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Yu JS, Rowe AR, Sackett JD. Complete genome sequence of iron-oxidizing Stutzerimonas stutzeri strain FeN3W isolated from Catalina Harbor sediment. Microbiol Resour Announc 2024; 13:e0003024. [PMID: 38700344 PMCID: PMC11237542 DOI: 10.1128/mra.00030-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/20/2024] [Indexed: 05/05/2024] Open
Abstract
Stutzerimonas stutzeri strain FeN3W is an iron-oxidizing bacterium isolated from marine sediment. FeN3W's 5.9 Mb genome encodes complete pathways for glycolysis, gluconeogenesis, TCA cycle, pentose phosphate pathway, and aerobic and anaerobic (nitrate) respiration. The genome contains 32 putative heme-binding proteins predicted to localize to the cell envelope.
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Affiliation(s)
- Jin-Sang Yu
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Annette R. Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Joshua D. Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
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2
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Barco RA, Merino N, Lam B, Budnik B, Kaplan M, Wu F, Amend JP, Nealson KH, Emerson D. Comparative proteomics of a versatile, marine, iron-oxidizing chemolithoautotroph. Environ Microbiol 2024; 26:e16632. [PMID: 38861374 DOI: 10.1111/1462-2920.16632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/20/2024] [Indexed: 06/13/2024]
Abstract
This study conducted a comparative proteomic analysis to identify potential genetic markers for the biological function of chemolithoautotrophic iron oxidation in the marine bacterium Ghiorsea bivora. To date, this is the only characterized species in the class Zetaproteobacteria that is not an obligate iron-oxidizer, providing a unique opportunity to investigate differential protein expression to identify key genes involved in iron-oxidation at circumneutral pH. Over 1000 proteins were identified under both iron- and hydrogen-oxidizing conditions, with differentially expressed proteins found in both treatments. Notably, a gene cluster upregulated during iron oxidation was identified. This cluster contains genes encoding for cytochromes that share sequence similarity with the known iron-oxidase, Cyc2. Interestingly, these cytochromes, conserved in both Bacteria and Archaea, do not exhibit the typical β-barrel structure of Cyc2. This cluster potentially encodes a biological nanowire-like transmembrane complex containing multiple redox proteins spanning the inner membrane, periplasm, outer membrane, and extracellular space. The upregulation of key genes associated with this complex during iron-oxidizing conditions was confirmed by quantitative reverse transcription-PCR. These findings were further supported by electromicrobiological methods, which demonstrated negative current production by G. bivora in a three-electrode system poised at a cathodic potential. This research provides significant insights into the biological function of chemolithoautotrophic iron oxidation.
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Affiliation(s)
- Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - N Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Lawrence Livermore National Lab, Biosciences and Biotechnology Division, Livermore, California, USA
| | - B Lam
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - B Budnik
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - M Kaplan
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - F Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang, China
| | - J P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - K H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - D Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
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3
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Tejedor-Sanz S, Li S, Kundu BB, Ajo-Franklin CM. Extracellular electron uptake from a cathode by the lactic acid bacterium Lactiplantibacillus plantarum. Front Microbiol 2023; 14:1298023. [PMID: 38075918 PMCID: PMC10701730 DOI: 10.3389/fmicb.2023.1298023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/03/2023] [Indexed: 01/28/2024] Open
Abstract
A subset of microorganisms that perform respiration can endogenously utilize insoluble electron donors, such as Fe(II) or a cathode, in a process called extracellular electron transfer (EET). However, it is unknown whether similar endogenous EET can be performed by primarily fermentative species like lactic acid bacteria. We report for the first time electron uptake from a cathode by Lactiplantibacillus plantarum, a primarily fermentative bacteria found in the gut of mammals and in fermented foods. L. plantarum consumed electrons from a cathode and coupled this oxidation to the reduction of both an endogenous organic (pyruvate) and an exogenous inorganic electron acceptor (nitrate). This electron uptake from a cathode reroutes glucose fermentation toward lactate degradation and provides cells with a higher viability upon sugar exhaustion. Moreover, the associated genes and cofactors indicate that this activity is mechanistically different from that one employed by lactic acid bacteria to reduce an anode and to perform respiration. Our results expand our knowledge of the diversity of electroactive species and of the metabolic and bioenergetic strategies used by lactic acid bacteria.
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Affiliation(s)
- Sara Tejedor-Sanz
- Department of BioSciences, Rice University, Houston, TX, United States
- Biological Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Siliang Li
- Department of BioSciences, Rice University, Houston, TX, United States
| | - Biki Bapi Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, United States
| | - Caroline M. Ajo-Franklin
- Department of BioSciences, Rice University, Houston, TX, United States
- Biological Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
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Yin X, Li X, Li Q, Wang B, Zheng L. Complete genome analysis reveals environmental adaptability of sulfur-oxidizing bacterium Thioclava nitratireducens M1-LQ-LJL-11 and symbiotic relationship with deep-sea hydrothermal vent Chrysomallon squamiferum. Mar Genomics 2023; 71:101058. [PMID: 37478643 DOI: 10.1016/j.margen.2023.101058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/23/2023]
Abstract
One sulfur-oxidizing bacterium Thioclava sp. M1-LQ-LJL-11 was isolated from the gill of Chrysomallon squamiferum collected from 2700 m deep hydrothermal named Longqi on the southwest Indian Ocean ridge. In order to understand its survival mechanism in hydrothermal extreme environment and symbiotic relationship with its host, the complete genome of strain M1-LQ-LJL-11 was sequenced and analyzed. A total of 6117 Mb of valid data was obtained, including 4096 coding genes, 61 non coding genes, including 9 rRNAs (among them, there are 3 in 23S rRNA, 3 in 5S rRNA, and 3 in 16S rRNA.), 52 tRNAs and 35 genomic islands. Strain M1-LQ-LJL-11 contains one chromosome and two plasmids. In the genome annotation information of the strain, we found 28 genes including cys sox, sor, sqr, tst related to sulfur metabolism and 17 metal resistance genes. Interestingly, a pair of quorum sensing system which probably regulating biofilm formation located in chromosome was found. These genes are critical for self-adaptation against severe environment as well as host survival. This study provides a basis understanding for the adaptive strategies of deep-sea hydrothermal bacteria and symbiotic relationship with its host in extreme environments through gene level.
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Affiliation(s)
- Xin Yin
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362200, China
| | - Xiang Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Qian Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Bingshu Wang
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362200, China
| | - Li Zheng
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362200, China; Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China.
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Thompson J, Barr C, Babcock-Adams L, Bird L, La Cava E, Garber A, Hongoh Y, Liu M, Nealson KH, Okamoto A, Repeta D, Suzuki S, Tacto C, Tashjian M, Merino N. Insights into the physiological and genomic characterization of three bacterial isolates from a highly alkaline, terrestrial serpentinizing system. Front Microbiol 2023; 14:1179857. [PMID: 37520355 PMCID: PMC10373932 DOI: 10.3389/fmicb.2023.1179857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/23/2023] [Indexed: 08/01/2023] Open
Abstract
The terrestrial serpentinite-hosted ecosystem known as "The Cedars" is home to a diverse microbial community persisting under highly alkaline (pH ~ 12) and reducing (Eh < -550 mV) conditions. This extreme environment presents particular difficulties for microbial life, and efforts to isolate microorganisms from The Cedars over the past decade have remained challenging. Herein, we report the initial physiological assessment and/or full genomic characterization of three isolates: Paenibacillus sp. Cedars ('Paeni-Cedars'), Alishewanella sp. BS5-314 ('Ali-BS5-314'), and Anaerobacillus sp. CMMVII ('Anaero-CMMVII'). Paeni-Cedars is a Gram-positive, rod-shaped, mesophilic facultative anaerobe that grows between pH 7-10 (minimum pH tested was 7), temperatures 20-40°C, and 0-3% NaCl concentration. The addition of 10-20 mM CaCl2 enhanced growth, and iron reduction was observed in the following order, 2-line ferrihydrite > magnetite > serpentinite ~ chromite ~ hematite. Genome analysis identified genes for flavin-mediated iron reduction and synthesis of a bacillibactin-like, catechol-type siderophore. Ali-BS5-314 is a Gram-negative, rod-shaped, mesophilic, facultative anaerobic alkaliphile that grows between pH 10-12 and temperatures 10-40°C, with limited growth observed 1-5% NaCl. Nitrate is used as a terminal electron acceptor under anaerobic conditions, which was corroborated by genome analysis. The Ali-BS5-314 genome also includes genes for benzoate-like compound metabolism. Anaero-CMMVII remained difficult to cultivate for physiological studies; however, growth was observed between pH 9-12, with the addition of 0.01-1% yeast extract. Anaero-CMMVII is a probable oxygen-tolerant anaerobic alkaliphile with hydrogenotrophic respiration coupled with nitrate reduction, as determined by genome analysis. Based on single-copy genes, ANI, AAI and dDDH analyses, Paeni-Cedars and Ali-BS5-314 are related to other species (P. glucanolyticus and A. aestuarii, respectively), and Anaero-CMMVII represents a new species. The characterization of these three isolates demonstrate the range of ecophysiological adaptations and metabolisms present in serpentinite-hosted ecosystems, including mineral reduction, alkaliphily, and siderophore production.
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Affiliation(s)
- Jaclyn Thompson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Casey Barr
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Lydia Babcock-Adams
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Lina Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - Eugenio La Cava
- National Institute for Materials Science, Tsukuba, Ibaraki, Japan
| | - Arkadiy Garber
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, United States
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Mark Liu
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Akihiro Okamoto
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Daniel Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Shino Suzuki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, Sagamihara, Kanagawa, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Clarissa Tacto
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Michelle Tashjian
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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6
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Tefft NM, Ford K, TerAvest MA. NADH dehydrogenases drive inward electron transfer in Shewanella oneidensis MR-1. Microb Biotechnol 2023; 16:560-568. [PMID: 36420671 PMCID: PMC9948175 DOI: 10.1111/1751-7915.14175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/17/2022] [Accepted: 10/31/2022] [Indexed: 11/25/2022] Open
Abstract
Shewanella oneidensis MR-1 is a promising chassis organism for microbial electrosynthesis because it has a well-defined biochemical pathway (the Mtr pathway) that can connect extracellular electrodes to respiratory electron carriers inside the cell. We previously found that the Mtr pathway can be used to transfer electrons from a cathode to intracellular electron carriers and drive reduction reactions. In this work, we hypothesized that native NADH dehydrogenases form an essential link between the Mtr pathway and NADH in the cytoplasm. To test this hypothesis, we compared the ability of various mutant strains to accept electrons from a cathode and transfer them to an NADH-dependent reaction in the cytoplasm, reduction of acetoin to 2,3-butanediol. We found that deletion of genes encoding NADH dehydrogenases from the genome blocked electron transfer from a cathode to NADH in the cytoplasm, preventing the conversion of acetoin to 2,3-butanediol. However, electron transfer to fumarate was not blocked by the gene deletions, indicating that NADH dehydrogenase deletion specifically impacted NADH generation and did not cause a general defect in extracellular electron transfer. Proton motive force (PMF) is linked to the function of the NADH dehydrogenases. We added a protonophore to collapse PMF and observed that it blocked inward electron transfer to acetoin but not fumarate. Together these results indicate a link between the Mtr pathway and intracellular NADH. Future work to optimize microbial electrosynthesis in S. oneidensis MR-1 should focus on optimizing flux through NADH dehydrogenases.
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Affiliation(s)
- Nicholas M Tefft
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Kathryne Ford
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Michaela A TerAvest
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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7
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Olmsted CN, Ort R, Tran PQ, McDaniel EA, Roden EE, Bond DR, He S, McMahon KD. Environmental predictors of electroactive bacterioplankton in small boreal lakes. Environ Microbiol 2023; 25:705-720. [PMID: 36529539 DOI: 10.1111/1462-2920.16314] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Extracellular electron transfer (EET) by electroactive bacteria in anoxic soils and sediments is an intensively researched subject, but EET's function in planktonic ecology has been less considered. Following the discovery of an unexpectedly high prevalence of EET genes in a bog lake's bacterioplankton, we hypothesized that the redox capacities of dissolved organic matter (DOM) enrich for electroactive bacteria by mediating redox chemistry. We developed the bioinformatics pipeline FEET (Find EET) to identify and summarize predicted EET protein-encoding genes from metagenomics data. We then applied FEET to 36 bog and thermokarst lakes and correlated gene occurrence with environmental data to test our predictions. Our results provide indirect evidence that DOM may participate in bacterioplankton EET. We found a similarly high prevalence of genes encoding putative EET proteins in most of these lakes, where oxidative EET strongly correlated with DOM. Numerous novel clusters of multiheme cytochromes that may enable EET were identified. Taxa previously not considered EET-capable were found to carry EET genes. We propose that EET and DOM interactions are of ecologically important to bacterioplankton in small boreal lakes, and that EET, particularly by methylotrophs and anoxygenic phototrophs, should be further studied and incorporated into methane emission models of melting permafrost.
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Affiliation(s)
- Charles N Olmsted
- Department of Molecular and Environmental Toxicology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Trout Lake Station, Center for Limnology, University of Wisconsin - Madison, Boulder, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Roger Ort
- Trout Lake Station, Center for Limnology, University of Wisconsin - Madison, Boulder, Wisconsin, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Department of Integrative Biology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Daniel R Bond
- Department of Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Shaomei He
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, Wisconsin, USA
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He Y, Zeng X, Xu F, Shao Z. Diversity of Mixotrophic Neutrophilic Thiosulfate- and Iron-Oxidizing Bacteria from Deep-Sea Hydrothermal Vents. Microorganisms 2022; 11:microorganisms11010100. [PMID: 36677390 PMCID: PMC9861301 DOI: 10.3390/microorganisms11010100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 01/04/2023] Open
Abstract
At deep-sea hydrothermal vents, sulfur oxidation and iron oxidation are of the highest importance to microbial metabolisms, which are thought to contribute mainly in chemolithoautotrophic groups. In this study, 17 mixotrophic neutrophilic thiosulfate- and iron-oxidizing bacteria were isolated from hydrothermal fields on the Carlsberg Ridge in the Indian Ocean, nine to the γ-proteobacteria (Halomonas (4), Pseudomonas (2), Marinobacter (2), and Rheinheimera (1)), seven to the α-proteobacteria (Thalassospira, Qipengyuania, Salipiger, Seohaeicola, Martelella, Citromicrobium, and Aurantimonas), and one to the Actinobacteria (Agromyces), as determined by their 16S rRNA and genome sequences. The physiological characterization of these isolates revealed wide versatility in electron donors (Fe(II) and Mn(II), or thiosulfate) and a variety of lifestyles as lithotrophic or heterotrophic, microaerobic, or anaerobic. As a representative strain, Pseudomonas sp. IOP_13 showed its autotrophic gowth from 105 cells/ml to 107 cells/ml;carbon dioxide fixation capacity with the δ13CVPDB in the biomass increased from -27.42‱ to 3460.06‱; the thiosulfate-oxidizing ability with produced SO42- increased from 60 mg/L to 287 mg/L; and the iron-oxidizing ability with Fe(II) decreased from 10 mM to 5.2 mM. In addition, iron-oxide crust formed outside the cells. Gene coding for energy metabolism involved in possible iron, manganese, and sulfur oxidation, and denitrification was identified by their genome analysis. This study sheds light on the function of the mixotrophic microbial community in the iron/manganese/sulfur cycles and the carbon fixation of the hydrothermal fields.
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Hashimoto Y, Shimamura S, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S. Physiological and comparative proteomic characterization of Desulfolithobacter dissulfuricans gen. nov., sp. nov., a novel mesophilic, sulfur-disproportionating chemolithoautotroph from a deep-sea hydrothermal vent. Front Microbiol 2022; 13:1042116. [PMID: 36532468 PMCID: PMC9751629 DOI: 10.3389/fmicb.2022.1042116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/31/2022] [Indexed: 03/19/2024] Open
Abstract
In deep-sea hydrothermal environments, inorganic sulfur compounds are important energy substrates for sulfur-oxidizing, -reducing, and -disproportionating microorganisms. Among these, sulfur-disproportionating bacteria have been poorly understood in terms of ecophysiology and phylogenetic diversity. Here, we isolated and characterized a novel mesophilic, strictly chemolithoautotrophic, diazotrophic sulfur-disproportionating bacterium, designated strain GF1T, from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan. Strain GF1T disproportionated elemental sulfur, thiosulfate, and tetrathionate in the presence of ferrihydrite. The isolate also grew by respiratory hydrogen oxidation coupled to sulfate reduction. Phylogenetic and physiological analyses support that strain GF1T represents the type strain of a new genus and species in the family Desulfobulbaceae, for which the name Desulfolithobacter dissulfuricans gen. nov. sp. nov. is proposed. Proteomic analysis revealed that proteins related to tetrathionate reductase were specifically and abundantly produced when grown via thiosulfate disproportionation. In addition, several proteins possibly involved in thiosulfate disproportionation, including those encoded by the YTD gene cluster, were also found. The overall findings pointed to a possible diversity of sulfur-disproportionating bacteria in hydrothermal systems and provided a refined picture of microbial sulfur disproportionation.
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Affiliation(s)
- Yurina Hashimoto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeru Shimamura
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Akihiro Tame
- General Affairs Department, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Department of Marine and Earth Sciences, Marine Works Japan Ltd., Yokosuka, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Junichi Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
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10
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Wei M, Zeng X, Han X, Shao Z, Xie Q, Dong C, Wang Y, Qiu Z. Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field. Front Microbiol 2022; 13:930601. [PMID: 36316996 PMCID: PMC9616709 DOI: 10.3389/fmicb.2022.930601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/09/2022] [Indexed: 12/02/2022] Open
Abstract
The genus Alcanivorax is common in various marine environments, including in hydrothermal fields. They were previously recognized as obligate hydrocarbonoclastic bacteria, but their potential for autotrophic carbon fixation and Fe(II)-oxidation remains largely elusive. In this study, an in situ enrichment experiment was performed using a hydrothermal massive sulfide slab deployed 300 m away from the Wocan hydrothermal vent. Furthermore, the biofilms on the surface of the slab were used as an inoculum, with hydrothermal massive sulfide powder from the same vent as an energy source, to enrich the potential iron oxidizer in the laboratory. Three dominant bacterial families, Alcanivoraceae, Pseudomonadaceae, and Rhizobiaceae, were enriched in the medium with hydrothermal massive sulfides. Subsequently, strain Alcanivorax sp. MM125-6 was isolated from the enrichment culture. It belongs to the genus Alcanivorax and is closely related to Alcanivorax profundimaris ST75FaO-1 T (98.9% sequence similarity) indicated by a phylogenetic analysis based on 16S rRNA gene sequences. Autotrophic growth experiments on strain MM125-6 revealed that the cell concentrations were increased from an initial 7.5 × 105 cells/ml to 3.13 × 108 cells/ml after 10 days, and that the δ13C VPDB in the cell biomass was also increased from 234.25‰ on day 2 to gradually 345.66 ‰ on day 10. The gradient tube incubation showed that bands of iron oxides and cells formed approximately 1 and 1.5 cm, respectively, below the air-agarose medium interface. In addition, the SEM-EDS data demonstrated that it can also secrete acidic exopolysaccharides and adhere to the surface of sulfide minerals to oxidize Fe(II) with NaHCO3 as the sole carbon source, which accelerates hydrothermal massive sulfide dissolution. These results support the conclusion that strain MM125-6 is capable of autotrophic carbon fixation and Fe(II) oxidization chemoautotrophically. This study expands our understanding of the metabolic versatility of the Alcanivorax genus as well as their important role(s) in coupling hydrothermal massive sulfide weathering and iron and carbon cycles in hydrothermal fields.
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Affiliation(s)
- Mingcong Wei
- Ocean College, Zhejiang University, Zhoushan, China
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xiqiu Han
- Ocean College, Zhejiang University, Zhoushan, China
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Qian Xie
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Chuanqi Dong
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Yejian Wang
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Zhongyan Qiu
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
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11
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Sackett JD, Kamble N, Leach E, Schuelke T, Wilbanks E, Rowe AR. Genome-Scale Mutational Analysis of Cathode-Oxidizing Thioclava electrotropha ElOx9 T. Front Microbiol 2022; 13:909824. [PMID: 35756027 PMCID: PMC9226611 DOI: 10.3389/fmicb.2022.909824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular electron transfer (EET) – the process by which microorganisms transfer electrons across their membrane(s) to/from solid-phase materials – has implications for a wide range of biogeochemically important processes in marine environments. Though EET is thought to play an important role in the oxidation of inorganic minerals by lithotrophic organisms, the mechanisms involved in the oxidation of solid particles are poorly understood. To explore the genetic basis of oxidative EET, we utilized genomic analyses and transposon insertion mutagenesis screens (Tn-seq) in the metabolically flexible, lithotrophic Alphaproteobacterium Thioclava electrotropha ElOx9T. The finished genome of this strain is 4.3 MB, and consists of 4,139 predicted ORFs, 54 contain heme binding motifs, and 33 of those 54 are predicted to localize to the cell envelope or have unknown localizations. To begin to understand the genetic basis of oxidative EET in ElOx9T, we constructed a transposon mutant library in semi-rich media which was comprised of >91,000 individual mutants encompassing >69,000 unique TA dinucleotide insertion sites. The library was subjected to heterotrophic growth on minimal media with acetate and autotrophic oxidative EET conditions on indium tin oxide coated glass electrodes poised at –278 mV vs. SHE or un-poised in an open circuit condition. We identified 528 genes classified as essential under these growth conditions. With respect to electrochemical conditions, 25 genes were essential under oxidative EET conditions, and 29 genes were essential in both the open circuit control and oxidative EET conditions. Though many of the genes identified under electrochemical conditions are predicted to be localized in the cytoplasm and lack heme binding motifs and/or homology to known EET proteins, we identified several hypothetical proteins and poorly characterized oxidoreductases that implicate a novel mechanism(s) for EET that warrants further study. Our results provide a starting point to explore the genetic basis of novel oxidative EET in this marine sediment microbe.
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Affiliation(s)
- Joshua D Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Nitin Kamble
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Edmund Leach
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Taruna Schuelke
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Elizabeth Wilbanks
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
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12
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Physiologic, Genomic, and Electrochemical Characterization of Two Heterotrophic Marine Sediment Microbes from the Idiomarina Genus. Microorganisms 2022; 10:microorganisms10061219. [PMID: 35744737 PMCID: PMC9230427 DOI: 10.3390/microorganisms10061219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 02/04/2023] Open
Abstract
Extracellular electron transfer (EET), the process that allows microbes to exchange electrons in a redox capacity with solid interfaces such as minerals or electrodes, has been predominantly described in microbes that use iron during respiration. In this work, we characterize the physiology, genome, and electrochemical properties of two obligately heterotrophic marine microbes that were previously isolated from marine sediment cathode enrichments. Phylogenetic analysis of isolate 16S rRNA genes showed two strains, SN11 and FeN1, belonging to the genus Idiomarina. Strain SN11 was found to be nearly identical to I. loihiensis L2-TRT, and strain FeN1 was most closely related to I. maritima 908087T. Each strain had a relatively small genome (~2.8–2.9 MB). Phenotypic similarities among FeN1, SN11, and the studied strains include being Gram-negative, motile, catalase- and oxidase-positive, and rod-shaped. Physiologically, all strains appeared to exclusively use amino acids as a primary carbon source for growth. This was consistent with genomic observations. Each strain contained 17 to 22 proteins with heme-binding motifs. None of these were predicted to be extracellular, although seven were of unknown localization and lacked functional annotation beyond cytochrome. Despite the lack of homology to known EET pathways, both FeN1 and SN11 were capable of sustained electron uptake over time in an electrochemical system linked to respiration. Given the association of these Idiomarina strains with electro-active biofilms in the environment and their lack of autotrophic capabilities, we predict that EET is used exclusively for respiration in these microbes.
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13
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De La Fuente MJ, Gallardo-Bustos C, De la Iglesia R, Vargas IT. Microbial Electrochemical Technologies for Sustainable Nitrogen Removal in Marine and Coastal Environments. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:2411. [PMID: 35206599 PMCID: PMC8875524 DOI: 10.3390/ijerph19042411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 02/01/2023]
Abstract
For many years, the world's coastal marine ecosystems have received industrial waste with high nitrogen concentrations, generating the eutrophication of these ecosystems. Different physicochemical-biological technologies have been developed to remove the nitrogen present in wastewater. However, conventional technologies have high operating costs and excessive production of brines or sludge which compromise the sustainability of the treatment. Microbial electrochemical technologies (METs) have begun to gain attention due to their cost-efficiency in removing nitrogen and organic matter using the metabolic capacity of microorganisms. This article combines a critical review of the environmental problems associated with the discharge of the excess nitrogen and the biological processes involved in its biogeochemical cycle; with a comparative analysis of conventional treatment technologies and METs especially designed for nitrogen removal. Finally, current METs limitations and perspectives as a sustainable nitrogen treatment alternative and efficient microbial enrichment techniques are included.
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Affiliation(s)
- María José De La Fuente
- Departamento de Ingeniería Hidráulica y Ambiental, Facultad de Ingeniería, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (M.J.D.L.F.); (C.G.B.)
- Marine Energy Research & Innovation Center (MERIC), Santiago 7550268, Chile;
| | - Carlos Gallardo-Bustos
- Departamento de Ingeniería Hidráulica y Ambiental, Facultad de Ingeniería, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (M.J.D.L.F.); (C.G.B.)
- Centro de Desarrollo Urbano Sustentable (CEDEUS), Santiago 7820436, Chile
| | - Rodrigo De la Iglesia
- Marine Energy Research & Innovation Center (MERIC), Santiago 7550268, Chile;
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Ignacio T. Vargas
- Departamento de Ingeniería Hidráulica y Ambiental, Facultad de Ingeniería, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (M.J.D.L.F.); (C.G.B.)
- Marine Energy Research & Innovation Center (MERIC), Santiago 7550268, Chile;
- Centro de Desarrollo Urbano Sustentable (CEDEUS), Santiago 7820436, Chile
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14
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Complete Genome Sequence of Halomonas sp. Strain FeN2, a Novel Cathode-Oxidizing Bacterium Isolated from Catalina Harbor Sediments. Microbiol Resour Announc 2021; 10:e0086221. [PMID: 34792381 PMCID: PMC8601139 DOI: 10.1128/mra.00862-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the complete, closed, circular genome of Halomonas sp. strain FeN2, a metabolically versatile electrotroph that was isolated from Catalina Harbor sediments. The 4.8-Mb genome contains 4,286 protein-coding genes and has complete glycolytic, tricarboxylic acid, glyoxylate, pentose phosphate, and reductive pentose phosphate pathways. FeN2 also contains genes for aerobic and anaerobic (denitrification) respiration.
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15
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Schulze-Makuch D, Fairén AG. Evaluating the Microbial Habitability of Rogue Planets and Proposing Speculative Scenarios on How They Might Act as Vectors for Panspermia. Life (Basel) 2021; 11:life11080833. [PMID: 34440576 PMCID: PMC8397938 DOI: 10.3390/life11080833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
There are two types of rogue planets, sub-brown dwarfs and “rocky” rogue planets. Sub-brown dwarfs are unlikely to be habitable or even host life, but rocky rogue planets may have a liquid ocean under a thick atmosphere or an ice layer. If they are overlain by an insulating ice layer, they are also referred to as Steppenwolf planets. However, given the poor detectability of rocky rogue planets, there is still no direct evidence of the presence of water or ice on them. Here we discuss the possibility that these types of rogue planets could harbor unicellular organisms, conceivably based on a variety of different energy sources, including chemical, osmotic, thermal, and luminous energy. Further, given the theoretically predicted high number of rogue planets in the galaxy, we speculate that rogue planets could serve as a source for galactic panspermia, transferring life to other planetary systems.
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Affiliation(s)
- Dirk Schulze-Makuch
- Astrobiology Group, Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany
- GFZ German Research Center for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775 Stechlin, Germany
- School of the Environment, Washington State University, Pullman, WA 99163, USA
- Correspondence: ; Tel.: +49-30-314-23736
| | - Alberto G. Fairén
- Centro de Astrobiología (CSIC-INTA), 28850 Madrid, Spain;
- Department of Astronomy, Cornell University, Ithaca, NY 14853, USA
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16
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Rowe AR, Salimijazi F, Trutschel L, Sackett J, Adesina O, Anzai I, Kugelmass LH, Baym MH, Barstow B. Identification of a pathway for electron uptake in Shewanella oneidensis. Commun Biol 2021; 4:957. [PMID: 34381156 PMCID: PMC8357807 DOI: 10.1038/s42003-021-02454-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/14/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular electron transfer (EET) could enable electron uptake into microbial metabolism for the synthesis of complex, energy dense organic molecules from CO2 and renewable electricity1-6. Theoretically EET could do this with an efficiency comparable to H2-oxidation7,8 but without the need for a volatile intermediate and the problems it causes for scale up9. However, significant gaps remain in understanding the mechanism and genetics of electron uptake. For example, studies of electron uptake in electroactive microbes have shown a role for the Mtr EET complex in the electroactive microbe Shewanella oneidensis MR-110-14, though there is substantial variation in the magnitude of effect deletion of these genes has depending on the terminal electron acceptor used. This speaks to the potential for previously uncharacterized and/or differentially utilized genes involved in electron uptake. To address this, we screened gene disruption mutants for 3667 genes, representing ≈99% of all nonessential genes, from the S. oneidensis whole genome knockout collection using a redox dye oxidation assay. Confirmation of electron uptake using electrochemical testing allowed us to identify five genes from S. oneidensis that are indispensable for electron uptake from a cathode. Knockout of each gene eliminates extracellular electron uptake, yet in four of the five cases produces no significant defect in electron donation to an anode. This result highlights both distinct electron uptake components and an electronic connection between aerobic and anaerobic electron transport chains that allow electrons from the reversible EET machinery to be coupled to different respiratory processes in S. oneidensis. Homologs to these genes across many different genera suggesting that electron uptake by EET coupled to respiration could be widespread. These gene discoveries provide a foundation for: studying this phenotype in exotic metal-oxidizing microbes, genetic optimization of electron uptake in S. oneidensis; and genetically engineering electron uptake into a highly tractable host like E. coli to complement recent advances in synthetic CO2 fixation15.
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Affiliation(s)
- Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
| | - Farshid Salimijazi
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Leah Trutschel
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Joshua Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | | | - Isao Anzai
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Liat H Kugelmass
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Michael H Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA.
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17
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Eddie BJ, Malanoski AP, Onderko EL, Phillips DA, Glaven SM. Marinobacter atlanticus electrode biofilms differentially regulate gene expression depending on electrode potential and lifestyle. Biofilm 2021; 3:100051. [PMID: 34195607 PMCID: PMC8233155 DOI: 10.1016/j.bioflm.2021.100051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/13/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
Marinobacter spp. are opportunitrophs with a broad metabolic range including interactions with metals and electrodes. Marinobacter atlanticus strain CP1 was previously isolated from a cathode biofilm microbial community enriched from a sediment microbial fuel cell. Like other Marinobacter spp., M. atlanticus generates small amounts of electrical current when grown as a biofilm on an electrode, which is enhanced by the addition of redox mediators. However, the molecular mechanism resulting in extracellular electron transfer is unknown. Here, RNA-sequencing was used to determine changes in gene expression in electrode-attached and planktonic cells of M. atlanticus when grown at electrode potentials that enable current production (310 and 510 mV vs. SHE) compared to a potential that enables electron uptake (160 mV). Cells grown at current-producing potentials had increased expression of genes for molybdate transport, regardless of planktonic or attached lifestyle. Electrode-attached cells at current-producing potentials showed increased expression of the major export protein for the type VI secretion system. Growth at 160 mV resulted in an increase in expression of genes related to stress response and DNA repair including both RecBCD and the LexA/RecA regulatory network, as well as genes for copper homeostasis. Changes in expression of proteins with PEP C-terminal extracellular export motifs suggests that M. atlanticus is remodeling the biofilm matrix in response to electrode potential. These results improve our understanding of the physiological adaptations required for M. atlanticus growth on electrodes, and suggest a role for metal acquisition, either as a requirement for metal cofactors of redox proteins or as a possible electron shuttling mechanism.
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Affiliation(s)
- Brian J. Eddie
- Naval Research Laboratory, 4555 Overlook Ave., SW, Washington, DC, 20375, USA
| | | | | | - Daniel A. Phillips
- Oak Ridge Institute for Science and Education / US Army DEVCOM Chemical Biological Center, Biochemistry Branch, Aberdeen Proving Grounds, MD, 21010 USA
| | - Sarah M. Glaven
- Naval Research Laboratory, 4555 Overlook Ave., SW, Washington, DC, 20375, USA
- Corresponding author. 4555 Overlook Ave, Washington, DC, 20375.
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18
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McRose DL, Newman DK. Redox-active antibiotics enhance phosphorus bioavailability. Science 2021; 371:1033-1037. [PMID: 33674490 DOI: 10.1126/science.abd1515] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 01/13/2021] [Indexed: 12/13/2022]
Abstract
Microbial production of antibiotics is common, but our understanding of their roles in the environment is limited. In this study, we explore long-standing observations that microbes increase the production of redox-active antibiotics under phosphorus limitation. The availability of phosphorus, a nutrient required by all life on Earth and essential for agriculture, can be controlled by adsorption to and release from iron minerals by means of redox cycling. Using phenazine antibiotic production by pseudomonads as a case study, we show that phenazines are regulated by phosphorus, solubilize phosphorus through reductive dissolution of iron oxides in the lab and field, and increase phosphorus-limited microbial growth. Phenazines are just one of many examples of phosphorus-regulated antibiotics. Our work suggests a widespread but previously unappreciated role for redox-active antibiotics in phosphorus acquisition and cycling.
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Affiliation(s)
- Darcy L McRose
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. .,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
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19
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Li XM, Ding LJ, Zhu D, Zhu YG. Long-Term Fertilization Shapes the Putative Electrotrophic Microbial Community in Paddy Soils Revealed by Microbial Electrosynthesis Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3430-3441. [PMID: 33600162 DOI: 10.1021/acs.est.0c08022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Electrotrophs play an important role in biogeochemical cycles, but the effects of long-term fertilization on electrotrophic communities in paddy soils remain unclear. Here, we explored the responses of electrotrophic communities in paddy soil-based microcosms to different long-term fertilization practices using microbial electrosynthesis systems (MESs), high-throughput quantitative PCR, and 16s rRNA gene-based Illumina sequencing techniques. Compared to the case in the unfertilized soil (CK), applications of only manure (M); only chemical nitrogen, phosphorous, and potassium fertilizers (NPK); and M plus NPK (MNPK) clearly changed the electrotrophic bacterial community structure. The Streptomyces genus of the Actinobacteria phylum was the dominant electrotroph in the CK, M, and MNPK soils. The latter two soils also favored Truepera of Deinococcus-Thermus or Arenimonas and Thioalkalispira of Proteobacteria. Furthermore, Pseudomonas of Proteobacteria and Bacillus of Firmicutes were major electrotrophs in the NPK soil. These electrotrophs consumed biocathodic currents coupled with nitrate reduction and recovered 18-38% of electrons via dissimilatory nitrate reduction to ammonium (DNRA). The increased abundances of the nrfA gene for DNRA induced by electrical potential further supported that the electrotrophs enhanced DNRA for all soils. These expand our knowledge about the diversity of electrotrophs and their roles in N cycle in paddy soils and highlight the importance of fertilization in shaping electrotrophic communities.
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Affiliation(s)
- Xiao-Min Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Jimei Road, No. 1799, Jimei District, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Zhongke Road 88, Beilun District, Ningbo 315830, China
- University of Chinese Academy of Sciences, Yuquan Road, No. 19A, Shijingshan District, Beijing 100049, China
| | - Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Jimei Road, No. 1799, Jimei District, Xiamen 361021, China
- University of Chinese Academy of Sciences, Yuquan Road, No. 19A, Shijingshan District, Beijing 100049, China
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20
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Rowe AR, Abuyen K, Lam BR, Kruger B, Casar CP, Osburn MR, El-Naggar MY, Amend JP. Electrochemical evidence for in situ microbial activity at the Deep Mine Microbial Observatory (DeMMO), South Dakota, USA. GEOBIOLOGY 2021; 19:173-188. [PMID: 33188587 DOI: 10.1111/gbi.12420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/07/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
The subsurface is Earth's largest reservoir of biomass. Micro-organisms are the dominant lifeforms in this habitat, but the nature of their in situ activities remains largely unresolved. At the Deep Mine Microbial Observatory (DeMMO) located in the Sanford Underground Research Facility (SURF) in Lead, South Dakota (USA), we performed in situ electrochemical incubations designed to assess the potential for deep groundwater microbial communities to utilize extracellular electron transfer to support microbial respiration. DeMMO 4 was chosen for its stable geochemistry and microbial community. Graphite and indium tin oxide electrodes poised at -200 mV versus SHE were incubated along with open circuit controls and various minerals in a parallel flow reactor that split access to fluids across different treatments. From the patterns of net current over time (fluctuating between anodic and cathodic currents over the course of a few days to weeks) and the catalytic features measured using periodic cyclic voltammetry, evidence of both oxidative and reductive microbe-electrode interactions was observed. The predominant catalytic activity ranged from -210 to -120 mV. The observed temporal variability in electrochemical activity was unexpected given the documented stability in major geochemical parameters. This suggests that the accessed fluids are more heterogeneous in electrochemically active microbial populations than previously predicted from the stable community composition. As previously reported, the fracture fluid and surface-attached microbial communities at SURF differed significantly. However, only minimal differences in community composition were observed between poised potential electrodes, open circuit electrodes, and mineral incubations. These data support that in this environment the ability to attach to surfaces is a stronger driver of microbial community structure than the type or reactivity of the surface. We demonstrate that insight into specific activities can be gained from electrochemical methods, specifically chronoamperometry coupled with routine cyclic voltammetry, which provide a sensitive approach to evaluate microbial activities in situ.
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Affiliation(s)
- Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Karla Abuyen
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Bonita R Lam
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Brittany Kruger
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Caitlin P Casar
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - Magdalena R Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL, USA
| | - Mohamed Y El-Naggar
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA
| | - Jan P Amend
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
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21
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Saito J, Deng X, Okamoto A. Single-Cell Mass Spectroscopic Analysis for Quantifying Active Metabolic Pathway Heterogeneity in a Bacterial Population on an Electrode. Anal Chem 2020; 92:15616-15623. [PMID: 33205944 DOI: 10.1021/acs.analchem.0c03869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial electrochemical catalysis based on respiratory reactions coupled with extracellular electron transport (EET), which is critical for bioenergy applications, strongly depends on the biocompatibility of the electrode material. However, the comparison of materials for such physiological responses has been difficult because of the lack of a quantitative assay for characterizing cellular metabolism at the electrode surface. Here, we developed a single-cell analysis method specific for the cells attached to the electrode to quantify active metabolic pathway heterogeneity as an index of physiological cell/electrode interaction, which generally increases with metabolic robustness in the microbial population. Nanoscale secondary ion mass spectrometry followed by microbial current production with model EET-capable bacteria, Shewanella oneidensis MR-1 and its mutant strains lacking carbon assimilation pathways, showed that different active metabolic pathways resulted in nearly identical 13C/15N assimilation ratios for individual cells in the presence of isotopically labeled nutrients, demonstrating a correlation between the 13C/15N ratio and the active metabolic pathway. Compared to the nonelectrode conditions, the heterogeneity of the assimilated 13C/15N ratio was highly enhanced on the electrode surface, suggesting that the metabolic robustness of the microbial population increased through the electrochemical interaction with the electrode. The present methodology enables us to quantitatively compare and screen electrode materials that increase the robustness of microbial electrocatalysis.
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Affiliation(s)
- Junki Saito
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Xiao Deng
- Land and Water, Commonwealth Scientific and Industrial Research Organization, 147 Underwood Avenue, Floreat, Western Australia 6014, Australia
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan.,Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
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22
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Chen Q, Liu C, Liu X, Sun D, Li P, Qiu B, Dang Y, Karpinski NA, Smith JA, Holmes DE. Magnetite enhances anaerobic digestion of high salinity organic wastewater. ENVIRONMENTAL RESEARCH 2020; 189:109884. [PMID: 32678736 DOI: 10.1016/j.envres.2020.109884] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/27/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Biological treatment of high salinity organic wastewater is a significant challenge because many microorganisms involved in the anaerobic digestion process cannot survive high osmotic pressures. In order to alleviate some of the stresses associated with the treatment of high salinity wastewater, two lab-scale up-flow anaerobic sludge bed reactors with or without magnetite (100 g/L) were used to treat high salinity organic wastewater. This study showed that the bioreactor amended with magnetite had higher chemical oxygen demand removal efficiencies (90.2% ± 0.54% vs 73.1% ± 1.9%) and methane production rates (4082 ± 334 ml (standard temperature and atmospheric pressure, STP)/d vs 2640 ± 120 ml (STP)/d) than the non-amended control reactor. In addition, the consumption of volatile fatty acids (20.9 ± 3.4 mM vs 61.7 ± 2.0 mM) was accelerated. Microbial community analysis revealed that the addition of magnetite caused the enrichment of many bacterial genera known to form robust biofilms (i.e. Pseudomonas) that are also capable of extracellular electron transfer and methanogens from the genus Methanosarcina which have been shown to participate in direct interspecies electron transfer. These results show that magnetite addition could enhance the performance of anaerobic digesters treating high salinity wastewater.
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Affiliation(s)
- Qian Chen
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Chuanqi Liu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Xinying Liu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Dezhi Sun
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Pengsong Li
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Bin Qiu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Yan Dang
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| | - Nicole A Karpinski
- Department of Biomolecular Sciences, Central Connecticut State University, 1615 Stanley Street, New Britain, CT, 06050, United States
| | - Jessica A Smith
- Department of Biomolecular Sciences, Central Connecticut State University, 1615 Stanley Street, New Britain, CT, 06050, United States
| | - Dawn E Holmes
- Department of Physical and Biological Sciences, Western New England University, 1215 Wilbraham Rd, Springfield, MA, 01119, United States
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23
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Electrochemical Bacterial Enrichment from Natural Seawater and Its Implications in Biocorrosion of Stainless-Steel Electrodes. MATERIALS 2020; 13:ma13102327. [PMID: 32438636 PMCID: PMC7288148 DOI: 10.3390/ma13102327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/29/2020] [Accepted: 05/09/2020] [Indexed: 11/17/2022]
Abstract
Microbial electrochemical technologies have revealed the opportunity of electrochemical enrichment for specific bacterial groups that are able to catalyze reactions of interest. However, there are unsolved challenges towards their application under aggressive environmental conditions, such as in the sea. This study demonstrates the impact of surface electrochemical potential on community composition and its corrosivity. Electrochemical bacterial enrichment was successfully carried out in natural seawater without nutrient amendments. Experiments were carried out for ten days of exposure in a closed-flow system over 316L stainless steel electrodes under three different poised potentials (−150 mV, +100 mV, and +310 mV vs. Ag/AgCl). Weight loss and atomic force microscopy showed a significant difference in corrosion when +310 mV (vs. Ag/AgCl) was applied in comparison to that produced under the other tested potentials (and an unpoised control). Bacterial community analysis conducted using 16S rRNA gene profiles showed that poised potentials are more positive as +310 mV (vs. Ag/AgCl) resulted in strong enrichment for Rhodobacteraceae and Sulfitobacter. Hence, even though significant enrichment of the known electrochemically active bacteria from the Rhodobacteraceae family was accomplished, the resultant bacterial community could accelerate pitting corrosion in 316 L stainless steel, thereby compromising the durability of the electrodes and the microbial electrochemical technologies.
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24
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Li X, Ding L, Yuan H, Li X, Zhu Y. Identification of potential electrotrophic microbial community in paddy soils by enrichment of microbial electrolysis cell biocathodes. J Environ Sci (China) 2020; 87:411-420. [PMID: 31791514 DOI: 10.1016/j.jes.2019.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Electrotrophs are microbes that can receive electrons directly from cathode in a microbial electrolysis cell (MEC). They not only participate in organic biosynthesis, but also be crucial in cathode-based bioremediation. However, little is known about the electrotrophic community in paddy soils. Here, the putative electrotrophs were enriched by cathodes of MECs constructed from five paddy soils with various properties using bicarbonate as an electron acceptor, and identified by 16S rRNA-gene based Illumina sequencing. The electrons were gradually consumed on the cathodes, and 25%-45% of which were recovered to reduce bicarbonate to acetic acid during MEC operation. Firmicutes was the dominant bacterial phylum on the cathodes, and Bacillus genus within this phylum was greatly enriched and was the most abundant population among the detected putative electrotrophs for almost all soils. Furthermore, several other members of Firmicutes and Proteobacteria may also participate in electrotrophic process in different soils. Soil pH, amorphous iron and electrical conductivity significantly influenced the putative electrotrophic bacterial community, which explained about 33.5% of the community structural variation. This study provides a basis for understanding the microbial diversity of putative electrotrophs in paddy soils, and highlights the importance of soil properties in shaping the community of putative electrotrophs.
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Affiliation(s)
- Xiaomin Li
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longjun Ding
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China.
| | - Haiyan Yuan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoming Li
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongguan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road, No. 18, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Jimei Road, No. 1799, Jimei District, Xiamen 361021, China
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25
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Meyer A, Saaem I, Silverman A, Varaljay VA, Mickol R, Blum S, Tobias AV, Schwalm ND, Mojadedi W, Onderko E, Bristol C, Liu S, Pratt K, Casini A, Eluere R, Moser F, Drake C, Gupta M, Kelley-Loughnane N, Lucks JP, Akingbade KL, Lux MP, Glaven S, Crookes-Goodson W, Jewett MC, Gordon DB, Voigt CA. Organism Engineering for the Bioproduction of the Triaminotrinitrobenzene (TATB) Precursor Phloroglucinol (PG). ACS Synth Biol 2019; 8:2746-2755. [PMID: 31750651 DOI: 10.1021/acssynbio.9b00393] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Organism engineering requires the selection of an appropriate chassis, editing its genome, combining traits from different source species, and controlling genes with synthetic circuits. When a strain is needed for a new target objective, for example, to produce a chemical-of-need, the best strains, genes, techniques, software, and expertise may be distributed across laboratories. Here, we report a project where we were assigned phloroglucinol (PG) as a target, and then combined unique capabilities across the United States Army, Navy, and Air Force service laboratories with the shared goal of designing an organism to produce this molecule. In addition to the laboratory strain Escherichia coli, organisms were screened from soil and seawater. Putative PG-producing enzymes were mined from a strain bank of bacteria isolated from aircraft and fuel depots. The best enzyme was introduced into the ocean strain Marinobacter atlanticus CP1 with its genome edited to redirect carbon flux from natural fatty acid ester (FAE) production. PG production was also attempted in Bacillus subtilis and Clostridium acetobutylicum. A genetic circuit was constructed in E. coli that responds to PG accumulation, which was then ported to an in vitro paper-based system that could serve as a platform for future low-cost strain screening or for in-field sensing. Collectively, these efforts show how distributed biotechnology laboratories with domain-specific expertise can be marshalled to quickly provide a solution for a targeted organism engineering project, and highlights data and material sharing protocols needed to accelerate future efforts.
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Affiliation(s)
- Adam Meyer
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ishtiaq Saaem
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Adam Silverman
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Vanessa A. Varaljay
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rebecca Mickol
- American Society for Engineering Education, 1818 N Street NW Suite 600, Washington, D.C. 20036, United States
| | - Steven Blum
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Alexander V. Tobias
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Nathan D. Schwalm
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Wais Mojadedi
- Oak Ridge Associate Universities, P.O.
Box 117, MS-29, Oak Ridge, Tennessee 37831, United States
| | - Elizabeth Onderko
- National Research Council, 500 5th Street NW, Washington, D.C. 20001, United States
| | - Cassandra Bristol
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Shangtao Liu
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
| | - Katelin Pratt
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Arturo Casini
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Raissa Eluere
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Felix Moser
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Carrie Drake
- UES, Inc., 4401 Dayton-Xenia Road, Dayton, Ohio 45432, United States
| | - Maneesh Gupta
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Nancy Kelley-Loughnane
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Julius P. Lucks
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Katherine L. Akingbade
- U.S. Army Research Laboratory, FCDD-RLS-EB, 2800 Powder Mill Road, Adelphi, Maryland 20783, United States
| | - Matthew P. Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Sarah Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Wendy Crookes-Goodson
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Michael C. Jewett
- Center for Synthetic Biology, Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - D. Benjamin Gordon
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Christopher A. Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Foundry, 75 Ames Street, Cambridge Massachusetts 02142, United States
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26
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Alqahtani MF, Bajracharya S, Katuri KP, Ali M, Ragab A, Michoud G, Daffonchio D, Saikaly PE. Enrichment of Marinobacter sp. and Halophilic Homoacetogens at the Biocathode of Microbial Electrosynthesis System Inoculated With Red Sea Brine Pool. Front Microbiol 2019; 10:2563. [PMID: 31787955 PMCID: PMC6855130 DOI: 10.3389/fmicb.2019.02563] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/23/2019] [Indexed: 11/13/2022] Open
Abstract
Homoacetogens are efficient CO2 fixing bacteria using H2 as electron donor to produce acetate. These organisms can be enriched at the biocathode of microbial electrosynthesis (MES) for electricity-driven CO2 reduction to acetate. Studies exploring homoacetogens in MES are mainly conducted using pure or mix-culture anaerobic inocula from samples with standard environmental conditions. Extreme marine environments host unique microbial communities including homoacetogens that may have unique capabilities due to their adaptation to harsh environmental conditions. Anaerobic deep-sea brine pools are hypersaline and metalliferous environments and homoacetogens can be expected to live in these environments due to their remarkable metabolic flexibility and energy-efficient biosynthesis. However, brine pools have never been explored as inocula for the enrichment of homacetogens in MES. Here we used the saline water from a Red Sea brine pool as inoculum for the enrichment of halophilic homoacetogens at the biocathode (-1 V vs. Ag/AgCl) of MES. Volatile fatty acids, especially acetate, along with hydrogen gas were produced in MES systems operated at 25 and 10% salinity. Acetate concentration increased when MES was operated at a lower salinity ∼3.5%, representing typical seawater salinity. Amplicon sequencing and genome-centric metagenomics of matured cathodic biofilm showed dominance of the genus Marinobacter and phylum Firmicutes at all tested salinities. Seventeen high-quality draft metagenome-assembled genomes (MAGs) were extracted from the biocathode samples. The recovered MAGs accounted for 87 ± 4% of the quality filtered sequence reads. Genome analysis of the MAGs suggested CO2 fixation via Wood-Ljundahl pathway by members of the phylum Firmicutes and the fixed CO2 was possibly utilized by Marinobacter sp. for growth by consuming O2 escaping from the anode to the cathode for respiration. The enrichment of Marinobacter sp. with homoacetogens was only possible because of the specific cathodic environment in MES. These findings suggest that in organic carbon-limited saline environments, Marinobacter spp. can live in consortia with CO2 fixing bacteria such as homoacetogens, which can provide them with fixed carbon as a source of carbon and energy.
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Affiliation(s)
- Manal F Alqahtani
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Suman Bajracharya
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Krishna P Katuri
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Muhammad Ali
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Ala'a Ragab
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Grégoire Michoud
- King Abdullah University of Science and Technology, Red Sea Research Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology, Red Sea Research Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Pascal E Saikaly
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
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27
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Lam BR, Barr CR, Rowe AR, Nealson KH. Differences in Applied Redox Potential on Cathodes Enrich for Diverse Electrochemically Active Microbial Isolates From a Marine Sediment. Front Microbiol 2019; 10:1979. [PMID: 31555224 PMCID: PMC6724507 DOI: 10.3389/fmicb.2019.01979] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/12/2019] [Indexed: 01/21/2023] Open
Abstract
The diversity of microbially mediated redox processes that occur in marine sediments is likely underestimated, especially with respect to the metabolisms that involve solid substrate electron donors or acceptors. Though electrochemical studies that utilize poised potential electrodes as a surrogate for solid substrate or mineral interactions have shed some much needed light on these areas, these studies have traditionally been limited to one redox potential or metabolic condition. This work seeks to uncover the diversity of microbes capable of accepting cathodic electrons from a marine sediment utilizing a range of redox potentials, by coupling electrochemical enrichment approaches to microbial cultivation and isolation techniques. Five lab-scale three-electrode electrochemical systems were constructed, using electrodes that were initially incubated in marine sediment at cathodic or electron-donating voltages (five redox potentials between -400 and -750 mV versus Ag/AgCl) as energy sources for enrichment. Electron uptake was monitored in the laboratory bioreactors and linked to the reduction of supplied terminal electron acceptors (nitrate or sulfate). Enriched communities exhibited differences in community structure dependent on poised redox potential and terminal electron acceptor used. Further cultivation of microbes was conducted using media with reduced iron (Fe0, FeCl2) and sulfur (S0) compounds as electron donors, resulting in the isolation of six electrochemically active strains. The isolates belong to the genera Vallitalea of the Clostridia, Arcobacter of the Epsilonproteobacteria, Desulfovibrio of the Deltaproteobacteria, and Vibrio and Marinobacter of the Gammaproteobacteria. Electrochemical characterization of the isolates with cyclic voltammetry yielded a wide range of midpoint potentials (99.20 to -389.1 mV versus Ag/AgCl), indicating diverse metabolic pathways likely support the observed electron uptake. Our work demonstrates culturing under various electrochemical and geochemical regimes allows for enhanced cultivation of diverse cathode-oxidizing microbes from one environmental system. Understanding the mechanisms of solid substrate oxidation from environmental microbes will further elucidation of the ecological relevance of these electron transfer interactions with implications for microbe-electrode technologies.
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Affiliation(s)
- Bonita R. Lam
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Casey R. Barr
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Annette R. Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Kenneth H. Nealson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
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28
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Guzman MS, Rengasamy K, Binkley MM, Jones C, Ranaivoarisoa TO, Singh R, Fike DA, Meacham JM, Bose A. Phototrophic extracellular electron uptake is linked to carbon dioxide fixation in the bacterium Rhodopseudomonas palustris. Nat Commun 2019; 10:1355. [PMID: 30902976 PMCID: PMC6430793 DOI: 10.1038/s41467-019-09377-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/07/2019] [Indexed: 01/06/2023] Open
Abstract
Extracellular electron uptake (EEU) is the ability of microbes to take up electrons from solid-phase conductive substances such as metal oxides. EEU is performed by prevalent phototrophic bacterial genera, but the electron transfer pathways and the physiological electron sinks are poorly understood. Here we show that electrons enter the photosynthetic electron transport chain during EEU in the phototrophic bacterium Rhodopseudomonas palustris TIE-1. Cathodic electron flow is also correlated with a highly reducing intracellular redox environment. We show that reducing equivalents are used for carbon dioxide (CO2) fixation, which is the primary electron sink. Deletion of the genes encoding ruBisCO (the CO2-fixing enzyme of the Calvin-Benson-Bassham cycle) leads to a 90% reduction in EEU. This work shows that phototrophs can directly use solid-phase conductive substances for electron transfer, energy transduction, and CO2 fixation. Extracellular electron uptake (EEU) is the ability of microbes to take up electrons from solid-phase conductive substances such as metal oxides. Here, Guzman et al. show that electrons enter the photosynthetic electron transport chain and are used for CO2 fixation during EEU in a phototrophic bacterium.
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Affiliation(s)
- Michael S Guzman
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Karthikeyan Rengasamy
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Michael M Binkley
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Clive Jones
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | | | - Rajesh Singh
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - David A Fike
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - J Mark Meacham
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Institute of Materials Science Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Arpita Bose
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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29
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Abstract
The Methanosarcinales, a lineage of cytochrome-containing methanogens, have recently been proposed to participate in direct extracellular electron transfer interactions within syntrophic communities. To shed light on this phenomenon, we applied electrochemical techniques to measure electron uptake from cathodes by Methanosarcina barkeri, which is an important model organism that is genetically tractable and utilizes a wide range of substrates for methanogenesis. Here, we confirm the ability of M. barkeri to perform electron uptake from cathodes and show that this cathodic current is linked to quantitative increases in methane production. The underlying mechanisms we identified include, but are not limited to, a recently proposed association between cathodes and methanogen-derived extracellular enzymes (e.g., hydrogenases) that can facilitate current generation through the formation of reduced and diffusible methanogenic substrates (e.g., hydrogen). However, after minimizing the contributions of such extracellular enzymes and using a mutant lacking hydrogenases, we observe a lower-potential hydrogen-independent pathway that facilitates cathodic activity coupled to methane production in M. barkeri Our electrochemical measurements of wild-type and mutant strains point to a novel and hydrogenase-free mode of electron uptake with a potential near -484 mV versus standard hydrogen electrode (SHE) (over 100 mV more reduced than the observed hydrogenase midpoint potential under these conditions). These results suggest that M. barkeri can perform multiple modes (hydrogenase-mediated and free extracellular enzyme-independent modes) of electrode interactions on cathodes, including a mechanism pointing to a direct interaction, which has significant applied and ecological implications.IMPORTANCE Methanogenic archaea are of fundamental applied and environmental relevance. This is largely due to their activities in a wide range of anaerobic environments, generating gaseous reduced carbon that can be utilized as a fuel source. While the bioenergetics of a wide variety of methanogens have been well studied with respect to soluble substrates, a mechanistic understanding of their interaction with solid-phase redox-active compounds is limited. This work provides insight into solid-phase redox interactions in Methanosarcina spp. using electrochemical methods. We highlight a previously undescribed mode of electron uptake from cathodes that is potentially informative of direct interspecies electron transfer interactions in the Methanosarcinales.
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30
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Bird LJ, Wang Z, Malanoski AP, Onderko EL, Johnson BJ, Moore MH, Phillips DA, Chu BJ, Doyle JF, Eddie BJ, Glaven SM. Development of a Genetic System for Marinobacter atlanticus CP1 ( sp. nov.), a Wax Ester Producing Strain Isolated From an Autotrophic Biocathode. Front Microbiol 2018; 9:3176. [PMID: 30622527 PMCID: PMC6308636 DOI: 10.3389/fmicb.2018.03176] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/07/2018] [Indexed: 11/13/2022] Open
Abstract
Here, we report on the development of a genetic system for Marinobacter sp. strain CP1, previously isolated from the Biocathode MCL community and shown to oxidize iron and grow as a cathodic biofilm. Sequence analysis of the small and large subunits of the 16S rRNA gene of CP1, as well as comparison of select conserved proteins, indicate that it is most closely related to Marinobacter adhaerens HP15 and Marinobacter sp. ES.042. In silico DNA–DNA hybridization using the genome-to-genome distance calculator (GGDC) predicts CP1 to be a new species of Marinobacter described here as Marinobacter atlanticus. CP1 is competent for transformation with plasmid DNA using conjugation with Escherichia coli donor strain WM3064 and constitutive expression of green fluorescent protein (GFP) is stable in the absence of antibiotic selection. Targeted double deletion mutagenesis of homologs for the M. aquaeoli fatty acyl-CoA reductase (acrB) and fatty aldehyde reductase (farA) genes resulted in a loss of production of wax esters; however, single deletion mutants for either gene resulted in an increase in total wax esters recovered. Genetic tools presented here for CP1 will enable further exploration of wax ester synthesis for biotechnological applications, as well as furthering our efforts to understand the role of CP1 within the Biocathode MCL community.
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Affiliation(s)
- Lina J Bird
- National Research Council, Washington, DC, United States
| | - Zheng Wang
- Center for Biomolecular Science and Engineering, United States Naval Research Laboratory, Washington, DC, United States
| | - Anthony P Malanoski
- Center for Biomolecular Science and Engineering, United States Naval Research Laboratory, Washington, DC, United States
| | | | - Brandy J Johnson
- Center for Biomolecular Science and Engineering, United States Naval Research Laboratory, Washington, DC, United States
| | - Martin H Moore
- Center for Biomolecular Science and Engineering, United States Naval Research Laboratory, Washington, DC, United States
| | - Daniel A Phillips
- American Society For Engineering Education, Washington, DC, United States
| | - Brandon J Chu
- Fischell Department of Bioengineering, University of Maryland, College Park, College Park, MD, United States
| | | | - Brian J Eddie
- Center for Biomolecular Science and Engineering, United States Naval Research Laboratory, Washington, DC, United States
| | - Sarah M Glaven
- Center for Biomolecular Science and Engineering, United States Naval Research Laboratory, Washington, DC, United States
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31
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Deng X, Okamoto A. Electrode Potential Dependency of Single-Cell Activity Identifies the Energetics of Slow Microbial Electron Uptake Process. Front Microbiol 2018; 9:2744. [PMID: 30483241 PMCID: PMC6243204 DOI: 10.3389/fmicb.2018.02744] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/26/2018] [Indexed: 12/22/2022] Open
Abstract
Electrochemical measurements have been widely applied to study microbial extracellular electron transport processes. However, because electrochemistry detects not only microbial electron transport but also other reactions, background signals comparable to or larger than microbial ones hamper the identification of microbial electrochemical properties. This problem is crucial especially for the detection of electron uptake processes by slow-growing microbes in low-energy subsurface sediments, as the environmental samples contain electrochemically active humus and mineral particles. In this study, we report a cell-specific stable isotope analysis to quantify the electrode potential dependency of anabolic activity in individual cells for identifying the electron uptake energetics of slow-growing bacteria. Followed by the incubation of Desulfovibrio ferrophilus IS5 cells with isotopic 15N-ammonium as the sole N source on electrodes poised at potentials of -0.2, -0.3, -0.4, and -0.5 V [vs. standard hydrogen electrode (SHE)], we conducted nanoscale secondary ion mass spectroscopy (NanoSIMS) to quantify 15N assimilation in more than 100 individual cells on the electrodes. We observed significant 15N assimilation at potentials of -0.4 and more 15N assimilation at -0.5 V, which is consistent with the onset potential for electron uptake via outer-membrane cytochromes (OMCs). The activation of cell energy metabolism was further examined by transcriptome analysis. Our results showed a novel methodology to study microbial electron uptake energetics. The results also serve as the first direct evidence that energy acquisition is coupled to the electron uptake process in sulfate-reducing bacteria that are ubiquitous in the subsurface environments, with implications on the electron-fueled subsurface biosphere hypothesis and other microbial processes, such as anaerobic iron corrosion and anaerobic methane oxidation.
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Affiliation(s)
- Xiao Deng
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo, Japan.,International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Japan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Japan.,Center for Functional Sensor and Actuator, National Institute for Materials Science, Tsukuba, Japan
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32
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Monteverde DR, Sylvan JB, Suffridge C, Baronas JJ, Fichot E, Fuhrman J, Berelson W, Sañudo-Wilhelmy SA. Distribution of Extracellular Flavins in a Coastal Marine Basin and Their Relationship to Redox Gradients and Microbial Community Members. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:12265-12274. [PMID: 30257556 DOI: 10.1021/acs.est.8b02822] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The flavins (including flavin mononucleotide (FMN) and riboflavin (RF)) are a class of organic compounds synthesized by organisms to assist in critical redox reactions. While known to be secreted extracellularly by some species in laboratory-based cultures, flavin concentrations are largely unreported in the natural environment. Here, we present pore water and water column profiles of extracellular flavins (FMN and RF) and two degradation products (lumiflavin and lumichrome) from a coastal marine basin in the Southern California Bight alongside ancillary geochemical and 16S rRNA microbial community data. Flavins were detectable at picomolar concentrations in the water column (93-300 pM FMN, 14-40 pM RF) and low nanomolar concentrations in pore waters (250-2070 pM FMN, 11-210 pM RF). Elevated pore water flavin concentrations displayed an increasing trend with sediment depth and were significantly correlated with the total dissolved Fe (negative) and Mn (positive) concentrations. Network analysis revealed a positive relationship between flavins and the relative abundance of Dehalococcoidia and the MSBL9 clade of Planctomycetes, indicating possible secretion by members of these lineages. These results suggest that flavins are a common component of the so-called shared extracellular metabolite pool, especially in anoxic marine sediments where they exist at physiologically relevant concentrations for metal oxide reduction.
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Affiliation(s)
- Danielle R Monteverde
- Department of Earth Sciences , University of Southern California , Los Angeles , California United States
| | - Jason B Sylvan
- Department of Oceanography , Texas A&M University , College Station , Texas United States
| | - Christopher Suffridge
- Department of Biological Sciences , University of Southern California , Los Angeles , California United States
| | - J Jotautas Baronas
- Department of Earth Sciences , University of Southern California , Los Angeles , California United States
| | - Erin Fichot
- Department of Biological Sciences , University of Southern California , Los Angeles , California United States
| | - Jed Fuhrman
- Department of Biological Sciences , University of Southern California , Los Angeles , California United States
| | - William Berelson
- Department of Earth Sciences , University of Southern California , Los Angeles , California United States
| | - Sergio A Sañudo-Wilhelmy
- Department of Earth Sciences , University of Southern California , Los Angeles , California United States
- Department of Biological Sciences , University of Southern California , Los Angeles , California United States
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Yung YL, Chen P, Nealson K, Atreya S, Beckett P, Blank JG, Ehlmann B, Eiler J, Etiope G, Ferry JG, Forget F, Gao P, Hu R, Kleinböhl A, Klusman R, Lefèvre F, Miller C, Mischna M, Mumma M, Newman S, Oehler D, Okumura M, Oremland R, Orphan V, Popa R, Russell M, Shen L, Sherwood Lollar B, Staehle R, Stamenković V, Stolper D, Templeton A, Vandaele AC, Viscardy S, Webster CR, Wennberg PO, Wong ML, Worden J. Methane on Mars and Habitability: Challenges and Responses. ASTROBIOLOGY 2018; 18:1221-1242. [PMID: 30234380 PMCID: PMC6205098 DOI: 10.1089/ast.2018.1917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 06/12/2018] [Indexed: 05/05/2023]
Abstract
Recent measurements of methane (CH4) by the Mars Science Laboratory (MSL) now confront us with robust data that demand interpretation. Thus far, the MSL data have revealed a baseline level of CH4 (∼0.4 parts per billion by volume [ppbv]), with seasonal variations, as well as greatly enhanced spikes of CH4 with peak abundances of ∼7 ppbv. What do these CH4 revelations with drastically different abundances and temporal signatures represent in terms of interior geochemical processes, or is martian CH4 a biosignature? Discerning how CH4 generation occurs on Mars may shed light on the potential habitability of Mars. There is no evidence of life on the surface of Mars today, but microbes might reside beneath the surface. In this case, the carbon flux represented by CH4 would serve as a link between a putative subterranean biosphere on Mars and what we can measure above the surface. Alternatively, CH4 records modern geochemical activity. Here we ask the fundamental question: how active is Mars, geochemically and/or biologically? In this article, we examine geological, geochemical, and biogeochemical processes related to our overarching question. The martian atmosphere and surface are an overwhelmingly oxidizing environment, and life requires pairing of electron donors and electron acceptors, that is, redox gradients, as an essential source of energy. Therefore, a fundamental and critical question regarding the possibility of life on Mars is, "Where can we find redox gradients as energy sources for life on Mars?" Hence, regardless of the pathway that generates CH4 on Mars, the presence of CH4, a reduced species in an oxidant-rich environment, suggests the possibility of redox gradients supporting life and habitability on Mars. Recent missions such as ExoMars Trace Gas Orbiter may provide mapping of the global distribution of CH4. To discriminate between abiotic and biotic sources of CH4 on Mars, future studies should use a series of diagnostic geochemical analyses, preferably performed below the ground or at the ground/atmosphere interface, including measurements of CH4 isotopes, methane/ethane ratios, H2 gas concentration, and species such as acetic acid. Advances in the fields of Mars exploration and instrumentation will be driven, augmented, and supported by an improved understanding of atmospheric chemistry and dynamics, deep subsurface biogeochemistry, astrobiology, planetary geology, and geophysics. Future Mars exploration programs will have to expand the integration of complementary areas of expertise to generate synergistic and innovative ideas to realize breakthroughs in advancing our understanding of the potential of life and habitable conditions having existed on Mars. In this spirit, we conducted a set of interdisciplinary workshops. From this series has emerged a vision of technological, theoretical, and methodological innovations to explore the martian subsurface and to enhance spatial tracking of key volatiles, such as CH4.
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Affiliation(s)
- Yuk L. Yung
- California Institute of Technology, Pasadena, California
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Pin Chen
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | | | | | | | - Jennifer G. Blank
- NASA Ames Research Center, Blue Marble Space Institute of Science, Mountain View, California
| | - Bethany Ehlmann
- California Institute of Technology, Pasadena, California
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - John Eiler
- California Institute of Technology, Pasadena, California
| | - Giuseppe Etiope
- Istituto Nazionale di Geofisica e Vulcanologia, Rome, Italy
- Faculty of Environmental Science and Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - James G. Ferry
- The Pennsylvania State University, University Park, Pennsylvania
| | - Francois Forget
- Laboratoire de Météorologie Dynamique, Institut Pierre Simon Laplace, CNRS, Paris, France
| | - Peter Gao
- University of California, Berkeley, California
| | - Renyu Hu
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Armin Kleinböhl
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | | | - Franck Lefèvre
- Laboratoire Atmospheres, Milieux, Observations Spatiales (LATMOS), IPSL, Paris, France
| | - Charles Miller
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Michael Mischna
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Michael Mumma
- NASA Goddard Space Flight Center, Greenbelt, Maryland
| | - Sally Newman
- California Institute of Technology, Pasadena, California
| | | | | | | | | | - Radu Popa
- University of Southern California, Los Angeles, California
| | - Michael Russell
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Linhan Shen
- California Institute of Technology, Pasadena, California
| | | | - Robert Staehle
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Vlada Stamenković
- California Institute of Technology, Pasadena, California
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | | | | | - Ann C. Vandaele
- The Royal Belgian Institute for Space Aeronomy (BIRA-IASB), Brussels, Belgium
| | - Sébastien Viscardy
- The Royal Belgian Institute for Space Aeronomy (BIRA-IASB), Brussels, Belgium
| | - Christopher R. Webster
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | | | | | - John Worden
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
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Lam BR, Rowe AR, Nealson KH. Variation in electrode redox potential selects for different microorganisms under cathodic current flow from electrodes in marine sediments. Environ Microbiol 2018; 20:2270-2287. [PMID: 29786168 DOI: 10.1111/1462-2920.14275] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 12/20/2022]
Abstract
Extracellular electron transport (EET) is a microbial process that allows microorganisms to transport electrons to and from insoluble substrates outside of the cell. Although progress has been made in understanding how microbes transfer electrons to insoluble substrates, the process of receiving electrons has largely remained unexplored. We investigated redox potentials favourable for donating electrons to dissolved and insoluble components in Catalina Harbor marine sediment by combining electrochemical techniques with geochemistry and molecular methods. Working electrodes buried in sediment microcosms were poised at seven redox potentials between -300 and -750 mV versus Ag/AgCl using a three-electrode system. In electrode biofilms recovered after 2-month incubations, overall community diversity increased with more negative redox potentials. Abundances of known EET-capable groups (e.g., Alteromonadales and Desulfuromonadales) varied with redox potential. Motility and chemotaxis genes were found in greater abundance in electrode communities, suggesting a possible selective advantage of these pathways for colonization and utilization of the electrode. Our enrichments demonstrated the validity of this approach in capturing groups known, as well as novel groups (e.g., Campylobacterales) that perform EET. The diverse nature of the enriched cathode communities suggest that insoluble substrate oxidation may be a critical, although poorly described microbial metabolic process in marine sediment.
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Affiliation(s)
- Bonita R Lam
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Kenneth H Nealson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
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35
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Cornejo JA, Sheng H, Edri E, M Ajo-Franklin C, Frei H. Nanoscale membranes that chemically isolate and electronically wire up the abiotic/biotic interface. Nat Commun 2018; 9:2263. [PMID: 29891950 PMCID: PMC5995903 DOI: 10.1038/s41467-018-04707-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/11/2018] [Indexed: 01/02/2023] Open
Abstract
By electrochemically coupling microbial and abiotic catalysts, bioelectrochemical systems such as microbial electrolysis cells and microbial electrosynthesis systems synthesize energy-rich chemicals from energy-poor precursors with unmatched efficiency. However, to circumvent chemical incompatibilities between the microbial cells and inorganic materials that result in toxicity, corrosion, fouling, and efficiency-degrading cross-reactions between oxidation and reduction environments, bioelectrochemical systems physically separate the microbial and inorganic catalysts by macroscopic distances, thus introducing ohmic losses, rendering these systems impractical at scale. Here we electrochemically couple an inorganic catalyst, a SnO2 anode, with a microbial catalyst, Shewanella oneidensis, via a 2-nm-thick silica membrane containing -CN and -NO2 functionalized p-oligo(phenylene vinylene) molecular wires. This membrane enables electron flow at 0.51 μA cm-2 from microbial catalysts to the inorganic anode, while blocking small molecule transport. Thus the modular architecture avoids chemical incompatibilities without ohmic losses and introduces an immense design space for scale up of bioelectrochemical systems.
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Affiliation(s)
- Jose A Cornejo
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA
| | - Hua Sheng
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA
| | - Eran Edri
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA.,Department of Chemical Engineering, Ben-Gurion University of the Negev Be'er Sheva, 8410501, Beersheba, Israel
| | - Caroline M Ajo-Franklin
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA. .,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA.
| | - Heinz Frei
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA.
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36
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Peng C, Sundman A, Bryce C, Catrouillet C, Borch T, Kappler A. Oxidation of Fe(II)-Organic Matter Complexes in the Presence of the Mixotrophic Nitrate-Reducing Fe(II)-Oxidizing Bacterium Acidovorax sp. BoFeN1. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5753-5763. [PMID: 29671587 DOI: 10.1021/acs.est.8b00953] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fe(II)-organic matter (Fe(II)-OM) complexes are abundant in the environment and may play a key role for the behavior of Fe and pollutants. Mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOx) reduce nitrate coupled to the oxidation of organic compounds and Fe(II). Fe(II) oxidation may occur enzymatically or abiotically by reaction with nitrite that forms during heterotrophic denitrification. However, it is unknown whether Fe(II)-OM complexes can be oxidized by NRFeOx. We used cell-suspension experiments with the mixotrophic nitrate-reducing Fe(II)-oxidizing bacterium Acidovorax sp. strain BoFeN1 to reveal the role of nonorganically bound Fe(II) (aqueous Fe(II)) and nitrite for the rates and extent of oxidation of Fe(II)-OM complexes (Fe(II)-citrate, Fe(II)-EDTA, Fe(II)-humic acid, and Fe(II)-fulvic acid). We found that Fe(II)-OM complexation inhibited microbial nitrate-reducing Fe(II) oxidation; large colloidal and negatively charged complexes showed lower oxidation rates than aqueous Fe(II). Accumulation of nitrite and fast abiotic oxidation of Fe(II)-OM complexes only happened in the presence of aqueous Fe(II) that probably interacted with (nitrite-reducing) enzymes in the periplasm causing nitrite accumulation in the periplasm and outside of the cells, whereas Fe(II)-OM complexes probably could not enter the periplasm and cause nitrite accumulation. These results suggest that Fe(II) oxidation by mixotrophic nitrate reducers in the environment depends on Fe(II) speciation, and that aqueous Fe(II) potentially plays a critical role in regulating microbial denitrification processes.
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Affiliation(s)
- Chao Peng
- Geomicrobiology, Center for Applied Geoscience , University of Tuebingen , Sigwartstrasse 10 , 72076 Tuebingen , Germany
| | - Anneli Sundman
- Geomicrobiology, Center for Applied Geoscience , University of Tuebingen , Sigwartstrasse 10 , 72076 Tuebingen , Germany
| | - Casey Bryce
- Geomicrobiology, Center for Applied Geoscience , University of Tuebingen , Sigwartstrasse 10 , 72076 Tuebingen , Germany
| | | | - Thomas Borch
- Department of Soil and Crop Sciences , Colorado State University , Fort Collins , Colorado 80523 , United States
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geoscience , University of Tuebingen , Sigwartstrasse 10 , 72076 Tuebingen , Germany
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37
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Chang R, Bird L, Barr C, Osburn M, Wilbanks E, Nealson K, Rowe A. Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments. Int J Syst Evol Microbiol 2018; 68:1652-1658. [DOI: 10.1099/ijsem.0.002723] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rachel Chang
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Lina Bird
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Casey Barr
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Magdalena Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Elizabeth Wilbanks
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Kenneth Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Annette Rowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
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38
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Tracking Electron Uptake from a Cathode into Shewanella Cells: Implications for Energy Acquisition from Solid-Substrate Electron Donors. mBio 2018; 9:mBio.02203-17. [PMID: 29487241 PMCID: PMC5829830 DOI: 10.1128/mbio.02203-17] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
While typically investigated as a microorganism capable of extracellular electron transfer to minerals or anodes, Shewanella oneidensis MR-1 can also facilitate electron flow from a cathode to terminal electron acceptors, such as fumarate or oxygen, thereby providing a model system for a process that has significant environmental and technological implications. This work demonstrates that cathodic electrons enter the electron transport chain of S. oneidensis when oxygen is used as the terminal electron acceptor. The effect of electron transport chain inhibitors suggested that a proton gradient is generated during cathode oxidation, consistent with the higher cellular ATP levels measured in cathode-respiring cells than in controls. Cathode oxidation also correlated with an increase in the cellular redox (NADH/FMNH2) pool determined with a bioluminescence assay, a proton uncoupler, and a mutant of proton-pumping NADH oxidase complex I. This work suggested that the generation of NADH/FMNH2 under cathodic conditions was linked to reverse electron flow mediated by complex I. A decrease in cathodic electron uptake was observed in various mutant strains, including those lacking the extracellular electron transfer components necessary for anodic-current generation. While no cell growth was observed under these conditions, here we show that cathode oxidation is linked to cellular energy acquisition, resulting in a quantifiable reduction in the cellular decay rate. This work highlights a potential mechanism for cell survival and/or persistence on cathodes, which might extend to environments where growth and division are severely limited. The majority of our knowledge of the physiology of extracellular electron transfer derives from studies of electrons moving to the exterior of the cell. The physiological mechanisms and/or consequences of the reverse processes are largely uncharacterized. This report demonstrates that when coupled to oxygen reduction, electrode oxidation can result in cellular energy acquisition. This respiratory process has potentially important implications for how microorganisms persist in energy-limited environments, such as reduced sediments under changing redox conditions. From an applied perspective, this work has important implications for microbially catalyzed processes on electrodes, particularly with regard to understanding models of cellular conversion of electrons from cathodes to microbially synthesized products.
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Kawaichi S, Yamada T, Umezawa A, McGlynn SE, Suzuki T, Dohmae N, Yoshida T, Sako Y, Matsushita N, Hashimoto K, Nakamura R. Anodic and Cathodic Extracellular Electron Transfer by the Filamentous Bacterium Ardenticatena maritima 110S. Front Microbiol 2018; 9:68. [PMID: 29467724 PMCID: PMC5808234 DOI: 10.3389/fmicb.2018.00068] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/11/2018] [Indexed: 11/13/2022] Open
Abstract
Ardenticatena maritima strain 110S is a filamentous bacterium isolated from an iron-rich coastal hydrothermal field, and it is a unique isolate capable of dissimilatory iron or nitrate reduction among the members of the bacterial phylum Chloroflexi. Here, we report the ability of A. maritima strain 110S to utilize electrodes as a sole electron acceptor and donor when coupled with the oxidation of organic compounds and nitrate reduction, respectively. In addition, multicellular filaments with hundreds of cells arranged end-to-end increased the extracellular electron transfer (EET) ability to electrodes by organizing filaments into bundled structures, with the aid of microbially reduced iron oxide minerals on the cell surface of strain 110S. Based on these findings, together with the attempt to detect surface-localized cytochromes in the genome sequence and the demonstration of redox-dependent staining and immunostaining of the cell surface, we propose a model of bidirectional electron transport by A. maritima strain 110S, in which surface-localized multiheme cytochromes and surface-associated iron minerals serve as a conduit of bidirectional EET in multicellular filaments.
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Affiliation(s)
- Satoshi Kawaichi
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Saitama, Japan
| | - Tetsuya Yamada
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Saitama, Japan.,Department of Electronic Chemistry, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo, Japan
| | - Akio Umezawa
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Saitama, Japan
| | - Shawn E McGlynn
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Saitama, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Center for Sustainable Resource Science, RIKEN, Wako, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Center for Sustainable Resource Science, RIKEN, Wako, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Nobuhiro Matsushita
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Ryuhei Nakamura
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, RIKEN, Saitama, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
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40
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A metabolic-activity-detecting approach to life detection: Restoring a chemostat from stop-feeding using a rapid bioactivity assay. Bioelectrochemistry 2017; 118:147-153. [DOI: 10.1016/j.bioelechem.2017.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 08/05/2017] [Accepted: 08/07/2017] [Indexed: 11/22/2022]
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Abstract
Electromicrobiology is the domain of those prokaryotes able to interact with charged electrodes, using them as electron donors and/or electron acceptors. This is performed via a process called extracellular electron transport, in which outer membrane cytochromes are used to oxidize and/or reduce otherwise unavailable insoluble electron acceptors. EET‐capable bacteria can thus be used for a variety of purposes, ranging from small power sources, water reclamation, to pollution remediation and electrosynthesis. Because the study of EET‐capable bacteria is in its nascent phase, the applications are mostly in developmental stages, but the potential for significant contributions to environmental quality is high and moving forward.
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Affiliation(s)
- Kenneth H Nealson
- Department of Earth Science and Biological Sciences, University of Southern California, 835 W. 37th Street, SHS Rm 560, Los Angeles, CA, 90089, USA
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42
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Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea. mBio 2017; 8:mBio.00530-17. [PMID: 28765215 PMCID: PMC5539420 DOI: 10.1128/mbio.00530-17] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors. Some archaea, known as anaerobic methanotrophs, are capable of converting methane into carbon dioxide when they are growing syntopically with sulfate-reducing bacteria. This partnership is the primary mechanism for methane removal in ocean sediments; however, there is still much to learn about how this syntrophy works. Previous studies have failed to identify the metabolic intermediate, such as hydrogen or formate, that is passed between partners. However, recent analysis of methanotrophic archaea has suggested that the syntrophy is formed through direct electron transfer. In this research, we analyzed the genomes of multiple partner bacteria and showed that they also contain the genes necessary to perform extracellular electron transfer, which are absent in related bacteria that do not form syntrophic partnerships with anaerobic methanotrophs. This genomic evidence shows a possible mechanism for direct electron transfer from methanotrophic archaea into the metabolism of the partner bacteria.
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43
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Li C, Lesnik KL, Liu H. Stay connected: Electrical conductivity of microbial aggregates. Biotechnol Adv 2017; 35:669-680. [PMID: 28768145 DOI: 10.1016/j.biotechadv.2017.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/25/2017] [Accepted: 07/27/2017] [Indexed: 01/01/2023]
Abstract
The discovery of direct extracellular electron transfer offers an alternative to the traditional understanding of diffusional electron exchange via small molecules. The establishment of electronic connections between electron donors and acceptors in microbial communities is critical to electron transfer via electrical currents. These connections are facilitated through conductivity associated with various microbial aggregates. However, examination of conductivity in microbial samples is still in its relative infancy and conceptual models in terms of conductive mechanisms are still being developed and debated. The present review summarizes the fundamental understanding of electrical conductivity in microbial aggregates (e.g. biofilms, granules, consortia, and multicellular filaments) highlighting recent findings and key discoveries. A greater understanding of electrical conductivity in microbial aggregates could facilitate the survey for additional microbial communities that rely on direct extracellular electron transfer for survival, inform rational design towards the aggregates-based production of bioenergy/bioproducts, and inspire the construction of new synthetic conductive polymers.
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Affiliation(s)
- Cheng Li
- Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, USA
| | - Keaton Larson Lesnik
- Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, USA
| | - Hong Liu
- Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, USA.
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Liu Y, Lai Q, Shao Z. A Multilocus Sequence Analysis Scheme for Phylogeny of Thioclava Bacteria and Proposal of Two Novel Species. Front Microbiol 2017; 8:1321. [PMID: 28751885 PMCID: PMC5508018 DOI: 10.3389/fmicb.2017.01321] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/29/2017] [Indexed: 11/13/2022] Open
Abstract
A multilocus sequence analysis (MLSA) was established and performed on the genus Thioclava, including 23 strains isolated from diverse marine environments, with the aim of better differentiation of strains and species within this genus. The study was based on sequences of 16S rRNA gene and five protein-coding housekeeping genes, gyrB, rpoD, dnaK, trpB, and recA. In contrast to 16S rRNA gene-based tree that was unable to separate some species within this genus, each tree based on a single housekeeping gene and MLSA had consistently defined seven clades, corresponding to the five established ones and two novel ones. The digital DNA-DNA hybridization and average nucleotide identity analyses based on genome sequences of the representative strains reconfirmed the validity of the MLSA analysis, and recommended a 97.3% MLSA similarity as the soft species threshold and nine species representing the five known and four putative novel species. Two of the four new species were identified as Thioclava sediminum sp. nov. (type strain TAW-CT134T = MCCC 1A10143T = LMG 29615T) and Thioclava marinus sp. nov. (type strain 11.10-0-13T = MCCC 1A03502T = LMG 29618T) by using a polyphasic taxonomic approach. Taken together, the newly established MLSA in this study first described the variability and phylogeny of the genus Thioclava which contributes to better understanding its ecology and evolution.
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Affiliation(s)
- Yang Liu
- School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian ProvinceXiamen, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian ProvinceXiamen, China
| | - Zongze Shao
- School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian ProvinceXiamen, China
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Malanoski AP, Lin B, Eddie BJ, Wang Z, Hervey WJ, Glaven SM. Relative abundance of 'Candidatus Tenderia electrophaga' is linked to cathodic current in an aerobic biocathode community. Microb Biotechnol 2017; 11:98-111. [PMID: 28696003 PMCID: PMC5743799 DOI: 10.1111/1751-7915.12757] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 01/18/2023] Open
Abstract
Biocathode microbial communities are proposed to catalyse a range of useful reactions. Unlike bioanodes, model biocathode organisms have not yet been successfully cultivated in isolation highlighting the need for culture‐independent approaches to characterization. Biocathode MCL (Marinobacter, Chromatiaceae, Labrenzia) is a microbial community proposed to couple CO2 fixation to extracellular electron transfer and O2 reduction. Previous metagenomic analysis of a single MCL bioelectrochemical system (BES) resulted in resolution of 16 bin genomes. To further resolve bin genomes and compare community composition across replicate MCL BES, we performed shotgun metagenomic and 16S rRNA gene (16S) sequencing at steady‐state current. Clustering pooled reads from replicate BES increased the number of resolved bin genomes to 20, over half of which were > 90% complete. Direct comparison of unassembled metagenomic reads and 16S operational taxonomic units (OTUs) predicted higher community diversity than the assembled/clustered metagenome and the predicted relative abundances did not match. However, when 16S OTUs were mapped to bin genomes and genome abundance was scaled by 16S gene copy number, estimated relative abundance was more similar to metagenomic analysis. The relative abundance of the bin genome representing ‘Ca. Tenderia electrophaga’ was correlated with increasing current, further supporting the hypothesis that this organism is the electroautotroph.
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Affiliation(s)
- Anthony P Malanoski
- United States Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC, 20375, USA
| | - Baochuan Lin
- Defense Threat Reduction Agency, 8725 John J Kingman Rd #6201, Fort Belvoir, VA, 22060, USA
| | - Brian J Eddie
- United States Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC, 20375, USA
| | - Zheng Wang
- United States Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC, 20375, USA
| | - W Judson Hervey
- United States Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC, 20375, USA
| | - Sarah M Glaven
- United States Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC, 20375, USA
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Liu Y, Lai Q, Shao Z. Thioclava nitratireducens sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2017; 67:2109-2113. [PMID: 28598317 DOI: 10.1099/ijsem.0.001844] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated 25B10_4T, was isolated from surface seawater of the Bering Sea and characterized using a polyphasic taxonomic approach. Cells of strain 25B10_4T were Gram-stain-negative, motile and short-rod-shaped. Growth was observed at 10-43 °C (optimum 28 °C), at pH 6-9 (optimum pH 7) and with 0-12 % NaCl (optimum 3-4 %, w/v). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 25B10_4T formed an independent branch within the genus Thioclava, sharing high similarities with four related type strains, Thioclava atlantica 13D2W-2T (98.9 %), Thioclava pacifica TL 2T (98.5 %), Thioclava dalianensis DLFJ1-1T (98.4 %) and Thioclava indica DT23-4T (96.9 %), and low similarities (less than 96.5 %) with other type strains within the family Rhodobacteraceae. The major fatty acid was identified as summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The quinone was Q-10. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, glycolipid and five unidentified phospholipids. The DNA G+C content was 63.8 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between strain 25B10_4T and the four above-mentioned type strains were, respectively, 20.5-25.7 % and 77.8-82.4 %. The phenotypic, phylogenetic and chemotaxonomic analyses clearly indicated that strain 25B10_4T represents a novel species within the genus Thioclava, for which the name Thioclava nitratireducens sp. nov. is proposed. The type strain is 25B10_4T (=MCCC 1A07302T=LMG 29614T).
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Affiliation(s)
- Yang Liu
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
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Matturro B, Cruz Viggi C, Aulenta F, Rossetti S. Cable Bacteria and the Bioelectrochemical Snorkel: The Natural and Engineered Facets Playing a Role in Hydrocarbons Degradation in Marine Sediments. Front Microbiol 2017; 8:952. [PMID: 28611751 PMCID: PMC5447156 DOI: 10.3389/fmicb.2017.00952] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/12/2017] [Indexed: 11/13/2022] Open
Abstract
The composition and metabolic traits of the microbial communities acting in an innovative bioelectrochemical system were here investigated. The system, known as Oil Spill Snorkel, was recently developed to stimulate the oxidative biodegradation of petroleum hydrocarbons in anoxic marine sediments. Next Generation Sequencing was used to describe the microbiome of the bulk sediment and of the biofilm growing attached to the surface of the electrode. The analysis revealed that sulfur cycling primarily drives the microbial metabolic activities occurring in the bioelectrochemical system. In the anoxic zone of the contaminated marine sediment, petroleum hydrocarbon degradation occurred under sulfate-reducing conditions and was lead by different families of Desulfobacterales (46% of total OTUs). Remarkably, the occurrence of filamentous Desulfubulbaceae, known to be capable to vehicle electrons deriving from sulfide oxidation to oxygen serving as a spatially distant electron acceptor, was demonstrated. Differently from the sediment, which was mostly colonized by Deltaproteobacteria, the biofilm at the anode hosted, at high extent, members of Alphaproteobacteria (59%) mostly affiliated to Rhodospirillaceae family (33%) and including several known sulfur- and sulfide-oxidizing genera. Overall, we showed the occurrence in the system of a variety of electroactive microorganisms able to sustain the contaminant biodegradation alone or by means of an external conductive support through the establishment of a bioelectrochemical connection between two spatially separated redox zones and the preservation of an efficient sulfur cycling.
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Rowe AR, Yoshimura M, LaRowe DE, Bird LJ, Amend JP, Hashimoto K, Nealson KH, Okamoto A. In situ
electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring. Environ Microbiol 2017; 19:2272-2285. [DOI: 10.1111/1462-2920.13723] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 03/05/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Annette R. Rowe
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Miho Yoshimura
- Department of Applied and Chemical Engineering; University of Tokyo; Tokyo Japan
| | - Doug E. LaRowe
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Lina J. Bird
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Jan P. Amend
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
- Department of Biological Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Kazuhito Hashimoto
- Center for Green Research on Energy and Environmental Materials; National Institute for Material Sciences; Tsukuba Ibaraki 305-0047 Japan
| | - Kenneth H. Nealson
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Akihiro Okamoto
- Center for Green Research on Energy and Environmental Materials; National Institute for Material Sciences; Tsukuba Ibaraki 305-0047 Japan
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Sudek LA, Wanger G, Templeton AS, Staudigel H, Tebo BM. Submarine Basaltic Glass Colonization by the Heterotrophic Fe(II)-Oxidizing and Siderophore-Producing Deep-Sea Bacterium Pseudomonas stutzeri VS-10: The Potential Role of Basalt in Enhancing Growth. Front Microbiol 2017; 8:363. [PMID: 28344573 PMCID: PMC5345036 DOI: 10.3389/fmicb.2017.00363] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 02/21/2017] [Indexed: 11/13/2022] Open
Abstract
Phylogenetically and metabolically diverse bacterial communities have been found in association with submarine basaltic glass surfaces. The driving forces behind basalt colonization are for the most part unknown. It remains ambiguous if basalt provides ecological advantages beyond representing a substrate for surface colonization, such as supplying nutrients and/or energy. Pseudomonas stutzeri VS-10, a metabolically versatile bacterium isolated from Vailulu'u Seamount, was used as a model organism to investigate the physiological responses observed when biofilms are established on basaltic glasses. In Fe-limited heterotrophic media, P. stutzeri VS-10 exhibited elevated growth in the presence of basaltic glass. Diffusion chamber experiments demonstrated that physical attachment or contact of soluble metabolites such as siderophores with the basaltic glass plays a pivotal role in this process. Electrochemical data indicated that P. stutzeri VS-10 is able to use solid substrates (electrodes) as terminal electron donors and acceptors. Siderophore production and heterotrophic Fe(II) oxidation are discussed as potential mechanisms enhancing growth of P. stutzeri VS-10 on glass surfaces. In correlation with that we discuss the possibility that metabolic versatility could represent a common and beneficial physiological trait in marine microbial communities being subject to oligotrophic and rapidly changing deep-sea conditions.
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Affiliation(s)
- Lisa A Sudek
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla CA, USA
| | - Greg Wanger
- Jet Propulsion Laboratory, California Institute of Technology, University of Southern California, Pasadena CA, USA
| | - Alexis S Templeton
- Department of Geological Sciences, University of Colorado Boulder, Boulder CO, USA
| | - Hubert Staudigel
- Institute of Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California, San Diego, La Jolla CA, USA
| | - Bradley M Tebo
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla CA, USA
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Eddie BJ, Wang Z, Hervey WJ, Leary DH, Malanoski AP, Tender LM, Lin B, Strycharz-Glaven SM. Metatranscriptomics Supports the Mechanism for Biocathode Electroautotrophy by " Candidatus Tenderia electrophaga". mSystems 2017; 2:e00002-17. [PMID: 28382330 PMCID: PMC5371394 DOI: 10.1128/msystems.00002-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/07/2017] [Indexed: 01/12/2023] Open
Abstract
Biocathodes provide a stable electron source to drive reduction reactions in electrotrophic microbial electrochemical systems. Electroautotrophic biocathode communities may be more robust than monocultures in environmentally relevant settings, but some members are not easily cultivated outside the electrode environment. We previously used metagenomics and metaproteomics to propose a pathway for coupling extracellular electron transfer (EET) to carbon fixation in "Candidatus Tenderia electrophaga," an uncultivated but dominant member of an electroautotrophic biocathode community. Here we validate and refine this proposed pathway using metatranscriptomics of replicate aerobic biocathodes poised at the growth potential level of 310 mV and the suboptimal 470 mV (versus the standard hydrogen electrode). At both potentials, transcripts were more abundant from "Ca. Tenderia electrophaga" than from any other constituent, and its relative activity was positively correlated with current. Several genes encoding key components of the proposed "Ca. Tenderia electrophaga" EET pathway were more highly expressed at 470 mV, consistent with a need for cells to acquire more electrons to obtain the same amount of energy as at 310 mV. These included cyc2, encoding a homolog of a protein known to be involved in iron oxidation. Mean expression of all CO2 fixation-related genes is 0.27 log2-fold higher at 310 mV, indicating that reduced energy availability at 470 mV decreased CO2 fixation. Our results substantiate the claim that "Ca. Tenderia electrophaga" is the key electroautotroph, which will help guide further development of this community for microbial electrosynthesis. IMPORTANCE Bacteria that directly use electrodes as metabolic electron donors (biocathodes) have been proposed for applications ranging from microbial electrosynthesis to advanced bioelectronics for cellular communication with machines. However, just as we understand very little about oxidation of analogous natural insoluble electron donors, such as iron oxide, the organisms and extracellular electron transfer (EET) pathways underlying the electrode-cell direct electron transfer processes are almost completely unknown. Biocathodes are a stable biofilm cultivation platform to interrogate both the rate and mechanism of EET using electrochemistry and to study the electroautotrophic organisms that catalyze these reactions. Here we provide new evidence supporting the hypothesis that the uncultured bacterium "Candidatus Tenderia electrophaga" directly couples extracellular electron transfer to CO2 fixation. Our results provide insight into developing biocathode technology, such as microbial electrosynthesis, as well as advancing our understanding of chemolithoautotrophy.
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Affiliation(s)
- Brian J Eddie
- United States Naval Research Laboratory, Washington, DC, USA
| | - Zheng Wang
- United States Naval Research Laboratory, Washington, DC, USA
| | - W Judson Hervey
- United States Naval Research Laboratory, Washington, DC, USA
| | - Dagmar H Leary
- United States Naval Research Laboratory, Washington, DC, USA
| | | | | | - Baochuan Lin
- United States Naval Research Laboratory, Washington, DC, USA
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