1
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Goff JL, Szink EG, Durrence KL, Lui LM, Nielsen TN, Kuehl JV, Hunt KA, Chandonia JM, Huang J, Thorgersen MP, Poole FL, Stahl DA, Chakraborty R, Deutschbauer AM, Arkin AP, Adams MWW. Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface. Environ Microbiome 2024; 19:26. [PMID: 38671539 PMCID: PMC11046850 DOI: 10.1186/s40793-024-00570-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
Castellaniella species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal-contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining microbial community composition and nitrate removal at ORR during biostimulation efforts reported increased abundances of members of the Castellaniella genus concurrent with increased denitrification rates. Thus, we asked how genomic and abiotic factors control the Castellaniella biogeography at the site to understand how these factors may influence nitrate transformation in an anthropogenically impacted setting. We report the isolation and characterization of several Castellaniella strains from the ORR subsurface. Five of these isolates match at 100% identity (at the 16S rRNA gene V4 region) to two Castellaniella amplicon sequence variants (ASVs), ASV1 and ASV2, that have persisted in the ORR subsurface for at least 2 decades. However, ASV2 has consistently higher relative abundance in samples taken from the site and was also the dominant blooming denitrifier population during a prior biostimulation effort. We found that the ASV2 representative strain has greater resistance to mixed metal stress than the ASV1 representative strains. We attribute this resistance, in part, to the large number of unique heavy metal resistance genes identified on a genomic island in the ASV2 representative genome. Additionally, we suggest that the relatively lower fitness of ASV1 may be connected to the loss of the nitrous oxide reductase (nos) operon (and associated nitrous oxide reductase activity) due to the insertion at this genomic locus of a mobile genetic element carrying copper resistance genes. This study demonstrates the value of integrating genomic, environmental, and phenotypic data to characterize the biogeography of key microorganisms in contaminated sites.
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Affiliation(s)
- Jennifer L Goff
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Elizabeth G Szink
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Konnor L Durrence
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Lauren M Lui
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jiawen Huang
- Earth and Environmental Science Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Romy Chakraborty
- Earth and Environmental Science Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
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2
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Hunt KA, Carr AV, Otwell AE, Valenzuela JJ, Walker KS, Dixon ER, Lui LM, Nielsen TN, Bowman S, von Netzer F, Moon JW, Schadt CW, Rodriguez M, Lowe K, Joyner D, Davis KJ, Wu X, Chakraborty R, Fields MW, Zhou J, Hazen TC, Arkin AP, Wankel SD, Baliga NS, Stahl DA. Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide. Environ Sci Technol 2024; 58:7056-7065. [PMID: 38608141 DOI: 10.1021/acs.est.3c07972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
The sources and sinks of nitrous oxide, as control emissions to the atmosphere, are generally poorly constrained for most environmental systems. Initial depth-resolved analysis of nitrous oxide flux from observation wells and the proximal surface within a nitrate contaminated aquifer system revealed high subsurface production but little escape from the surface. To better understand the environmental controls of production and emission at this site, we used a combination of isotopic, geochemical, and molecular analyses to show that chemodenitrification and bacterial denitrification are major sources of nitrous oxide in this subsurface, where low DO, low pH, and high nitrate are correlated with significant nitrous oxide production. Depth-resolved metagenomes showed that consumption of nitrous oxide near the surface was correlated with an enrichment of Clade II nitrous oxide reducers, consistent with a growing appreciation of their importance in controlling release of nitrous oxide to the atmosphere. Our work also provides evidence for the reduction of nitrous oxide at a pH of 4, well below the generally accepted limit of pH 5.
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Affiliation(s)
- Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Alex V Carr
- Department of Molecular Engineering Sciences, University of Washington, Seattle, Washington 98105, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Anne E Otwell
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195, United States
| | | | - Kathleen S Walker
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Emma R Dixon
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Lauren M Lui
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Samuel Bowman
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02540, United States
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Ji-Won Moon
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Kenneth Lowe
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Dominique Joyner
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Katherine J Davis
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana 59717, United States
| | - Xiaoqin Wu
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Romy Chakraborty
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717, United States
| | - Jizhong Zhou
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, United States
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Terry C Hazen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02540, United States
| | - Nitin S Baliga
- Department of Molecular Engineering Sciences, University of Washington, Seattle, Washington 98105, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195, United States
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3
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Cavoto G, Chakraborty R, Doinaki A, Dutsov C, Giovannozzi M, Hume T, Kirch K, Michielsen K, Morvaj L, Papa A, Renga F, Sakurai M, Schmidt-Wellenburg P. Anomalous spin precession systematic effects in the search for a muon EDM using the frozen-spin technique. Eur Phys J C Part Fields 2024; 84:262. [PMID: 38487792 PMCID: PMC10933177 DOI: 10.1140/epjc/s10052-024-12604-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
At the Paul Scherrer Institut (PSI), we are developing a high-precision apparatus with the aim of searching for the muon electric dipole moment (EDM) with unprecedented sensitivity. The underpinning principle of this experiment is the frozen-spin technique, a method that suppresses the spin precession due to the anomalous magnetic moment, thereby enhancing the signal-to-noise ratio for EDM signals. This increased sensitivity enables measurements that would be difficult to achieve with conventional g - 2 muon storage rings. Given the availability of the 125 MeV / c muon beam at PSI, the anticipated statistical sensitivity for the EDM after a year of data collection is 6 × 10 - 23 e · cm . To achieve this goal, it is imperative to do a detailed analysis of any potential spurious effects that could mimic EDM signals. In this study, we present a quantitative methodology to evaluate the systematic effects that might arise in the context of the frozen-spin technique utilised within a compact storage ring. Our approach involves the analytical derivation of equations governing the motion of the muon spin in the electromagnetic (EM) fields intrinsic to the experimental setup, validated through numerical simulations. We also illustrate a method to calculate the cumulative geometric (Berry's) phase. This work complements ongoing experimental efforts to detect a muon EDM at PSI and contributes to a broader understanding of spin-precession systematic effects.
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Affiliation(s)
- G. Cavoto
- Istituto Nazionale di Fisica Nucleare, Sez. di Roma, P.le A. Moro 2, 00185 Rome, Italy
| | | | - A. Doinaki
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
- ETH Zürich, 8092 Zurich, Switzerland
| | - C. Dutsov
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - M. Giovannozzi
- CERN Beams Department, Esplanade des Particules 1, 1211 Meyrin, Switzerland
| | - T. Hume
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
- ETH Zürich, 8092 Zurich, Switzerland
| | - K. Kirch
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
- ETH Zürich, 8092 Zurich, Switzerland
| | - K. Michielsen
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
- ETH Zürich, 8092 Zurich, Switzerland
- École Polytechnique, Route de Saclay, 91128 Palaiseau Cedex, France
| | - L. Morvaj
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - A. Papa
- Istituto Nazionale di Fisica Nucleare, Sez. di Pisa, Largo B. Pontecorvo 3, 56127 Pisa, Italy
| | - F. Renga
- Istituto Nazionale di Fisica Nucleare, Sez. di Roma, P.le A. Moro 2, 00185 Rome, Italy
| | - M. Sakurai
- ETH Zürich, 8092 Zurich, Switzerland
- Present Address: University College London, Gower Street, London, WC1E 6BT UK
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4
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Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, Chakraborty R, Stahl DA, Adams PD, Arkin AP, He Z, Zhou J. Environmental stress mediates groundwater microbial community assembly. Nat Microbiol 2024; 9:490-501. [PMID: 38212658 DOI: 10.1038/s41564-023-01573-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.
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Affiliation(s)
- Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yajiao Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yupeng Fan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Jianjun Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Ping Zhang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Daniel J Curtis
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Renmao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Lauren Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Terry C Hazen
- Department of Earth and Planetary Sciences, Bredesen Center, Department of Civil and Environmental Sciences, Center for Environmental Biotechnology, and Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Eric J Alm
- Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew W Fields
- Center for Biofilm Engineering and Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Farris Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Paul D Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Adam P Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
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5
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Aguillard DP, Albahri T, Allspach D, Anisenkov A, Badgley K, Baeßler S, Bailey I, Bailey L, Baranov VA, Barlas-Yucel E, Barrett T, Barzi E, Bedeschi F, Berz M, Bhattacharya M, Binney HP, Bloom P, Bono J, Bottalico E, Bowcock T, Braun S, Bressler M, Cantatore G, Carey RM, Casey BCK, Cauz D, Chakraborty R, Chapelain A, Chappa S, Charity S, Chen C, Cheng M, Chislett R, Chu Z, Chupp TE, Claessens C, Convery ME, Corrodi S, Cotrozzi L, Crnkovic JD, Dabagov S, Debevec PT, Di Falco S, Di Sciascio G, Drendel B, Driutti A, Duginov VN, Eads M, Edmonds A, Esquivel J, Farooq M, Fatemi R, Ferrari C, Fertl M, Fienberg AT, Fioretti A, Flay D, Foster SB, Friedsam H, Froemming NS, Gabbanini C, Gaines I, Galati MD, Ganguly S, Garcia A, George J, Gibbons LK, Gioiosa A, Giovanetti KL, Girotti P, Gohn W, Goodenough L, Gorringe T, Grange J, Grant S, Gray F, Haciomeroglu S, Halewood-Leagas T, Hampai D, Han F, Hempstead J, Hertzog DW, Hesketh G, Hess E, Hibbert A, Hodge Z, Hong KW, Hong R, Hu T, Hu Y, Iacovacci M, Incagli M, Kammel P, Kargiantoulakis M, Karuza M, Kaspar J, Kawall D, Kelton L, Keshavarzi A, Kessler DS, Khaw KS, Khechadoorian Z, Khomutov NV, Kiburg B, Kiburg M, Kim O, Kinnaird N, Kraegeloh E, Krylov VA, Kuchinskiy NA, Labe KR, LaBounty J, Lancaster M, Lee S, Li B, Li D, Li L, Logashenko I, Lorente Campos A, Lu Z, Lucà A, Lukicov G, Lusiani A, Lyon AL, MacCoy B, Madrak R, Makino K, Mastroianni S, Miller JP, Miozzi S, Mitra B, Morgan JP, Morse WM, Mott J, Nath A, Ng JK, Nguyen H, Oksuzian Y, Omarov Z, Osofsky R, Park S, Pauletta G, Piacentino GM, Pilato RN, Pitts KT, Plaster B, Počanić D, Pohlman N, Polly CC, Price J, Quinn B, Qureshi MUH, Ramachandran S, Ramberg E, Reimann R, Roberts BL, Rubin DL, Santi L, Schlesier C, Schreckenberger A, Semertzidis YK, Shemyakin D, Sorbara M, Stöckinger D, Stapleton J, Still D, Stoughton C, Stratakis D, Swanson HE, Sweetmore G, Sweigart DA, Syphers MJ, Tarazona DA, Teubner T, Tewsley-Booth AE, Tishchenko V, Tran NH, Turner W, Valetov E, Vasilkova D, Venanzoni G, Volnykh VP, Walton T, Weisskopf A, Welty-Rieger L, Winter P, Wu Y, Yu B, Yucel M, Zeng Y, Zhang C. Measurement of the Positive Muon Anomalous Magnetic Moment to 0.20 ppm. Phys Rev Lett 2023; 131:161802. [PMID: 37925710 DOI: 10.1103/physrevlett.131.161802] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/05/2023] [Indexed: 11/07/2023]
Abstract
We present a new measurement of the positive muon magnetic anomaly, a_{μ}≡(g_{μ}-2)/2, from the Fermilab Muon g-2 Experiment using data collected in 2019 and 2020. We have analyzed more than 4 times the number of positrons from muon decay than in our previous result from 2018 data. The systematic error is reduced by more than a factor of 2 due to better running conditions, a more stable beam, and improved knowledge of the magnetic field weighted by the muon distribution, ω[over ˜]_{p}^{'}, and of the anomalous precession frequency corrected for beam dynamics effects, ω_{a}. From the ratio ω_{a}/ω[over ˜]_{p}^{'}, together with precisely determined external parameters, we determine a_{μ}=116 592 057(25)×10^{-11} (0.21 ppm). Combining this result with our previous result from the 2018 data, we obtain a_{μ}(FNAL)=116 592 055(24)×10^{-11} (0.20 ppm). The new experimental world average is a_{μ}(exp)=116 592 059(22)×10^{-11} (0.19 ppm), which represents a factor of 2 improvement in precision.
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Affiliation(s)
| | - T Albahri
- University of Liverpool, Liverpool, United Kingdom
| | - D Allspach
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - A Anisenkov
- Budker Institute of Nuclear Physics, Novosibirsk, Russia
| | - K Badgley
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - S Baeßler
- University of Virginia, Charlottesville, Virginia, USA
| | - I Bailey
- Lancaster University, Lancaster, United Kingdom
| | - L Bailey
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - V A Baranov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - E Barlas-Yucel
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - T Barrett
- Cornell University, Ithaca, New York, USA
| | - E Barzi
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | | | - M Berz
- Michigan State University, East Lansing, Michigan, USA
| | - M Bhattacharya
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - H P Binney
- University of Washington, Seattle, Washington, USA
| | - P Bloom
- North Central College, Naperville, Illinois, USA
| | - J Bono
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - E Bottalico
- University of Liverpool, Liverpool, United Kingdom
| | - T Bowcock
- University of Liverpool, Liverpool, United Kingdom
| | - S Braun
- University of Washington, Seattle, Washington, USA
| | - M Bressler
- Department of Physics, University of Massachusetts, Amherst, Massachusetts, USA
| | | | - R M Carey
- Boston University, Boston, Massachusetts, USA
| | - B C K Casey
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - D Cauz
- Università di Udine, Udine, Italy
| | | | | | - S Chappa
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - S Charity
- University of Liverpool, Liverpool, United Kingdom
| | - C Chen
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
- Tsung-Dao Lee Institute, Shanghai Jiao Tong University, Shanghai, China
| | - M Cheng
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - R Chislett
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Z Chu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - T E Chupp
- University of Michigan, Ann Arbor, Michigan, USA
| | - C Claessens
- University of Washington, Seattle, Washington, USA
| | - M E Convery
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - S Corrodi
- Argonne National Laboratory, Lemont, Illinois, USA
| | | | - J D Crnkovic
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - S Dabagov
- INFN, Laboratori Nazionali di Frascati, Frascati, Italy
| | - P T Debevec
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | | | - B Drendel
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | | | - V N Duginov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - M Eads
- Northern Illinois University, DeKalb, Illinois, USA
| | - A Edmonds
- Boston University, Boston, Massachusetts, USA
| | - J Esquivel
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - M Farooq
- University of Michigan, Ann Arbor, Michigan, USA
| | - R Fatemi
- University of Kentucky, Lexington, Kentucky, USA
| | | | - M Fertl
- Institute of Physics and Cluster of Excellence PRISMA+, Johannes Gutenberg University Mainz, Mainz, Germany
| | - A T Fienberg
- University of Washington, Seattle, Washington, USA
| | | | - D Flay
- Department of Physics, University of Massachusetts, Amherst, Massachusetts, USA
| | - S B Foster
- Boston University, Boston, Massachusetts, USA
| | - H Friedsam
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | | | | | - I Gaines
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | | | - S Ganguly
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - A Garcia
- University of Washington, Seattle, Washington, USA
| | - J George
- Department of Physics, University of Massachusetts, Amherst, Massachusetts, USA
| | | | - A Gioiosa
- Università del Molise, Campobasso, Italy
| | - K L Giovanetti
- Department of Physics and Astronomy, James Madison University, Harrisonburg, Virginia, USA
| | | | - W Gohn
- University of Kentucky, Lexington, Kentucky, USA
| | - L Goodenough
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - T Gorringe
- University of Kentucky, Lexington, Kentucky, USA
| | - J Grange
- University of Michigan, Ann Arbor, Michigan, USA
| | - S Grant
- Argonne National Laboratory, Lemont, Illinois, USA
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - F Gray
- Regis University, Denver, Colorado, USA
| | - S Haciomeroglu
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | | | - D Hampai
- INFN, Laboratori Nazionali di Frascati, Frascati, Italy
| | - F Han
- University of Kentucky, Lexington, Kentucky, USA
| | - J Hempstead
- University of Washington, Seattle, Washington, USA
| | - D W Hertzog
- University of Washington, Seattle, Washington, USA
| | - G Hesketh
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - E Hess
- INFN, Sezione di Pisa, Pisa, Italy
| | - A Hibbert
- University of Liverpool, Liverpool, United Kingdom
| | - Z Hodge
- University of Washington, Seattle, Washington, USA
| | - K W Hong
- University of Virginia, Charlottesville, Virginia, USA
| | - R Hong
- Argonne National Laboratory, Lemont, Illinois, USA
- University of Kentucky, Lexington, Kentucky, USA
| | - T Hu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
- Tsung-Dao Lee Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Y Hu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | | | | | - P Kammel
- University of Washington, Seattle, Washington, USA
| | | | - M Karuza
- INFN, Sezione di Trieste, Trieste, Italy
| | - J Kaspar
- University of Washington, Seattle, Washington, USA
| | - D Kawall
- Department of Physics, University of Massachusetts, Amherst, Massachusetts, USA
| | - L Kelton
- University of Kentucky, Lexington, Kentucky, USA
| | - A Keshavarzi
- Department of Physics and Astronomy, University of Manchester, Manchester, United Kingdom
| | - D S Kessler
- Department of Physics, University of Massachusetts, Amherst, Massachusetts, USA
| | - K S Khaw
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
- Tsung-Dao Lee Institute, Shanghai Jiao Tong University, Shanghai, China
| | | | - N V Khomutov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - B Kiburg
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - M Kiburg
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
- North Central College, Naperville, Illinois, USA
| | - O Kim
- University of Mississippi, University, Mississippi, USA
| | - N Kinnaird
- Boston University, Boston, Massachusetts, USA
| | - E Kraegeloh
- University of Michigan, Ann Arbor, Michigan, USA
| | - V A Krylov
- Joint Institute for Nuclear Research, Dubna, Russia
| | | | - K R Labe
- Cornell University, Ithaca, New York, USA
| | - J LaBounty
- University of Washington, Seattle, Washington, USA
| | - M Lancaster
- Department of Physics and Astronomy, University of Manchester, Manchester, United Kingdom
| | - S Lee
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - B Li
- Argonne National Laboratory, Lemont, Illinois, USA
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - D Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - L Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - I Logashenko
- Budker Institute of Nuclear Physics, Novosibirsk, Russia
| | | | - Z Lu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - A Lucà
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - G Lukicov
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | | | - A L Lyon
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - B MacCoy
- University of Washington, Seattle, Washington, USA
| | - R Madrak
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - K Makino
- Michigan State University, East Lansing, Michigan, USA
| | | | - J P Miller
- Boston University, Boston, Massachusetts, USA
| | - S Miozzi
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
| | - B Mitra
- University of Mississippi, University, Mississippi, USA
| | - J P Morgan
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - W M Morse
- Brookhaven National Laboratory, Upton, New York, USA
| | - J Mott
- Boston University, Boston, Massachusetts, USA
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - A Nath
- INFN, Sezione di Napoli, Naples, Italy
| | - J K Ng
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
- Tsung-Dao Lee Institute, Shanghai Jiao Tong University, Shanghai, China
| | - H Nguyen
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - Y Oksuzian
- Argonne National Laboratory, Lemont, Illinois, USA
| | - Z Omarov
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - R Osofsky
- University of Washington, Seattle, Washington, USA
| | - S Park
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | | | | | - R N Pilato
- University of Liverpool, Liverpool, United Kingdom
| | - K T Pitts
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - B Plaster
- University of Kentucky, Lexington, Kentucky, USA
| | - D Počanić
- University of Virginia, Charlottesville, Virginia, USA
| | - N Pohlman
- Northern Illinois University, DeKalb, Illinois, USA
| | - C C Polly
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - J Price
- University of Liverpool, Liverpool, United Kingdom
| | - B Quinn
- University of Mississippi, University, Mississippi, USA
| | - M U H Qureshi
- Institute of Physics and Cluster of Excellence PRISMA+, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - E Ramberg
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - R Reimann
- Institute of Physics and Cluster of Excellence PRISMA+, Johannes Gutenberg University Mainz, Mainz, Germany
| | - B L Roberts
- Boston University, Boston, Massachusetts, USA
| | - D L Rubin
- Cornell University, Ithaca, New York, USA
| | - L Santi
- Università di Udine, Udine, Italy
| | - C Schlesier
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Y K Semertzidis
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - D Shemyakin
- Budker Institute of Nuclear Physics, Novosibirsk, Russia
| | - M Sorbara
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
| | - D Stöckinger
- Institut für Kern- und Teilchenphysik, Technische Universität Dresden, Dresden, Germany
| | - J Stapleton
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - D Still
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - C Stoughton
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - D Stratakis
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - H E Swanson
- University of Washington, Seattle, Washington, USA
| | - G Sweetmore
- Department of Physics and Astronomy, University of Manchester, Manchester, United Kingdom
| | | | - M J Syphers
- Northern Illinois University, DeKalb, Illinois, USA
| | - D A Tarazona
- Cornell University, Ithaca, New York, USA
- Michigan State University, East Lansing, Michigan, USA
- University of Liverpool, Liverpool, United Kingdom
| | - T Teubner
- University of Liverpool, Liverpool, United Kingdom
| | - A E Tewsley-Booth
- University of Kentucky, Lexington, Kentucky, USA
- University of Michigan, Ann Arbor, Michigan, USA
| | - V Tishchenko
- Brookhaven National Laboratory, Upton, New York, USA
| | - N H Tran
- Boston University, Boston, Massachusetts, USA
| | - W Turner
- University of Liverpool, Liverpool, United Kingdom
| | - E Valetov
- Michigan State University, East Lansing, Michigan, USA
| | - D Vasilkova
- Department of Physics and Astronomy, University College London, London, United Kingdom
- University of Liverpool, Liverpool, United Kingdom
| | - G Venanzoni
- University of Liverpool, Liverpool, United Kingdom
| | - V P Volnykh
- Joint Institute for Nuclear Research, Dubna, Russia
| | - T Walton
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - A Weisskopf
- Michigan State University, East Lansing, Michigan, USA
| | - L Welty-Rieger
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - P Winter
- Argonne National Laboratory, Lemont, Illinois, USA
| | - Y Wu
- Argonne National Laboratory, Lemont, Illinois, USA
| | - B Yu
- University of Mississippi, University, Mississippi, USA
| | - M Yucel
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - Y Zeng
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
- Tsung-Dao Lee Institute, Shanghai Jiao Tong University, Shanghai, China
| | - C Zhang
- University of Liverpool, Liverpool, United Kingdom
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6
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Acharya SM, Yee MO, Diamond S, Andeer PF, Baig NF, Aladesanmi OT, Northen TR, Banfield JF, Chakraborty R. Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots. ISME Commun 2023; 3:54. [PMID: 37280433 PMCID: PMC10244434 DOI: 10.1038/s43705-023-00265-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.
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Affiliation(s)
- Shwetha M Acharya
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mon Oo Yee
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Peter F Andeer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nameera F Baig
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Omolara T Aladesanmi
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Romy Chakraborty
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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7
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Wu X, Gushgari-Doyle S, Lui LM, Hendrickson AJ, Liu Y, Jagadamma S, Nielsen TN, Justice NB, Simmons T, Hess NJ, Joyner DC, Hazen TC, Arkin AP, Chakraborty R. Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone. Appl Environ Microbiol 2023:e0050023. [PMID: 37272792 DOI: 10.1128/aem.00500-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ. IMPORTANCE In this study, we explored the links between geochemical parameters, microbial community structure and metabolic potential across the depth of sediment, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone. Our results revealed that microbes in the terrestrial subsurface can be highly localized, with communities rarely being interconnected along the depth. Overall, our research demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolic potential in different depths of subsurface terrestrial sediment. Such studies correlating microbial community analyses and geochemistry analyses, including high resolution mass spectrometry analyses of natural organic carbon, will further the fundamental understanding of microbial ecology and biogeochemistry in subsurface terrestrial ecosystems and will benefit the future development of predictive models on nutrient turnover in these environments.
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Affiliation(s)
- Xiaoqin Wu
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sara Gushgari-Doyle
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Andrew J Hendrickson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yina Liu
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Torben N Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicholas B Justice
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tuesday Simmons
- University of California, Berkeley, Berkeley, California, USA
| | - Nancy J Hess
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Terry C Hazen
- University of Tennessee, Knoxville, Tennessee, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- University of California, Berkeley, Berkeley, California, USA
| | - Romy Chakraborty
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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8
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Pak MC, Chakraborty R, Kanso MA, Tontiwattanakul K, Kim KI, Giacomin AJ. Coronavirus peplomer interaction. Phys Fluids (1994) 2022; 34:113109. [PMID: 36505011 PMCID: PMC9728042 DOI: 10.1063/5.0120167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/19/2022] [Indexed: 06/17/2023]
Abstract
By virtue of their lack of motility, viruses rely entirely on their own temperature (Brownian motion) to position themselves properly for cell attachment. Spiked viruses use one or more spikes (called peplomers) to attach. The coronavirus uses adjacent peplomer pairs. These peplomers, identically charged, repel one another over the surface of their convex capsids to form beautiful polyhedra. We identify the edges of these polyhedra with the most important peplomer hydrodynamic interactions. These convex capsids may or may not be spherical, and their peplomer population declines with infection time. These peplomers are short, equidimensional, and bulbous with triangular bulbs. In this short paper, we explore the interactions between nearby peplomer bulbs. By interactions, we mean the hydrodynamic interferences between the velocity profiles caused by the drag of the suspending fluid when the virus rotates. We find that these peplomer hydrodynamic interactions raise rotational diffusivity of the virus, and thus affect its ability to infect.
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Affiliation(s)
- Myong Chol Pak
- Department of Physics, Kim Il Sung University,
Taesong District, Pyongyang 999093, Democratic People's Republic of
Korea
| | - R. Chakraborty
- Chemical Engineering Department, Jadavpur
University, Kolkata 700032, India
| | - M. A. Kanso
- Chemical Engineering Department, Polymers Research Group,
Queen's University, Kingston, Ontario K7L 3N6,
Canada
| | - K. Tontiwattanakul
- Department of Mechanical and Aerospace Engineering, King
Mongkut's University of Technology North Bangkok, Bangkok,
Thailand
| | - Kwang-Il Kim
- Department of Physics, Kim Il Sung University,
Taesong District, Pyongyang 999093, Democratic People's Republic of
Korea
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9
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Chakravarty B, Kalapahar S, Sharma S, Chattopadhyay R, Ghosh S, Chakraborty M, Chakraborty R, Bose U, Chakraborty P. O-031 Activation of NLRP3 inflammasome enhances neutrophil extracellular traps in women with stage III/IV endometriosis: convergence of multiple signaling portray association between genetics and lesion type. Hum Reprod 2022. [DOI: 10.1093/humrep/deac104.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Study question
Do NOD-like receptor pyrin-containing 3 (NLRP3) signaling affect neutrophil extracellular traps (NET)-osis in women with stage III/IV endometriosis?
Summary answer
Inflammasome activation whether due to pathogen (disease itself) or damage-associated molecular pattern (through NET) might be one mechanism involved in establishing perturbed endometrium in endometriosis.
What is known already
Endometriosis is characterized by number of processes like vascularization, hypernociception, and fibrosis, cardinal cause being inflammation. Recently, expression of inflammasome components, including NLRP3 and apoptosis signal-regulating kinase has been demonstrated in human endometrium cueing involvement in uterine innate immunity. Moreover, a novel extracellular killing mechanism, NET, is documented to reflect an inflammatory status in deep infiltrating endometriosis. Since, endometriosis demonstrates similarities with chronic inflammatory and autoimmune disorders; we postulated inflammatory responses in endometriosis may become modulated through a feed-forward loop of NET-induced specific cytokine production thus providing insights against potentiality of endometriotic cells to limit progression of the disease.
Study design, size, duration
Twenty-two consented women (24-39 years) with endometriosis (Group A) (Stages III–IV) (based on ASRM-2018 guidelines) and age-matched counterpart/s of male sub-fertility (Group B; control), free of uterine abnormalities (n = 18) were recruited between January to December 2021 from Institute of Reproductive Medicine, Kolkata. Eutopic endometrium, were collected from women undergoing diagnostic laparoscopy (Group A) or by curettage from women undergoing endometrial ablation (Group B). Serum was collected during window-of-implantation (LH + 7) for both the group/s.
Participants/materials, setting, methods
Pro-(IFN-g, TNF-a, IL-6, TGF-b) and anti-inflammatory (IL-10, IL-13, IL-4, IL-5) cytokines was evaluated by western blot. Expression level of inflammasome-related proteins (NLRP3, ASC, CASPASE1, PYCARD, IL-1-b) and mRNA expression was estimated by western-blot and quantitative-real-time PCR (qRT-PCR) respectively from tissue biopsies in Group A and B. SYTOX® green assay by flow-cytometry and neutrophil-elastase activity by immunofluorescence was done to quantify and characterize NET production in blood monocytes. P < 0.05 was considered statistically significant.
Main results and the role of chance
The mean (±SD) age of study population was 31.6±5.2 years. Hyperestrogenic milieu possibly stimulated (p < 0.001) pro-inflammatory molecules (IFN-g, TNF-a, IL-6, TGF-b) in endometriosis as observed by western-blot and qRT-PCR. A significant up-regulation (p < 0.001) was observed in relative mRNA expression of NLRP3 and PYCARD gene in Group A. However, caspase 1 expression documented non-significant variation in biopsies from endometriosis patients. Western blot corroborated the finding/s. The outcome of NLRP3 activation was supported by increased (p < 0.002) mRNA expression of IL-1b. NETs were detected significantly higher (p < 0.01) in 54.54% (12/22) patients in group A compared to control (16.66%; (3/18)). Moreover, quantification of NETs showed a significantly higher amount in endometriosis compared to group B (0.097 vs. 0.02, p < 0.03).
Spermann-rank correlation by SPSS version22 revealed positive correlation between IL-1b with NLRP3 (r = 0.56, p< 0.001), PYCARD (r = 0.11, p< 0.01); and caspase1 (r = 0.16, p< 0.01) and IL-1b (r = 0.47, p< 0.01) with NET-positive cell/s in endometriosis. Moreover, posterior cul-de-sac lesions correlated positively with NET-positive cell/s (r = 0.29; p < 0.01) cueing to possible prognostic marker/s. In summary, a coordinated-fashioned action of components of NLRP3 inflammasome machinery may regulate production of NET/s forming a complex network allowing communication between cell-types in order to maintain viability and development of endometrial lesion/s.
Limitations, reasons for caution
Our findings need to be replicated in larger study cohort/s, especially stratified by severity of endometriosis sub-groups and in women of different ethnicities. Another limitation is the missing information about NETs in normal functioning human endometrium throughout the menstrual cycle.
Wider implications of the findings
The proposed study aims to understand potential role of NLRP3 inflammasome complex as a “double-edged sword” in the development and pathophysiology of endometriosis. Therapeutic alternatives that aim to re-balance the pro- to anti-inflammatory milieu in the endometrium should consider the inflammasome as part of the equation.
Trial registration number
Not applicable
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Affiliation(s)
- B Chakravarty
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - S Kalapahar
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - S Sharma
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - R Chattopadhyay
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - S Ghosh
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - M Chakraborty
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - R Chakraborty
- Melaka Manipal Medical College, Department of Microbiology, Manipal , India
| | - U Bose
- Melaka Manipal Medical College, Department of Pharmacology, Manipal , India
| | - P Chakraborty
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
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10
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de Raad M, Li YV, Kuehl JV, Andeer PF, Kosina SM, Hendrickson A, Saichek NR, Golini AN, Han LZ, Wang Y, Bowen BP, Deutschbauer AM, Arkin AP, Chakraborty R, Northen TR. A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria. Front Microbiol 2022; 13:855331. [PMID: 35694313 PMCID: PMC9174792 DOI: 10.3389/fmicb.2022.855331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse soil bacteria but also is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested and all of its metabolites were trackable through LC–MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities.
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Affiliation(s)
- Markus de Raad
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Yifan V. Li
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jennifer V. Kuehl
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Peter F. Andeer
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Suzanne M. Kosina
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Andrew Hendrickson
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Nicholas R. Saichek
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Amber N. Golini
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - La Zhen Han
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Ying Wang
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Benjamin P. Bowen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Adam M. Deutschbauer
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Adam P. Arkin
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R. Northen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
- *Correspondence: Trent R. Northen,
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11
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Cabugao KGM, Gushgari-Doyle S, Chacon SS, Wu X, Bhattacharyya A, Bouskill N, Chakraborty R. Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges. Front Microbiol 2022; 13:864895. [PMID: 35602028 PMCID: PMC9114703 DOI: 10.3389/fmicb.2022.864895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.
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Affiliation(s)
- Kristine Grace M Cabugao
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sara Gushgari-Doyle
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Stephany S Chacon
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Xiaoqin Wu
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Amrita Bhattacharyya
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas Bouskill
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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12
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Gushgari-Doyle S, Lui LM, Nielsen TN, Wu X, Malana RG, Hendrickson AJ, Carion H, Poole FL, Adams MWW, Arkin AP, Chakraborty R. Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions. ISME Commun 2022; 2:32. [PMID: 37938300 PMCID: PMC9723602 DOI: 10.1038/s43705-022-00113-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 07/04/2023]
Abstract
Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.
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Affiliation(s)
| | - Lauren M Lui
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Xiaoqin Wu
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ria G Malana
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Heloise Carion
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
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13
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Kosina SM, Rademacher P, Wetmore KM, de Raad M, Zemla M, Zane GM, Zulovich JJ, Chakraborty R, Bowen BP, Wall JD, Auer M, Arkin AP, Deutschbauer AM, Northen TR. Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms. Front Microbiol 2021; 12:757856. [PMID: 34956122 PMCID: PMC8696352 DOI: 10.3389/fmicb.2021.757856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.
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Affiliation(s)
- Suzanne M. Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter Rademacher
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kelly M. Wetmore
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Markus de Raad
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcin Zemla
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | | | - Romy Chakraborty
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Manfred Auer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
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14
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Gushgari-Doyle S, Schicklberger M, Li YV, Walker R, Chakraborty R. Plant Growth Promotion Diversity in Switchgrass-Colonizing, Diazotrophic Endophytes. Front Microbiol 2021; 12:730440. [PMID: 34867848 PMCID: PMC8633415 DOI: 10.3389/fmicb.2021.730440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022] Open
Abstract
Endophytic nitrogen-fixing (diazotrophic) bacteria are essential members of the microbiome of switchgrass (Panicum virgatum), considered to be an important commodity crop in bioenergy production. While endophytic diazotrophs are known to provide fixed atmospheric nitrogen to their host plant, there are many other plant growth-promoting (PGP) capabilities of these organisms to be demonstrated. The diversity of PGP traits across different taxa of switchgrass-colonizing endophytes is understudied, yet critical for understanding endophytic function and improving cultivation methods of important commodity crops. Here, we present the isolation and characterization of three diazotrophic endophytes: Azospirillum agricola R1C, Klebsiella variicola F10Cl, and Raoultella terrigena R1Gly. Strains R1C and F10Cl were isolated from switchgrass and strain R1Gly, while isolated from tobacco, is demonstrated herein to colonize switchgrass. Each strain exhibited highly diverse genomic and phenotypic PGP capabilities. Strain F10Cl and R1Gly demonstrated the highest functional similarity, suggesting that, while endophyte community structure may vary widely based on host species, differences in functional diversity are not a clearly delineated. The results of this study advance our understanding of diazotrophic endophyte diversity, which will allow us to design robust strategies to improve cultivation methods of many economically important commodity crops.
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Affiliation(s)
- Sara Gushgari-Doyle
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcus Schicklberger
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yifan V Li
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Robert Walker
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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15
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Cheon IS, Li C, Son YM, Goplen NP, Wu Y, Cassmann T, Wang Z, Wei X, Tang J, Li Y, Marlow H, Hughes S, Hammel L, Cox TM, Goddery E, Ayasoufi K, Weiskopf D, Boonyaratanakornkit J, Dong H, Li H, Chakraborty R, Johnson AJ, Edell E, Taylor JJ, Kaplan MH, Sette A, Bartholmai BJ, Kern R, Vassallo R, Sun J. Immune signatures underlying post-acute COVID-19 lung sequelae. Sci Immunol 2021; 6:eabk1741. [PMID: 34591653 DOI: 10.1126/sciimmunol.abk1741] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- I S Cheon
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - C Li
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Y M Son
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - N P Goplen
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Y Wu
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - T Cassmann
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Z Wang
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - X Wei
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - J Tang
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Y Li
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - H Marlow
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - S Hughes
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - L Hammel
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - T M Cox
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - E Goddery
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - K Ayasoufi
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - D Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - J Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - H Dong
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - H Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - R Chakraborty
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA.,Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - A J Johnson
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - E Edell
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - J J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - M H Kaplan
- Department of Microbiology and Immunology, Indiana University of School of Medicine, Indianapolis, IN 46202, USA
| | - A Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego (UCSD), La Jolla, CA 92037, USA
| | - B J Bartholmai
- Department of Radiology, Mayo Clinic, Rochester, MN 5590, USA
| | - R Kern
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - R Vassallo
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - J Sun
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA.,Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA.,Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA.,Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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16
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Carim S, Azadeh AL, Kazakov AE, Price MN, Walian PJ, Lui LM, Nielsen TN, Chakraborty R, Deutschbauer AM, Mutalik VK, Arkin AP. Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins. ISME J 2021; 15:2289-2305. [PMID: 33649553 PMCID: PMC8319346 DOI: 10.1038/s41396-021-00921-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/14/2021] [Accepted: 02/01/2021] [Indexed: 12/13/2022]
Abstract
Tailocins are bactericidal protein complexes produced by a wide variety of bacteria that kill closely related strains and may play a role in microbial community structure. Thanks to their high specificity, tailocins have been proposed as precision antibacterial agents for therapeutic applications. Compared to tailed phages, with whom they share an evolutionary and morphological relationship, bacterially produced tailocins kill their host upon production but producing strains display resistance to self-intoxication. Though lipopolysaccharide (LPS) has been shown to act as a receptor for tailocins, the breadth of factors involved in tailocin sensitivity, and the mechanisms behind resistance to self-intoxication, remain unclear. Here, we employed genome-wide screens in four non-model pseudomonads to identify mutants with altered fitness in the presence of tailocins produced by closely related pseudomonads. Our mutant screens identified O-antigen composition and display as most important in defining sensitivity to our tailocins. In addition, the screens suggest LPS thinning as a mechanism by which resistant strains can become more sensitive to tailocins. We validate many of these novel findings, and extend these observations of tailocin sensitivity to 130 genome-sequenced pseudomonads. This work offers insights into tailocin-bacteria interactions, informing the potential use of tailocins in microbiome manipulation and antibacterial therapy.
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Affiliation(s)
- Sean Carim
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Ashley L Azadeh
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Morgan N Price
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Peter J Walian
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lauren M Lui
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Romy Chakraborty
- Climate and Ecosystem Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vivek K Mutalik
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Adam P Arkin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, CA, USA.
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17
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Kothari A, Roux S, Zhang H, Prieto A, Soneja D, Chandonia JM, Spencer S, Wu X, Altenburg S, Fields MW, Deutschbauer AM, Arkin AP, Alm EJ, Chakraborty R, Mukhopadhyay A. Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance. mSystems 2021; 6:e0053721. [PMID: 34184913 PMCID: PMC8269241 DOI: 10.1128/msystems.00537-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 05/26/2021] [Indexed: 01/21/2023] Open
Abstract
Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes; however, little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes (the entire plasmid content of an environment) and identified 200 viral sequences, which clustered into 41 genus-level viral clusters (approximately equivalent to viral genera) including 9 known and 32 putative new genera. We used publicly available bacterial whole-genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with Proteobacteria, followed by Firmicutes, Bacteroidetes, and Actinobacteria. The publicly available WGS enabled mapping bacterial hosts to several viral sequences. The WGS of groundwater isolates increased the depth of host prediction by allowing host identification at the strain level. The latter included 4 viruses that were almost entirely (>99% query coverage, >99% identity) identified as integrated in the genomes of Pseudomonas, Acidovorax, and Castellaniella strains, resulting in high-confidence host assignments. Lastly, 21 of these viruses carried putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they are key players in microbial adaption to environmental stress. IMPORTANCE To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications. Using this method, we detected several novel phage genera along with those previously established. Our approach of using the whole-genome sequences of hundreds of bacterial isolates from the same site enabled us to make host assignments with high confidence, several at strain levels. Certain phage genes suggest that they provide an environment-specific selective advantage to their bacterial hosts. Our study lays the foundation for future research on directed phage isolations using specific bacterial host strains to further characterize groundwater phages, their life cycles, and their effects on groundwater microbiome and biogeochemistry.
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Affiliation(s)
- Ankita Kothari
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hanqiao Zhang
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Anatori Prieto
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Drishti Soneja
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sarah Spencer
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xiaoqin Wu
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sara Altenburg
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Matthew W. Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana, USA
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Energy Biosciences Institute, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Eric J. Alm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute of MIT Cambridge, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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18
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Wang S, Walker R, Schicklberger M, Nico PS, Fox PM, Karaoz U, Chakraborty R, Brodie EL. Microbial Phosphorus Mobilization Strategies Across a Natural Nutrient Limitation Gradient and Evidence for Linkage With Iron Solubilization Traits. Front Microbiol 2021; 12:572212. [PMID: 34248859 PMCID: PMC8261140 DOI: 10.3389/fmicb.2021.572212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 03/12/2021] [Indexed: 01/04/2023] Open
Abstract
Microorganisms have evolved several mechanisms to mobilize and mineralize occluded and insoluble phosphorus (P), thereby promoting plant growth in terrestrial ecosystems. However, the linkages between microbial P-solubilization traits and the preponderance of insoluble P in natural ecosystems are not well known. We tested the P solubilization traits of hundreds of culturable bacteria representative of the rhizosphere from a natural gradient where P concentration and bioavailability decline as soil becomes progressively more weathered. Aluminum, iron phosphate and organic P (phytate) were expected to dominate in more weathered soils. A defined cultivation medium with these chemical forms of P was used for isolation. A combination of soil chemical, spectroscopic analyses and 16S rRNA gene sequencing were used to understand the in situ ability for solubilization of these predominant forms of P. Locations with more occluded and organic P harbored the greatest abundance of P-mobilizing microorganisms, especially Burkholderiaceae (Caballeronia and Paraburkholderia spp.). Nearly all bacteria utilized aluminum phosphate, however fewer could subsist on iron phosphate (FePO4) or phytate. Microorganisms isolated from phytic acid were also most effective at solubilizing FePO4, suggesting that phytate solubilization may be linked to the ability to solubilize Fe. Significantly, we observed Fe to be co-located with P in organic patches in soil. Siderophore addition in lab experiments reinstated phytase mediated P-solubilization from Fe-phytate complexes. Taken together, these results indicate that metal-organic-P complex formation may limit enzymatic P solubilization from phytate in soil. Additionally, the linked traits of phytase and siderophore production were mostly restricted to specific clades within the Burkholderiaceae. We propose that Fe complexation of organic P (e.g., phytate) represents a major constraint on P turnover and availability in acidic soils, as only a limited subset of bacteria appear to possess the traits required to access this persistent pool of soil P.
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Affiliation(s)
- Shi Wang
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Robert Walker
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Marcus Schicklberger
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter S Nico
- Energy Geosciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Patricia M Fox
- Energy Geosciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ulas Karaoz
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eoin L Brodie
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
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19
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Kim J, Goldstein AH, Chakraborty R, Jardine K, Weber R, Sorensen PO, Wang S, Faybishenko B, Misztal PK, Brodie EL. Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt. Front Microbiol 2021; 12:679671. [PMID: 34248891 PMCID: PMC8261151 DOI: 10.3389/fmicb.2021.679671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/31/2021] [Indexed: 11/24/2022] Open
Abstract
Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.
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Affiliation(s)
- Junhyeong Kim
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Allen H Goldstein
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Romy Chakraborty
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Kolby Jardine
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Robert Weber
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Patrick O Sorensen
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Shi Wang
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Boris Faybishenko
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Pawel K Misztal
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Eoin L Brodie
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States.,Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
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Abi B, Albahri T, Al-Kilani S, Allspach D, Alonzi LP, Anastasi A, Anisenkov A, Azfar F, Badgley K, Baeßler S, Bailey I, Baranov VA, Barlas-Yucel E, Barrett T, Barzi E, Basti A, Bedeschi F, Behnke A, Berz M, Bhattacharya M, Binney HP, Bjorkquist R, Bloom P, Bono J, Bottalico E, Bowcock T, Boyden D, Cantatore G, Carey RM, Carroll J, Casey BCK, Cauz D, Ceravolo S, Chakraborty R, Chang SP, Chapelain A, Chappa S, Charity S, Chislett R, Choi J, Chu Z, Chupp TE, Convery ME, Conway A, Corradi G, Corrodi S, Cotrozzi L, Crnkovic JD, Dabagov S, De Lurgio PM, Debevec PT, Di Falco S, Di Meo P, Di Sciascio G, Di Stefano R, Drendel B, Driutti A, Duginov VN, Eads M, Eggert N, Epps A, Esquivel J, Farooq M, Fatemi R, Ferrari C, Fertl M, Fiedler A, Fienberg AT, Fioretti A, Flay D, Foster SB, Friedsam H, Frlež E, Froemming NS, Fry J, Fu C, Gabbanini C, Galati MD, Ganguly S, Garcia A, Gastler DE, George J, Gibbons LK, Gioiosa A, Giovanetti KL, Girotti P, Gohn W, Gorringe T, Grange J, Grant S, Gray F, Haciomeroglu S, Hahn D, Halewood-Leagas T, Hampai D, Han F, Hazen E, Hempstead J, Henry S, Herrod AT, Hertzog DW, Hesketh G, Hibbert A, Hodge Z, Holzbauer JL, Hong KW, Hong R, Iacovacci M, Incagli M, Johnstone C, Johnstone JA, Kammel P, Kargiantoulakis M, Karuza M, Kaspar J, Kawall D, Kelton L, Keshavarzi A, Kessler D, Khaw KS, Khechadoorian Z, Khomutov NV, Kiburg B, Kiburg M, Kim O, Kim SC, Kim YI, King B, Kinnaird N, Korostelev M, Kourbanis I, Kraegeloh E, Krylov VA, Kuchibhotla A, Kuchinskiy NA, Labe KR, LaBounty J, Lancaster M, Lee MJ, Lee S, Leo S, Li B, Li D, Li L, Logashenko I, Lorente Campos A, Lucà A, Lukicov G, Luo G, Lusiani A, Lyon AL, MacCoy B, Madrak R, Makino K, Marignetti F, Mastroianni S, Maxfield S, McEvoy M, Merritt W, Mikhailichenko AA, Miller JP, Miozzi S, Morgan JP, Morse WM, Mott J, Motuk E, Nath A, Newton D, Nguyen H, Oberling M, Osofsky R, Ostiguy JF, Park S, Pauletta G, Piacentino GM, Pilato RN, Pitts KT, Plaster B, Počanić D, Pohlman N, Polly CC, Popovic M, Price J, Quinn B, Raha N, Ramachandran S, Ramberg E, Rider NT, Ritchie JL, Roberts BL, Rubin DL, Santi L, Sathyan D, Schellman H, Schlesier C, Schreckenberger A, Semertzidis YK, Shatunov YM, Shemyakin D, Shenk M, Sim D, Smith MW, Smith A, Soha AK, Sorbara M, Stöckinger D, Stapleton J, Still D, Stoughton C, Stratakis D, Strohman C, Stuttard T, Swanson HE, Sweetmore G, Sweigart DA, Syphers MJ, Tarazona DA, Teubner T, Tewsley-Booth AE, Thomson K, Tishchenko V, Tran NH, Turner W, Valetov E, Vasilkova D, Venanzoni G, Volnykh VP, Walton T, Warren M, Weisskopf A, Welty-Rieger L, Whitley M, Winter P, Wolski A, Wormald M, Wu W, Yoshikawa C. Measurement of the Positive Muon Anomalous Magnetic Moment to 0.46 ppm. Phys Rev Lett 2021; 126:141801. [PMID: 33891447 DOI: 10.1103/physrevlett.126.141801] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
We present the first results of the Fermilab National Accelerator Laboratory (FNAL) Muon g-2 Experiment for the positive muon magnetic anomaly a_{μ}≡(g_{μ}-2)/2. The anomaly is determined from the precision measurements of two angular frequencies. Intensity variation of high-energy positrons from muon decays directly encodes the difference frequency ω_{a} between the spin-precession and cyclotron frequencies for polarized muons in a magnetic storage ring. The storage ring magnetic field is measured using nuclear magnetic resonance probes calibrated in terms of the equivalent proton spin precession frequency ω[over ˜]_{p}^{'} in a spherical water sample at 34.7 °C. The ratio ω_{a}/ω[over ˜]_{p}^{'}, together with known fundamental constants, determines a_{μ}(FNAL)=116 592 040(54)×10^{-11} (0.46 ppm). The result is 3.3 standard deviations greater than the standard model prediction and is in excellent agreement with the previous Brookhaven National Laboratory (BNL) E821 measurement. After combination with previous measurements of both μ^{+} and μ^{-}, the new experimental average of a_{μ}(Exp)=116 592 061(41)×10^{-11} (0.35 ppm) increases the tension between experiment and theory to 4.2 standard deviations.
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Affiliation(s)
- B Abi
- University of Oxford, Oxford, United Kingdom
| | - T Albahri
- University of Liverpool, Liverpool, United Kingdom
| | - S Al-Kilani
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - D Allspach
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - L P Alonzi
- University of Washington, Seattle, Washington, USA
| | | | - A Anisenkov
- Budker Institute of Nuclear Physics, Novosibirsk, Russia
| | - F Azfar
- University of Oxford, Oxford, United Kingdom
| | - K Badgley
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - S Baeßler
- University of Virginia, Charlottesville, Virginia, USA
| | - I Bailey
- Lancaster University, Lancaster, United Kingdom
| | - V A Baranov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - E Barlas-Yucel
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - T Barrett
- Cornell University, Ithaca, New York, USA
| | - E Barzi
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - A Basti
- INFN, Sezione di Pisa, Pisa, Italy
- Università di Pisa, Pisa, Italy
| | | | - A Behnke
- Northern Illinois University, DeKalb, Illinois, USA
| | - M Berz
- Michigan State University, East Lansing, Michigan, USA
| | | | - H P Binney
- University of Washington, Seattle, Washington, USA
| | | | - P Bloom
- North Central College, Naperville, Illinois, USA
| | - J Bono
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - E Bottalico
- INFN, Sezione di Pisa, Pisa, Italy
- Università di Pisa, Pisa, Italy
| | - T Bowcock
- University of Liverpool, Liverpool, United Kingdom
| | - D Boyden
- Northern Illinois University, DeKalb, Illinois, USA
| | - G Cantatore
- INFN, Sezione di Trieste, Trieste, Italy
- Università di Trieste, Trieste, Italy
| | - R M Carey
- Boston University, Boston, Massachusetts, USA
| | - J Carroll
- University of Liverpool, Liverpool, United Kingdom
| | - B C K Casey
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - D Cauz
- INFN Gruppo Collegato di Udine, Sezione di Trieste, Udine, Italy
- Università di Udine, Udine, Italy
| | - S Ceravolo
- INFN, Laboratori Nazionali di Frascati, Frascati, Italy
| | | | - S P Chang
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | | | - S Chappa
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - S Charity
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - R Chislett
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - J Choi
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Z Chu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - T E Chupp
- University of Michigan, Ann Arbor, Michigan, USA
| | - M E Convery
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - A Conway
- Department of Physics, University of Massachusetts, Amherst, Massachusetts, USA
| | - G Corradi
- INFN, Laboratori Nazionali di Frascati, Frascati, Italy
| | - S Corrodi
- Argonne National Laboratory, Lemont, Illinois, USA
| | - L Cotrozzi
- INFN, Sezione di Pisa, Pisa, Italy
- Università di Pisa, Pisa, Italy
| | - J D Crnkovic
- Brookhaven National Laboratory, Upton, New York, USA
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- University of Mississippi, University, Mississippi, USA
| | - S Dabagov
- INFN, Laboratori Nazionali di Frascati, Frascati, Italy
| | | | - P T Debevec
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - P Di Meo
- INFN, Sezione di Napoli, Napoli, Italy
| | | | - R Di Stefano
- INFN, Sezione di Napoli, Napoli, Italy
- Università di Cassino e del Lazio Meridionale, Cassino, Italy
| | - B Drendel
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - A Driutti
- INFN, Sezione di Trieste, Trieste, Italy
- Università di Udine, Udine, Italy
- University of Kentucky, Lexington, Kentucky, USA
| | - V N Duginov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - M Eads
- Northern Illinois University, DeKalb, Illinois, USA
| | - N Eggert
- Cornell University, Ithaca, New York, USA
| | - A Epps
- Northern Illinois University, DeKalb, Illinois, USA
| | - J Esquivel
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - M Farooq
- University of Michigan, Ann Arbor, Michigan, USA
| | - R Fatemi
- University of Kentucky, Lexington, Kentucky, USA
| | - C Ferrari
- INFN, Sezione di Pisa, Pisa, Italy
- Istituto Nazionale di Ottica-Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - M Fertl
- Institute of Physics and Cluster of Excellence PRISMA+, Johannes Gutenberg University Mainz, Mainz, Germany
- University of Washington, Seattle, Washington, USA
| | - A Fiedler
- Northern Illinois University, DeKalb, Illinois, USA
| | - A T Fienberg
- University of Washington, Seattle, Washington, USA
| | - A Fioretti
- INFN, Sezione di Pisa, Pisa, Italy
- Istituto Nazionale di Ottica-Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - D Flay
- Department of Physics, University of Massachusetts, Amherst, Massachusetts, USA
| | - S B Foster
- Boston University, Boston, Massachusetts, USA
| | - H Friedsam
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - E Frlež
- University of Virginia, Charlottesville, Virginia, USA
| | - N S Froemming
- Northern Illinois University, DeKalb, Illinois, USA
- University of Washington, Seattle, Washington, USA
| | - J Fry
- University of Virginia, Charlottesville, Virginia, USA
| | - C Fu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - C Gabbanini
- INFN, Sezione di Pisa, Pisa, Italy
- Istituto Nazionale di Ottica-Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - M D Galati
- INFN, Sezione di Pisa, Pisa, Italy
- Università di Pisa, Pisa, Italy
| | - S Ganguly
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - A Garcia
- University of Washington, Seattle, Washington, USA
| | - D E Gastler
- Boston University, Boston, Massachusetts, USA
| | - J George
- Department of Physics, University of Massachusetts, Amherst, Massachusetts, USA
| | | | - A Gioiosa
- INFN, Sezione di Pisa, Pisa, Italy
- Università del Molise, Campobasso, Italy
| | - K L Giovanetti
- Department of Physics and Astronomy, James Madison University, Harrisonburg, Virginia, USA
| | - P Girotti
- INFN, Sezione di Pisa, Pisa, Italy
- Università di Pisa, Pisa, Italy
| | - W Gohn
- University of Kentucky, Lexington, Kentucky, USA
| | - T Gorringe
- University of Kentucky, Lexington, Kentucky, USA
| | - J Grange
- Argonne National Laboratory, Lemont, Illinois, USA
- University of Michigan, Ann Arbor, Michigan, USA
| | - S Grant
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - F Gray
- Regis University, Denver, Colorado, USA
| | - S Haciomeroglu
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - D Hahn
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | | | - D Hampai
- INFN, Laboratori Nazionali di Frascati, Frascati, Italy
| | - F Han
- University of Kentucky, Lexington, Kentucky, USA
| | - E Hazen
- Boston University, Boston, Massachusetts, USA
| | - J Hempstead
- University of Washington, Seattle, Washington, USA
| | - S Henry
- University of Oxford, Oxford, United Kingdom
| | - A T Herrod
- University of Liverpool, Liverpool, United Kingdom
| | - D W Hertzog
- University of Washington, Seattle, Washington, USA
| | - G Hesketh
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - A Hibbert
- University of Liverpool, Liverpool, United Kingdom
| | - Z Hodge
- University of Washington, Seattle, Washington, USA
| | - J L Holzbauer
- University of Mississippi, University, Mississippi, USA
| | - K W Hong
- University of Virginia, Charlottesville, Virginia, USA
| | - R Hong
- Argonne National Laboratory, Lemont, Illinois, USA
- University of Kentucky, Lexington, Kentucky, USA
| | - M Iacovacci
- INFN, Sezione di Napoli, Napoli, Italy
- Università di Napoli, Napoli, Italy
| | | | - C Johnstone
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - J A Johnstone
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - P Kammel
- University of Washington, Seattle, Washington, USA
| | | | - M Karuza
- INFN, Sezione di Trieste, Trieste, Italy
- University of Rijeka, Rijeka, Croatia
| | - J Kaspar
- University of Washington, Seattle, Washington, USA
| | - D Kawall
- Department of Physics, University of Massachusetts, Amherst, Massachusetts, USA
| | - L Kelton
- University of Kentucky, Lexington, Kentucky, USA
| | - A Keshavarzi
- Department of Physics and Astronomy, University of Manchester, Manchester, United Kingdom
| | - D Kessler
- Department of Physics, University of Massachusetts, Amherst, Massachusetts, USA
| | - K S Khaw
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
- Tsung-Dao Lee Institute, Shanghai Jiao Tong University, Shanghai, China
- University of Washington, Seattle, Washington, USA
| | | | - N V Khomutov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - B Kiburg
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - M Kiburg
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
- North Central College, Naperville, Illinois, USA
| | - O Kim
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - S C Kim
- Cornell University, Ithaca, New York, USA
| | - Y I Kim
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - B King
- University of Liverpool, Liverpool, United Kingdom
| | - N Kinnaird
- Boston University, Boston, Massachusetts, USA
| | | | - I Kourbanis
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - E Kraegeloh
- University of Michigan, Ann Arbor, Michigan, USA
| | - V A Krylov
- Joint Institute for Nuclear Research, Dubna, Russia
| | - A Kuchibhotla
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - K R Labe
- Cornell University, Ithaca, New York, USA
| | - J LaBounty
- University of Washington, Seattle, Washington, USA
| | - M Lancaster
- Department of Physics and Astronomy, University of Manchester, Manchester, United Kingdom
| | - M J Lee
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - S Lee
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - S Leo
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - B Li
- Argonne National Laboratory, Lemont, Illinois, USA
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - D Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - L Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - I Logashenko
- Budker Institute of Nuclear Physics, Novosibirsk, Russia
| | | | - A Lucà
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - G Lukicov
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - G Luo
- Northern Illinois University, DeKalb, Illinois, USA
| | - A Lusiani
- INFN, Sezione di Pisa, Pisa, Italy
- Scuola Normale Superiore, Pisa, Italy
| | - A L Lyon
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - B MacCoy
- University of Washington, Seattle, Washington, USA
| | - R Madrak
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - K Makino
- Michigan State University, East Lansing, Michigan, USA
| | - F Marignetti
- INFN, Sezione di Napoli, Napoli, Italy
- Università di Cassino e del Lazio Meridionale, Cassino, Italy
| | | | - S Maxfield
- University of Liverpool, Liverpool, United Kingdom
| | - M McEvoy
- Northern Illinois University, DeKalb, Illinois, USA
| | - W Merritt
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | | | - J P Miller
- Boston University, Boston, Massachusetts, USA
| | - S Miozzi
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
| | - J P Morgan
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - W M Morse
- Brookhaven National Laboratory, Upton, New York, USA
| | - J Mott
- Boston University, Boston, Massachusetts, USA
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - E Motuk
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - A Nath
- INFN, Sezione di Napoli, Napoli, Italy
- Università di Napoli, Napoli, Italy
| | - D Newton
- University of Liverpool, Liverpool, United Kingdom
| | - H Nguyen
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - M Oberling
- Argonne National Laboratory, Lemont, Illinois, USA
| | - R Osofsky
- University of Washington, Seattle, Washington, USA
| | - J-F Ostiguy
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - S Park
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - G Pauletta
- INFN Gruppo Collegato di Udine, Sezione di Trieste, Udine, Italy
- Università di Udine, Udine, Italy
| | - G M Piacentino
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
- Università del Molise, Campobasso, Italy
| | - R N Pilato
- INFN, Sezione di Pisa, Pisa, Italy
- Università di Pisa, Pisa, Italy
| | - K T Pitts
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - B Plaster
- University of Kentucky, Lexington, Kentucky, USA
| | - D Počanić
- University of Virginia, Charlottesville, Virginia, USA
| | - N Pohlman
- Northern Illinois University, DeKalb, Illinois, USA
| | - C C Polly
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - M Popovic
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - J Price
- University of Liverpool, Liverpool, United Kingdom
| | - B Quinn
- University of Mississippi, University, Mississippi, USA
| | - N Raha
- INFN, Sezione di Pisa, Pisa, Italy
| | | | - E Ramberg
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - N T Rider
- Cornell University, Ithaca, New York, USA
| | - J L Ritchie
- Department of Physics, University of Texas at Austin, Austin, Texas, USA
| | - B L Roberts
- Boston University, Boston, Massachusetts, USA
| | - D L Rubin
- Cornell University, Ithaca, New York, USA
| | - L Santi
- INFN Gruppo Collegato di Udine, Sezione di Trieste, Udine, Italy
- Università di Udine, Udine, Italy
| | - D Sathyan
- Boston University, Boston, Massachusetts, USA
| | - H Schellman
- Northwestern University, Evanston, Illinois, USA
| | - C Schlesier
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - A Schreckenberger
- Boston University, Boston, Massachusetts, USA
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Physics, University of Texas at Austin, Austin, Texas, USA
| | - Y K Semertzidis
- Center for Axion and Precision Physics (CAPP)/Institute for Basic Science (IBS), Daejeon, Republic of Korea
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Y M Shatunov
- Budker Institute of Nuclear Physics, Novosibirsk, Russia
| | - D Shemyakin
- Budker Institute of Nuclear Physics, Novosibirsk, Russia
| | - M Shenk
- Northern Illinois University, DeKalb, Illinois, USA
| | - D Sim
- University of Liverpool, Liverpool, United Kingdom
| | - M W Smith
- INFN, Sezione di Pisa, Pisa, Italy
- University of Washington, Seattle, Washington, USA
| | - A Smith
- University of Liverpool, Liverpool, United Kingdom
| | - A K Soha
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - M Sorbara
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
- Università di Roma Tor Vergata, Rome, Italy
| | - D Stöckinger
- Institut für Kern-und Teilchenphysik, Technische Universität Dresden, Dresden, Germany
| | - J Stapleton
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - D Still
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - C Stoughton
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - D Stratakis
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - C Strohman
- Cornell University, Ithaca, New York, USA
| | - T Stuttard
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - H E Swanson
- University of Washington, Seattle, Washington, USA
| | - G Sweetmore
- Department of Physics and Astronomy, University of Manchester, Manchester, United Kingdom
| | | | - M J Syphers
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
- Northern Illinois University, DeKalb, Illinois, USA
| | - D A Tarazona
- Michigan State University, East Lansing, Michigan, USA
| | - T Teubner
- University of Liverpool, Liverpool, United Kingdom
| | | | - K Thomson
- University of Liverpool, Liverpool, United Kingdom
| | - V Tishchenko
- Brookhaven National Laboratory, Upton, New York, USA
| | - N H Tran
- Boston University, Boston, Massachusetts, USA
| | - W Turner
- University of Liverpool, Liverpool, United Kingdom
| | - E Valetov
- Lancaster University, Lancaster, United Kingdom
- Michigan State University, East Lansing, Michigan, USA
- Tsung-Dao Lee Institute, Shanghai Jiao Tong University, Shanghai, China
| | - D Vasilkova
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | | | - V P Volnykh
- Joint Institute for Nuclear Research, Dubna, Russia
| | - T Walton
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - M Warren
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - A Weisskopf
- Michigan State University, East Lansing, Michigan, USA
| | - L Welty-Rieger
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
| | - M Whitley
- University of Liverpool, Liverpool, United Kingdom
| | - P Winter
- Argonne National Laboratory, Lemont, Illinois, USA
| | - A Wolski
- University of Liverpool, Liverpool, United Kingdom
| | - M Wormald
- University of Liverpool, Liverpool, United Kingdom
| | - W Wu
- University of Mississippi, University, Mississippi, USA
| | - C Yoshikawa
- Fermi National Accelerator Laboratory, Batavia, Illinois, USA
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21
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Yee MO, Kim P, Li Y, Singh AK, Northen TR, Chakraborty R. Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions. Front Microbiol 2021; 12:625752. [PMID: 33841353 PMCID: PMC8032546 DOI: 10.3389/fmicb.2021.625752] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
The rhizosphere is a dynamic ecosystem shaped by complex interactions between plant roots, soil, microbial communities and other micro- and macro-fauna. Although studied for decades, critical gaps exist in the study of plant roots, the rhizosphere microbiome and the soil system surrounding roots, partly due to the challenges associated with measuring and parsing these spatiotemporal interactions in complex heterogeneous systems such as soil. To overcome the challenges associated with in situ study of rhizosphere interactions, specialized plant growth chamber systems have been developed that mimic the natural growth environment. This review discusses the currently available lab-based systems ranging from widely known rhizotrons to other emerging devices designed to allow continuous monitoring and non-destructive sampling of the rhizosphere ecosystems in real-time throughout the developmental stages of a plant. We categorize them based on the major rhizosphere processes it addresses and identify their unique challenges as well as advantages. We find that while some design elements are shared among different systems (e.g., size exclusion membranes), most of the systems are bespoke and speaks to the intricacies and specialization involved in unraveling the details of rhizosphere processes. We also discuss what we describe as the next generation of growth chamber employing the latest technology as well as the current barriers they face. We conclude with a perspective on the current knowledge gaps in the rhizosphere which can be filled by innovative chamber designs.
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Affiliation(s)
- Mon Oo Yee
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter Kim
- CBRN Defense and Energy Technologies, Sandia National Laboratories, Livermore, CA, United States
| | - Yifan Li
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anup K. Singh
- CBRN Defense and Energy Technologies, Sandia National Laboratories, Livermore, CA, United States
| | - Trent R. Northen
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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22
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Balarjishvili N, Kvachadze L, Tevdoradze E, Skhirtladze N, Leshkasheli L, Bolkvadze D, Pataridze T, Meskhi T, Chakraborty R, Kutateladze M, Torok T. Significance of lysogeny for the metabolism of Desulfovibrio spp. strains isolated from aquatic environments of Georgia. J Appl Microbiol 2021; 131:1344-1359. [PMID: 33555060 DOI: 10.1111/jam.15030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 01/21/2023]
Abstract
AIMS Sulphate-reducing bacteria (SRB) are ecologically important group of anaerobic micro-organisms that can reduce sulphate to form hydrogen sulphide-a toxic gas causing iron corrosion on metal surfaces. In this work, SRB strains were isolated from aquatic environments in the country of Georgia to determine their lysogenicity and the role of temperate phages in host metabolism. METHODS AND RESULTS SRB strains were isolated in samples from the Black Sea coast of Georgia. Based on their genetic, cytological and physiological properties of bacteria, 10 Georgian isolates were assigned to the genus Desulfovibrio. Temperate bacteriophages were induced from three out of ten strains by UV-exposure. Comparison of metal (Fe and Cr) reduction and utilization of various carbon sources by the wild-type (lysogenic) bacterial strains and their UV-irradiated counterparts was done. CONCLUSIONS Temperate phage in the cells of SRB could alter significant functions of bacteria and may have a contribution in the acquisition of different traits by SRB. SIGNIFICANCE AND IMPACT OF THE STUDY This article pointed to a significant role for temperate bacteriophages in the metabolism and metabolic potential of host strains of SRB, which were first isolated from the aquatic environment of Georgia.
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Affiliation(s)
- N Balarjishvili
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - L Kvachadze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - E Tevdoradze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - N Skhirtladze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - L Leshkasheli
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - D Bolkvadze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA.,Ilia State University, Tbilisi, GA, USA
| | - T Pataridze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - T Meskhi
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - R Chakraborty
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - M Kutateladze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, GA, USA
| | - T Torok
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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23
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Baindara P, Chakraborty R, Holliday Z, Mandal S, Schrum A. Oral probiotics in coronavirus disease 2019: connecting the gut-lung axis to viral pathogenesis, inflammation, secondary infection and clinical trials. New Microbes New Infect 2021; 40:100837. [PMID: 33425362 PMCID: PMC7785423 DOI: 10.1016/j.nmni.2021.100837] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/12/2020] [Accepted: 12/31/2020] [Indexed: 01/07/2023] Open
Abstract
Defined as helpful live bacteria that can provide medical advantages to the host when administered in tolerable amounts, oral probiotics might be worth considering as a possible preventive or therapeutic modality to mitigate coronavirus disease 2019 (COVID-19) symptom severity. This hypothesis stems from an emerging understanding of the gut-lung axis wherein probiotic microbial species in the digestive tract can influence systemic immunity, lung immunity, and possibly viral pathogenesis and secondary infection co-morbidities. We review the principles underlying the gut-lung axis, examples of probiotic-associated antiviral activities, and current clinical trials in COVID-19 based on oral probiotics.
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Affiliation(s)
- P. Baindara
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO, USA,Corresponding author: P. Baindara, Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
| | - R. Chakraborty
- Department of Biotechnology, North Bengal University, Darjeeling, India
| | - Z.M. Holliday
- Pulmonary Disease, Critical Care Medicine, School of Medicine, University of Missouri, Columbia, MO, USA
| | - S.M. Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, India,Corresponding author: S.M. Mandal, Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur, India.
| | - A.G. Schrum
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO, USA,Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, USA,Department of Biomedical, Biological, & Chemical Engineering, College of Engineering, University of Missouri, Columbia, MO, USA,Corresponding author: A. Schrum, Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
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24
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Raina R, DeCoy M, Chakraborty R, Mahajan S, Moran R, Gibson K, Kumar D, Bergmann C. Renal cystic diseases during the perinatal and neonatal period. J Neonatal Perinatal Med 2021; 14:163-176. [PMID: 32986687 DOI: 10.3233/npm-200520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Renal cystic diseases are a clinically and genetically diverse group of renal diseases that can manifest in utero, infancy, or throughout childhood and adulthood. These diseases may be unilateral or bilateral with a single cyst or multiple cysts, or with increased echogenicity of the renal cortex without macroscopic cysts. Certain cystic renal diseases are life-threatening, with many developing chronic kidney and hepatic disease if not recognized early enough. Therefore, due to the prevalence and life-altering complications of this specific group of diseases in vulnerable populations, it is crucial for clinicians and healthcare providers to have an overall understanding of cystic diseases and how to pre-emptively detect and manage these conditions. In this review, we discuss in detail the epidemiology, genetics and pathophysiology, diagnosis, presentation, and management of numerous genetic and sporadic renal cystic diseases, such as polycystic kidney disease, multicystic dysplastic kidney, and calyceal diverticula, with an emphasis on prenatal care and pregnancy counseling.
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Affiliation(s)
- R Raina
- Department of Nephrology, Akron Children's Hospital, Akron, OH, USA
- Akron Nephrology Associates/Cleveland Clinic Akron General, Akron, OH, USA
| | - M DeCoy
- Department of Pediatrics, Akron Children's Hospital, Akron, OH, USA
| | - R Chakraborty
- Department of Nephrology, Akron Children's Hospital, Akron, OH, USA
- Akron Nephrology Associates/Cleveland Clinic Akron General, Akron, OH, USA
| | - S Mahajan
- Revere High School, Richfield, OH, USA
| | - R Moran
- Department of Genetics, MetroHealth Medical Center/Case Western Reserve University, Cleveland, OH, USA
| | - K Gibson
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, MetroHealth Medical Center/Case Western Reserve University, Cleveland, OH, USA
| | - D Kumar
- Department of Pediatrics, Division of Neonatology, MetroHealth Medical Center/Case Western Reserve University, Cleveland, OH, USA
| | - C Bergmann
- Department of Medicine, Nephrology, University Hospital Freiburg, Freiburg, Germany
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25
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Wu X, Spencer S, Gushgari-Doyle S, Yee MO, Voriskova J, Li Y, Alm EJ, Chakraborty R. Culturing of "Unculturable" Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater. Front Microbiol 2020; 11:610001. [PMID: 33391234 PMCID: PMC7773641 DOI: 10.3389/fmicb.2020.610001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/19/2020] [Indexed: 11/23/2022] Open
Abstract
Recovery and cultivation of diverse environmentally-relevant microorganisms from the terrestrial subsurface remain a challenge despite recent advances in modern molecular technology. Here, we applied complex carbon (C) sources, i.e., sediment dissolved organic matter (DOM) and bacterial cell lysate, to enrich groundwater microbial communities for 30 days. As comparisons, we also included enrichments amended with simple C sources including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins. Our results demonstrate that complex C is far more effective in enriching diverse and distinct microorganisms from groundwater than simple C. Simple C enrichments yield significantly lower biodiversity, and are dominated by few phyla (e.g., Proteobacteria and Bacteroidetes), while microcosms enriched with complex C demonstrate significantly higher biodiversity including phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia, Planctomycetes, and Armatimonadetes). Subsequent isolation from complex C enrichments yielded 228 bacterial isolates representing five phyla, 17 orders, and 56 distinct species, including candidate novel, rarely cultivated, and undescribed organisms. Results from this study will substantially advance cultivation and isolation strategies for recovering diverse and novel subsurface microorganisms. Obtaining axenic representatives of “once-unculturable” microorganisms will enhance our understanding of microbial physiology and function in different biogeochemical niches of terrestrial subsurface ecosystems.
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Affiliation(s)
- Xiaoqin Wu
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sarah Spencer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sara Gushgari-Doyle
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mon Oo Yee
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jana Voriskova
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yifan Li
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Romy Chakraborty
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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26
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Ge X, Thorgersen MP, Poole FL, Deutschbauer AM, Chandonia JM, Novichkov PS, Gushgari-Doyle S, Lui LM, Nielsen T, Chakraborty R, Adams PD, Arkin AP, Hazen TC, Adams MWW. Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation. Front Microbiol 2020; 11:587127. [PMID: 33193240 PMCID: PMC7604516 DOI: 10.3389/fmicb.2020.587127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
A nitrate- and metal-contaminated site at the Oak Ridge Reservation (ORR) was previously shown to contain the metal molybdenum (Mo) at picomolar concentrations. This potentially limits microbial nitrate reduction, as Mo is required by the enzyme nitrate reductase, which catalyzes the first step of nitrate removal. Enrichment for anaerobic nitrate-reducing microbes from contaminated sediment at the ORR yielded Bacillus strain EB106-08-02-XG196. This bacterium grows in the presence of multiple metals (Cd, Ni, Cu, Co, Mn, and U) but also exhibits better growth compared to control strains, including Pseudomonas fluorescens N2E2 isolated from a pristine ORR environment under low molybdate concentrations (<1 nM). Molybdate is taken up by the molybdate binding protein, ModA, of the molybdate ATP-binding cassette transporter. ModA of XG196 is phylogenetically distinct from those of other characterized ModA proteins. The genes encoding ModA from XG196, P. fluorescens N2E2 and Escherichia coli K12 were expressed in E. coli and the recombinant proteins were purified. Isothermal titration calorimetry analysis showed that XG196 ModA has a higher affinity for molybdate than other ModA proteins with a molybdate binding constant (KD) of 2.2 nM, about one order of magnitude lower than those of P. fluorescens N2E2 (27.0 nM) and E. coli K12 (25.0 nM). XG196 ModA also showed a fivefold higher affinity for molybdate than for tungstate (11 nM), whereas the ModA proteins from P. fluorescens N2E2 [KD (Mo) 27.0 nM, KD (W) 26.7 nM] and E. coli K12[(KD (Mo) 25.0 nM, KD (W) 23.8 nM] had similar affinities for the two oxyanions. We propose that high molybdate affinity coupled with resistance to multiple metals gives strain XG196 a competitive advantage in Mo-limited environments contaminated with high concentrations of metals and nitrate, as found at ORR.
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Affiliation(s)
- Xiaoxuan Ge
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Pavel S Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sara Gushgari-Doyle
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Torben Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Paul D Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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27
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Acharya SM, Chakraborty R, Tringe SG. Emerging Trends in Biological Treatment of Wastewater From Unconventional Oil and Gas Extraction. Front Microbiol 2020; 11:569019. [PMID: 33013800 PMCID: PMC7509137 DOI: 10.3389/fmicb.2020.569019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/19/2020] [Indexed: 01/16/2023] Open
Abstract
Unconventional oil and gas exploration generates an enormous quantity of wastewater, commonly referred to as flowback and produced water (FPW). Limited freshwater resources and stringent disposal regulations have provided impetus for FPW reuse. Organic and inorganic compounds released from the shale/brine formation, microbial activity, and residual chemicals added during hydraulic fracturing bestow a unique as well as temporally varying chemical composition to this wastewater. Studies indicate that many of the compounds found in FPW are amenable to biological degradation, indicating biological treatment may be a viable option for FPW processing and reuse. This review discusses commonly characterized contaminants and current knowledge on their biodegradability, including the enzymes and organisms involved. Further, a perspective on recent novel hybrid biological treatments and application of knowledge gained from omics studies in improving these treatments is explored.
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Affiliation(s)
- Shwetha M Acharya
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Susannah G Tringe
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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28
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Moon JW, Paradis CJ, Joyner DC, von Netzer F, Majumder EL, Dixon ER, Podar M, Ge X, Walian PJ, Smith HJ, Wu X, Zane GM, Walker KF, Thorgersen MP, Poole Ii FL, Lui LM, Adams BG, De León KB, Brewer SS, Williams DE, Lowe KA, Rodriguez M, Mehlhorn TL, Pfiffner SM, Chakraborty R, Arkin AP, Wall JD, Fields MW, Adams MWW, Stahl DA, Elias DA, Hazen TC. Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer. Chemosphere 2020; 255:126951. [PMID: 32417512 DOI: 10.1016/j.chemosphere.2020.126951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/17/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.
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Affiliation(s)
- Ji-Won Moon
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA; current U.S. Geological Survey, National Minerals Information Center, Reston, VA, USA
| | - Charles J Paradis
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Dominique C Joyner
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Frederick von Netzer
- University of Washington, Department of Civil and Environmental Engineering, Seattle, WA, USA
| | - Erica L Majumder
- University of Missouri, Department of Biochemistry, Columbia, MO, USA
| | - Emma R Dixon
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Mircea Podar
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Xiaoxuan Ge
- University of Georgia, Department of Biochemistry and Molecular Biology, Athens, GA, USA
| | - Peter J Walian
- Lawrence Berkeley National Laboratory, Molecular Biophysics and Integrated Bioimaging, Berkeley, CA, USA
| | - Heidi J Smith
- Montana State University, Center for Biofilm Engineering, Department of Microbiology & Immunology, Bozeman, MT, USA
| | - Xiaoqin Wu
- Lawrence Berkeley National Laboratory, Department of Ecology, Earth and Environmental Sciences Area, Berkeley, CA, USA
| | - Grant M Zane
- University of Missouri, Department of Biochemistry, Columbia, MO, USA
| | - Kathleen F Walker
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Michael P Thorgersen
- University of Georgia, Department of Biochemistry and Molecular Biology, Athens, GA, USA
| | - Farris L Poole Ii
- University of Georgia, Department of Biochemistry and Molecular Biology, Athens, GA, USA
| | - Lauren M Lui
- Lawrence Berkeley National Laboratory Environmental Genomics and Systems Biology, Berkeley, CA, USA
| | - Benjamin G Adams
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Kara B De León
- University of Missouri, Department of Biochemistry, Columbia, MO, USA
| | - Sheridan S Brewer
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Daniel E Williams
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Kenneth A Lowe
- Oak Ridge National Laboratory, Environmental Science Division, Oak Ridge, TN, USA
| | - Miguel Rodriguez
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Tonia L Mehlhorn
- Oak Ridge National Laboratory, Environmental Science Division, Oak Ridge, TN, USA
| | - Susan M Pfiffner
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Romy Chakraborty
- Lawrence Berkeley National Laboratory, Department of Ecology, Earth and Environmental Sciences Area, Berkeley, CA, USA
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory Environmental Genomics and Systems Biology, Berkeley, CA, USA
| | - Judy D Wall
- University of Missouri, Department of Biochemistry, Columbia, MO, USA
| | - Matthew W Fields
- Montana State University, Center for Biofilm Engineering, Department of Microbiology & Immunology, Bozeman, MT, USA
| | - Michael W W Adams
- University of Georgia, Department of Biochemistry and Molecular Biology, Athens, GA, USA
| | - David A Stahl
- University of Washington, Department of Civil and Environmental Engineering, Seattle, WA, USA
| | - Dwayne A Elias
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Terry C Hazen
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA; University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA.
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29
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Sanber K, Nawas Z, Salsman V, Gad A, Mathew P, Landi D, Lee C, Sengal A, Chakraborty R, Joseph S, Ahmed N, Hegde M. Modulation of inhibitory receptor signaling pathways improves CAR T cell activity against glioblastoma. Cytotherapy 2020. [DOI: 10.1016/j.jcyt.2020.03.489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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30
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Bajpai V, Singh P, Chakraborty R, Bhardwaj N, Mathur P. Anti-microbial-resistance and profile of exotoxins of invasive beta-haemolytic-streptococci infections in trauma patients. J Infect Public Health 2020. [DOI: 10.1016/j.jiph.2020.01.140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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31
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Couradeau E, Sasse J, Goudeau D, Nath N, Hazen TC, Bowen BP, Chakraborty R, Malmstrom RR, Northen TR. Probing the active fraction of soil microbiomes using BONCAT-FACS. Nat Commun 2019; 10:2770. [PMID: 31235780 PMCID: PMC6591230 DOI: 10.1038/s41467-019-10542-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 05/07/2019] [Indexed: 01/17/2023] Open
Abstract
The ability to link soil microbial diversity to soil processes requires technologies that differentiate active microbes from extracellular DNA and dormant cells. Here, we use BONCAT (bioorthogonal non-canonical amino acid tagging) to measure translationally active cells in soils. We compare the active population of two soil depths from Oak Ridge (Tennessee, USA) and find that a maximum of 25-70% of the extractable cells are active. Analysis of 16S rRNA sequences from BONCAT-positive cells recovered by fluorescence-activated cell sorting (FACS) reveals that the phylogenetic composition of the active fraction is distinct from the total population of extractable cells. Some members of the community are found to be active at both depths independently of their abundance rank, suggesting that the incubation conditions favor the activity of similar organisms. We conclude that BONCAT-FACS is effective for interrogating the active fraction of soil microbiomes in situ and provides a new approach for uncovering the links between soil processes and specific microbial groups.
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Affiliation(s)
- Estelle Couradeau
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joelle Sasse
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danielle Goudeau
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Nandita Nath
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Terry C Hazen
- University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ben P Bowen
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Romy Chakraborty
- Earth Science and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex R Malmstrom
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA.
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32
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Xia M, Fu D, Chakraborty R, Singh RP, Terry N. Enhanced crude oil depletion by constructed bacterial consortium comprising bioemulsifier producer and petroleum hydrocarbon degraders. Bioresour Technol 2019; 282:456-463. [PMID: 30889537 DOI: 10.1016/j.biortech.2019.01.131] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 05/26/2023]
Abstract
The aim of this work was to study the production of bioemulsifier by Rhodococcus erythropolis OSDS1, and the improvement of crude oil depletion efficiency using a consortium of petroleum hydrocarbon degraders and OSDS1. The results showed that R. erythropolis OSDS1 produced highly stable bioemulsifier under various salinity (0-35 g/L NaCl) and pH (5.0-9.0) conditions; more than 90% of the initial emulsification activity was retained after 168 h. Emulsification capacity of the bioemulsifier on different petroleum hydrocarbons was diesel > mineral oil/crude oil > gasoline. A mixed bacterial consortium combining OSDS1 and four other petroleum hydrocarbon degraders was constructed. GC-MS results revealed that the constructed consortium achieved 85.26% depletion efficiency of crude oil in 15 days, which was significantly higher than that of individual strains. During the process, alkane hydroxylase gene (alkB) was successfully amplified from the consortium, confirming presence of crude oil degrading enzymes.
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Affiliation(s)
- Mingqian Xia
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 210096, China; Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, United States
| | - Dafang Fu
- School of Civil Engineering, Southeast University, Nanjing, Jiangsu 210096, China.
| | - Romy Chakraborty
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | | | - Norman Terry
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, United States
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33
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Vuono DC, Read RW, Hemp J, Sullivan BW, Arnone JA, Neveux I, Blank RR, Loney E, Miceli D, Winkler MKH, Chakraborty R, Stahl DA, Grzymski JJ. Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium. Front Microbiol 2019; 10:3. [PMID: 30723459 PMCID: PMC6349771 DOI: 10.3389/fmicb.2019.00003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/07/2019] [Indexed: 11/30/2022] Open
Abstract
Respiratory ammonification and denitrification are two evolutionarily unrelated dissimilatory nitrogen (N) processes central to the global N cycle, the activity of which is thought to be controlled by carbon (C) to nitrate (NO3 -) ratio. Here we find that Intrasporangium calvum C5, a novel dual-pathway denitrifier/respiratory ammonifier, disproportionately utilizes ammonification rather than denitrification when grown under low C concentrations, even at low C:NO3 - ratios. This finding is in conflict with the paradigm that high C:NO3 - ratios promote ammonification and low C:NO3 - ratios promote denitrification. We find that the protein atomic composition for denitrification modules (NirK) are significantly cost minimized for C and N compared to ammonification modules (NrfA), indicating that limitation for C and N is a major evolutionary selective pressure imprinted in the architecture of these proteins. The evolutionary precedent for these findings suggests ecological importance for microbial activity as evidenced by higher growth rates when I. calvum grows predominantly using its ammonification pathway and by assimilating its end-product (ammonium) for growth under ammonium-free conditions. Genomic analysis of I. calvum further reveals a versatile ecophysiology to cope with nutrient stress and redox conditions. Metabolite and transcriptional profiles during growth indicate that enzyme modules, NrfAH and NirK, are not constitutively expressed but rather induced by nitrite production via NarG. Mechanistically, our results suggest that pathway selection is driven by intracellular redox potential (redox poise), which may be lowered when resource concentrations are low, thereby decreasing catalytic activity of upstream electron transport steps (i.e., the bc1 complex) needed for denitrification enzymes. Our work advances our understanding of the biogeochemical flexibility of N-cycling organisms, pathway evolution, and ecological food-webs.
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Affiliation(s)
- David C. Vuono
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Robert W. Read
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - James Hemp
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Benjamin W. Sullivan
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, Reno, NV, United States
| | - John A. Arnone
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - Iva Neveux
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - Robert R. Blank
- Agricultural Research Service, United States Department of Agriculture, Reno, NV, United States
| | - Evan Loney
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - David Miceli
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - Mari-Karoliina H. Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Joseph J. Grzymski
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
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34
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Carlson HK, Price MN, Callaghan M, Aaring A, Chakraborty R, Liu H, Kuehl JV, Arkin AP, Deutschbauer AM. The selective pressures on the microbial community in a metal-contaminated aquifer. ISME J 2018; 13:937-949. [PMID: 30523276 PMCID: PMC6461962 DOI: 10.1038/s41396-018-0328-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/12/2018] [Accepted: 11/22/2018] [Indexed: 12/25/2022]
Abstract
In many environments, toxic compounds restrict which microorganisms persist. However, in complex mixtures of inhibitory compounds, it is challenging to determine which specific compounds cause changes in abundance and prevent some microorganisms from growing. We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions. In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus. Rhodanobacter abundance is positively correlated with low pH and high concentrations of uranium and 13 other ions and we sought to determine which of these ions are selective pressures that favor the growth of Rhodanobacter over other taxa. Of these ions, low pH and high UO22+, Mn2+, Al3+, Cd2+, Zn2+, Co2+, and Ni2+ are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well, and (b) reach toxic concentrations (for the Pseudomonas isolate) in the Rhodanobacter-dominated wells. We used mixtures of ions to simulate the groundwater conditions in the most contaminated wells and verified that few isolates aside from Rhodanobacter can tolerate these eight ions. These results clarify which ions are likely causal factors that impact the microbial community at this field site and are not merely correlated with taxonomic shifts. Furthermore, our general high-throughput approach can be applied to other environments, isolates, and conditions to systematically help identify selective pressures on microbial communities.
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Affiliation(s)
- Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mark Callaghan
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex Aaring
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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35
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Smith HJ, Zelaya AJ, De León KB, Chakraborty R, Elias DA, Hazen TC, Arkin AP, Cunningham AB, Fields MW. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. FEMS Microbiol Ecol 2018; 94:5107865. [PMID: 30265315 PMCID: PMC6192502 DOI: 10.1093/femsec/fiy191] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/26/2018] [Indexed: 12/12/2022] Open
Abstract
Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.
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Affiliation(s)
- H J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A J Zelaya
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - K B De León
- Department of Biochemistry, University of Missouri, Columbia, MO
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - R Chakraborty
- Climate and Ecosystems Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - D A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - T C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A P Arkin
- Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A B Cunningham
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Civil Engineering, Montana State University, Montana State University, Bozeman, MT
| | - M W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
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36
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Wu X, Wu L, Liu Y, Zhang P, Li Q, Zhou J, Hess NJ, Hazen TC, Yang W, Chakraborty R. Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession. Front Microbiol 2018; 9:1234. [PMID: 29937762 PMCID: PMC6002664 DOI: 10.3389/fmicb.2018.01234] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/22/2018] [Indexed: 01/06/2023] Open
Abstract
Knowledge of dynamic interactions between natural organic matter (NOM) and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C) fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM) to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soft X-ray absorption spectroscopy (sXAS). We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC) decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in subsurface groundwater.
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Affiliation(s)
- Xiaoqin Wu
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States
| | - Yina Liu
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.,Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, United States
| | - Ping Zhang
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States
| | - Qinghao Li
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,National Key Laboratory of Crystal Materials, School of Physics, Shandong University, Jinan, China
| | - Jizhong Zhou
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Nancy J Hess
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Institute for a Secure and Sustainable Environment, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wanli Yang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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37
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Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 2018; 557:503-509. [PMID: 29769716 DOI: 10.1038/s41586-018-0124-0] [Citation(s) in RCA: 285] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 04/09/2018] [Indexed: 01/25/2023]
Abstract
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth conditions. We identified mutant phenotypes for 11,779 protein-coding genes that had not been annotated with a specific function. Many genes could be associated with a specific condition because the gene affected fitness only in that condition, or with another gene in the same bacterium because they had similar mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that have high confidence because they are conserved in other bacteria. By combining these conserved associations with comparative genomics, we identified putative DNA repair proteins; in addition, we propose specific functions for poorly annotated enzymes and transporters and for uncharacterized protein families. Our study demonstrates the scalability of microbial genetics and its utility for improving gene annotations.
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Affiliation(s)
- Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R Jordan Waters
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mark Callaghan
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jayashree Ray
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ryan A Melnyk
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jacob S Lamson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yumi Suh
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zuelma Esquivel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Harini Sadeeshkumar
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Romy Chakraborty
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Benjamin E Rubin
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Axel Visel
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Natural Sciences, University of California, Merced, CA, USA
| | - James Bristow
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew J Blow
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, CA, USA.
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
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38
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Jenkins S, Swenson TL, Lau R, Rocha AM, Aaring A, Hazen TC, Chakraborty R, Northen TR. Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites. Front Microbiol 2017; 8:2618. [PMID: 29312276 PMCID: PMC5744445 DOI: 10.3389/fmicb.2017.02618] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/15/2017] [Indexed: 11/13/2022] Open
Abstract
Exometabolomics enables analysis of metabolite utilization of low molecular weight organic substances by soil bacteria. Environmentally-based defined media are needed to examine ecologically relevant patterns of substrate utilization. Here, we describe an approach for the construction of defined media using untargeted characterization of water soluble soil microbial metabolites from a saprolite soil collected from the Oak Ridge Field Research Center (ORFRC). To broadly characterize metabolites, both liquid chromatography mass spectrometry (LC/MS) and gas chromatography mass spectrometry (GC/MS) were used. With this approach, 96 metabolites were identified, including amino acids, amino acid derivatives, sugars, sugar alcohols, mono- and di-carboxylic acids, nucleobases, and nucleosides. From this pool of metabolites, 25 were quantified. Molecular weight cut-off filtration determined the fraction of carbon accounted for by the quantified metabolites and revealed that these soil metabolites have an uneven quantitative distribution (e.g., trehalose accounted for 9.9% of the <1 kDa fraction). This quantitative information was used to formulate two soil defined media (SDM), one containing 23 metabolites (SDM1) and one containing 46 (SDM2). To evaluate the viability of the SDM, we examined the growth of 30 phylogenetically diverse soil bacterial isolates from the ORFRC field site. The simpler SDM1 supported the growth of 13 isolates while the more complex SDM2 supported 15 isolates. To investigate SDM1 substrate preferences, one isolate, Pseudomonas corrugata strain FW300-N2E2 was selected for a time-series exometabolomics analysis. Interestingly, it was found that this organism preferred lower-abundance substrates such as guanine, glycine, proline and arginine and glucose and did not utilize the more abundant substrates maltose, mannitol, trehalose and uridine. These results demonstrate the viability and utility of using exometabolomics to construct a tractable environmentally relevant media. We anticipate that this approach can be expanded to other environments to enhance isolation and characterization of diverse microbial communities.
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Affiliation(s)
- Stefan Jenkins
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tami L Swenson
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rebecca Lau
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Andrea M Rocha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Geosyntec Consultants, Knoxville, TN, United States
| | - Alex Aaring
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Terry C Hazen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Civil and Environmental Engineering, University of Tennessee-Knoxville, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, University of Tennessee-Knoxville, Knoxville, TN, United States.,Department of Microbiology, University of Tennessee-Knoxville, Knoxville, TN, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Joint Genome Institute, Walnut Creek, CA, United States
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39
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Kozieł S, Chakraborty R, Bose K. Relationship between temperament and fatness in 11-year-old children and 17-year-old adolescents from Wrocław, Poland. Homo 2017; 68:479-486. [PMID: 29175059 DOI: 10.1016/j.jchb.2017.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 10/12/2017] [Indexed: 11/29/2022]
Abstract
Childhood obesity is increasing globally, and Poland is no exception. Studies indicate that relationship between obesity and psychological well-being is a complex issue and this needs further research. The objective of the present cross sectional study was to analyze the relationship between some temperament components and fatness among children in two developmental periods, approximately before and after adolescence. Participants included 122 children aged 11 years (57 boys and 65 girls), and 153 adolescents aged 17 years (64 boys and 89 girls) from 6 primary and 4 secondary schools in Wrocław, Poland. Height, weight, triceps-, subscapular and abdominal skinfold thicknesses were measured. Temperament was assessed by a questionnaire of Buss and Plomin (1984) in two versions: EAS-C for children completed by parents and EAS-D for youth and adults. Physical activity (PAL) was also assessed by a questionnaire. Mean, median and standard deviation (SD) were calculated and Student's t tests were performed to test for significance of differences between groups. Chi squared (χ2) statistic was used to test the significance of differences in frequencies. Analyses of covariance (ANCOVA) were performed to show the effect of the social - psychological factors on fatness. Controlling for socioeconomic status and physical activity level, activity, as a component of temperament had a significant effect on body fatness. The only component of temperament, which significantly influenced level of fatness in girls, was emotionality. These relationships differed according to sex and the two age groups concerned.
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Affiliation(s)
- S Kozieł
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Science, Rudolf Weigiel 12, 53-114 Wroclaw, Poland.
| | - R Chakraborty
- Department of Anthropology, Dinabandhu Mahavidyalaya, Bongaon, West Bengal, India
| | - K Bose
- Department of Anthropology, Vidyasagar University, Midnapore, West Bengal, India
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Chakraborty R, Muchtar E, Kumar SK, Buadi FK, Dingli D, Dispenzieri A, Hayman SR, Hogan WJ, Kapoor P, Lacy MQ, Leung N, Gertz MA. Elevated pre-transplant C-reactive protein identifies a high-risk subgroup in multiple myeloma patients undergoing delayed autologous stem cell transplantation. Bone Marrow Transplant 2017; 53:155-161. [PMID: 29131152 DOI: 10.1038/bmt.2017.228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/01/2017] [Accepted: 09/06/2017] [Indexed: 01/12/2023]
Abstract
The significance of elevated C-reactive protein (CRP) prior to autologous stem cell transplantation (ASCT) in multiple myeloma (MM) has not been studied. We analyzed 1111 MM patients who underwent ASCT at Mayo Clinic from 2007 to 2015. A total of 840 patients (76%) received early ASCT (⩽12 months from diagnosis) and 271 patients (24%) received delayed ASCT (>12 months from diagnosis). Elevated CRP (> upper normal limit (8 mg/L)) was seen in 14% and 22% of patients undergoing early and delayed ASCT, respectively (P=0.003). There was no correlation of CRP with pre-transplant response, bone marrow plasma cell percentage or labeling index. Patients with an elevated CRP had a higher likelihood of having circulating plasma cells prior to ASCT (33 vs 19%; P<0.001). In the early ASCT cohort, the median overall survival (OS) in patients with normal and elevated CRP was not reached and 91 months respectively (P=0.011). In the delayed ASCT cohort, the median OS in respective groups were 73 and 30 months respectively (P<0.001), with elevated CRP being an independent prognostic marker on multivariate analysis (hazard ratio 2.0; 95% confidence interval, 1.0-3.8; P=0.045). Elevated pre-transplant CRP identifies a high-risk population especially in patients undergoing delayed ASCT and should be incorporated in the pre-transplant evaluation.
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Affiliation(s)
- R Chakraborty
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - E Muchtar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - S K Kumar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - F K Buadi
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - D Dingli
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - A Dispenzieri
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - S R Hayman
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - W J Hogan
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - P Kapoor
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - M Q Lacy
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - N Leung
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - M A Gertz
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
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Chakraborty R, Muchtar E, Kumar SK, Buadi FK, Dingli D, Dispenzieri A, Hayman SR, Hogan WJ, Kapoor P, Lacy MQ, Leung N, Warsame R, Kourelis T, Gonsalves W, Gertz MA. Outcomes of maintenance therapy with lenalidomide or bortezomib in multiple myeloma in the setting of early autologous stem cell transplantation. Leukemia 2017; 32:712-718. [PMID: 28848227 DOI: 10.1038/leu.2017.256] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/20/2017] [Accepted: 08/02/2017] [Indexed: 01/04/2023]
Abstract
Post-transplant maintenance is widely used in multiple myeloma (MM); however, there is a lack of data on real-world outcomes. We have analyzed 577 patients with newly diagnosed MM undergoing early auto-transplantation between 2010 and 2015. A total of 341, 132 and 104 patients received no, lenalidomide (Len) or bortezomib (Bort) maintenance, respectively. Patients receiving Len or Bort maintenance had a higher incidence of high-risk cytogenetics by fluorescence in situ hybridization (31% (Len) vs 58% (Bort) vs 8% (No); P<0.001). Len maintenance led to a superior progression-free survival (PFS) compared with no maintenance (median, 37 vs 28 months, respectively; P=0.002; adjusted hazard ratio 0.48 (95% CI, 0.35-0.66)), including in subgroups with ISS stage III disease (median, 40 vs 24 months; P=0.008) and high-risk cytogenetics (median, 27 vs 16 months; P=0.032). Bort maintenance did not confer PFS benefit for the entire cohort, but improved PFS in the high-risk cytogenetic subgroup (median, 28 vs 16 months; P=0.035). Discontinuation due to toxicity was seen in 17 and 7% of patients receiving Len or Bort maintenance, respectively. Our results indicate that post-transplant maintenance with Len or Bort is well tolerated in clinical practice and improves PFS in high-risk subgroups of MM patients.
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Affiliation(s)
- R Chakraborty
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - E Muchtar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - S K Kumar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - F K Buadi
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - D Dingli
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - A Dispenzieri
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - S R Hayman
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - W J Hogan
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - P Kapoor
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - M Q Lacy
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - N Leung
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - R Warsame
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - T Kourelis
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - W Gonsalves
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - M A Gertz
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
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Wu X, Deutschbauer AM, Kazakov AE, Wetmore KM, Cwick BA, Walker RM, Novichkov PS, Arkin AP, Chakraborty R. Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center. Genome Announc 2017; 5:e00582-17. [PMID: 28663297 PMCID: PMC5638281 DOI: 10.1128/genomea.00582-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 05/15/2017] [Indexed: 11/20/2022]
Abstract
We present here the draft genome sequences of two Janthinobacterium lividum strains, GW456P and GW458P, isolated from groundwater samples collected from a background site at the Oak Ridge Field Research Center. Production of a purple pigment by these two strains was observed when grown on diluted (1/10) LB agar plates.
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Affiliation(s)
- Xiaoqin Wu
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Program in Comparative Biochemistry, University of California, Berkeley, California, USA
| | - Bryson A Cwick
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Robert M Walker
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Pavel S Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Tiwary B, Ghosh R, Moktan S, Ranjan V, Dey P, Choudhury D, Dutta S, Deb D, Das A, Chakraborty R. Prospective bacterial quorum sensing inhibitors from Indian medicinal plant extracts. Lett Appl Microbiol 2017; 65:2-10. [DOI: 10.1111/lam.12748] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 11/27/2022]
Affiliation(s)
- B.K. Tiwary
- Omics Laboratory; Department of Biotechnology; University of North Bengal; Siliguri India
- Department of Microbiology; North Bengal St. Xavier's College; Rajganj Jalpaiguri India
| | - R. Ghosh
- Omics Laboratory; Department of Biotechnology; University of North Bengal; Siliguri India
| | - S. Moktan
- Department of Botany; University of Calcutta; Ballygunge India
| | - V.K. Ranjan
- Omics Laboratory; Department of Biotechnology; University of North Bengal; Siliguri India
| | - P. Dey
- Cellular Immunology Laboratory; Department of Zoology; University of North Bengal; Siliguri India
| | - D. Choudhury
- Taxonomy & Environmental Biology Laboratory; Department of Botany; University of North Bengal; Siliguri India
| | - S. Dutta
- Cellular Immunology Laboratory; Department of Zoology; University of North Bengal; Siliguri India
| | - D. Deb
- Omics Laboratory; Department of Biotechnology; University of North Bengal; Siliguri India
| | - A.P. Das
- Taxonomy & Environmental Biology Laboratory; Department of Botany; University of North Bengal; Siliguri India
| | - R. Chakraborty
- Omics Laboratory; Department of Biotechnology; University of North Bengal; Siliguri India
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Muchtar E, Dean DS, Dispenzieri A, Dingli D, Buadi FK, Lacy MQ, Hayman SR, Kapoor P, Leung N, Russell S, Lust JA, Lin Y, Warsame R, Gonsalves W, Kourelis TV, Go RS, Chakraborty R, Zeldenrust S, Kyle RA, Rajkumar SV, Kumar SK, Gertz MA. Prevalence and predictors of thyroid functional abnormalities in newly diagnosed AL amyloidosis. J Intern Med 2017; 281:611-619. [PMID: 28439924 DOI: 10.1111/joim.12617] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Data on the effect of systemic immunoglobulin light chain amyloidosis (AL amyloidosis) on thyroid function are limited. OBJECTIVE To assess the prevalence of hypothyroidism in AL amyloidosis patients and determine its predictors. METHODS 1142 newly diagnosed AL amyloidosis patients were grouped based on the thyroid-stimulating hormone (TSH) measurement at diagnosis: hypothyroid group (TSH above upper normal reference; >5 mIU L-1 ; n = 217, 19% of study participants) and euthyroid group (n = 925, 81%). Predictors for hypothyroidism were assessed in a binary multivariate model. Survival between groups was compared using the log-rank test and a multivariate analysis. RESULTS Patients with hypothyroidism were older, more likely to present with renal and hepatic involvement and had a higher light chain burden compared to patients in the euthyroid group. Higher proteinuria in patients with renal involvement and lower albumin in patients with hepatic involvement were associated with hypothyroidism. In a binary logistic regression model, age ≥65 years, female sex, renal involvement, hepatic involvement, kappa light chain restriction and amiodarone use were independently associated with hypothyroidism. Ninety-three per cent of patients in the hypothyroid group with free thyroxine measurement had normal values, consistent with subclinical hypothyroidism. Patients in the hypothyroid group had a shorter survival compared to patients in the euthyroid group (4-year survival 36% vs 43%; P = 0.008), a difference that was maintained in a multivariate analysis. CONCLUSION A significant proportion of patients with AL amyloidosis present with hypothyroidism, predominantly subclinical, which carries a survival disadvantage. Routine assessment of TSH in these patients is warranted.
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Affiliation(s)
- E Muchtar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - D S Dean
- Division of Diabetes, Endocrinology, Metabolism, and Nutrition, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - A Dispenzieri
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - D Dingli
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - F K Buadi
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - M Q Lacy
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - S R Hayman
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - P Kapoor
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - N Leung
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.,Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - S Russell
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - J A Lust
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Yi Lin
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - R Warsame
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - W Gonsalves
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - T V Kourelis
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - R S Go
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - R Chakraborty
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.,Hospitalist Services, Essentia Health St. Joseph's Hospital, Brainerd, MN, USA
| | - S Zeldenrust
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - R A Kyle
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | - S K Kumar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - M A Gertz
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
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Wendt FR, Pathak G, Sajantila A, Chakraborty R, Budowle B. Global genetic variation of select opiate metabolism genes in self-reported healthy individuals. Pharmacogenomics J 2017; 18:281-294. [PMID: 28398354 DOI: 10.1038/tpj.2017.13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/16/2017] [Accepted: 02/21/2017] [Indexed: 12/26/2022]
Abstract
CYP2D6 is a key pharmacogene encoding an enzyme impacting poor, intermediate, extensive and ultrarapid phase I metabolism of many marketed drugs. The pharmacogenetics of opiate drug metabolism is particularly interesting due to the relatively high incidence of addiction and overdose. Recently, trans-acting opiate metabolism and analgesic response enzymes (UGT2B7, ABCB1, OPRM1 and COMT) have been incorporated into pharmacogenetic studies to generate more comprehensive metabolic profiles of patients. With use of massively parallel sequencing, it is possible to identify additional polymorphisms that fine tune, or redefine, previous pharmacogenetic findings, which typically rely on targeted approaches. The 1000 Genomes Project data were analyzed to describe population genetic variation and statistics for these five genes in self-reported healthy individuals in five global super- and 26 sub-populations. Findings on the variation of these genes in various populations expand baseline understanding of pharmacogenetically relevant polymorphisms for future studies of affected cohorts.
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Affiliation(s)
- F R Wendt
- Institute for Molecular Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - G Pathak
- Institute for Molecular Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - A Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - R Chakraborty
- Institute for Molecular Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - B Budowle
- Institute for Molecular Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA.,Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX USA.,Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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46
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Tandon N, Muchtar E, Sidana S, Dispenzieri A, Lacy MQ, Dingli D, Buadi FK, Hayman SR, Chakraborty R, Hogan WJ, Gonsalves W, Warsame R, Kourelis TV, Leung N, Kapoor P, Kumar SK, Gertz MA. Revisiting conditioning dose in newly diagnosed light chain amyloidosis undergoing frontline autologous stem cell transplant: impact on response and survival. Bone Marrow Transplant 2017; 52:1126-1132. [DOI: 10.1038/bmt.2017.68] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/17/2017] [Accepted: 03/01/2017] [Indexed: 11/09/2022]
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47
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Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, Goodwin LA, Kazakov A, Novichkov P, Arkin AP, Hazen TC. Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Stand Genomic Sci 2017; 12:23. [PMID: 28194258 PMCID: PMC5299692 DOI: 10.1186/s40793-017-0233-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 01/08/2017] [Indexed: 01/21/2023] Open
Abstract
Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier. Experiments with anaerobic washed cell suspension of strain RCH2 revealed it could reduce Cr(VI) and Fe(III). The genome of strain RCH2 was sequenced using a combination of Illumina and 454 sequencing technologies and contained a circular chromosome of 4.6 Mb and three plasmids. Global genome comparisons of strain RCH2 with six other fully sequenced P. stutzeri strains revealed most genomic regions are conserved, however strain RCH2 has an additional 244 genes, some of which are involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex formation.
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Affiliation(s)
| | - Hannah Woo
- University Of Tennessee, Knoxville, TN USA
| | | | - Robert Walker
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Marcin Zemla
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Manfred Auer
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Lynne A Goodwin
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | | | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Terry C Hazen
- Lawrence Berkeley National Laboratory, Berkeley, CA USA.,University Of Tennessee, Knoxville, TN USA
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Jewell TNM, Karaoz U, Bill M, Chakraborty R, Brodie EL, Williams KH, Beller HR. Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer. Front Microbiol 2017; 8:40. [PMID: 28179898 PMCID: PMC5264521 DOI: 10.3389/fmicb.2017.00040] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 01/06/2017] [Indexed: 02/05/2023] Open
Abstract
Organic matter deposits in alluvial aquifers have been shown to result in the formation of naturally reduced zones (NRZs), which can modulate aquifer redox status and influence the speciation and mobility of metals, affecting groundwater geochemistry. In this study, we sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (NRZs) in a shallow alluvial aquifer at the Rifle (CO) site. We conducted a 20-day microcosm experiment in which NRZ sediments, which were enriched in buried woody plant material, served as the sole source of electron donors and microorganisms. The microcosms were constructed and incubated under anaerobic conditions in serum bottles with an initial N2 headspace and were sampled every 5 days for metagenome and metatranscriptome profiles in combination with biogeochemical measurements. Biogeochemical data indicated that the decomposition of native organic matter occurred in different phases, beginning with mineralization of dissolved organic matter (DOM) to CO2 during the first week of incubation, followed by a pulse of acetogenesis that dominated carbon flux after 2 weeks. A pulse of methanogenesis co-occurred with acetogenesis, but only accounted for a small fraction of carbon flux. The depletion of DOM over time was strongly correlated with increases in expression of many genes associated with heterotrophy (e.g., amino acid, fatty acid, and carbohydrate metabolism) belonging to a Hydrogenophaga strain that accounted for a relatively large percentage (~8%) of the metatranscriptome. This Hydrogenophaga strain also expressed genes indicative of chemolithoautotrophy, including CO2 fixation, H2 oxidation, S-compound oxidation, and denitrification. The pulse of acetogenesis appears to have been collectively catalyzed by a number of different organisms and metabolisms, most prominently pyruvate:ferredoxin oxidoreductase. Unexpected genes were identified among the most highly expressed (>98th percentile) transcripts, including acetone carboxylase and cell-wall-associated hydrolases with unknown substrates (numerous lesser expressed cell-wall-associated hydrolases targeted peptidoglycan). Many of the most highly expressed hydrolases belonged to a Ca. Bathyarchaeota strain and may have been associated with recycling of bacterial biomass. Overall, these results highlight the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.
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Affiliation(s)
- Talia N M Jewell
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Markus Bill
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Kenneth H Williams
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Harry R Beller
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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Patra P, Divinakumar KJ, Prakash J, Patra B, Chakraborty R. Clinico-psycho-social profile of patients brought under consultation-liaison psychiatry care in a large tertiary care referral hospital. Ind Psychiatry J 2017; 26:24-27. [PMID: 29456317 PMCID: PMC5810162 DOI: 10.4103/ipj.ipj_13_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE The aim of this study was to access the clinico-psycho-social profile of patients brought under consultation-liaison (CL) psychiatry care in a large tertiary care referral hospital. MATERIALS AND METHODS This study included all patients who were referred for CL psychiatry from among the inpatients in the hospital and the emergency department (during off working hours of the hospital) over a period of 1 year. Data were obtained and analyzed in terms of where was the referral placed, by whom, the reason for placing the referral, the primary medical/surgical diagnosis of the patient, the presenting complaints, any past psychiatric history, the psychiatric diagnosis (as per the International Classification of Diseases, Tenth Edition), the investigations advised and their reports, the treatment advised (psychotherapeutic and psychopharmacological), the sociodemographic profile of the patients, and the follow-up details. RESULTS A total of 157 patients were referred to the CL unit over the study period. Out of these, 125 patients were referred among the inpatients and 32 from the emergency department of the hospital. Majority of the patients were in the age group of 25-50 years and were male. The majority of the referrals were made by general physician; most of the referrals were placed from emergency department. The most common reason for referral was for altered sensorium and behavioral abnormalities. The most common diagnosis was delirium followed by depressive episode and alcohol dependence syndrome. CONCLUSION There was higher representation of delirium and alcohol-related cases in our study compared to older studies.
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Affiliation(s)
- P Patra
- Department of Psychiatry, Command Hospital (Eastern Command), Kolkata, West Bengal, India
| | - K J Divinakumar
- Department of Psychiatry, Command Hospital (Eastern Command), Kolkata, West Bengal, India
| | - Jyoti Prakash
- Department of Psychiatry, Command Hospital (Eastern Command), Kolkata, West Bengal, India
| | - B Patra
- Department of Psychiatry, Katihar Medical College, Katihar, Bihar, India
| | - R Chakraborty
- Department of Psychiatry, Command Hospital (Eastern Command), Kolkata, West Bengal, India
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Rahman MA, Chakraborty R, Ferdousi KR, Alam A, Chowdhury MK, Paul BK. New Therapeutic Approach to Treat Allergic Rhinitis & Bronchial Asthma, Considering These Two as One United Airway Disease. Mymensingh Med J 2017; 26:216-221. [PMID: 28260781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The relationship between allergic rhinitis and asthma is now established, and most of the clinical, epidemiological and biological data recommend integrated management. This review discusses rhinosinusitis as a co-morbid condition, a precipitating or triggering condition, and an epiphenomenon as an integrated part of the disease. A better understanding and a more pragmatic method of diagnosis and management is needed using cost-effective long-term strategies. Allergic Rhinitis, though a non-life threatening disease, its pathogenesis reveals that Bronchial Asthma also develops by the same aetiopathogenesis. The United airway disease hypothesis proposes that the upper & lower airway diseases are both manifestations of a single inflammatory process and studies have already proved it. Allergic Rhinitis when once develops if not treated vigorously, can later turn up to Asthma. As chronic inflammation is the central process which is actually continuously changing pathologically the lower respiratory tract & helping to develop Bronchial Asthma. The conventional therapies for Allergic Rhinitis such as antihistamines & decongestants are only symptom relievers, to stop the ongoing pathogenesis of Bronchial Asthma to develop it, the chronic inflammatory process should have to be stopped. This can be done by corticosteroid nasal sprays. Also Asthma with Rhinitis is better controlled by them. Even Bronchial Asthma treatment should be started with inhaler corticosteroid therapy rather than getting it after intermittent use of only bronchodilators (salbutamol) only.
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Affiliation(s)
- M A Rahman
- Professor Mohammed Atiqur Rahman, Professor, Department of Respiratory Medicine, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh; E-mail:
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