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Di S, Li Y, Song B, Guo C, Qi P, Wang Z, Liu Z, Zhao H, Wang X. Potential effects of individual and combined exposure to tetraconazole and cadmium on zebrafish from the perspective of enantioselectivity and intestinal microbiota. Sci Total Environ 2024; 921:170899. [PMID: 38350559 DOI: 10.1016/j.scitotenv.2024.170899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/25/2024] [Accepted: 02/09/2024] [Indexed: 02/15/2024]
Abstract
As the wide use of pesticides, they could form combined pollution with heavy metals, which would affect their environmental behaviors and toxic effects. Particularly, the effects would be more intricate for chiral pesticides. In this study, the accumulation and dissipation trends of tetraconazole enantiomers in zebrafish were investigated by individual and combined exposure of cadmium (Cd) and tetraconazole (including racemate and enantiomers) after confirming the absolute configuration of tetraconazole enantiomer. For the enantiomer treatments, Cd enhanced the accumulation of S-(+)-tetraconazole, but declined the concentrations of R-(-)-tetraconazole in zebrafish. The dissipation half-lives of tetraconazole enantiomers were extended by 1.65-1.44 times after the combined exposure of Cd and enantiomers. The community richness and diversity of intestinal microbiota were reduced in all treatments, and there were significant differences in R + Cd treatment. There was synergistic effect between Cd and S-(+)-tetraconazole for the effects on the relative abundances of Fusobacteria, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. For R-(-)-tetraconazole, Cd mainly exhibited antagonistic effects. In the combined exposure of Cd and S-(+)-tetraconazole, the relative abundance changes of Cetobacterium (Fusobacteria, increase) and Edwardsiella (Proteobacteria, decrease) might affect the carbohydrate metabolism and energy metabolism, and led to the increase of S-(+)-tetraconazole bioaccumulation concentration. In the combined exposure of Cd and R-(-)-tetraconazole, Cd could increase the relative abundance of Edwardsiella (Proteobacteria), and affect the amino acid metabolism, which might reduce the bioaccumulation concentration of R-(-)-tetraconazole. This study reported for the first time that the abundance of intestinal microbiota in zebrafish might affect the bioaccumulation and dissipation of tetraconazole enantiomers, and would provide new insight for the study of combined pollutions.
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Affiliation(s)
- Shanshan Di
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Ying Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Beibei Song
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Chao Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Peipei Qi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Zhiwei Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Zhenzhen Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Huiyu Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China
| | - Xinquan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China; Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou 310021, PR China.
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Kis M, Szabó T, Tandori J, Maróti P. Roadmap of electrons from donor side to the reaction center of photosynthetic purple bacteria with mutated cytochromes. Photosynth Res 2024; 159:261-272. [PMID: 38032488 PMCID: PMC10991045 DOI: 10.1007/s11120-023-01059-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 10/28/2023] [Indexed: 12/01/2023]
Abstract
In photosynthetic bacteria, the absorbed light drives the canonical cyclic electron transfer between the reaction center and the cytochrome bc1 complexes via the pools of mobile electron carriers. If kinetic or structural barriers hinder the participation of the bc1 complex in the cyclic flow of electrons, then the pools of mobile redox agents must supply the electrons for the multiple turnovers of the reaction center. These conditions were achieved by continuous high light excitation of intact cells of bacterial strains Rba. sphaeroides and Rvx. gelatinosus with depleted donor side cytochromes c2 (cycA) and tetraheme cytochrome subunit (pufC), respectively. The gradual oxidation by ferricyanide further reduced the availability of electron donors to pufC. Electron transfer through the reaction center was tracked by absorption change and by induction and relaxation of the fluorescence of the bacteriochlorophyll dimer. The rate constants of the electron transfer (~ 3 × 103 s‒1) from the mobile donors of Rvx. gelatinosus bound either to the RC (pufC) or to the tetraheme subunit (wild type) were similar. The electrons transferred through the reaction center dimer were supplied entirely by the donor pool; their number amounted to about 5 in wild type Rvx. gelatinosus and decreased to 1 in pufC oxidized by ferricyanide. Fluorescence yield was measured as a function of the oxidized fraction of the dimer and its complex shape reveals the contribution of two competing processes: the migration of the excitation energy among the photosynthetic units and the availability of electron donors to the oxidized dimer. The experimental results were simulated and rationalized by a simple kinetic model of the two-electron cycling of the acceptor side combined with aperiodic one-electron redox function of the donor side.
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Affiliation(s)
- M Kis
- Balaton Limnological Research Institute, Klebelsberg K. Utca 3, Tihany, 8237, Hungary
| | - T Szabó
- Institute of Medical Physics, University of Szeged, Korányi Fasor 9, Szeged, 6720, Hungary
| | - J Tandori
- Institute of Medical Physics, University of Szeged, Korányi Fasor 9, Szeged, 6720, Hungary
| | - P Maróti
- Institute of Medical Physics, University of Szeged, Korányi Fasor 9, Szeged, 6720, Hungary.
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Sana TG, Notopoulou A, Puygrenier L, Decossas M, Moreau S, Carlier A, Krasteva PV. Structures and roles of BcsD and partner scaffold proteins in proteobacterial cellulose secretion. Curr Biol 2024; 34:106-116.e6. [PMID: 38141614 DOI: 10.1016/j.cub.2023.11.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Cellulose is the world's most abundant biopolymer, and similar to its role as a cell wall component in plants, it is a prevalent constituent of the extracellular matrix in bacterial biofilms. Although bacterial cellulose (BC) was first described in the 19th century, it was only recently revealed that it is produced by several distinct types of Bcs secretion systems that feature multiple accessory subunits in addition to a catalytic BcsAB synthase tandem. We recently showed that crystalline cellulose secretion in the Gluconacetobacter genus (α-Proteobacteria) is driven by a supramolecular BcsH-BcsD scaffold-the "cortical belt"-which stabilizes the synthase nanoarrays through an unexpected inside-out mechanism for secretion system assembly. Interestingly, while bcsH is specific for Gluconacetobacter, bcsD homologs are widespread in Proteobacteria. Here, we examine BcsD homologs and their gene neighborhoods from several plant-colonizing β- and γ-Proteobacteria proposed to secrete a variety of non-crystalline and/or chemically modified cellulosic polymers. We provide structural and mechanistic evidence that through different quaternary structure assemblies BcsD acts with proline-rich BcsH, BcsP, or BcsO partners across the proteobacterial clade to form synthase-interacting intracellular scaffolds that, in turn, determine the biofilm strength and architecture in species with strikingly different physiology and secreted biopolymers.
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Affiliation(s)
- Thibault G Sana
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac 33600, France; "Structural Biology of Biofilms" Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac 33600, France
| | - Areti Notopoulou
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac 33600, France; "Structural Biology of Biofilms" Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac 33600, France
| | - Lucie Puygrenier
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac 33600, France; "Structural Biology of Biofilms" Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac 33600, France
| | - Marion Decossas
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac 33600, France; "Structural Biology of Biofilms" Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac 33600, France
| | - Sandra Moreau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
| | - Aurélien Carlier
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France; Laboratory of Microbiology, Ghent University, Ghent 9000, Belgium
| | - Petya V Krasteva
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac 33600, France; "Structural Biology of Biofilms" Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac 33600, France.
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Sepúlveda-Rebolledo P, González-Rosales C, Dopson M, Pérez-Rueda E, Holmes DS, Valdés JH. Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives. Res Microbiol 2024; 175:104135. [PMID: 37678513 DOI: 10.1016/j.resmic.2023.104135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
Extreme acidophiles thrive in acidic environments, confront a multitude of challenges, and demonstrate remarkable adaptability in their metabolism to cope with the ever-changing environmental fluctuations, which encompass variations in temperature, pH levels, and the availability of electron acceptors and donors. The survival and proliferation of members within the Acidithiobacillia class rely on the deployment of transcriptional regulatory systems linked to essential physiological traits. The study of these transcriptional regulatory systems provides valuable insights into critical processes, such as energy metabolism and nutrient assimilation, and how they integrate into major genetic-metabolic circuits. In this study, we examined the transcriptional regulatory repertoires and potential interactions of forty-three Acidithiobacillia complete and draft genomes, encompassing nine species. To investigate the function and diversity of Transcription Factors (TFs) and their DNA Binding Sites (DBSs), we conducted a genome-wide comparative analysis, which allowed us to identify these regulatory elements in representatives of Acidithiobacillia. We classified TFs into gene families and compared their occurrence among all representatives, revealing conservation patterns across the class. The results identified conserved regulators for several pathways, including iron and sulfur oxidation, the main pathways for energy acquisition, providing new evidence for viable regulatory interactions and branch-specific conservation in Acidithiobacillia. The identification of TFs and DBSs not only corroborates existing experimental information for selected species, but also introduces novel candidates for experimental validation. Moreover, these promising candidates have the potential for further extension to new representatives within the class.
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Affiliation(s)
- Pedro Sepúlveda-Rebolledo
- Centro de Genómica y Bioinformática and PhD. Program on Integrative Genomics, Facultad de Ciencias, Universidad Mayor, Santiago (8580745), Chile.
| | - Carolina González-Rosales
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago (8580638), Chile; Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Yucatán, Mexico.
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago (8580638), Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago (7510156), Chile.
| | - Jorge H Valdés
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago (8370146), Chile.
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Weber L, Gilat A, Maillot N, Byrne D, Arnoux P, Giudici-Orticoni MT, Méjean V, Ilbert M, Genest O, Rosenzweig R, Dementin S. Bacterial adaptation to cold: Conservation of a short J-domain co-chaperone and its protein partners in environmental proteobacteria. Environ Microbiol 2023; 25:2447-2464. [PMID: 37549929 DOI: 10.1111/1462-2920.16478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
Bacterial genomes are a huge reservoir of genes encoding J-domain protein co-chaperones that recruit the molecular chaperone DnaK to assist protein substrates involved in survival, adaptation, or fitness. The atc operon of the aquatic mesophilic bacterium Shewanella oneidensis encodes the proteins AtcJ, AtcA, AtcB, and AtcC, and all of them, except AtcA, are required for growth at low temperatures. AtcJ is a short J-domain protein that interacts with DnaK, but also with AtcC through its 21 amino acid C-terminal domain. This interaction network is critical for cold growth. Here, we show that AtcJ represents a subfamily of short J-domain proteins that (i) are found in several environmental, mostly aquatic, β- or ɣ-proteobacteria and (ii) contain a conserved PX7 W motif in their C-terminal extension. Using a combination of NMR, biochemical and genetic approaches, we show that the hydrophobic nature of the tryptophan of the S. oneidensis AtcJ PX7 W motif determines the strong AtcJ-AtcC interaction essential for cold growth. The AtcJ homologues are encoded by operons containing at least the S. oneidensis atcA, atcB, and atcC homologues. These findings suggest a conserved network of DnaK and Atc proteins necessary for low-temperature growth and, given the variation in the atc operons, possibly for other biological functions.
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Affiliation(s)
- Lana Weber
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Atar Gilat
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nathanael Maillot
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Deborah Byrne
- Protein Expression Facility, Aix-Marseille University, French National Center for Scientific Research (CNRS), IMM FR3479, Marseille, France
| | - Pascal Arnoux
- Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM UMR7265), Aix-Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), French National Center for Scientific Research (CNRS), Saint Paul-Lez-Durance, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Vincent Méjean
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Marianne Ilbert
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Olivier Genest
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sébastien Dementin
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
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Satoh I, Gotou K, Nagatsuma S, Nagashima KVP, Kobayashi M, Yu LJ, Madigan MT, Kimura Y, Wang-Otomo ZY. Selective expression of light-harvesting complexes alters phospholipid composition in the intracytoplasmic membrane and core complex of purple phototrophic bacteria. Biochim Biophys Acta Bioenerg 2023; 1864:149001. [PMID: 37527691 DOI: 10.1016/j.bbabio.2023.149001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023]
Abstract
Phospholipid-protein interactions play important roles in regulating the function and morphology of photosynthetic membranes in purple phototrophic bacteria. Here, we characterize the phospholipid composition of intracytoplasmic membrane (ICM) from Rhodobacter (Rba.) sphaeroides that has been genetically altered to selectively express light-harvesting (LH) complexes. In the mutant strain (DP2) that lacks a peripheral light-harvesting (LH2) complex, the phospholipid composition was significantly different from that of the wild-type strain; strain DP2 showed a marked decrease in phosphatidylglycerol (PG) and large increases in cardiolipin (CL) and phosphatidylcholine (PC) indicating preferential interactions between the complexes and specific phospholipids. Substitution of the core light-harvesting (LH1) complex of Rba. sphaeroides strain DP2 with that from the purple sulfur bacterium Thermochromatium tepidum further altered the phospholipid composition, with substantial increases in PG and PE and decreases in CL and PC, indicating that the phospholipids incorporated into the ICM depend on the nature of the LH1 complex expressed. Purified LH1-reaction center core complexes (LH1-RC) from the selectively expressing strains also contained different phospholipid compositions than did core complexes from their corresponding wild-type strains, suggesting different patterns of phospholipid association between the selectively expressed LH1-RC complexes and those purified from native strains. Effects of carotenoids on the phospholipid composition were also investigated using carotenoid-suppressed cells and carotenoid-deficient species. The findings are discussed in relation to ICM morphology and specific LH complex-phospholipid interactions.
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Affiliation(s)
- I Satoh
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
| | - K Gotou
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
| | - S Nagatsuma
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan
| | - K V P Nagashima
- Research Institute for Integrated Science, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa 221-8686, Japan
| | - M Kobayashi
- National Institute of Technology, Ariake College, Omuta, Fukuoka 836-8585, Japan
| | - L-J Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - M T Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA
| | - Y Kimura
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Z-Y Wang-Otomo
- Faculty of Science, Ibaraki University, Mito 310-8512, Japan.
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Wang D, Fiebig OC, Harris D, Toporik H, Ji Y, Chuang C, Nairat M, Tong AL, Ogren JI, Hart SM, Cao J, Sturgis JN, Mazor Y, Schlau-Cohen GS. Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria. Proc Natl Acad Sci U S A 2023; 120:e2220477120. [PMID: 37399405 PMCID: PMC10334754 DOI: 10.1073/pnas.2220477120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/21/2023] [Indexed: 07/05/2023] Open
Abstract
In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical reactions. While the energy transfer dynamics within individual antenna proteins have been extensively studied over the past decades, the dynamics between the proteins are poorly understood due to the heterogeneous organization of the network. Previously reported timescales averaged over such heterogeneity, obscuring individual interprotein energy transfer steps. Here, we isolated and interrogated interprotein energy transfer by embedding two variants of the primary antenna protein from purple bacteria, light-harvesting complex 2 (LH2), together into a near-native membrane disc, known as a nanodisc. We integrated ultrafast transient absorption spectroscopy, quantum dynamics simulations, and cryogenic electron microscopy to determine interprotein energy transfer timescales. By varying the diameter of the nanodiscs, we replicated a range of distances between the proteins. The closest distance possible between neighboring LH2, which is the most common in native membranes, is 25 Å and resulted in a timescale of 5.7 ps. Larger distances of 28 to 31 Å resulted in timescales of 10 to 14 ps. Corresponding simulations showed that the fast energy transfer steps between closely spaced LH2 increase transport distances by ∼15%. Overall, our results introduce a framework for well-controlled studies of interprotein energy transfer dynamics and suggest that protein pairs serve as the primary pathway for the efficient transport of solar energy.
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Affiliation(s)
- Dihao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Olivia C. Fiebig
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Dvir Harris
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Hila Toporik
- School of Molecular Sciences, Arizona State University, Tempe, AZ85281
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ85281
| | - Yi Ji
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Chern Chuang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Muath Nairat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Ashley L. Tong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - John I. Ogren
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Stephanie M. Hart
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - James N. Sturgis
- LISM UMR 7255, CNRS and Aix-Marseille University, Marseille Cedex 913402, France
| | - Yuval Mazor
- School of Molecular Sciences, Arizona State University, Tempe, AZ85281
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ85281
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Yao K, Cai A, Han J, Che R, Hao J, Wang F, Ye M, Jiang X. The characteristics and metabolic potentials of the soil bacterial community of two typical military demolition ranges in China. Sci Total Environ 2023; 874:162562. [PMID: 36871728 DOI: 10.1016/j.scitotenv.2023.162562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/25/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
The response mechanism of soil microbiota in military polluted sites can effectively indicate the biotoxicity of ammunition. In this study, two military demolition ranges polluted soils of grenades and bullet were collected. According to high-throughput sequencing, after grenade explosion, the dominant bacteria in Site 1 (S1) are Proteobacteria (97.29 %) and Actinobacteria (1.05 %). The dominant bacterium in Site 2 (S2) is Proteobacteria (32.95 %), followed by Actinobacteria (31.17 %). After the military exercise, the soil bacterial diversity index declined significantly, and the bacterial communities interacted more closely. The indigenous bacteria in S1 were influenced more compared to those in S2. According to the environmental factor analysis, the bacteria composition can easily be influenced by heavy metals and organic pollutants, including Cu, Pb, Cr and Trinitrotoluene (TNT). About 269 metabolic pathways annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were detected in bacterial communities, including nutrition metabolism (C, 4.09 %; N, 1.14 %; S, 0.82 %), external pollutant metabolism (2.52 %) and heavy metal detoxication (2.12 %), respectively. The explosion of ammunition changes the basic metabolism of indigenous bacteria, and heavy metal stress inhibits the TNT degradation ability of bacterial communities. The pollution degree and community structure influence the metal detoxication strategy at the contaminated sites together. Heavy metal ions in S1 are mainly discharged through membrane transporters, while heavy metal ions in S2 are mainly degraded through lipid metabolism and biosynthesis of secondary metabolites. The results obtained in this study can provide deep insight into the response mechanism of the soil bacterial community in military demolition ranges with composite pollutions of heavy metals and organic substances. CAPSULE: Heavy metal stress changed the composition, interaction and metabolism of indigenous communities in military demolition ranges, especially the TNT degradation process.
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Affiliation(s)
- Keyu Yao
- National Engineering Laboratory of Soil Nutrients Management, Pollution Control and Remediation Technologies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Anjuan Cai
- Jiangsu Environmental Engineering Technology Co., Ltd, 210019, China
| | - Jin Han
- Jiangsu Environmental Engineering Technology Co., Ltd, 210019, China
| | - Ruijie Che
- Key Laboratory for Soft Chemistry and Functional Materials of Ministry of Education, Nanjing University of Science and Technology, Nanjing 210094, China; Jiangsu Province Engineering Research Center of Environmental Risk Prevention and Emergency Response Technology, School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Jiarong Hao
- Key Laboratory for Soft Chemistry and Functional Materials of Ministry of Education, Nanjing University of Science and Technology, Nanjing 210094, China; Jiangsu Province Engineering Research Center of Environmental Risk Prevention and Emergency Response Technology, School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Fenghe Wang
- Key Laboratory for Soft Chemistry and Functional Materials of Ministry of Education, Nanjing University of Science and Technology, Nanjing 210094, China; Jiangsu Province Engineering Research Center of Environmental Risk Prevention and Emergency Response Technology, School of Environment, Nanjing Normal University, Nanjing 210023, China.
| | - Mao Ye
- National Engineering Laboratory of Soil Nutrients Management, Pollution Control and Remediation Technologies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xin Jiang
- National Engineering Laboratory of Soil Nutrients Management, Pollution Control and Remediation Technologies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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9
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Cupellini L, Qian P, Nguyen-Phan TC, Gardiner AT, Cogdell RJ. Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex. Photosynth Res 2023; 156:75-87. [PMID: 35672557 PMCID: PMC10070313 DOI: 10.1007/s11120-022-00925-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The light-harvesting complex 2 (LH2) of purple bacteria is one of the most studied photosynthetic antenna complexes. Its symmetric structure and ring-like bacteriochlorophyll arrangement make it an ideal system for theoreticians and spectroscopists. LH2 complexes from most bacterial species are thought to have eightfold or ninefold symmetry, but recently a sevenfold symmetric LH2 structure from the bacterium Mch. purpuratum was solved by Cryo-Electron microscopy. This LH2 also possesses unique near-infrared absorption and circular dichroism (CD) spectral properties. Here we use an atomistic strategy to elucidate the spectral properties of Mch. purpuratum LH2 and understand the differences with the most commonly studied LH2 from Rbl. acidophilus. Our strategy exploits a combination of molecular dynamics simulations, multiscale polarizable quantum mechanics/molecular mechanics calculations, and lineshape simulations. Our calculations reveal that the spectral properties of LH2 complexes are tuned by site energies and exciton couplings, which in turn depend on the structural fluctuations of the bacteriochlorophylls. Our strategy proves effective in reproducing the absorption and CD spectra of the two LH2 complexes, and in uncovering the origin of their differences. This work proves that it is possible to obtain insight into the spectral tuning strategies of purple bacteria by quantitatively simulating the spectral properties of their antenna complexes.
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Affiliation(s)
- Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124, Pisa, Italy.
| | - Pu Qian
- Materials and Structure Analysis, Thermofisher Scientific, Achtseweg Nordic 5, 5651 GTC, Eindhoven, The Netherlands
| | - Tu C Nguyen-Phan
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Alastair T Gardiner
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Novohradská 237 - Opatovický mlýn, 379 01, Třeboň, Czech Republic
| | - Richard J Cogdell
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
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10
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Chen Y, Lyu Y, Zhang J, Li Q, Lyu L, Zhou Y, Kong J, Zeng X, Zhang S, Li J. Riddles of Lost City: Chemotrophic Prokaryotes Drives Carbon, Sulfur, and Nitrogen Cycling at an Extinct Cold Seep, South China Sea. Microbiol Spectr 2023; 11:e0333822. [PMID: 36511717 PMCID: PMC9927161 DOI: 10.1128/spectrum.03338-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Deep-sea cold seeps are one of the most productive ecosystems that sustained by hydrocarbons carried by the fluid. Once the seep fluid ceases, the thriving autotrophic communities die out, terming as the extinct seep. But heterotrophic fauna can still survive even for thousands of years. The critical role of prokaryotes in active seeps are well defined, but their functions in extinct seeps are poorly understood to date. Here, we clarified the diversity, taxonomic specificity, interspecies correlation, and metabolic profiles of sediment prokaryotes at an extinct seep site of Haima cold seep, South China Sea. Alpha diversity of archaea significantly increased, while that of bacteria remained unchanged in extinct seep compared to active seep. However, archaea composition did not differ significantly at extinct seep from active or nonseep sites based on weighted-unifrac dissimilarity, while bacteria composition exhibited significant difference. Distribution of archaea and bacteria showed clear specificity to extinct seeps, indicating the unique life strategies here. Prokaryotes might live chemolithoautotrophically on cycling of inorganic carbon, sulfur, and nitrogen, or chemoorganotrophically on recycling of hydrocarbons. Notably, many of the extinct seep specific species and networked keystone lineages are classified as Proteobacteria. Regarding the functional diversity and metabolic flexibility of this clade, Proteobacteria is supposed to integrate the geochemical cycles and play a critical role in energy and resource supplement for microbiome in extinct seep. Collectively, our findings shed lights on the microbial ecology and functional diversity in extinct seeps, providing new understanding of biogeochemical cycling after fluid cessation. IMPORTANCE This research paper uncovered the potential mechanisms for microbiota mediated geochemical cycling in extinct cold seep, advancing our understanding in deep sea microbiology ecology.
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Affiliation(s)
- Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Yuanjiao Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Yingli Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Jie Kong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Xinyang Zeng
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Si Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Jie Li
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
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11
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Jin Q, Chen L, Yang S, Zhu C, Li J, Chen J, Li W, Peng X. Carbon Reduction and Pollutant Abatement by a Bio-Ecological Combined Process for Rural Sewage. Int J Environ Res Public Health 2023; 20:1643. [PMID: 36674396 PMCID: PMC9866468 DOI: 10.3390/ijerph20021643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 06/17/2023]
Abstract
In order to explore the treatment effect of a bio-ecological combined process on pollution reduction and carbon abatement of rural domestic wastewater under seasonal changes, the rural area of Lingui District, Guilin City, Guangxi Province, China was selected to construct a combined process of regulating a pond, biological filter, subsurface flow constructed wetland, and ecological purification pond. The influent water, effluent water, and the characteristics of pollutant treatment in each unit were investigated. The results showed that the average removal rates of COD, TN, and NH3-N in summer were 87.57, 72.18, and 80.98%, respectively, while they were 77.46, 57.52, and 64.48% in winter. There were significant seasonal differences in wastewater treatment results in Guilin. Meanwhile, in view of the low carbon:nitrogen ratio in the influent and the poor decontamination effect, the method of adding additional carbon sources such as sludge fermentation and rice straw is proposed to strengthen resource utilization and achieve carbon reduction and emission reduction. The treatment effect of ecological units, especially constructed wetland units, had a high contribution rate of TN treatment, but it was greatly impacted by seasons. The analysis of the relative abundance of the microbial community at the phylum level in constructed wetlands revealed that Proteobacteria, Acidobacteria, Chloroflexi, Firmicutes, Bacteroidetes, Planctomycetota, and Actinobacteria were the dominant phyla. The relative abundance of microbial communities of Proteobacteria, Chloroflexi, and Acidobacteria decreased to a large extent from summer to winter, while Firmicutes, Bacteroidetes, and Planctomycetota increased to varying degrees. These dominant bacteria played an important role in the degradation of pollutants such as COD, NH3-N, and TN in wetland systems.
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Affiliation(s)
- Qiu Jin
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210029, China
| | - Liangang Chen
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210029, China
| | - Shengyun Yang
- School of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China
| | - Chaochao Zhu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210029, China
- School of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China
| | - Jingang Li
- School of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China
| | - Jing Chen
- School of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China
| | - Wei Li
- Department of Ecological Sciences and Engineering, College of Environment and Ecology, Chongqing University, Chongqing 400030, China
| | - Xinxin Peng
- Department of Ecological Sciences and Engineering, College of Environment and Ecology, Chongqing University, Chongqing 400030, China
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12
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Ma X, Liu S, Wang H, Wang Y, Li Z, Gu T, Li Y, Xin F, Wen B. In Vitro Fermentation of Beechwood Lignin-Carbohydrate Complexes Provides Evidence for Utilization by Gut Bacteria. Nutrients 2023; 15:nu15010220. [PMID: 36615876 PMCID: PMC9824187 DOI: 10.3390/nu15010220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/24/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Lignin-carbohydrate complexes (LCCs) are emerging as a new and natural product with pharmacological and nutraceutical potential. It is uncertain, however, whether LCCs have a positive effect on the microbiota of the gut based on the current evidence. Here, the LCC extracted from beechwood (BW-LCC) was used as a substrate for in vitro fermentation. The lignin in BW-LCC consisted of guaiacyl (G) and syringyl (S) units, which are mainly linked by β-O-4 bonds. After 24 h of in vitro fermentation, the pH had evidently declined. The concentrations of acetic acid and propionic acid, the two main short-chain fatty acids (SCFAs), were significantly higher than in the control group (CK). In addition, BW-LCC altered the microbial diversity and composition of gut microbes, including a reduction in the relative abundance of Firmicutes and an increase in the relative abundance of Proteobacteria and Bacteroidetes. The relative abundance of Escherichia coli-Shigella and Bacteroides were the most variable at the genus level. The genes of carbohydrate-active enzymes (CAZymes) also changed significantly with the fermentation and were related to the changes in microbes. Notably, the auxiliary actives (AAs), especially AA1, AA2, and AA3_2, play important roles in lignin degradation and were significantly enriched and concentrated in Proteobacteria. From this study, we are able to provide new perspectives on how gut microbes utilize LCC.
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Affiliation(s)
- Xiaochen Ma
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shujun Liu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongliang Wang
- Center of Biomass Engineering, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yulu Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhen Li
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianyi Gu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulong Li
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (F.X.); (B.W.)
| | - Boting Wen
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (F.X.); (B.W.)
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13
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Wang F, Wei L, Guo M, Yang W, Li Z, Hu D, Lu P. Insights of microbial community evolution under benzisothiazolinone exposure in different soil environments. Chemosphere 2022; 307:135868. [PMID: 35932925 DOI: 10.1016/j.chemosphere.2022.135868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Benzisothiazolinones (1, 2-benzisothiazoline-3-one; BIT) is widely used to control bacterial and fungal diseases of various crops, and their residues in soil may play an important role in the interaction between soil microorganisms. We studied microbial remediation in five representative soils under different soil conditions (unsterilized, sterilized and flooded) using 16S rRNA gene sequencing to investigate the effect of microorganisms on the degradation of BIT residues in soils to minimize the potentially toxic effects of BIT. High-throughput sequencing data showed that the structure and abundance of bacterial communities in BIT soils changed greatly, which might affect their degradation pathways, while Principal Coordinates Analysis (PCoA) results showed that there was no significant difference in the fungal community in different treatments of the five soils, but the degradation rate of BIT was more influenced by anaerobic microorganisms. Furthermore, Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria were the predominant bacterial phyla, accounting for 93.74% of all OTUs, which played an important role in the degradation of BIT. Lysinibacillus had a high relative abundance (21.10%) under flooded treatment conditions in Jilin soil, and its bioremediation may be a reason for the rapid degradation of BIT in flooded treatment. Besides, only soil organic matter (SOM) and pH among the soil properties had significant effects on the microbial community. Based on the further analysis of bacterial phenotype, some microorganisms related to the biodegradation of BIT were found, mainly belonging to Proteobacteria, Bacteroidetes and Firmicutes. This study provides a useful theoretical basis for the biodegradation of BIT using isolated microorganisms.
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Affiliation(s)
- Fang Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Longfeng Wei
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, China
| | - Meiting Guo
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Wansheng Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Zhu Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, China
| | - Deyu Hu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China.
| | - Ping Lu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China.
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14
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Wachira JM, Kiplimo D, Thuita M, Masso C, Mwirichia R. Community Structure of Nitrifying and Denitrifying Bacteria from Effluents Discharged into Lake Victoria, Kenya. Curr Microbiol 2022; 79:252. [PMID: 35834125 DOI: 10.1007/s00284-022-02950-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 06/23/2022] [Indexed: 11/26/2022]
Abstract
An active microbial community of nitrifying and denitrifying bacteria is needed for efficient utilization of nitrogenous compounds from wastewater. In this study, we explored the bacterial community diversity and structure within rivers, treated and untreated wastewater treatment plants (WWTPs) discharging into Lake Victoria. Water samples were collected from rivers and WWTPs that drain into Lake Victoria. Physicochemical analysis was done to determine the level of nutrients or pollutant loading in the samples. Total community DNA was extracted, followed by Illumina high throughput sequencing to determine the total microbial community and abundance. Enrichment and isolation were then done to recover potential nitrifiers and denitrifiers. Physicochemical analysis pointed to high levels total nitrogen and ammonia in both treated and untreated WWTPs as compared to the samples from the lake and rivers. A total of 1,763 operational taxonomic units (OTUs) spread across 26 bacterial phyla were observed with the most dominant phylum being Proteobacteria. We observed a decreasing trend in diversity from the lake, rivers to WWTPs. The genus Planktothrix constituted 19% of the sequence reads in sample J2 collected from the lagoon. All the isolates recovered in this study were affiliated to three genera: Pseudomonas, Klebsiella and Enterobacter in the phylum Proteobacteria. A combination of metagenomic analysis and a culture-dependent approach helped us understand the relative abundance as well as potential nitrifiers and denitrifiers present in different samples. The recovered isolates could be used for in situ removal of nitrogenous compounds from contaminated wastewater.
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Affiliation(s)
- James M Wachira
- Department of Biological Sciences, University of Embu, Embu, 6-60100, Kenya
| | - Denis Kiplimo
- Department of Biological Sciences, University of Embu, Embu, 6-60100, Kenya
| | - Moses Thuita
- International Institute of Tropical Agriculture, Nairobi, 30772-00100, Kenya
| | - Cargele Masso
- International Institute of Tropical Agriculture, PMB 5320, Ibadan, 200001, Oyo State, Nigeria
| | - Romano Mwirichia
- Department of Biological Sciences, University of Embu, Embu, 6-60100, Kenya.
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15
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Daszczyńska A, Krucoń T, Stasiuk R, Koblowska M, Matlakowska R. Lanthanide-Dependent Methanol Metabolism of a Proteobacteria-Dominated Community in a Light Lanthanide-Rich Deep Environment. Int J Mol Sci 2022; 23:ijms23073947. [PMID: 35409305 PMCID: PMC8999231 DOI: 10.3390/ijms23073947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/01/2023] Open
Abstract
This study investigated the occurrence and diversity of proteobacterial XoxF-type methanol dehydrogenases (MDHs) in the microbial community that inhabits a fossil organic matter- and sedimentary lanthanide (Ln3+)-rich underground mine environment using a metagenomic and metaproteomic approach. A total of 8 XoxF-encoding genes (XoxF-EGs) and 14 protein sequences matching XoxF were identified. XoxF-type MDHs were produced by Alpha-, Beta-, and Gammaproteobacteria represented by the four orders Methylococcales, Nitrosomonadales, Rhizobiales, and Xanthomonadales. The highest number of XoxF-EG- and XoxF-matching protein sequences were affiliated with Nitrosomonadales and Rhizobiales, respectively. Among the identified XoxF-EGs, two belonged to the XoxF1 clade, five to the XoxF4 clade, and one to the XoxF5 clade, while seven of the identified XoxF proteins belonged to the XoxF1 clade, four to the XoxF4 clade, and three to the XoxF5 clade. Moreover, the accumulation of light lanthanides and the presence of methanol in the microbial mat were confirmed. This study is the first to show the occurrence of XoxF in the metagenome and metaproteome of a deep microbial community colonizing a fossil organic matter- and light lanthanide-rich sedimentary environment. The presented results broaden our knowledge of the ecology of XoxF-producing bacteria as well as of the distribution and diversity of these enzymes in the natural environment.
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Affiliation(s)
- Agnieszka Daszczyńska
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (A.D.); (R.S.)
| | - Tomasz Krucoń
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland;
| | - Robert Stasiuk
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (A.D.); (R.S.)
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland;
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Renata Matlakowska
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (A.D.); (R.S.)
- Correspondence:
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16
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Yin F, Zhang F, Wang H. Rhizosphere bacteria community and functions under typical natural halophyte communities in North China salinized areas. PLoS One 2021; 16:e0259515. [PMID: 34762689 PMCID: PMC8584676 DOI: 10.1371/journal.pone.0259515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/20/2021] [Indexed: 11/18/2022] Open
Abstract
Soil salinity is a serious environmental issue in arid China. Halophytes show extreme salt tolerance and are grow in saline-alkaline environments. There rhizosphere have complex bacterial communities, which mediate a variety of interactions between plants and soil. High-throughput sequencing was used to investigated rhizosphere bacterial community changes under the typical halophyte species in arid China. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria and Bacteroidetes, Suaeda glauca rhizosphere has stronger enrichment of Nitrospirae and Cyanobacteria. The Ace, Chao and Shannon indices were significantly higher in soils under LC and SG (P<0.05). Functional predictions, based on 16S rRNA gene by PICRUSt, indicated that Energy metabolism, Amino acid metabolism, Carbohydrate metabolism and Fatty acid metabolism are dominant bacterial functions in three halophytes rhizosphere soil. Carbon metabolism, Oxidative phosphorylation, Methane metabolism, Sulfur metabolism and Nitrogen metabolism in SG were significantly higher than that in LC and PT. Regression analysis revealed that rhizosphere soil bacterial community structure is influenced by soil organic matter (SOM) and soil water content (SWC), while soil bacterial community diversity is affected by soil pH. This study contributes to our understanding of the distribution characteristics and metabolic functions under different halophyte rhizosphere bacterial communities, and will provide references for the use of rhizosphere bacteria to regulate the growth of halophytes and ecological restoration of saline soil.
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Affiliation(s)
- Fating Yin
- Agricultural College, Shihezi University, Shihezi City, China
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, Xinjiang, China
| | - Fenghua Zhang
- Agricultural College, Shihezi University, Shihezi City, China
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, Xinjiang, China
- * E-mail:
| | - Haoran Wang
- Agricultural College, Shihezi University, Shihezi City, China
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17
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Abstract
In host-associated bacteria, surface and secreted proteins mediate acquisition of nutrients, interactions with host cells, and specificity of tissue localization. In Gram-negative bacteria, the mechanism by which many proteins cross and/or become tethered to the outer membrane remains unclear. The domain of unknown function 560 (DUF560) occurs in outer membrane proteins throughout Proteobacteria and has been implicated in host-bacterium interactions and lipoprotein surface exposure. We used sequence similarity networking to reveal three subfamilies of DUF560 homologs. One subfamily includes those DUF560 proteins experimentally characterized thus far: NilB, a host range determinant of the nematode-mutualist Xenorhabdus nematophila, and the surface lipoprotein assembly modulators Slam1 and Slam2, which facilitate lipoprotein surface exposure in Neisseria meningitidis (Y. Hooda, C. C. Lai, A. Judd, C. M. Buckwalter, et al., Nat Microbiol 1:16009, 2016, https://doi.org/10.1038/nmicrobiol.2016.9; Y. Hooda, C. C. L. Lai, T. F. Moraes, Front Cell Infect Microbiol 7:207, 2017, https://doi.org/10.3389/fcimb.2017.00207). We show that DUF560 proteins from a second subfamily facilitate secretion of soluble, nonlipidated proteins across the outer membrane. Using in silico analysis, we demonstrate that DUF560 gene complement correlates with bacterial environment at a macro level and host association at a species level. The DUF560 protein superfamily represents a newly characterized Gram-negative secretion system capable of lipoprotein surface exposure and soluble protein secretion with conserved roles in facilitating symbiosis. In light of these data, we propose that it be titled the type 11 secretion system (TXISS). IMPORTANCE The microbial constituency of a host-associated microbiome emerges from a complex physical and chemical interplay of microbial colonization factors, host surface conditions, and host immunological responses. To fill unique niches within a host, bacteria encode surface and secreted proteins that enable interactions with and responses to the host and co-occurring microbes. Bioinformatic predictions of putative bacterial colonization factor localization and function facilitate hypotheses about the potential of bacteria to engage in pathogenic, mutualistic, or commensal activities. This study uses publicly available genome sequence data alongside experimental results from Xenorhabdus nematophila to demonstrate a role for DUF560 family proteins in secretion of bacterial effectors of host interactions. Our research delineates a broadly distributed family of proteins and enables more accurate predictions of the localization of colonization factors throughout Proteobacteria.
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Affiliation(s)
- Alex S. Grossman
- University of Tennessee—Knoxville, Department of Microbiology, Knoxville, Tennessee, USA
| | - Terra J. Mauer
- University of Wisconsin—Madison, Department of Bacteriology, Madison, Wisconsin, USA
| | - Katrina T. Forest
- University of Wisconsin—Madison, Department of Bacteriology, Madison, Wisconsin, USA
| | - Heidi Goodrich-Blair
- University of Tennessee—Knoxville, Department of Microbiology, Knoxville, Tennessee, USA
- University of Wisconsin—Madison, Department of Bacteriology, Madison, Wisconsin, USA
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18
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Liu S, Chen Y, Xiao L. Metagenomic insights into mixotrophic denitrification facilitated nitrogen removal in a full-scale A2/O wastewater treatment plant. PLoS One 2021; 16:e0250283. [PMID: 33857258 PMCID: PMC8049308 DOI: 10.1371/journal.pone.0250283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/01/2021] [Indexed: 11/18/2022] Open
Abstract
Wastewater treatment plants (WWTPs) are important for pollutant removal from wastewater, elimination of point discharges of nutrients into the environment and water resource protection. The anaerobic/anoxic/oxic (A2/O) process is widely used in WWTPs for nitrogen removal, but the requirement for additional organics to ensure a suitable nitrogen removal efficiency makes this process costly and energy consuming. In this study, we report mixotrophic denitrification at a low COD (chemical oxygen demand)/TN (total nitrogen) ratio in a full-scale A2/O WWTP with relatively high sulfate in the inlet. Nitrogen and sulfur species analysis in different units of this A2/O WWTP showed that the internal sulfur cycle of sulfate reduction and reoxidation occurred and that the reduced sulfur species might contribute to denitrification. Microbial community analysis revealed that Thiobacillus, an autotrophic sulfur-oxidizing denitrifier, dominated the activated sludge bacterial community. Metagenomics data also supported the potential of sulfur-based denitrification when high levels of denitrification occurred, and sulfur oxidation and sulfate reduction genes coexisted in the activated sludge. Although most of the denitrification genes were affiliated with heterotrophic denitrifiers with high abundance, the narG and napA genes were mainly associated with autotrophic sulfur-oxidizing denitrifiers. The functional genes related to nitrogen removal were actively expressed even in the unit containing relatively highly reduced sulfur species, indicating that the mixotrophic denitrification process in A2/O could overcome not only a shortage of carbon sources but also the inhibition by reduced sulfur of nitrification and denitrification. Our results indicate that a mixotrophic denitrification process could be developed in full-scale WWTPs and reduce the requirement for additional carbon sources, which could endow WWTPs with more flexible and adaptable nitrogen removal.
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Affiliation(s)
- Shulei Liu
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing, China
| | - Yasong Chen
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing, China
| | - Lin Xiao
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing, China
- * E-mail:
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19
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Affiliation(s)
- Navdeep S Chandel
- Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, USA
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20
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Cui W, Ma Z, Li X, Hu X. Structural rearrangement of native and processed pea starches following simulated digestion in vitro and fermentation characteristics of their resistant starch residues using human fecal inoculum. Int J Biol Macromol 2021; 172:490-502. [PMID: 33472022 DOI: 10.1016/j.ijbiomac.2021.01.092] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/27/2020] [Accepted: 01/14/2021] [Indexed: 12/11/2022]
Abstract
Pea starches, in both native (NPS) and retrograded-autoclaved forms (RAPS), were subjected to simulated gastrointestinal (GI) digestion in vitro, their multi-scale structural characteristics, morphological features, molecular distribution and thermal properties were characterized. A gradual increase in the short-/long-range crystallinity, melting enthalpy of gelatinization on increasing digestion time was observed for both the native and retrograded-autoclaved pea starch samples based on the X-ray diffraction, Fourier-transform infrared spectra, solid-state 13CNMR and differential scanning calorimetry measurements. It was especially noticed that the growth rate of crystallinity and double helices, as well as the decrease in Mw values were evidently greater for RAPS than for NPS. To investigate how different molecular fine structure of pea starch substrate affects the gut microbiota shifts and dynamic short-chain fatty acid profile, their resistant starch residues obtained from both native and retrograded-autoclaved pea starch after 8 h of simulated GI tract digestion was used as the fermentation substrate. The levels of acetate, propionate and butyrate gradually increased with the increasing fermentation time for NPS and RAPS. In comparison to the blank control (i.e., the group without the addition of carbohydrate), the fermented NPS and RAPS obviously resulted in an increased abundance of Firmicutes and Bacteroidetes, accompanied by a decrease in Proteobacteria, Actinobacteria and Verrucomicrobia. Both NPS and RAPS promoted different shifts in the microbial community at the genus level, with an increase in the abundance of Bacteroides, Megamonas and Bifidobacterium, as well as a reduction in the abundance of Fusobacterium, Faecalibacterium and Lachnoclostridium in comparison to the blank control samples.
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Affiliation(s)
- Wenxin Cui
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Zhen Ma
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China.
| | - Xiaoping Li
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Xinzhong Hu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
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21
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Song J, Min L, Wu J, He Q, Chen F, Wang Y. Response of the microbial community to phosphate-solubilizing bacterial inoculants on Ulmus chenmoui Cheng in Eastern China. PLoS One 2021; 16:e0247309. [PMID: 33630914 PMCID: PMC7906385 DOI: 10.1371/journal.pone.0247309] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/04/2021] [Indexed: 11/24/2022] Open
Abstract
Phosphate-solubilizing bacteria (PSB) have beneficial effects on plant health and soil composition. To date, studies of PSB in soil have largely been performed under field or greenhouse conditions. However, less is known about the impact of introducing indigenous PSB in the field, including their effects on the local microbial community. In this study, we conducted greenhouse and field experiments to explore the effects of the addition of indigenous PSB on the growth of Chenmou elm (Ulmus chenmoui) and on the diversity and composition of the bacterial community in the soil. We obtained four bacterial isolates with the highest phosphate-solubilizing activity: UC_1 (Pseudomonas sp.), UC_M (Klebsiella sp.), UC_J (Burkholderia sp.), and UC_3 (Chryseobacterium sp.). Sequencing on the Illumina MiSeq platform showed that the inoculated PSB did not become the dominant strains in the U. chenmoui rhizosphere. However, the soil bacterial community structure was altered by the addition of these PSB. The relative abundance of Chloroflexi decreased significantly in response to PSB application in all treatment groups, whereas the populations of several bacteria, including Proteobacteria and Bacteroidetes, increased. Network analysis indicated that Chloroflexi was the most strongly negatively correlated with Proteobacteria, whereas Proteobacteria was strongly positively correlated with Bacteroidetes. Our findings indicate that inoculation with PSB (UC_1, UC_M, UC_J, and UC_3) can improve the growth of U. chenmoui and regulate its rhizosphere microbial community. Therefore, inoculation with these bacterial strains could promote the efficient cultivation and production of high-quality plant materials.
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Affiliation(s)
- Juan Song
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - LiJing Min
- College of Life Science, Huzhou University, Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou, Zhejiang, China
| | - JunRong Wu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Qingfang He
- Department of Biology, University of Arkansas at Little Rock, Little Rock, Arkansas, United States of America
| | - FengMao Chen
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yang Wang
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
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22
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Razjivin AP, Kozlovsky VS. Unique features of the 'photo-energetics' of purple bacteria: a critical survey by the late Aleksandr Yuryevich Borisov (1930-2019). Photosynth Res 2020; 146:17-24. [PMID: 31655967 DOI: 10.1007/s11120-019-00683-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
We provide here an edited version of the "Farewell discussion" by the late Aleksandr (Alex) Yuryevich (Yu) Borisov (1930-2019) on several aspects related to the excitation energy transfer in photosynthetic bacteria. It is preceded by a prolog giving the events that led to our decision to publish it. Further, we include here a few photographs to give a personal glimpse of this unique biophysicist of our time. In addition, we provide here a reminiscence, by Andrei B. Rubin, on the scientific beginnings of Borisov. This article follows a Tribute to Borisov by Semenov et al. (2019, Photosynthesis Research, this issue).
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Affiliation(s)
- Andrei P Razjivin
- Department of Photosynthesis, A.N.Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir S Kozlovsky
- Department of Photosynthesis, A.N.Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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23
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Hamid H, Li LY, Grace JR. Effect of substrate concentrations on aerobic biotransformation of 6:2 fluorotelomer sulfonate (6:2 FTS) in landfill leachate. Chemosphere 2020; 261:128108. [PMID: 33113640 DOI: 10.1016/j.chemosphere.2020.128108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 08/05/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Biotransformation of 6:2 fluorotelomer sulfonate (FTS) results in the formation of short-chain (C4 - C6) perfluorocarboxylic acids (PFCAs) in landfill leachate. Although leachate substrate concentrations (i.e., organic carbon, ammonia) vary widely, their effects on 6:2 FTS biotransformation and PFCAs formation are unknown. This study investigated the effect of organic carbon and ammonia concentration in 6:2 FTS aerobic biotransformation and PFCA formation in leachate. Biotransformation experiments were conducted with sediment collected from a landfill leachate ditch, to which deionized (DI) water and various amounts of leachate were added. Microbial community analysis using 16S rRNA indicated that while phylum Proteobacteria dominated the bacterial composition throughout the 60 days, Actinobacteria increased with time. Many genera from Proteobacteria and Actinobacteria can synthesize a wide array of enzymes, indicating that these phyla are likely to play an important role in 6:2 FTS biotransformation. Higher biotransformation of 6:2 FTS was observed in leachate-added microcosms (∼21%), compared to DI water microcosm (∼14%), likely reflecting the substrate dependency of 6:2 FTS biotransformation. Substrate limiting conditions in DI water microcosm resulted in slightly greater formation of ∑(C4 - C6) PFCAs (∼14 mol%), compared with leachate added microcosms (10-13 mol%). The findings suggest that dilution of landfill leachate, (e.g., during wet seasons), likely results in reduced 6:2 FTS biotransformation and increased PFCAs formation compared to dry conditions. Observed formation of C7 - C8 PFCAs in the live microcosms suggested that landfills act as secondary sources of legacy PFCAs (e.g., perfluorooctanoic acid) in the environment.
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Affiliation(s)
- Hanna Hamid
- Civil Engineering, University of British Columbia, 6250 Applied Science Lane, Vancouver, BC, V6T 1Z4, Canada
| | - Loretta Y Li
- Civil Engineering, University of British Columbia, 6250 Applied Science Lane, Vancouver, BC, V6T 1Z4, Canada.
| | - John R Grace
- Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
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24
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Abstract
Escherichia coli is considered to be the best-known microorganism given the large number of published studies detailing its genes, its genome and the biochemical functions of its molecular components. This vast literature has been systematically assembled into a reconstruction of the biochemical reaction networks that underlie E. coli's functions, a process which is now being applied to an increasing number of microorganisms. Genome-scale reconstructed networks are organized and systematized knowledge bases that have multiple uses, including conversion into computational models that interpret and predict phenotypic states and the consequences of environmental and genetic perturbations. These genome-scale models (GEMs) now enable us to develop pan-genome analyses that provide mechanistic insights, detail the selection pressures on proteome allocation and address stress phenotypes. In this Review, we first discuss the overall development of GEMs and their applications. Next, we review the evolution of the most complete GEM that has been developed to date: the E. coli GEM. Finally, we explore three emerging areas in genome-scale modelling of microbial phenotypes: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses.
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Affiliation(s)
- Xin Fang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Colton J Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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25
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Gureev AP, Syromyatnikov MY, Ignatyeva DA, Valuyskikh VV, Solodskikh SA, Panevina AV, Gryaznova MV, Kokina AV, Popov VN. Effect of long-term methylene blue treatment on the composition of mouse gut microbiome and its relationship with the cognitive abilities of mice. PLoS One 2020; 15:e0241784. [PMID: 33206681 PMCID: PMC7673545 DOI: 10.1371/journal.pone.0241784] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/20/2020] [Indexed: 12/22/2022] Open
Abstract
In recent years, methylene blue (MB) has attracted considerable interest as a potential drug for the treatment of methemoglobinemia and neurodegenerative diseases. MB is active against microorganisms from various taxonomic groups. However, no studies have yet been conducted on the effect of MB on the intestinal microbiome of model animals. The aim of this work was to study the effect of different concentrations of MB on the mouse gut microbiome and its relationship with the cognitive abilities of mice. We showed that a low MB concentration (15 mg/kg/day) did not cause significant changes in the microbiome composition. The Bacteroidetes/Firmicutes ratio decreased relative to the control on the 2nd and 3rd weeks. A slight decrease in the levels Actinobacteria was detected on the 3rd week of the experiment. Changes in the content of Delta, Gamma, and Epsilonproteobacteria have been also observed. We did not find significant alterations in the composition of intestinal microbiome, which could be an indication of the development of dysbiosis or other gut dysfunction. At the same time, a high concentration of MB (50 mg/kg/day) led to pronounced changes, primarily an increase in the levels of Delta, Gamma and Epsilonproteobacteria. Over 4 weeks of therapy, the treatment with high MB concentration has led to an increase in the median content of Proteobacteria to 7.49% vs. 1.61% in the control group. Finally, we found that MB at a concentration of 15 mg/kg/day improved the cognitive abilities of mice, while negative correlation between the content of Deferribacteres and cognitive parameters was revealed. Our data expand the understanding of the relationship between MB, cognitive abilities, and gut microbiome in respect to the antibacterial properties of MB.
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Affiliation(s)
- Artem P. Gureev
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
| | - Mikhail Yu. Syromyatnikov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia
- Laboratory of Innovative Recombinant Proteomics, All-Russian Veterinary Research Institute of Pathology, Pharmacology and Therapy, Voronezh, Russia
| | - Daria A. Ignatyeva
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
| | - Valeria V. Valuyskikh
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
| | - Sergey A. Solodskikh
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia
| | - Anna V. Panevina
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia
| | - Maria V. Gryaznova
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia
| | - Anastasia V. Kokina
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia
| | - Vasily N. Popov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia
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26
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Li Q, You P, Hu Q, Leng B, Wang J, Chen J, Wan S, Wang B, Yuan C, Zhou R, Ouyang K. Effects of co-contamination of heavy metals and total petroleum hydrocarbons on soil bacterial community and function network reconstitution. Ecotoxicol Environ Saf 2020; 204:111083. [PMID: 32791359 DOI: 10.1016/j.ecoenv.2020.111083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 06/07/2020] [Accepted: 07/25/2020] [Indexed: 05/25/2023]
Abstract
Due to the accumulation of heavy metals in soil ecosystems, the response of soil microorganisms to the disturbance of heavy metals were widely studied. However, little was known about the interactions among microorganisms in heavy metals and total petroleum hydrocarbons (TPH) co-contaminated soils. In the present study, the microbiota shifts of 2 different contamination types of heavy metal-TPH polluted soils were investigated. NGS sequencing approach was adopted to illustrate the microbial community structure and to predict community function. Networks were established to reveal the interactions between microbes and environmental pollutants. Results showed that the alpha diversity and OTUs number of soil microbiota were reduced under heavy metals and TPH pollutants. TPH was the major pollutant in HT1 group, in which Proteobacteria phylum increased significantly, including Arenimonas genus, Sphingomonadaceae family and Burkholderiaceae family. Moreover, the function structures based on the KEGG database of HT1 group was enriched in the benzene matter metabolism and bacterial motoricity in microbiota. In contrast, severe Cr-Pb-TPH co-pollutants in HT2 increased the abundance of Firmicutes. In details, the relative abundance of Streptococcus genus and Bacilli class raised sharply. The DNA replication functions in microbiota were enriched under severely contaminated soil as a result of high concentrations of heavy metals and TPH pollutants' damage to bacteria. Furthermore, according to the correlation analysis between microbes and the pollutants, Streptococcus, Neisseria, Aeromonas, Porphyromonas and Acinetobacter were suggested as the bioremediation bacteria for Cr and Pb polluted soils, while Syntrophaceae spp. and Immundisolibacter were suggested as the bioremediation bacteria for TPH polluted soil. The study took a survey on the microbiota shifts of the heavy metals and TPH polluted soils, and the microbe's biomarkers provided new insights for the candidate strains of biodegradation, while further researches are required to verify the biodegradation mechanism of these biomarkers.
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Affiliation(s)
- Qian Li
- Hunan Research Institute for Nonferrous Metals, Changsha, China.
| | - Ping You
- Hunan Research Institute for Nonferrous Metals, Changsha, China
| | - Qi Hu
- NEOMICS Institute, Shenzhen, China
| | | | | | - Jiali Chen
- Hunan Research Institute for Nonferrous Metals, Changsha, China
| | - Si Wan
- Hunan Research Institute for Nonferrous Metals, Changsha, China; Kunming University of Science and Technology, Kunming, China
| | - Bing Wang
- Hunan Research Institute for Nonferrous Metals, Changsha, China; Kunming University of Science and Technology, Kunming, China
| | - Cuiyu Yuan
- Hunan Research Institute for Nonferrous Metals, Changsha, China
| | - Rui Zhou
- Hunan Research Institute for Nonferrous Metals, Changsha, China
| | - Kun Ouyang
- Hunan Research Institute for Nonferrous Metals, Changsha, China.
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27
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M A Basher AR, McLaughlin RJ, Hallam SJ. Metabolic pathway inference using multi-label classification with rich pathway features. PLoS Comput Biol 2020; 16:e1008174. [PMID: 33001968 PMCID: PMC7529316 DOI: 10.1371/journal.pcbi.1008174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Metabolic inference from genomic sequence information is a necessary step in determining the capacity of cells to make a living in the world at different levels of biological organization. A common method for determining the metabolic potential encoded in genomes is to map conceptually translated open reading frames onto a database containing known product descriptions. Such gene-centric methods are limited in their capacity to predict pathway presence or absence and do not support standardized rule sets for automated and reproducible research. Pathway-centric methods based on defined rule sets or machine learning algorithms provide an adjunct or alternative inference method that supports hypothesis generation and testing of metabolic relationships within and between cells. Here, we present mlLGPR, multi-label based on logistic regression for pathway prediction, a software package that uses supervised multi-label classification and rich pathway features to infer metabolic networks in organismal and multi-organismal datasets. We evaluated mlLGPR performance using a corpora of 12 experimental datasets manifesting diverse multi-label properties, including manually curated organismal genomes, synthetic microbial communities and low complexity microbial communities. Resulting performance metrics equaled or exceeded previous reports for organismal genomes and identify specific challenges associated with features engineering and training data for community-level metabolic inference.
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Affiliation(s)
- Abdur Rahman M A Basher
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, British Columbia, Canada
| | - Ryan J McLaughlin
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, British Columbia, Canada
| | - Steven J Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, University of British Columbia, 2552-2350 Health Sciences Mall, Vancouver, British Columbia, Canada
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, BC, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
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28
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Francoeur CB, Khadempour L, Moreira-Soto RD, Gotting K, Book AJ, Pinto-Tomás AA, Keefover-Ring K, Currie CR. Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System. mBio 2020; 11:e02146-20. [PMID: 32934088 PMCID: PMC7492740 DOI: 10.1128/mbio.02146-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Herbivores must overcome a variety of plant defenses, including coping with plant secondary compounds (PSCs). To help detoxify these defensive chemicals, several insect herbivores are known to harbor gut microbiota with the metabolic capacity to degrade PSCs. Leaf-cutter ants are generalist herbivores, obtaining sustenance from specialized fungus gardens that act as external digestive systems and which degrade the diverse collection of plants foraged by the ants. There is in vitro evidence that certain PSCs harm Leucoagaricus gongylophorus, the fungal cultivar of leaf-cutter ants, suggesting a role for the Proteobacteria-dominant bacterial community present within fungus gardens. In this study, we investigated the ability of symbiotic bacteria present within fungus gardens of leaf-cutter ants to degrade PSCs. We cultured fungus garden bacteria, sequenced the genomes of 42 isolates, and identified genes involved in PSC degradation, including genes encoding cytochrome P450 enzymes and genes in geraniol, cumate, cinnamate, and α-pinene/limonene degradation pathways. Using metatranscriptomic analysis, we showed that some of these degradation genes are expressed in situ Most of the bacterial isolates grew unhindered in the presence of PSCs and, using gas chromatography-mass spectrometry (GC-MS), we determined that isolates from the genera Bacillus, Burkholderia, Enterobacter, Klebsiella, and Pseudomonas degrade α-pinene, β-caryophyllene, or linalool. Using a headspace sampler, we show that subcolonies of fungus gardens reduced α-pinene and linalool over a 36-h period, while L. gongylophorus strains alone reduced only linalool. Overall, our results reveal that the bacterial communities in fungus gardens play a pivotal role in alleviating the effect of PSCs on the leaf-cutter ant system.IMPORTANCE Leaf-cutter ants are dominant neotropical herbivores capable of deriving energy from a wide range of plant substrates. The success of leaf-cutter ants is largely due to their external gut, composed of key microbial symbionts, specifically, the fungal mutualist L. gongylophorus and a consistent bacterial community. Both symbionts are known to have critical roles in extracting energy from plant material, yet comparatively little is known about their roles in the detoxification of plant secondary compounds. In this study, we assessed if the bacterial communities associated with leaf-cutter ant fungus gardens can degrade harmful plant chemicals. We identify plant secondary compound detoxification in leaf-cutter ant gardens as a process that depends on the degradative potential of both the bacterial community and L. gongylophorus Our findings suggest that the fungus garden and its associated microbial community influence the generalist foraging abilities of the ants, underscoring the importance of microbial symbionts in plant substrate suitability for herbivores.
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Affiliation(s)
- Charlotte B Francoeur
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lily Khadempour
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Rolando D Moreira-Soto
- Sección de Entomología Medica, Departamento de Parasitología, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Kirsten Gotting
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Adam J Book
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Adrián A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San José, Costa Rica
- Departamento de Bioquímica, Facultad de Medicina, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Giddings LA, Chlipala G, Kunstman K, Green S, Morillo K, Bhave K, Peterson H, Driscoll H, Maienschein-Cline M. Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site. PLoS One 2020; 15:e0237599. [PMID: 32785287 PMCID: PMC7423320 DOI: 10.1371/journal.pone.0237599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/29/2020] [Indexed: 01/20/2023] Open
Abstract
The microbial oxidation of metal sulfides plays a major role in the formation of acid rock drainage (ARD). We aimed to broadly characterize the ARD at Ely Brook, which drains the Ely Copper Mine Superfund site in Vermont, USA, using metagenomics and metatranscriptomics to assess the metabolic potential and seasonal ecological roles of microorganisms in water and sediment. Using Centrifuge against the NCBI "nt" database, ~25% of reads in sediment and water samples were classified as acid-tolerant Proteobacteria (61 ± 4%) belonging to the genera Pseudomonas (2.6-3.3%), Bradyrhizobium (1.7-4.1%), and Streptomyces (2.9-5.0%). Numerous genes (12%) were differentially expressed between seasons and played significant roles in iron, sulfur, carbon, and nitrogen cycling. The most abundant RNA transcript encoded the multidrug resistance protein Stp, and most expressed KEGG-annotated transcripts were involved in amino acid metabolism. Biosynthetic gene clusters involved in secondary metabolism (BGCs, 449) as well as metal- (133) and antibiotic-resistance (8501) genes were identified across the entire dataset. Several antibiotic and metal resistance genes were colocalized and coexpressed with putative BGCs, providing insight into the protective roles of the molecules BGCs produce. Our study shows that ecological stimuli, such as metal concentrations and seasonal variations, can drive ARD taxa to produce novel bioactive metabolites.
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Affiliation(s)
- Lesley-Ann Giddings
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
- Department of Chemistry, Smith College, Northampton, Massachusetts, United States of America
| | - George Chlipala
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Kevin Kunstman
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Stefan Green
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Katherine Morillo
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
| | - Kieran Bhave
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
| | - Holly Peterson
- Department of Geology, Guilford College, Greensboro, North Carolina, United States of America
| | - Heather Driscoll
- Vermont Genetics Network, Department of Biology, Norwich University, Northfield, Vermont, United States of America
| | - Mark Maienschein-Cline
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
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Sunwoo J, Ji SC, Kim AH, Yu K, Cho J, Jang I, Lee S. Impact of Vancomycin-Induced Changes in the Intestinal Microbiota on the Pharmacokinetics of Simvastatin. Clin Transl Sci 2020; 13:752-760. [PMID: 32058642 PMCID: PMC7359932 DOI: 10.1111/cts.12761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
The pharmacokinetic (PK) properties of drugs are affected in several ways by interactions with microbiota. The aim of this study was to investigate the effects of oral vancomycin on the gut microbiota and, consequently, on the PKs of simvastatin. An open-label, single arm, sequential crossover study was conducted in six healthy Korean male subjects. After 6 days on a control diet, simvastatin 40 mg was orally administered to the subjects before and after 1 week of oral vancomycin treatment. Blood samples for PK analysis and fecal samples for metagenomic and metabolomic analyses were collected. After vancomycin treatment, the richness of microbiota considerably decreased, and the composition was altered. In particular, the relative abundance of Bacteroidetes decreased, whereas that of proteobacteria increased. In addition, changes in fecal metabolites, including D-glucuronic acid, were observed. However, systemic exposure of simvastatin was not changed whereas that of hydroxysimvastatin showed a tendency to increase. The relationship between the change of PKs of simvastatin and the change of gut microbiota and fecal metabolites were not clearly observed.
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Affiliation(s)
- Jung Sunwoo
- Department of Clinical Pharmacology and TherapeuticsSeoul National University College of Medicine and HospitalSeoulKorea
| | - Sang Chun Ji
- Department of Clinical Pharmacology and TherapeuticsSeoul National University College of Medicine and HospitalSeoulKorea
| | - Andrew HyoungJin Kim
- Department of MedicineDivision of Infectious DiseasesWashington University School of MedicineSt. LouisMissouriUSA
| | - Kyung‐Sang Yu
- Department of Clinical Pharmacology and TherapeuticsSeoul National University College of Medicine and HospitalSeoulKorea
| | - Joo‐Youn Cho
- Department of Clinical Pharmacology and TherapeuticsSeoul National University College of Medicine and HospitalSeoulKorea
| | - In‐Jin Jang
- Department of Clinical Pharmacology and TherapeuticsSeoul National University College of Medicine and HospitalSeoulKorea
| | - SeungHwan Lee
- Department of Clinical Pharmacology and TherapeuticsSeoul National University College of Medicine and HospitalSeoulKorea
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Tao X, Feng J, Yang Y, Wang G, Tian R, Fan F, Ning D, Bates CT, Hale L, Yuan MM, Wu L, Gao Q, Lei J, Schuur EAG, Yu J, Bracho R, Luo Y, Konstantinidis KT, Johnston ER, Cole JR, Penton CR, Tiedje JM, Zhou J. Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria. Microbiome 2020; 8:84. [PMID: 32503635 PMCID: PMC7275452 DOI: 10.1186/s40168-020-00838-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/15/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed. RESULTS The β-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, α-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling. CONCLUSIONS Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated. Video Abstract.
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Affiliation(s)
- Xuanyu Tao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Jiajie Feng
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Gangsheng Wang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Renmao Tian
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Fenliang Fan
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Daliang Ning
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Colin T Bates
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Lauren Hale
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Mengting M Yuan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Linwei Wu
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Edward A G Schuur
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Julian Yu
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, 85212, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Rosvel Bracho
- School of Forest Resources and Conservation, Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Yiqi Luo
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, School of Biology, and Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Eric R Johnston
- School of Civil and Environmental Engineering, School of Biology, and Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - C Ryan Penton
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, 85212, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Honarmand Ebrahimi K. SARS-CoV-2 spike glycoprotein-binding proteins expressed by upper respiratory tract bacteria may prevent severe viral infection. FEBS Lett 2020; 594:1651-1660. [PMID: 32449939 PMCID: PMC7280584 DOI: 10.1002/1873-3468.13845] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 12/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a major global challenge. The virus infects host cells using its spike glycoprotein (S-protein) and has significantly higher infectivity and mortality rates among the aged population. Here, based on bioinformatic analysis, I provide evidence that some members of the upper respiratory tract (URT) commensal bacteria express viral S-protein -binding proteins. Based on this analysis and available data showing a decline in the population of these bacteria in the elderly, I propose that some URT commensal bacteria hamper SARS-CoV-2 infectivity and that a decline in the population of these bacteria contributes to the severity of infection. Further studies should provide a better understanding of the interaction of URT bacteria and SARS-CoV-2, which may lead to new therapeutic approaches.
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Keren-Khadmy N, Zeytuni N, Kutnowski N, Perriere G, Monteil C, Zarivach R. From conservation to structure, studies of magnetosome associated cation diffusion facilitators (CDF) proteins in Proteobacteria. PLoS One 2020; 15:e0231839. [PMID: 32310978 PMCID: PMC7170241 DOI: 10.1371/journal.pone.0231839] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/01/2020] [Indexed: 12/24/2022] Open
Abstract
Magnetotactic bacteria (MTB) are prokaryotes that sense the geomagnetic field lines to geolocate and navigate in aquatic sediments. They are polyphyletically distributed in several bacterial divisions but are mainly represented in the Proteobacteria. In this phylum, magnetotactic Deltaproteobacteria represent the most ancestral class of MTB. Like all MTB, they synthesize membrane-enclosed magnetic nanoparticles, called magnetosomes, for magnetic sensing. Magnetosome biogenesis is a complex process involving a specific set of genes that are conserved across MTB. Two of the most conserved genes are mamB and mamM, that encode for the magnetosome-associated proteins and are homologous to the cation diffusion facilitator (CDF) protein family. In magnetotactic Alphaproteobacteria MTB species, MamB and MamM proteins have been well characterized and play a central role in iron-transport required for biomineralization. However, their structural conservation and their role in more ancestral groups of MTB like the Deltaproteobacteria have not been established. Here we studied magnetite cluster MamB and MamM cytosolic C-terminal domain (CTD) structures from a phylogenetically distant magnetotactic Deltaproteobacteria species represented by BW-1 strain, which has the unique ability to biomineralize magnetite and greigite. We characterized them in solution, analyzed their crystal structures and compared them to those characterized in Alphaproteobacteria MTB species. We showed that despite the high phylogenetic distance, MamBBW-1 and MamMBW-1 CTDs share high structural similarity with known CDF-CTDs and will probably share a common function with the Alphaproteobacteria MamB and MamM.
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Affiliation(s)
- Noa Keren-Khadmy
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Natalie Zeytuni
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Nitzan Kutnowski
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Guy Perriere
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Villeurbanne Cedex, France
| | - Caroline Monteil
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université de Lyon, Villeurbanne Cedex, France
- CNRS, CEA, Aix-Marseille Université, UMR7265 Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail:
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Abis L, Loubet B, Ciuraru R, Lafouge F, Houot S, Nowak V, Tripied J, Dequiedt S, Maron PA, Sadet-Bourgeteau S. Reduced microbial diversity induces larger volatile organic compound emissions from soils. Sci Rep 2020; 10:6104. [PMID: 32269288 PMCID: PMC7142124 DOI: 10.1038/s41598-020-63091-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/29/2020] [Indexed: 12/11/2022] Open
Abstract
Microorganisms in soil are known to be a source and a sink of volatile organic compounds (VOCs). The role of the microbial VOCs on soil ecosystem regulation has been increasingly demonstrated in the recent years. Nevertheless, little is known about the influence of the microbial soil community structure and diversity on VOC emissions. This novel study analyzed the effect of reduced microbial diversity in soil on VOC emissions. We found that reduced levels of microbial diversity in soil increased VOC emissions from soils, while the number of different VOCs emitted decreased. Furthermore, we found that Proteobacteria, Bacteroidetes and fungi phyla were positively correlated to VOC emissions, and other prokaryotic phyla were either negatively correlated or very slightly positively correlated to VOCs emissions. Our interpretation is that Proteobacteria, Bacteroidetes and fungi were VOC producers while the other prokaryotic phyla were consumers. Finally, we discussed the possible role of VOCs as mediators of microbial interactions in soil.
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Affiliation(s)
- Letizia Abis
- Sorbonne Université, UPMC, Paris, France.
- INRA, UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France.
- Technische Universität Berlin, Umweltchemie und Luftrinhaltunz, Straße des 17. Juni 135, Berlin, 10623, Germany.
| | - Benjamin Loubet
- INRA, UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Raluca Ciuraru
- INRA, UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Florence Lafouge
- INRA, UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Sabine Houot
- INRA, UMR ECOSYS, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Virginie Nowak
- INRA, UMR AgroEcologie, AgroSup Dijon, BP 87999, 21079, Dijon, cedex, France
| | - Julie Tripied
- INRA, UMR AgroEcologie, AgroSup Dijon, BP 87999, 21079, Dijon, cedex, France
| | - Samuel Dequiedt
- INRA, UMR AgroEcologie, AgroSup Dijon, BP 87999, 21079, Dijon, cedex, France
| | - Pierre Alain Maron
- INRA, UMR AgroEcologie, AgroSup Dijon, BP 87999, 21079, Dijon, cedex, France
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Ding Q, Liu K, Song Z, Sun R, Zhang J, Yin L, Pu Y. Effects of Microcystin-LR on Metabolic Functions and Structure Succession of Sediment Bacterial Community under Anaerobic Conditions. Toxins (Basel) 2020; 12:toxins12030183. [PMID: 32183408 PMCID: PMC7150748 DOI: 10.3390/toxins12030183] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/05/2020] [Accepted: 03/14/2020] [Indexed: 01/02/2023] Open
Abstract
Microcystins (MCs), which are produced by harmful cyanobacteria blooms, pose a serious threat to environmental health. However, the effect of MCs on the bacterial community under anaerobic conditions is still unclear. This study examined the dynamic changes of MC-degrading capacity, metabolic activity, and structure of the bacterial community in lake sediment repeatedly treated with 1 mg/L microcystin-LR (MC-LR) under anaerobic conditions. The results showed that the MC-degrading capacity of the bacterial community was increased nearly three-fold with increased treatment frequency. However, the metabolic profile behaved in exactly opposite trend, in which the overall carbon metabolic activity was inhibited by repeated toxin addition. Microbial diversity was suppressed by the first addition of MC-LR and then gradually recovered. The 16S amplicon sequencing showed that the dominant genera were changed from Exiguobacterium and Acinetobacter to Prosthecobacter, Dechloromonas, and Agrobacterium. Furthermore, the increase in the relative abundance of Dechloromonas, Pseudomonas, Hydrogenophaga, and Agrobacterium was positively correlated with the MC-LR treatment times. This indicates that they might be responsible for MC degradation under anaerobic conditions. Our findings reveal the relationship between MC-LR and the sediment bacterial community under anaerobic conditions and indicate that anaerobic biodegradation is an effective and promising method to remediate MCs pollution.
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Affiliation(s)
- Qin Ding
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
| | - Kaiyan Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
| | - Zhiquan Song
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697, USA
| | - Rongli Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
| | - Juan Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
- Correspondence: ; Tel.: +86-25-83272582
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Farukh M. Comparative genomic analysis of selenium utilization traits in different marine environments. J Microbiol 2020; 58:113-122. [PMID: 31993987 DOI: 10.1007/s12275-020-9250-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/02/2019] [Accepted: 10/31/2019] [Indexed: 11/25/2022]
Abstract
Selenium (Se) is an essential trace element for many organisms, which is required in the biosynthesis of proteins with selenocysteine, tRNAs with selenouridine, and certain enzymes with Se as a cofactor. Recent large-scale metagenomics projects provide a unique opportunity for studying the global trends of Se utilization in marine environments. Here, we analyzed samples from different marine microbial communities, revealed by the Tara Oceans project, to characterize the Se utilization traits. We found that the selenophosphate synthetase gene, which defines the overall Se utilization, and Se utilization traits are present in all samples. Regions with samples rich and poor in Se utilization traits were categorized. From the analysis of environmental factors, the mesopelagic zone and high temperature (> 15°C) of water are favorable, while geographical location has little influence on Se utilization. All Se utilization traits showed a relatively independent occurrence. The taxonomic classification of Se traits shows that most of the sequences corresponding to Se utilization traits belong to the phylum Proteobacteria. Overall, our study provides useful insights into the general features of Se utilization in ocean samples and may help to understand the evolutionary dynamics of Se utilization in different marine environments.
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Affiliation(s)
- Muhammad Farukh
- Department of Biotechnology, School of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Hongshan District, Wuhan, 430074, P. R. China.
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, P. R. China.
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Grattieri M, Patterson S, Copeland J, Klunder K, Minteer SD. Purple Bacteria and 3D Redox Hydrogels for Bioinspired Photo-bioelectrocatalysis. ChemSusChem 2020; 13:230-237. [PMID: 31600418 DOI: 10.1002/cssc.201902116] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/18/2019] [Indexed: 06/10/2023]
Abstract
A major challenge for the implementation of intact bacterial cells in photo-bioelectrochemical systems remains the hindered extracellular electron transfer. This study focuses on purple bacteria, photosynthetic microorganisms particularly interesting for the development of bioelectrochemical systems because of their versatile metabolisms. Although soluble monomeric redox mediators have been proven as effective systems for electron transfer mediation, their application in the field is not preferable owing to their toxicity and unwanted release into the environment. An abiotic/biotic photoanode is reported in which a bioinspired redox mediating system is implemented in a 3D geometry allowing to "electrically wire" intact bacterial cells. The 3D photoanode decreased the overpotential required for harvesting photoexcited electrons, operating at +0.073 V versus the saturated calomel electrode (SCE). Accordingly, the overpotential was significantly reduced compared with a pioneering Os-redox polymer reported in literature, which required operation at +0.303 V versus SCE. These results provide the basis for further development of bio-photoanodes for light-powered biosensing and power generation.
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Affiliation(s)
- Matteo Grattieri
- Departments of Chemistry and Materials Science & Engineering, University of Utah, 315 S 1400 E Rm 2020, Salt Lake City, UT, 84112, USA
| | - Sarai Patterson
- Departments of Chemistry and Materials Science & Engineering, University of Utah, 315 S 1400 E Rm 2020, Salt Lake City, UT, 84112, USA
| | - Jeffrey Copeland
- Departments of Chemistry and Materials Science & Engineering, University of Utah, 315 S 1400 E Rm 2020, Salt Lake City, UT, 84112, USA
| | - Kevin Klunder
- Departments of Chemistry and Materials Science & Engineering, University of Utah, 315 S 1400 E Rm 2020, Salt Lake City, UT, 84112, USA
| | - Shelley D Minteer
- Departments of Chemistry and Materials Science & Engineering, University of Utah, 315 S 1400 E Rm 2020, Salt Lake City, UT, 84112, USA
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Berkessa YW, Yan B, Li T, Jegatheesan V, Zhang Y. Treatment of anthraquinone dye textile wastewater using anaerobic dynamic membrane bioreactor: Performance and microbial dynamics. Chemosphere 2020; 238:124539. [PMID: 31470310 DOI: 10.1016/j.chemosphere.2019.124539] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
The performance and microbial community structure of anaerobic dynamic membrane bioreactor (AnDMBR) treating textile wastewater was investigated. The reactor showed excellent soluble COD and color removal of 98.5% and >97.5%, respectively. Dynamic membrane layer grown over the 3D printed dynamic membrane support showed decent rejection for high molecular weight compounds (>20 kDa); and the total suspended solid rejection by the dynamic layer was >98.8%. Gel permeation chromatography analysis of extracellular polymeric substance (EPS) and effluent samples revealed EPS accounted for more than 76.7% of low molecular weight fractions (<20 kDa) that end up in the effluent. Higher applied flux facilitated the rapid formation dynamic layer which enabled a satisfactory effluent quality. Microbial community analysis revealed that during the operation the archaeal community was relatively stable while obvious changes took place in the bacterial community. Introduction of dye Remazol Brilliant Blue R (RBBR) to the AnDMBR increased the abundances of phyla of Proteobacteria and Spirochaetae whereas fractions of Firmicutes and Euryarchaeota decreased obviously. Furthermore, relative stable abundances of phyla Aminicenantes, Bacteroidetes, Thermotogae and Chloroflexi among the top six phyla detected in the system ensured a healthy anaerobic degradation environment for RBBR wastewater treatment.
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Affiliation(s)
- Yifru Waktole Berkessa
- Lab of Waste Valorization and Water Reuse, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Laoshan District, Qingdao, 266101, PR China; State Key Laboratory of Petroleum Pollution Control, Beijing, 102206, PR China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, PR China
| | - Binghua Yan
- Lab of Waste Valorization and Water Reuse, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Laoshan District, Qingdao, 266101, PR China; Qingdao Key Laboratory of Functional Membrane Material and Membrane Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
| | - Tengfei Li
- Lab of Waste Valorization and Water Reuse, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Laoshan District, Qingdao, 266101, PR China
| | | | - Yang Zhang
- Lab of Waste Valorization and Water Reuse, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Laoshan District, Qingdao, 266101, PR China; Qingdao Key Laboratory of Functional Membrane Material and Membrane Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
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Abstract
Photosynthetic organisms use networks of chromophores to absorb and deliver solar energy to reaction centers. We present a detailed model of the light-harvesting complexes in purple bacteria, including explicit interaction with sunlight, radiative and nonradiative energy loss, and dephasing and thermalizing effects of coupling to a vibrational bath. We capture the effect of slow vibrations by introducing time-dependent disorder. Our model describes the experimentally observed high efficiency of light harvesting, despite the absence of long-range quantum coherence. The one-exciton part of the quantum state fluctuates continuously but remains highly mixed at all times. These results suggest a relatively minor role for structure in determining efficiency. We build hypothetical models with randomly arranged chromophores but still observe high efficiency when nearest-neighbor distances are comparable to those in nature. This helps explain the high transport efficiency in organisms with widely differing antenna structures and suggests new design criteria for artificial light-harvesting devices.
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Affiliation(s)
- Susannah Bourne Worster
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
| | - Clement Stross
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
- School of Mathematics , University of Bristol , Bristol BS8 1UG , U.K
| | - Felix M W C Vaughan
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
- School of Mathematics , University of Bristol , Bristol BS8 1UG , U.K
- Bristol Centre for Complexity Sciences , University of Bristol , Bristol BS2 8BB , U.K
| | - Noah Linden
- School of Mathematics , University of Bristol , Bristol BS8 1UG , U.K
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
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Wang M, Deng B, Fu X, Sun H, Xu Z. Characterizations of microbial diversity and machine oil degrading microbes in machine oil contaminated soil. Environ Pollut 2019; 255:113190. [PMID: 31541828 DOI: 10.1016/j.envpol.2019.113190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/02/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Microbial diversity in machine oil contaminated soil was determined by high-throughput amplicon sequencing technology. The diversity of culturable microbes in the contaminated soil was further characterized using polymerase chain reaction method. Proteobacteria and Bacteroidetes were the most dominant phyla and occupied 52.73 and 16.77%, respectively, while the most abundant genera were Methylotenera (21.62%) and Flavobacterium (3.06%) in the soil. In the culturable microbes, the major phyla were Firmicutes (46.15%) and Proteobacteria (37.36%) and the most abundant genera were Bacillus (42.86%) and Aeromonas (34.07%). Four isolated microbes with high machine oil degradation efficiency were selected to evaluate their characteristics on the oil degradation. All of them reached their highest oil degradation rate after 7 days of incubation. Most of them significantly increased their oil degradation rate by additional carbon or organic nitrogen source in the incubation medium. The oil degradation rate by combination of the four microbes at the same inoculation level was also higher than the rate from each individual microbe. The protocol and findings of this study are very useful for developing micro-bioremediation method to eliminate machine oil contaminants from soil.
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Affiliation(s)
- Mengjiao Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China; Shaanxi Provincial Engineering Research Center of Edible and Medicinal Microbes, Shaanxi University of Technology, Hanzhong, Shaanxi, China; Shaanxi Key Laboratory of Bio-resources, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Baiwan Deng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China; Shaanxi Provincial Engineering Research Center of Edible and Medicinal Microbes, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Xun Fu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Haiyan Sun
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China; Shaanxi Key Laboratory of Bio-resources, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Zhimin Xu
- School of Nutrition and Food Sciences, Louisiana State University, Baton Rouge, LA, USA.
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Yu X, Kang X, Li Y, Cui Y, Tu W, Shen T, Yan M, Gu Y, Zou L, Ma M, Xiang Q, Zhao K, Liang Y, Zhang X, Chen Q. Rhizobia population was favoured during in situ phytoremediation of vanadium-titanium magnetite mine tailings dam using Pongamia pinnata. Environ Pollut 2019; 255:113167. [PMID: 31522008 DOI: 10.1016/j.envpol.2019.113167] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/27/2019] [Accepted: 09/02/2019] [Indexed: 05/28/2023]
Abstract
Mine tailings contain toxic metals and can lead to serious pollution of soil environment. Phytoremediation using legumes has been regarded as an eco-friendly way for the rehabilitation of tailings-laden lands but little is known about the changes of microbial structure during the process. In the present study, we monitored the dynamic change of microbiota in the rhizosphere of Pongamia pinnata during a 2-year on-site remediation of vanadium-titanium magnetite tailings. After remediation, overall soil health conditions were significantly improved as increased available N and P contents and enzyme activities were discovered. There was also an increase of microbial carbon and nitrogen contents. The Illumina sequencing technique revealed that the abundance of taxa under Proteobacteria was increased and rhizobia-related OTUs were preferentially enriched. A significant difference was discovered for sample groups before and after remediation. Rhizobium and Nordella were identified as the keystone taxa at genus rank. The functional prediction indicated that nitrogen fixation was enhanced, corresponding well with qPCR results which showed a significant increase of nifH gene copy numbers by the 2nd year. Our findings for the first time elucidated that legume phytoremediation can effectively cause microbial communities to shift in favour of rhizobia in heavy metal contaminated soil.
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Affiliation(s)
- Xiumei Yu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xia Kang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Yanmei Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yongliang Cui
- Sichuan Provincial Academy of Natural Resource and Sciences, Chengdu 610015, China
| | - Weiguo Tu
- Sichuan Provincial Academy of Natural Resource and Sciences, Chengdu 610015, China
| | - Tian Shen
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Min Yan
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yunfu Gu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Menggen Ma
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Quanju Xiang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yueyang Liang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoping Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang Chen
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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López-Serna R, García D, Bolado S, Jiménez JJ, Lai FY, Golovko O, Gago-Ferrero P, Ahrens L, Wiberg K, Muñoz R. Photobioreactors based on microalgae-bacteria and purple phototrophic bacteria consortia: A promising technology to reduce the load of veterinary drugs from piggery wastewater. Sci Total Environ 2019; 692:259-266. [PMID: 31349167 DOI: 10.1016/j.scitotenv.2019.07.126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Traditional swine manure treatments are not fully effective in the removal of veterinary drugs. Moreover, they are costly and entail a significant carbon footprint in many cases. Innovative biological approaches based on phototrophic microorganisms have recently emerged as promising alternatives to overcome those limitations. This work evaluated the removal of 19 veterinary drugs (i.e., 16 antibiotics, 1 analgesic, 1 anti-parasitic and 1 hormone) from piggery wastewater (PWW) in two open photobioreactors (PBR) operated with a consortium of microalgae-bacteria (AB-PBR) and purple photosynthetic bacteria (PPB-PBR). Multiple hydraulic retention times (HRT), in particular 11, 8 and 4 days, were tested during stage I, II and III, respectively. Ten out of 19 target compounds were detected with inlet drug concentrations ranging from 'non-detected' (n.d.) to almost 23,000 ng L-1 for the antibiotic oxytetracycline. Moreover, three of the antibiotics (i.e., enrofloxacin, sulfadiazine and oxytetracycline) were found at concentrations above the analytical linearity range in some or all of the samples under study. AB-PBR supported higher removal efficiencies (REs) than PPB-PBR, except for danofloxacin. Overall, REs progressively decreased when decreasing the HRT. The highest REs (>90%) were observed for doxycycline (95 ± 3%) and oxytetracycline (93 ± 3%) in AB-PBR during stage I. The other drugs, except sulfadimidine that was the most recalcitrant, showed REs above 70% during stage I in the same photobioreactor. In contrast, no removal was observed for danofloxacin in AB-PBR during stage III, sulfadimidine in PPB-PBR during stage III or marbofloxacin in PPB-PBR during the entire experiment.
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Affiliation(s)
- Rebeca López-Serna
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes (ISP), Dr. Mergelina, s/n, 47011 Valladolid, Spain.
| | - Dimas García
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes (ISP), Dr. Mergelina, s/n, 47011 Valladolid, Spain; Centro para la Investigación en Recursos Acuáticos de Nicaragua, CIRA/UNAN, Managua 4598, Nicaragua
| | - Silvia Bolado
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes (ISP), Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Juan José Jiménez
- Institute of Sustainable Processes (ISP), Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Analytical Chemistry, Faculty of Sciences, University of Valladolid, Campus Miguel Delibes, Paseo de Belén 7, 47011 Valladolid, Spain
| | - Foon Yin Lai
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Uppsala, SE-75007, Sweden
| | - Oksana Golovko
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Uppsala, SE-75007, Sweden
| | - Pablo Gago-Ferrero
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Uppsala, SE-75007, Sweden; Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, 101-E-17003 Girona, Spain
| | - Lutz Ahrens
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Uppsala, SE-75007, Sweden
| | - Karin Wiberg
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Uppsala, SE-75007, Sweden
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineerings, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes (ISP), Dr. Mergelina, s/n, 47011 Valladolid, Spain
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Park JH, Han HJ. Effect of tungsten-resistant bacteria on uptake of tungsten by lettuce and tungsten speciation in plants. J Hazard Mater 2019; 379:120825. [PMID: 31279307 DOI: 10.1016/j.jhazmat.2019.120825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 06/07/2019] [Accepted: 06/25/2019] [Indexed: 06/09/2023]
Abstract
Tungsten is an emerging contaminant because of its potential toxicity to humans. However, tungsten-plant-microbe interactions remains unknown. The objective of the study was to evaluate the effect of tungsten-resistant bacteria on tungsten species in plants and microbial community structure in soil. Although bacterial inoculation did not affect lettuce (Lactuca sativa L.) growth or tungsten uptake via root, tungsten-resistant bacteria increased translocation of tungsten from root to shoot. Bacterial inoculation slightly oxidized tungsten in lettuce based on tungsten L3 x-ray absorption near-edge structure (XANES). Tungsten in lettuce roots and shoots grown in tungsten(VI)-spiked soil existed as a mixture of tungsten(IV) and tungsten(VI). Tungsten accumulated as polytungstate in the root and monotungstate in the shoot. Inoculation with tungsten-resistant bacteria and plant growth increased microbial diversity in tungsten-contaminated soil. In tungsten-spiked soils without plants, metal-resistant or reducing bacteria were found while bacteria growing in rhizosphere were detected in soils supporting plant growth. These results indicate a role of the bacteria and plants in phytoremediation of tungsten-contaminated soil.
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Affiliation(s)
- Jin Hee Park
- Department of Environmental & Biological Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea.
| | - Hyeop-Jo Han
- Department of Energy and Resources Engineering, Chonnam National University, Gwangju 61186, Republic of Korea
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Liu B, Su G, Yang Y, Yao Y, Huang Y, Hu L, Zhong H, He Z. Vertical distribution of microbial communities in chromium-contaminated soil and isolation of Cr(Ⅵ)-Reducing strains. Ecotoxicol Environ Saf 2019; 180:242-251. [PMID: 31100590 DOI: 10.1016/j.ecoenv.2019.05.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
Soil ecosystems surrounding chromium slag undergo continuous harsh physicochemical conditions due to multiple heavy metals contamination. Previous studies of soil microbial communities mainly focused on surface soil layer, while little was known about the depth-related distributions of the microbial communities in chromium (Cr)-contaminated soil. In this study, a comprehensive analysis of depth-related distributions of microbial communities in Cr-contaminated soil was carried out by Illumina sequencing of 16s rRNA genes. The results revealed that bacterial diversities at 0 cm depth layer were significantly higher than those below 20 cm depths. And there was a remarkable difference in bacterial compositions along with the sampling depths especially for the dominant phyla of Proteobacteria, Actinobacteria, Chloroflexi and Fimicutes (p < 0.05). While the archaea accounted for a relatively low proportion of the microbes and showed stability in the compositions with the predominant phyla of Thaumarchaeota and Euryarchaeota. The linear discriminate analysis (LDA) and effect size (LEfSe) analysis showed that there were thirty-seven kinds of biomarker microbes existing in the five soil layers with LDA threshold of 4.0, and each layer showed distinct microbial divisions, indicating that microbes with different biological functions might survive along with the sampling depths. The environmental variables including total chromium (Cr), Cr(Ⅵ), Mn, Ni, and Zn had considerable influences on microbial community composition in the contaminated soil. A total of 25 Cr(Ⅵ)-reducing strains were further isolated and identified, which were phylogenetically affiliated to Proteobacteria, Actinobacteria and Firmicutes. Among the isolated Cr(Ⅵ)-reducing strains, Bacillus stratosphericus was the first time to be reported with Cr(Ⅵ) reducing capacity.
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Affiliation(s)
- Bang Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Guirong Su
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yiran Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yang Yao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yongji Huang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Liang Hu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Hui Zhong
- School of Life Science, Central South University, Changsha, 410012, China.
| | - Zhiguo He
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China.
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Abstract
Light energy is first captured in animal and microbial rhodopsins by ultrafast photoisomerization, whose relaxation accompanies protein structural changes for each function. Here, we report a microbial rhodopsin, marine bacterial TAT rhodopsin, that displays no formation of photointermediates at >10-5 s. Low-temperature ultraviolet-visible and Fourier transform infrared spectroscopy revealed that TAT rhodopsin features all-trans to 13-cis photoisomerization like other microbial rhodopsins, but a planar 13-cis chromophore in the primary K intermediate seems to favor thermal back isomerization to the original state without photocycle completion. The molecular mechanism of the early photoreaction in TAT rhodopsin will be discussed.
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Affiliation(s)
- Chihiro Kataoka
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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Yim SS, Johns NI, Park J, Gomes ALC, McBee RM, Richardson M, Ronda C, Chen SP, Garenne D, Noireaux V, Wang HH. Multiplex transcriptional characterizations across diverse bacterial species using cell-free systems. Mol Syst Biol 2019; 15:e8875. [PMID: 31464371 PMCID: PMC6692573 DOI: 10.15252/msb.20198875] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/01/2019] [Accepted: 07/03/2019] [Indexed: 12/14/2022] Open
Abstract
Cell-free expression systems enable rapid prototyping of genetic programs in vitro. However, current throughput of cell-free measurements is limited by the use of channel-limited fluorescent readouts. Here, we describe DNA Regulatory element Analysis by cell-Free Transcription and Sequencing (DRAFTS), a rapid and robust in vitro approach for multiplexed measurement of transcriptional activities from thousands of regulatory sequences in a single reaction. We employ this method in active cell lysates developed from ten diverse bacterial species. Interspecies analysis of transcriptional profiles from > 1,000 diverse regulatory sequences reveals functional differences in promoter activity that can be quantitatively modeled, providing a rich resource for tuning gene expression in diverse bacterial species. Finally, we examine the transcriptional capacities of dual-species hybrid lysates that can simultaneously harness gene expression properties of multiple organisms. We expect that this cell-free multiplex transcriptional measurement approach will improve genetic part prototyping in new bacterial chassis for synthetic biology.
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Affiliation(s)
- Sung Sun Yim
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Nathan I Johns
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
- Present address:
Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Jimin Park
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
| | - Antonio LC Gomes
- Department of ImmunologyMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Ross M McBee
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Department of Biological SciencesColumbia UniversityNew YorkNYUSA
| | - Miles Richardson
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
| | - Carlotta Ronda
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Sway P Chen
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
| | - David Garenne
- School of Physics and AstronomyUniversity of MinnesotaMinneapolisMNUSA
| | - Vincent Noireaux
- School of Physics and AstronomyUniversity of MinnesotaMinneapolisMNUSA
| | - Harris H Wang
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNYUSA
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47
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Sáez-Blázquez R, Feist J, Romero E, Fernández-Domínguez AI, García-Vidal FJ. Cavity-Modified Exciton Dynamics in Photosynthetic Units. J Phys Chem Lett 2019; 10:4252-4258. [PMID: 31291109 PMCID: PMC6907886 DOI: 10.1021/acs.jpclett.9b01495] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/10/2019] [Indexed: 06/09/2023]
Abstract
Recently, exciton-photon strong coupling has been proposed as a means to control and enhance energy transfer in ensembles of organic molecules. Here, we demonstrate that the exciton dynamics in an archetypal purple bacterial photosynthetic unit, composed of six LH2 antennas surrounding a single LH1 complex, is greatly modified by its interaction with an optical cavity. We develop a Bloch-Redfield master equation approach that accounts for the interplay between the B800 and B850 bacteriochlorophyll molecules within each LH2 antenna, as well as their interactions with the central LH1 complex. Using a realistic parametrization of both the photosynthetic unit and optical cavity, we investigate the formation of polaritons in the system, revealing that these can be tuned to accelerate its exciton dynamics by 3 orders of magnitude. This yields a significant occupation of the LH1 complex, the stage immediately prior to the reaction center, with only a few-femtosecond delay after the initial excitation of the LH2 B800 pigments. Our theoretical findings unveil polaritonic phenomena as a promising route for the characterization, tailoring, and optimization of light-harvesting mechanisms in natural and artificial photosynthetic processes.
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Affiliation(s)
- Rocío Sáez-Blázquez
- Departamento
de Física Teórica de la Materia Condensada and Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
| | - Johannes Feist
- Departamento
de Física Teórica de la Materia Condensada and Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
| | - Elisabet Romero
- Institute
of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science
and Technology (BIST), E-43007 Tarragona, Spain
| | - Antonio I. Fernández-Domínguez
- Departamento
de Física Teórica de la Materia Condensada and Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
| | - Francisco J. García-Vidal
- Departamento
de Física Teórica de la Materia Condensada and Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
- Donostia
International Physics Center (DIPC), E-20018 Donostia−San Sebastián, Spain
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48
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Lu C, Hong Y, Liu J, Gao Y, Ma Z, Yang B, Ling W, Waigi MG. A PAH-degrading bacterial community enriched with contaminated agricultural soil and its utility for microbial bioremediation. Environ Pollut 2019; 251:773-782. [PMID: 31121542 DOI: 10.1016/j.envpol.2019.05.044] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/21/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
A bacterial community was enriched with polycyclic aromatic hydrocarbons (PAHs) polluted soil to better study PAH degradation by indigenous soil bacteria. The consortium degraded more than 52% of low molecular weight and 35% of high molecular weight (HMW) PAHs during 16 days in a soil leachate medium. 16S rRNA gene high-throughput sequencing and quantitative polymerase chain reaction analyses for alpha subunit genes of ring-hydroxylating-dioxygenase (RHDα) suggested that Proteobacteria and Actinobacteria at the phylum level, Pseudomonas, Methylobacillus, Nocardioides, Methylophilaceae, Achromobacter, Pseudoxanthomonas, and Caulobacter at the generic level were involved in PAH degradation and might have the ability to carry RHDα genes (nidA and nahAc). The community was selected and collected according to biomass and RHDα gene contents, and added back to the PAH-polluted soil. The 16 EPA priority PAHs decreased from 95.23 to 23.41 mg kg-1 over 35 days. Compared with soil without the introduction of this bacterial community, adding the community with RHDα genes significantly decreased soil PAH contents, particularly HMW PAHs. The metabolic rate of PAHs in soil was positively correlated with nidA and nahAc gene contents. These results indicate that adding an indigenous bacterial consortium containing RHDα genes to contaminated soil may be a feasible and environmentally friendly method to clean up PAHs in agricultural soil.
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Affiliation(s)
- Chao Lu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Hong
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zhao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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49
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Juntawang C, Rongsayamanont C, Khan E. Entrapped-cells-based anaerobic forward osmosis membrane bioreactor treating medium-strength domestic wastewater: Fouling characterization and performance evaluation. Chemosphere 2019; 225:226-237. [PMID: 30877917 DOI: 10.1016/j.chemosphere.2019.03.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/07/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
A novel entrapped cells-based-anaerobic forward osmosis membrane bioreactor (E-FOMBR) was developed. Its performance and fouling were investigated in comparison with suspended cells-based-anaerobic forward osmosis membrane bioreactor (S-FOMBR). E-FOMBR and S-FOMBR were operated under the same conditions with two widely used draw solutions (NaCl and (NH4)2SO4). The membrane fouling especially irreversible fouling in S-FOMBR was more severe than that in E-FOMBR regardless of the type of draw solution. The permeate flux of E-FOMBR were 1.79 and 1.85 LMH while those of S-FOMBR were 1.49 and 1.14 LMH with NaCl and (NH4)2SO4 as draw solutions, respectively. More deterioration of biological activity (suggested by lower organic removal) due to accumulation of salt was observed in S-FOMBR compared to E-FOMBR. Proteobacteria dominated in both FOMBRs but was more abundant in E-FOMBR than S-FOMBR. The superiority of E-FOMBR over S-FOMBR included higher and stable system performance, higher flux, and longer operation time.
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Affiliation(s)
- Chaipon Juntawang
- Environmental and Conservation Sciences Program, North Dakota State University, Fargo, ND, 58108-6050, USA.
| | - Chaiwat Rongsayamanont
- Research Center for Environmental Assessment and Technology for Hazardous Waste Management, Faculty of Environmental Management, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand.
| | - Eakalak Khan
- Department of Civil and Environmental Engineering and Construction, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA.
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50
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Zhang J, Tian H, Wang P, Xiao Q, Zhu S, Jiang H. Variations in pH significantly affect cadmium uptake in grafted muskmelon (Cucumis melo L.) plants and drive the diversity of bacterial communities in a seedling substrate. Plant Physiol Biochem 2019; 139:132-140. [PMID: 30889478 DOI: 10.1016/j.plaphy.2019.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Substrates are fundamental prerequisites for growing grafted seedlings. In this study, substrates with different pH levels (5.0, 5.5, 6.0, 6.5, 7.0, and 8.0) were set up to elucidate the effect of pH on cadmium (Cd) uptake in grafted muskmelon (Cucumis melo L.) plants. Bacterial diversity was also investigated. Results showed that pH and high Cd concentration greatly affected the growth of grafted plants. The chlorophyll content of the muskmelon leaves decreased at 100 μM Cd. The majority of the Cd ions accumulated in the rootstock rather than in the shoot tissue in all of the treatments. The shoots and roots showed the highest Cd content at pH 5.5 and the lowest Cd content at pH 8.0 regardless of the Cd concentration. The operational taxonomic units belonging to Proteobacteria and Bacteroidetes were significantly (p < 0.05) enriched at different substrate pH levels compared with those at pH 5.0. The operational taxonomic units belonging to the phyla Firmicutes, Acidobacteria, and Chloroflexi were significantly decreased. The available nitrogen, phosphorus, Cd, and pH were strongly linked to bacterial community compositions. On the contrary, the available potassium was weakly correlated with the bacterial structure. This study demonstrates that pH greatly affects Cd uptake in grafted muskmelon plants and predicts microbial community structures in breeding substrates with different pH levels. Our results suggest that Cd accumulation in grafted plants can be reduced by setting the appropriate substrate pH. This work can serve as a reference for growing high-quality grafted plants and ensuring food safety in the presence of Cd contamination.
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Affiliation(s)
- Jian Zhang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui Province, China; Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, 230031, Anhui Province, China.
| | - Hongmei Tian
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui Province, China; Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, 230031, Anhui Province, China
| | - Pengcheng Wang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui Province, China; Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, 230031, Anhui Province, China.
| | - Qingqing Xiao
- Department of Biological and Environmental Engineering, Hefei University, 230601, Anhui Province, China
| | - Shoujing Zhu
- College of Life Science and Resources and Environment, Yichun University, Yichun, 336000, Jiangxi Province, China
| | - Haikun Jiang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui Province, China; Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Hefei, 230031, Anhui Province, China; School of Horticulture, Anhui Agricultural University, Hefei, 230036, Anhui Province, China
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