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Ferreira D, Venceslau SS, Bernardino R, Preto A, Zhang L, Waldbauer JR, Leavitt WD, Pereira IAC. DsrC is involved in fermentative growth and interacts directly with the FlxABCD-HdrABC complex in Desulfovibrio vulgaris Hildenborough. Environ Microbiol 2023; 25:962-976. [PMID: 36602077 DOI: 10.1111/1462-2920.16335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023]
Abstract
DsrC is a key protein in dissimilatory sulfur metabolism, where it works as co-substrate of the dissimilatory sulfite reductase DsrAB. DsrC has two conserved cysteines in a C-terminal arm that are converted to a trisulfide upon reduction of sulfite. In sulfate-reducing bacteria, DsrC is essential and previous works suggested additional functions beyond sulfite reduction. Here, we studied whether DsrC also plays a role during fermentative growth of Desulfovibrio vulgaris Hildenborough, by studying two strains where the functionality of DsrC is impaired by a lower level of expression (IPFG07) and additionally by the absence of one conserved Cys (IPFG09). Growth studies coupled with metabolite and proteomic analyses reveal that fermentation leads to lower levels of DsrC, but impairment of its function results in reduced growth by fermentation and a shift towards more fermentative metabolism during sulfate respiration. In both respiratory and fermentative conditions, there is increased abundance of the FlxABCD-HdrABC complex and Adh alcohol dehydrogenase in IPFG09 versus the wild type, which is reflected in higher production of ethanol. Pull-down experiments confirmed a direct interaction between DsrC and the FlxABCD-HdrABC complex, through the HdrB subunit. Dissimilatory sulfur metabolism, where sulfur compounds are used for energy generation, is a key process in the ecology of anoxic environments, and is more widespread among bacteria than previously believed. Two central proteins for this type of metabolism are DsrAB dissimilatory sulfite reductase and its co-substrate DsrC. Using physiological, proteomic and biochemical studies of Desulfovibrio vulgaris Hildenborough and mutants affected in DsrC functionality, we show that DsrC is also relevant for fermentative growth of this model organism and that it interacts directly with the soluble FlxABCD-HdrABC complex that links the NAD(H) pool with dissimilatory sulfite reduction.
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Affiliation(s)
- Delfim Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Raquel Bernardino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André Preto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Guo H, Zhong R, Liu B, Yang J, Liu Z, Du C, Li X. Characteristic and Mechanistic Investigation of Stress-Assisted Microbiologically Influenced Corrosion of X80 Steel in Near-Neutral Solutions. MATERIALS (BASEL, SWITZERLAND) 2022; 16:390. [PMID: 36614728 PMCID: PMC9822082 DOI: 10.3390/ma16010390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
The behavior and mechanisms of the stress-assisted microbiologically influenced corrosion (MIC) of X80 pipeline steel induced by sulfate-reducing bacteria (SRB) were investigated using focused ion beam-scanning electron microscopy (FIB). Electrochemical results show that SRB and stress have a synergistic effect on the corrosion of X80 steel. SRB accelerated the transformation of Fe3O4 into iron-sulfur compounds and may have caused the film breakage of X80 steel products. The obtained FIB results provide direct evidence that SRB promotes the corrosion of X80 steel.
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Affiliation(s)
- Huihua Guo
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China
| | - Rui Zhong
- Collaborative Innovation Center of Steel Technology, University of Science and Technology Beijing, Beijing 100083, China
| | - Bo Liu
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China
| | - Jike Yang
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China
| | - Zhiyong Liu
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China
- National Materials Corrosion and Protection Data Center, Beijing 100083, China
| | - Cuiwei Du
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China
- National Materials Corrosion and Protection Data Center, Beijing 100083, China
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Xiaogang Li
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China
- National Materials Corrosion and Protection Data Center, Beijing 100083, China
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
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3
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McLeish AG, Greenfield P, Midgley DJ, Paulsen IT. Desulfuromonas sp. 'CSMB_57', isolation and genomic insights from the most abundant bacterial taxon in eastern Australian coals. Microb Genom 2022; 8. [PMID: 35997693 PMCID: PMC9484754 DOI: 10.1099/mgen.0.000857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One of the most abundant and ubiquitous taxa observed in eastern Australian coal seams is an uncultured Desulfuromonas species and part of the Coal Seam Microbiome dataset assigned as 'CSMB_57'. Despite this abundance and ubiquity, knowledge about this taxon is limited. The present study aimed to generate an enrichment culture of Desulfuromonas sp. 'CSMB_57' using culturing strategies that exploit its sulphur-reducing capabilities by utilizing a polysulfide solution in a liquid medium. Using dilution to extinction methods, a highly enriched culture was successfully generated. The full-length 16S rRNA sequence revealed that all closely related taxa were observed in subsurface environments suggesting that D. sp. 'CSMB_57' may be a subsurface specialist. Subsequently, the DNA from the enrichment culture was sequenced and the genome of D. sp. 'CSMB_57' was assembled. Genomic annotation revealed a high number of CRISPR arrays for viral defence, a large array of ABC transporters for amino acid and peptide uptake, as well as genes likely associated with syntrophy such as genes associated with type-IVa pilus, often used for direct interspecies electron transfer, and multiple hydrogenases capable of producing hydrogen. From the various genomic observations, a conceptual ecological model was developed that explores its possible syntrophic roles with hydrogenotrophic methanogens and acetogenic bacteria within coal-seam environments.
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Affiliation(s)
- Andrew G McLeish
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, Australia.,Department of Energy, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, Sydney, Australia
| | - Paul Greenfield
- Department of Energy, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, Sydney, Australia.,Department of Biological Sciences, Macquarie University, North Ryde, Sydney, Australia
| | - David J Midgley
- Department of Energy, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, Sydney, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, Australia
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Wang X, Xie GJ, Tian N, Dang CC, Cai C, Ding J, Liu BF, Xing DF, Ren NQ, Wang Q. Anaerobic microbial manganese oxidation and reduction: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153513. [PMID: 35101498 DOI: 10.1016/j.scitotenv.2022.153513] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Manganese is a vital heavy metal abundant in terrestrial and aquatic environments. Anaerobic manganese redox reactions mediated by microorganisms have been recognized for a long time, which promote elements mobility and bioavailability in the environment. Biological anaerobic redox of manganese serves two reactions, including Mn(II) oxidation and Mn(IV) reduction. This review provides a comprehensive analysis of manganese redox cycles in the environment, closely related to greenhouse gas mitigation, the fate of nutrients, microbial bioremediation, and global biogeochemical cycle, including nitrogen, sulfur, and carbon. The oxidation and reduction of manganese occur cyclically and simultaneously in the environment. Anaerobic reduction of Mn(IV) receives electrons from methane, ammonium and sulfide, while Mn(II) can function as an electron source for manganese-oxidizing microorganisms for autotrophic denitrification and photosynthesis. The anaerobic redox transition between Mn(II) and Mn(IV) promotes a dynamic biogeochemical cycle coupled to microorganisms in water, soil and sediment environments. The discussion of reaction mechanisms, microorganism diversity, environmental influence bioremediation and application identify the research gaps for future investigation, which provides promising opportunities for further development of biotechnological applications to remediate contaminated environments.
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Affiliation(s)
- Xuan Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Ning Tian
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Cheng-Cheng Dang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Chen Cai
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
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Mostafa A, Im S, Kim J, Lim KH, Kim I, Kim DH. Electron bifurcation reactions in dark fermentation: An overview for better understanding and improvement. BIORESOURCE TECHNOLOGY 2022; 344:126327. [PMID: 34785332 DOI: 10.1016/j.biortech.2021.126327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Electron bifurcation (EB) is the most recently found mode of energy conservation, which involves both exergonic and endergonic electron transfer reactions to minimize energy loss. Several works have been devoted on EB reactions (EBRs) in anaerobic digestion but limited in dark fermentative hydrogen production (DF). Two main electron carriers in DF are ferredoxin (Fd) and reduced nicotinamide adenine dinucleotide (NADH), complicatedly involved in EB. Here, i) the importance of EB involvement in DF, ii) all EBRs possible to present in DF, as well as iii) the limitation of previous studies that tried incorporating any of EBRs in DF metabolic model, were highlighted. In addition, the concept of using metagenomic analysis for estimating the share of each EB reaction in the metabolic model, was proposed. This review is expected to initiate a new wave for studying EB, as a tool for explaining and predicting DF products.
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Affiliation(s)
- Alsayed Mostafa
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Seongwon Im
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Jimin Kim
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Kyeong-Ho Lim
- Department of Civil and Environmental Engineering, Kongju National University, Cheonan, Chungnam 31080, Republic of Korea
| | - Ijung Kim
- Department of Civil and Environmental Engineering, Hongik University, 94 Wausan-ro, Mapo-gu, Seoul 04066, Republic of Korea
| | - Dong-Hoon Kim
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea.
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Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea. THE ISME JOURNAL 2022; 16:168-177. [PMID: 34285362 PMCID: PMC8692474 DOI: 10.1038/s41396-021-01047-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023]
Abstract
Sulfate-coupled anaerobic oxidation of methane (AOM) is a major methane sink in marine sediments. Multiple lineages of anaerobic methanotrophic archaea (ANME) often coexist in sediments and catalyze this process syntrophically with sulfate-reducing bacteria (SRB), but the potential differences in ANME ecophysiology and mechanisms of syntrophy remain unresolved. A humic acid analog, anthraquinone 2,6-disulfonate (AQDS), could decouple archaeal methanotrophy from bacterial sulfate reduction and serve as the terminal electron acceptor for AOM (AQDS-coupled AOM). Here in sediment microcosm experiments, we examined variations in physiological response between two co-occurring ANME-2 families (ANME-2a and ANME-2c) and tested the hypothesis of sulfate respiration by ANME-2. Sulfate concentrations as low as 100 µM increased AQDS-coupled AOM nearly 2-fold matching the rates of sulfate-coupled AOM. However, the SRB partners remained inactive in microcosms with sulfate and AQDS and neither ANME-2 families respired sulfate, as shown by their cellular sulfur contents and anabolic activities measured using nanoscale secondary ion mass spectrometry. ANME-2a anabolic activity was significantly higher than ANME-2c, suggesting that ANME-2a was primarily responsible for the observed sulfate stimulation of AQDS-coupled AOM. Comparative transcriptomics showed significant upregulation of ANME-2a transcripts linked to multiple ABC transporters and downregulation of central carbon metabolism during AQDS-coupled AOM compared to sulfate-coupled AOM. Surprisingly, genes involved in sulfur anabolism were not differentially expressed during AQDS-coupled AOM with and without sulfate amendment. Collectively, this data indicates that ANME-2 archaea are incapable of respiring sulfate, but sulfate availability differentially stimulates the growth and AOM activity of different ANME lineages.
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Draft Genome Sequence of Desulfovibrio sp. Strain CSMB_222, Isolated from Coal Seam Formation Water. Microbiol Resour Announc 2021; 10:e0056421. [PMID: 34854698 PMCID: PMC8638610 DOI: 10.1128/mra.00564-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Subsurface coal seams contain microbial consortia with various taxa, each with a different role in the degradation of coal organic matter. This study presents the sequenced and annotated genome of Desulfovibrio sp. strain CSMB_222, a bacterium isolated from eastern Australian coal seams.
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8
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A Distinct, Flocculent, Acidogenic Microbial Community Accompanies Methanogenic Granules in Anaerobic Digesters. Microbiol Spectr 2021; 9:e0078421. [PMID: 34756083 PMCID: PMC8579839 DOI: 10.1128/spectrum.00784-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The formation of dense, well-settling methanogenic granules is essential for the operation of high-rate, up-flow anaerobic bioreactors used for wastewater treatment. Granule formation (granulation) mechanisms have been previously proposed, but an ecological understanding of granule formation is still lacking. Additionally, much of the current research on granulation only examines the start-up phase of bioreactor operation, rather than monitoring the fate of established granules and how new granules emerge over time. This paper, therefore, attempts to provide an insight into the microbial ecology of granule formation outside the start-up phase of bioreactor operation and develop an ecological granulation model. The microbial communities of granules actively undergoing growth, breakage, and reformation were examined, and an ecological granulation model was proposed. A distinct pregranular microbial community, with a high proportion of acidogenic organisms, such as the Streptococcaceae, was identified and suggested to have a role in initiating granulation by providing simpler substrates for the methanogenic and syntrophic communities which developed during granule growth. After initial granule formation, deterministic influences on microbial community assembly increased with granule size and indicated that microbial community succession was influenced by granule growth, leading to the formation of a stepwise ecological model for granulation. IMPORTANCE Complex microbial communities in engineered environments can aggregate to form surface-attached biofilms. Others form suspended biofilms, such as methanogenic granules. The formation of dense, methanogenic granules underpins the performance of high-rate, anaerobic bioreactors in industrial wastewater treatment. Granule formation (granulation) has been well studied from a physico-chemical perspective, but the ecological basis is poorly understood. We identified a distinct, flocculent, microbial community, which was present alongside granules, comprising primary consumers likely key in providing simpler substrates to granules. This flocculent community is understudied in anaerobic digestion and may initiate, or perpetuate, granule formation. We propose that it may be possible to influence bioreactor performance (e.g., to regulate volatile fatty acid concentrations) by manipulating this community. The patterns of microbial community diversity and assembly revealed by the study indicate that cycles of granule growth and breakage lead to overall diversification of the bioreactor meta-community, with implications for bioreactor process stability.
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Cong S, Xu Y, Lu Y. Growth Coordination Between Butyrate-Oxidizing Syntrophs and Hydrogenotrophic Methanogens. Front Microbiol 2021; 12:742531. [PMID: 34603271 PMCID: PMC8481629 DOI: 10.3389/fmicb.2021.742531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/18/2021] [Indexed: 11/13/2022] Open
Abstract
Syntrophy is a thermodynamically required mutualistic cooperation between fatty acid-oxidizing bacteria and methanogens that plays the important role in organic decomposition and methanogenesis in anoxic environments. In this study, three experiments were conducted to evaluate the cell-to-cell interaction in a thermophilic coculture consisting of Syntrophothermus lipocalidus and Methanocella conradii and a mesophilic coculture consisting of Syntrophomonas wolfei and Methanococcus maripaludis. First, syntrophs and methanogens were inoculated at different initial cell ratios to evaluate the growth synchronization. The quantitative PCR analysis revealed that the organism with a lower relative abundance at the beginning always grew faster, and the cell ratio converged over time to relative constant values in both the thermophilic and mesophilic cocultures. Next, intermittent ultrasound and constant shaking treatments were used to evaluate the influence of physical disturbance on microbial aggregation in the mesophilic coculture. The fluorescence in situ hybridization and scanning electron microscopy revealed that the tendency of syntrophic aggregation was not affected by the physical disturbances, although the activity was slightly depressed. Syntrophomonas dominated in the initial microbial aggregates, which, however, did not grow until Methanococcus was attached and increased to a significant extent, indicating the local growth synchronization during the formation and maturation of syntrophic aggregates. Last, microfluidic experiments revealed that whether or not Syntrophomonas or Methanococcus was loaded first, the second organism preferred moving to the place where the first organism was located, suggesting the cell-to-cell attraction between Syntrophomonas and Methanococcus. Collectively, our study demonstrated the growth synchronization and cell-to-cell attraction between the butyrate-oxidizing bacteria and methanogens for optimizing the syntrophic cooperation.
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Affiliation(s)
- Shuqi Cong
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yiqin Xu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
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10
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Turkarslan S, Stopnisek N, Thompson AW, Arens CE, Valenzuela JJ, Wilson J, Hunt KA, Hardwicke J, de Lomana ALG, Lim S, Seah YM, Fu Y, Wu L, Zhou J, Hillesland KL, Stahl DA, Baliga NS. Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions. THE ISME JOURNAL 2021; 15:2233-2247. [PMID: 33612833 PMCID: PMC8319347 DOI: 10.1038/s41396-021-00919-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/18/2020] [Accepted: 01/29/2021] [Indexed: 01/31/2023]
Abstract
Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR- and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.
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Affiliation(s)
- Serdar Turkarslan
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA 98109 USA
| | - Nejc Stopnisek
- grid.34477.330000000122986657Civil and Environmental Engineering, University of Washington, Seattle, WA 98195 USA
| | - Anne W. Thompson
- grid.262075.40000 0001 1087 1481Department of Biology, Portland State University, Portland, OR 97201 USA
| | - Christina E. Arens
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA 98109 USA
| | - Jacob J. Valenzuela
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA 98109 USA
| | - James Wilson
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA 98109 USA
| | - Kristopher A. Hunt
- grid.34477.330000000122986657Civil and Environmental Engineering, University of Washington, Seattle, WA 98195 USA
| | - Jessica Hardwicke
- grid.34477.330000000122986657Civil and Environmental Engineering, University of Washington, Seattle, WA 98195 USA
| | | | - Sujung Lim
- grid.20861.3d0000000107068890Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 USA
| | - Yee Mey Seah
- grid.462982.30000 0000 8883 2602Biological Sciences, University of Washington Bothell, Bothell, WA 98011 USA
| | - Ying Fu
- grid.266900.b0000 0004 0447 0018Institute for Environmental Genomics and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, OK 73072 USA
| | - Liyou Wu
- grid.266900.b0000 0004 0447 0018Institute for Environmental Genomics and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, OK 73072 USA
| | - Jizhong Zhou
- grid.266900.b0000 0004 0447 0018Institute for Environmental Genomics and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, OK 73072 USA
| | - Kristina L. Hillesland
- grid.462982.30000 0000 8883 2602Biological Sciences, University of Washington Bothell, Bothell, WA 98011 USA
| | - David A. Stahl
- grid.34477.330000000122986657Civil and Environmental Engineering, University of Washington, Seattle, WA 98195 USA
| | - Nitin S. Baliga
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, Seattle, WA 98109 USA
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11
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Torres K, Álvarez-Hornos FJ, Gabaldón C, Marzal P. Start-Up of Chitosan-Assisted Anaerobic Sludge Bed Reactors Treating Light Oxygenated Solvents under Intermittent Operation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18094986. [PMID: 34067161 PMCID: PMC8125441 DOI: 10.3390/ijerph18094986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 01/20/2023]
Abstract
Quality of the granular sludge developed during the start-up of anaerobic up-flow sludge bed reactors is of crucial importance to ensure the process feasibility of treating industrial wastewater such as those containing solvents. In this study, the microbial granule formation from suspended-growth biomass was investigated in two chitosan-assisted reactors. These reactors operated mimicking industrial sites working with night closures treating a mixture of ethanol, ethyl acetate, and 1-ethoxy-2-propanol. Each reactor operated under different hydrodynamic regimes typical from UASB (R1: <0.15 m h−1) and EGSB (R2: 3 m h−1). High soluble COD removal efficiencies (>90%) accompanied by rapid formation of robust anaerobic granules were achieved at both up-flow velocity levels. After three weeks from the start-up, mean size diameters of 475 µm and 354 µm were achieved for R1 and R2, respectively. The performance of the process was found to be stable for the whole operational period of 106 days treating intermittent OLR up to 13 kg COD m−3 d−1. A memory dose of chitosan at day 42 was beneficial to guarantee good quality of the granules by offsetting the negative impact of intermittent water supply on the granular size. Methanocorpusculum was identified as the dominant archaea at both up-flow velocities. Acetobacterium, Geobacter and Desulfovibrio bacteria were also abundant, demonstrating its role on the degradation of light-oxygenated solvents.
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12
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Tang WT, Hao TW, Chen GH. Comparative metabolic modeling of multiple sulfate-reducing prokaryotes reveals versatile energy conservation mechanisms. Biotechnol Bioeng 2021; 118:2676-2693. [PMID: 33844295 DOI: 10.1002/bit.27787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/21/2021] [Accepted: 03/11/2021] [Indexed: 11/07/2022]
Abstract
Sulfate-reducing prokaryotes (SRPs) are crucial participants in the cycling of sulfur, carbon, and various metals in the natural environment and in engineered systems. Despite recent advances in genetics and molecular biology bringing a huge amount of information about the energy metabolism of SRPs, little effort has been made to link this important information with their biotechnological studies. This study aims to construct multiple metabolic models of SRPs that systematically compile genomic, genetic, biochemical, and molecular information about SRPs to study their energy metabolism. Pan-genome analysis was conducted to compare the genomes of SRPs, from which a list of orthologous genes related to central and energy metabolism was obtained. Twenty-four SRP metabolic models via the inference of pan-genome analysis were efficiently constructed. The metabolic model of the well-studied model SRP Desulfovibrio vulgaris Hildenborough (DvH) was validated via flux balance analysis (FBA). The DvH model predictions matched reported experimental growth and energy yields, which demonstrated that the core metabolic model worked successfully. Further, steady-state simulation of SRP metabolic models under different growth conditions showed how the use of different electron transfer pathways leads to energy generation. Three energy conservation mechanisms were identified, including menaquinone-based redox loop, hydrogen cycling, and proton pumping. Flavin-based electron bifurcation (FBEB) was also demonstrated to be an essential mechanism for supporting energy conservation. The developed models can be easily extended to other species of SRPs not examined in this study. More importantly, the present work develops an accurate and efficient approach for constructing metabolic models of multiple organisms, which can be applied to other critical microbes in environmental and industrial systems, thereby enabling the quantitative prediction of their metabolic behaviors to benefit relevant applications.
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Affiliation(s)
- Wen-Tao Tang
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Tian-Wei Hao
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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13
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Du J, Gu M, Yin Q, Wu G. Temporary addition of carbon fibers facilitates methanogenic degradation of ethanol during anaerobic treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142724. [PMID: 33082040 DOI: 10.1016/j.scitotenv.2020.142724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Syntrophic methanogenesis can be improved by the addition of conductive materials. In this study, conductive carbon fibers (CFs) were applied to efficiently enrich syntrophic microorganisms with potential direct interspecies electron transfer (DIET) ability and promote methanogenic activity. With ethanol as the substrate, CFs shortened the acclimation time remarkably. The maximum methane production rate and the ethanol degradation rate of suspended biomass were increased by 40% and 68%, respectively, even when CFs were subsequently removed. However, with acetate and propionate as the mixed substrate, CFs decreased the methanogenic activity. In the reactor fed with ethanol, CFs increased the relative abundance of Geobacter, Desulfovibrio, and methanogens by 57%, 39%, and 63%, respectively. Methanosaeta possessed most methane production genes and might involve in DIET. Furthermore, CFs increased the relative abundance of ethanol-degradation genes assigned to Geobacter, Desulfovibrio and Pelobacter, suggesting the promoted ethanol-degradation. The triggered electron transport system activity and acetoclastic methanogenesis also explained the accelerated effects on ethanol-degradation by long-term acclimation with CFs. Notably, the dominance of Geobacter and Methanosaeta combined with the increased electron transfer constant in the CFs-amended ethanol reactor indicated the potential role of DIET after the removal of CFs, which deserved further clarification.
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Affiliation(s)
- Jin Du
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Mengqi Gu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Qidong Yin
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Guangxue Wu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
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14
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Duarte AG, Barbosa ACC, Ferreira D, Manteigas G, Domingos RM, Pereira IAC. Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148416. [PMID: 33753023 DOI: 10.1016/j.bbabio.2021.148416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/25/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023]
Abstract
In prokaryotes, the proton or sodium motive force required for ATP synthesis is produced by respiratory complexes that present an ion-pumping mechanism or are involved in redox loops performed by membrane proteins that usually have substrate and quinone-binding sites on opposite sides of the membrane. Some respiratory complexes include a dimeric redox module composed of a quinone-interacting membrane protein of the NrfD family and an iron‑sulfur protein of the NrfC family. The QrcABCD complex of sulfate reducers, which includes the QrcCD module homologous to NrfCD, was recently shown to perform electrogenic quinone reduction providing the first conclusive evidence for energy conservation among this family. Similar redox modules are present in multiple respiratory complexes, which can be associated with electroneutral, energy-driven or electrogenic reactions. This work discusses the presence of the NrfCD/PsrBC dimeric redox module in different bioenergetics contexts and its role in prokaryotic energy conservation mechanisms.
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Affiliation(s)
- Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal.
| | - Ana C C Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Delfim Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Gonçalo Manteigas
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Renato M Domingos
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal.
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15
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Fiévet A, Merrouch M, Brasseur G, Eve D, Biondi EG, Valette O, Pauleta SR, Dolla A, Dermoun Z, Burlat B, Aubert C. OrpR is a σ 54 -dependent activator using an iron-sulfur cluster for redox sensing in Desulfovibrio vulgaris Hildenborough. Mol Microbiol 2021; 116:231-244. [PMID: 33595838 PMCID: PMC8359166 DOI: 10.1111/mmi.14705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 01/15/2023]
Abstract
Enhancer binding proteins (EBPs) are key players of σ54 -regulation that control transcription in response to environmental signals. In the anaerobic microorganism Desulfovibrio vulgaris Hildenborough (DvH), orp operons have been previously shown to be coregulated by σ54 -RNA polymerase, the integration host factor IHF and a cognate EBP, OrpR. In this study, ChIP-seq experiments indicated that the OrpR regulon consists of only the two divergent orp operons. In vivo data revealed that (i) OrpR is absolutely required for orp operons transcription, (ii) under anaerobic conditions, OrpR binds on the two dedicated DNA binding sites and leads to high expression levels of the orp operons, (iii) increasing the redox potential of the medium leads to a drastic down-regulation of the orp operons expression. Moreover, combining functional and biophysical studies on the anaerobically purified OrpR leads us to propose that OrpR senses redox potential variations via a redox-sensitive [4Fe-4S]2+ cluster in the sensory PAS domain. Overall, the study herein presents the first characterization of a new Fe-S redox regulator belonging to the σ54 -dependent transcriptional regulator family probably advantageously selected by cells adapted to the anaerobic lifestyle to monitor redox stress conditions.
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Affiliation(s)
| | | | | | - Danaé Eve
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | | | | | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Dept. Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Alain Dolla
- Aix Marseille Univ, Toulon Univ, CNRS, IRD, MIO, Marseille, France
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16
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Zhang Y, Yu Z, Zhang Y, Zhang H. Regeneration of unconventional natural gas by methanogens co-existing with sulfate-reducing prokaryotes in deep shale wells in China. Sci Rep 2020; 10:16042. [PMID: 32994524 PMCID: PMC7525477 DOI: 10.1038/s41598-020-73010-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/08/2020] [Indexed: 02/01/2023] Open
Abstract
Biogenic methane in shallow shale reservoirs has been proven to contribute to economic recovery of unconventional natural gas. However, whether the microbes inhabiting the deeper shale reservoirs at an average depth of 4.1 km and even co-occurring with sulfate-reducing prokaryote (SRP) have the potential to produce biomethane is still unclear. Stable isotopic technique with culture-dependent and independent approaches were employed to investigate the microbial and functional diversity related to methanogenic pathways and explore the relationship between SRP and methanogens in the shales in the Sichuan Basin, China. Although stable isotopic ratios of the gas implied a thermogenic origin for methane, the decreased trend of stable carbon and hydrogen isotope value provided clues for increasing microbial activities along with sustained gas production in these wells. These deep shale-gas wells harbored high abundance of methanogens (17.2%) with ability of utilizing various substrates for methanogenesis, which co-existed with SRP (6.7%). All genes required for performing methylotrophic, hydrogenotrophic and acetoclastic methanogenesis were present. Methane production experiments of produced water, with and without additional available substrates for methanogens, further confirmed biomethane production via all three methanogenic pathways. Statistical analysis and incubation tests revealed the partnership between SRP and methanogens under in situ sulfate concentration (~ 9 mg/L). These results suggest that biomethane could be produced with more flexible stimulation strategies for unconventional natural gas recovery even at the higher depths and at the presence of SRP.
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Affiliation(s)
- Yimeng Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing, 100049, People's Republic of China.,Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Open Studio for Marine Corrosion and Protection, Pilot National Laboratory for Marine Science and Technology (Qingdao), No.1 Wenhai Road, Qingdao, 266237, People's Republic of China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing, 100049, People's Republic of China.
| | - Yiming Zhang
- Beijing Municipal Ecological Environment Bureau, Beijing, 100048, People's Republic of China
| | - Hongxun Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing, 100049, People's Republic of China
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17
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Smith NW, Shorten PR, Altermann E, Roy NC, McNabb WC. Competition for Hydrogen Prevents Coexistence of Human Gastrointestinal Hydrogenotrophs in Continuous Culture. Front Microbiol 2020; 11:1073. [PMID: 32547517 PMCID: PMC7272605 DOI: 10.3389/fmicb.2020.01073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/29/2020] [Indexed: 01/24/2023] Open
Abstract
Understanding the metabolic dynamics of the human gastrointestinal tract (GIT) microbiota is of growing importance as research continues to link the microbiome to host health status. Microbial strains that metabolize hydrogen have been associated with a variety of both positive and negative host nutritional and health outcomes, but limited data exists for their competition in the GIT. To enable greater insight into the behaviour of these microbes, a mathematical model was developed for the metabolism and growth of the three major hydrogenotrophic groups: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens. In batch culture simulations with abundant sulphate and hydrogen, the SRB outcompeted the methanogen for hydrogen due to having a half-saturation constant 106 times lower than that of the methanogen. The acetogen, with a high model threshold for hydrogen uptake of around 70 mM, was the least competitive. Under high lactate and zero sulphate conditions, hydrogen exchange between the SRB and the methanogen was the dominant interaction. The methanogen grew at 70% the rate of the SRB, with negligible acetogen growth. In continuous culture simulations, both the SRB and the methanogen were washed out at dilution rates above 0.15 h−1 regardless of substrate availability, whereas the acetogen could survive under abundant hydrogen conditions. Specific combinations of conditions were required for survival of more than one hydrogenotroph in continuous culture, and survival of all three was not possible. The stringency of these requirements and the inability of the model to simulate survival of all three hydrogenotrophs in continuous culture demonstrates that factors outside of those modelled are vital to allow hydrogenotroph coexistence in the GIT.
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Affiliation(s)
- Nick W Smith
- School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand.,AgResearch, Ruakura Research Centre, Hamilton, New Zealand.,AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Paul R Shorten
- Riddet Institute, Massey University, Palmerston North, New Zealand.,AgResearch, Ruakura Research Centre, Hamilton, New Zealand
| | - Eric Altermann
- Riddet Institute, Massey University, Palmerston North, New Zealand.,AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Nicole C Roy
- Riddet Institute, Massey University, Palmerston North, New Zealand.,AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand.,Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Warren C McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand
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18
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Chen J, Wade MJ, Dolfing J, Soyer OS. Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer. J R Soc Interface 2020; 16:20190129. [PMID: 31064258 PMCID: PMC6544901 DOI: 10.1098/rsif.2019.0129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Methane-producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulfate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulfate availability are not well understood. Here, we construct model synthetic communities using a sulfate reducer and two types of methanogens representing different methanogenesis routes. We find that tri-cultures with both routes increase methane production by almost twofold compared to co-cultures and are stable in the absence of sulfate. With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate. We show that this is due to a shift in the metabolism of these methanogens towards co-utilization of hydrogen with acetate. These findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities.
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Affiliation(s)
- Jing Chen
- 1 School of Life Sciences, University of Warwick , Coventry CV4 7AL , UK
| | - Matthew J Wade
- 3 School of Engineering, Newcastle University , Newcastle NE1 7RU , UK.,4 School of Mathematics and Statistics, McMaster University , Hamilton, Ontario , Canada L8S 4K1
| | - Jan Dolfing
- 3 School of Engineering, Newcastle University , Newcastle NE1 7RU , UK
| | - Orkun S Soyer
- 1 School of Life Sciences, University of Warwick , Coventry CV4 7AL , UK.,2 Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick , Coventry CV4 7AL , UK
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19
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Schoelmerich MC, Müller V. Energy-converting hydrogenases: the link between H 2 metabolism and energy conservation. Cell Mol Life Sci 2019; 77:1461-1481. [PMID: 31630229 DOI: 10.1007/s00018-019-03329-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/17/2019] [Accepted: 10/01/2019] [Indexed: 10/25/2022]
Abstract
The reversible interconversion of molecular hydrogen and protons is one of the most ancient microbial metabolic reactions and catalyzed by hydrogenases. A widespread yet largely enigmatic group comprises multisubunit [NiFe] hydrogenases, that directly couple H2 metabolism to the electrochemical ion gradient across the membranes of bacteria and of archaea. These complexes are collectively referred to as energy-converting hydrogenases (Ech), as they reversibly transform redox energy into physicochemical energy. Redox energy is typically provided by a low potential electron donor such as reduced ferredoxin to fuel H2 evolution and the establishment of a transmembrane electrochemical ion gradient ([Formula: see text]). The [Formula: see text] is then utilized by an ATP synthase for energy conservation by generating ATP. This review describes the modular structure/function of Ech complexes, focuses on insights into the energy-converting mechanisms, describes the evolutionary context and delves into the implications of relying on an Ech complex as respiratory enzyme for microbial metabolism.
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Affiliation(s)
- Marie Charlotte Schoelmerich
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.,Microbiology and Biotechnology, Institute of Plant Sciences and Microbiology, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
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20
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Smith NW, Shorten PR, Altermann E, Roy NC, McNabb WC. A Mathematical Model for the Hydrogenotrophic Metabolism of Sulphate-Reducing Bacteria. Front Microbiol 2019; 10:1652. [PMID: 31379794 PMCID: PMC6653664 DOI: 10.3389/fmicb.2019.01652] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Sulphate-reducing bacteria (SRB) are studied across a range of scientific fields due to their characteristic ability to metabolise sulphate and produce hydrogen sulphide, which can lead to significant consequences for human activities. Importantly, they are members of the human gastrointestinal microbial population, contributing to the metabolism of dietary and host secreted molecules found in this environment. The role of the microbiota in host digestion is well studied, but the full role of SRB in this process has not been established. Moreover, from a human health perspective, SRB have been implicated in a number of functional gastrointestinal disorders such as Irritable Bowel Syndrome and the development of colorectal cancer. To assist with the study of SRB, we present a mathematical model for the growth and metabolism of the well-studied SRB, Desulfovibrio vulgaris in a closed system. Previous attempts to model SRB have resulted in complex or highly specific models that are not easily adapted to the study of SRB in different environments, such as the gastrointestinal tract. We propose a simpler, Monod-based model that allows for easy alteration of both key parameter values and the governing equations to enable model adaptation. To prevent any incorrect assumptions about the nature of SRB metabolic pathways, we structure the model to consider only the concentrations of initial and final metabolites in a pathway, which circumvents the current uncertainty around hydrogen cycling by SRB. We parameterise our model using experiments with varied initial substrate conditions, obtaining parameter values that compare well with experimental estimates in the literature. We then validate our model against four independent experiments involving D. vulgaris with further variations to substrate availability. Further use of the model will be possible in a number of settings, notably as part of larger models studying the metabolic interactions between SRB and other hydrogenotrophic microbes in the human gastrointestinal tract and how this relates to functional disorders.
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Affiliation(s)
- Nick W Smith
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand.,AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand.,School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand
| | - Paul R Shorten
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Eric Altermann
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Nicole C Roy
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, The University of Auckland, Auckland, New Zealand
| | - Warren C McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, The University of Auckland, Auckland, New Zealand
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21
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Baffert C, Kpebe A, Avilan L, Brugna M. Hydrogenases and H 2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus. Adv Microb Physiol 2019; 74:143-189. [PMID: 31126530 DOI: 10.1016/bs.ampbs.2019.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H2 metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H2 metabolism.
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Affiliation(s)
- Carole Baffert
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Arlette Kpebe
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Luisana Avilan
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Myriam Brugna
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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22
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Rajeev L, Luning EG, Zane GM, Juba TR, Kazakov AE, Novichkov PS, Wall JD, Mukhopadhyay A. LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species. PLoS One 2019; 14:e0214960. [PMID: 30964892 PMCID: PMC6456213 DOI: 10.1371/journal.pone.0214960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/22/2019] [Indexed: 11/18/2022] Open
Abstract
The central carbon/lactate utilization pathway in the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, is encoded by the highly conserved operon DVU3025-3033. Our earlier in vitro genome-wide study had suggested a network of four two-component system regulators that target this large operon; however, how these four regulators control this operon was not known. Here, we probe the regulation of the lactate utilization operon with mutant strains and DNA-protein binding assays. We show that the LurR response regulator is required for optimal growth and complete lactate utilization, and that it activates the DVU3025-3033 lactate oxidation operon as well as DVU2451, a lactate permease gene, in the presence of lactate. We show by electrophoretic mobility shift assays that LurR binds to three sites in the upstream region of DVU3025, the first gene of the operon. NrfR, a response regulator that is activated under nitrite stress, and LurR share similar binding site motifs and bind the same sites upstream of DVU3025. The DVU3025 promoter also has a binding site motif (Pho box) that is bound by PhoB, a two-component response regulator activated under phosphate limitation. The lactate utilization operon, the regulator LurR, and LurR binding sites are conserved across the order Desulfovibrionales whereas possible modulation of the lactate utilization genes by additional regulators such as NrfR and PhoB appears to be limited to D. vulgaris.
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Affiliation(s)
- Lara Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Eric G. Luning
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Thomas R. Juba
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Alexey E. Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Pavel S. Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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23
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Chen Z, Gao SH, Jin M, Sun S, Lu J, Yang P, Bond PL, Yuan Z, Guo J. Physiological and transcriptomic analyses reveal CuO nanoparticle inhibition of anabolic and catabolic activities of sulfate-reducing bacterium. ENVIRONMENT INTERNATIONAL 2019; 125:65-74. [PMID: 30710801 DOI: 10.1016/j.envint.2019.01.058] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
The widespread use of CuO nanoparticles (NPs) results in their continuous release into the environment, which could pose risks to public health and to microbial ecosystems. Following consumption, NPs will initially enter into sewer systems and interact with and potentially influence sewer microbial communities. An understanding of the response of microbes in sewers, particularly sulfate-reducing bacteria (SRB), to the CuO NPs induced stress is important as hydrogen sulfide produced by SRB can cause sewer corrosion and odour emissions. In this study, we elucidated how the anabolic and catabolic processes of a model SRB, Desulfovibrio vulgaris Hidenborough (D. vulgaris), respond to CuO NPs. Physiological analyses indicated that the exposure of the culture to CuO NPs at elevated concentrations (>50 mg/L) inhibited both its anabolic and catabolic activities, as revealed by lowered cell proliferation and sulfate reduction rate. The antibacterial effects of CuO NPs were mainly attributed to the overproduction of reactive oxygen species. Transcriptomic analysis indicated that genes encoding for flagellar assembly and some genes involved in electron transfer and respiration were down-regulated, while genes for the ferric uptake regulator (Fur) were up-regulated. Moreover, the CuO NPs exposure significantly up-regulated genes involved in protein synthesis and ATP synthesis. These results suggest that CuO NPs inhibited energy conversion, cell mobility, and iron starvation to D. vulgaris. Meanwhile, D. vulgaris attempted to respond to the stress of CuO NPs by increasing protein and ATP synthesis. These findings offer new insights into the bacterial-nanoparticles interaction at the transcriptional level, and advance our understanding of impacts of CuO NPs on SRB in the environment.
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Affiliation(s)
- Zhaoyu Chen
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Department of Environmental Science & Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Shu-Hong Gao
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Min Jin
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Shengjie Sun
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Ji Lu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Ping Yang
- Department of Environmental Science & Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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24
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Duarte AG, Catarino T, White GF, Lousa D, Neukirchen S, Soares CM, Sousa FL, Clarke TA, Pereira IAC. An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation. Nat Commun 2018; 9:5448. [PMID: 30575735 PMCID: PMC6303296 DOI: 10.1038/s41467-018-07839-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/27/2018] [Indexed: 02/02/2023] Open
Abstract
The bioenergetics of anaerobic metabolism frequently relies on redox loops performed by membrane complexes with substrate- and quinone-binding sites on opposite sides of the membrane. However, in sulfate respiration (a key process in the biogeochemical sulfur cycle), the substrate- and quinone-binding sites of the QrcABCD complex are periplasmic, and their role in energy conservation has not been elucidated. Here we show that the QrcABCD complex of Desulfovibrio vulgaris is electrogenic, as protons and electrons required for quinone reduction are extracted from opposite sides of the membrane, with a H+/e− ratio of 1. Although the complex does not act as a H+-pump, QrcD may include a conserved proton channel leading from the N-side to the P-side menaquinone pocket. Our work provides evidence of how energy is conserved during dissimilatory sulfate reduction, and suggests mechanisms behind the functions of related bacterial respiratory complexes in other bioenergetic contexts. The bacterial complex QrcABCD plays a key role in the bioenergetics of sulfate respiration. Here, Duarte et al. show that this complex is electrogenic, with protons and electrons required for quinone reduction being extracted from opposite sides of the membrane.
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Affiliation(s)
- Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.,Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Gaye F White
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Sinje Neukirchen
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14 UZA I, 1090, Vienna, Austria
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipa L Sousa
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14 UZA I, 1090, Vienna, Austria
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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25
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Park C, Park W. Survival and Energy Producing Strategies of Alkane Degraders Under Extreme Conditions and Their Biotechnological Potential. Front Microbiol 2018; 9:1081. [PMID: 29910779 PMCID: PMC5992423 DOI: 10.3389/fmicb.2018.01081] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/07/2018] [Indexed: 11/17/2022] Open
Abstract
Many petroleum-polluted areas are considered as extreme environments because of co-occurrence of low and high temperatures, high salt, and acidic and anaerobic conditions. Alkanes, which are major constituents of crude oils, can be degraded under extreme conditions, both aerobically and anaerobically by bacteria and archaea of different phyla. Alkane degraders possess exclusive metabolic pathways and survival strategies, which involve the use of protein and RNA chaperones, compatible solutes, biosurfactants, and exopolysaccharide production for self-protection during harsh environmental conditions such as oxidative and osmotic stress, and ionic nutrient-shortage. Recent findings suggest that the thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus uses a novel alkylsuccinate synthase for long-chain alkane degradation, and the thermophilic Candidatus Syntrophoarchaeum butanivorans anaerobically oxidizes butane via alkyl-coenzyme M formation. In addition, gene expression data suggest that extremophiles produce energy via the glyoxylate shunt and the Pta-AckA pathway when grown on a diverse range of alkanes under stress conditions. Alkane degraders possess biotechnological potential for bioremediation because of their unusual characteristics. This review will provide genomic and molecular insights on alkane degraders under extreme conditions.
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Affiliation(s)
- Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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26
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Flowers JJ, Richards MA, Baliga N, Meyer B, Stahl DA. Constraint-based modelling captures the metabolic versatility of Desulfovibrio vulgaris. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:190-201. [PMID: 29377633 DOI: 10.1111/1758-2229.12619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/18/2018] [Indexed: 06/07/2023]
Abstract
A refined Desulfovibrio vulgaris Hildenborough flux balance analysis (FBA) model (iJF744) was developed, incorporating 1016 reactions that include 744 genes and 951 metabolites. A draft model was first developed through automatic model reconstruction using the ModelSeed Server and then curated based on existing literature. The curated model was further refined by incorporating three recently proposed redox reactions involving the Hdr-Flx and Qmo complexes and a lactate dehydrogenase (LdhAB, DVU 3027-3028) indicated by mutation and transcript analyses to serve electron transfer reactions central to syntrophic and respiratory growth. Eight different variations of this model were evaluated by comparing model predictions to experimental data determined for four different growth conditions - three for sulfate respiration (with lactate, pyruvate or H2 /CO2 -acetate) and one for fermentation in syntrophic coculture. The final general model supports (i) a role for Hdr-Flx in the oxidation of DsrC and ferredoxin, and reduction of NAD+ in a flavin-based electron confurcating reaction sequence, (ii) a function of the Qmo complex in receiving electrons from the menaquinone pool and potentially from ferredoxin to reduce APS and (iii) a reduction of the soluble DsrC by LdhAB and a function of DsrC in electron transfer reactions other than sulfite reduction.
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Affiliation(s)
- Jason J Flowers
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | | | | | - Birte Meyer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
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27
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Christensen GA, Moon J, Veach AM, Mosher JJ, Wymore AM, van Nostrand JD, Zhou J, Hazen TC, Arkin AP, Elias DA. Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition. PLoS One 2018; 13:e0194663. [PMID: 29558522 PMCID: PMC5860781 DOI: 10.1371/journal.pone.0194663] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/07/2018] [Indexed: 02/01/2023] Open
Abstract
Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion of the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.
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Affiliation(s)
- Geoff A. Christensen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - JiWon Moon
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Allison M. Veach
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jennifer J. Mosher
- Marshall University, Biological Sciences, Huntington, West Virginia, United States of America
| | - Ann M. Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | - Jizhong Zhou
- University of Oklahoma, Norman, Oklahoma, United States of America
| | - Terry C. Hazen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- University of Tennessee, Knoxville, Tennessee, United States of America
| | - Adam P. Arkin
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- University of California at Berkeley, Berkeley, California, United States of America
| | - Dwayne A. Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
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28
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Müller N, Timmers P, Plugge CM, Stams AJM, Schink B. Syntrophy in Methanogenic Degradation. (ENDO)SYMBIOTIC METHANOGENIC ARCHAEA 2018. [DOI: 10.1007/978-3-319-98836-8_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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29
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Leng L, Yang P, Singh S, Zhuang H, Xu L, Chen WH, Dolfing J, Li D, Zhang Y, Zeng H, Chu W, Lee PH. A review on the bioenergetics of anaerobic microbial metabolism close to the thermodynamic limits and its implications for digestion applications. BIORESOURCE TECHNOLOGY 2018; 247:1095-1106. [PMID: 28958887 DOI: 10.1016/j.biortech.2017.09.103] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/09/2017] [Accepted: 09/15/2017] [Indexed: 05/24/2023]
Abstract
The exploration of the energetics of anaerobic digestion systems can reveal how microorganisms cooperate efficiently for cell growth and methane production, especially under low-substrate conditions. The establishment of a thermodynamically interdependent partnership, called anaerobic syntrophy, allows unfavorable reactions to proceed. Interspecies electron transfer and the concentrations of electron carriers are crucial for maintaining this mutualistic activity. This critical review summarizes the functional microorganisms and syntroph partners, particularly in the metabolic pathways and energy conservation of syntrophs. The kinetics and thermodynamics of propionate degradation to methane, reversibility of the acetate oxidation process, and estimation of microbial growth are summarized. The various routes of interspecies electron transfer, reverse electron transfer, and Poly-β-hydroxyalkanoate formation in the syntrophic community are also reviewed. Finally, promising and critical directions of future research are proposed. Fundamental insight in the activities and interactions involved in AD systems could serve as a guidance for engineered systems optimization and upgrade.
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Affiliation(s)
- Ling Leng
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Peixian Yang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Shubham Singh
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Huichuan Zhuang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Linji Xu
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Wen-Hsing Chen
- Department of Environmental Engineering, National Ilan University, Yilan 260, Taiwan
| | - Jan Dolfing
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle NE1 7RU, UK
| | - Dong Li
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Yan Zhang
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Huiping Zeng
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, China
| | - Wei Chu
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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30
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Weatherill JJ, Atashgahi S, Schneidewind U, Krause S, Ullah S, Cassidy N, Rivett MO. Natural attenuation of chlorinated ethenes in hyporheic zones: A review of key biogeochemical processes and in-situ transformation potential. WATER RESEARCH 2018; 128:362-382. [PMID: 29126033 DOI: 10.1016/j.watres.2017.10.059] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 10/12/2017] [Accepted: 10/28/2017] [Indexed: 06/07/2023]
Abstract
Chlorinated ethenes (CEs) are legacy contaminants whose chemical footprint is expected to persist in aquifers around the world for many decades to come. These organohalides have been reported in river systems with concerning prevalence and are thought to be significant chemical stressors in urban water ecosystems. The aquifer-river interface (known as the hyporheic zone) is a critical pathway for CE discharge to surface water bodies in groundwater baseflow. This pore water system may represent a natural bioreactor where anoxic and oxic biotransformation process act in synergy to reduce or even eliminate contaminant fluxes to surface water. Here, we critically review current process understanding of anaerobic CE respiration in the competitive framework of hyporheic zone biogeochemical cycling fuelled by in-situ fermentation of natural organic matter. We conceptualise anoxic-oxic interface development for metabolic and co-metabolic mineralisation by a range of aerobic bacteria with a focus on vinyl chloride degradation pathways. The superimposition of microbial metabolic processes occurring in sediment biofilms and bulk solute transport delivering reactants produces a scale dependence in contaminant transformation rates. Process interpretation is often confounded by the natural geological heterogeneity typical of most riverbed environments. We discuss insights from recent field experience of CE plumes discharging to surface water and present a range of practical monitoring technologies which address this inherent complexity at different spatial scales. Future research must address key dynamics which link supply of limiting reactants, residence times and microbial ecophysiology to better understand the natural attenuation capacity of hyporheic systems.
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Affiliation(s)
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Uwe Schneidewind
- Department of Engineering Geology and Hydrogeology, RWTH Aachen University, Aachen, Germany
| | - Stefan Krause
- School of Geography, Earth and Environmental Science, University of Birmingham, UK
| | - Sami Ullah
- School of Geography, Earth and Environmental Science, University of Birmingham, UK
| | | | - Michael O Rivett
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, UK; GroundH(2)O Plus Ltd., Quinton, Birmingham, UK
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31
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Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes. mBio 2017; 8:mBio.02022-17. [PMID: 29259088 PMCID: PMC5736913 DOI: 10.1128/mbio.02022-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi. The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments and provide evidence for a homacetogenic lifestyle of these abundant marine Chloroflexi. Moreover, genome signature and key metabolic genes indicate an evolutionary relationship between these deep-sea sediment microbes and terrestrial, reductively dehalogenating Dehalococcoides.
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32
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Zhou C, Zhou Y, Rittmann BE. Reductive precipitation of sulfate and soluble Fe(III) by Desulfovibrio vulgaris: Electron donor regulates intracellular electron flow and nano-FeS crystallization. WATER RESEARCH 2017; 119:91-101. [PMID: 28436827 DOI: 10.1016/j.watres.2017.04.044] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/15/2017] [Accepted: 04/17/2017] [Indexed: 06/07/2023]
Abstract
Fully understanding the metabolism of SRB provides fundamental guidelines for allowing the microorganisms to provide more beneficial services in water treatment and resource recovery. The electron-transfer pathway of sulfate respiration by Desulfovibrio vulgaris is well studied, but still partly unresolved. Here we provide deeper insight by comprehensively monitoring metabolite changes during D. vulgaris metabolism with two electron donors, lactate and pyruvate, in presence or absence of citrate-chelated soluble FeIII as an additional competing electron acceptor. H2 was produced from lactate oxidation to pyruvate, but pyruvate oxidation produced mostly formate. Accumulation of lactate-originated H2 during lag phases inhibited pyruvate transformation to acetate. Sulfate reduction was initiated by lactate-originated H2, but MQ-mediated e- flow initiated sulfate reduction without delay when pyruvate was the donor. When H2-induced electron flow gave priority to FeIII reduction over sulfate reduction, the long lag phase before sulfate reduction shortened the time for iron-sulfide crystallite growth and led to smaller mackinawite (Fe1+xS) nanocrystallites. Synthesizing all the results, we propose that electron flow from lactate or pyruvate towards SO42- reduction to H2S are through at least three routes that are regulated by the e- donor (lactate or pyruvate) and the presence or absence of another e- acceptor (FeIII here). These routes are not competing, but complementary: e.g., H2 or formate production and oxidation were necessary for sulfite and disulfide/trisulfide reduction to sulfide. Our study suggests that the e- donor provides a practical tool to regulate and optimize SRB-predominant bioremediation systems.
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Affiliation(s)
- Chen Zhou
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA.
| | - Yun Zhou
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA; College of Environmental Science and Engineering, Tongji University, China
| | - Bruce E Rittmann
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
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33
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Baba R, Morita M, Asakawa S, Watanabe T. Transcription of [FeFe]-Hydrogenase Genes during H 2 Production in Clostridium and Desulfovibrio spp. Isolated from a Paddy Field Soil. Microbes Environ 2017; 32:125-132. [PMID: 28502969 PMCID: PMC5478535 DOI: 10.1264/jsme2.me16171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Changes in the relative abundances of the transcripts of hydA gene paralogs for [FeFe]-hydrogenase in Clostridium sp. strain H2 and Desulfovibrio sp. strain A1 isolated from paddy field soil were analyzed during H2 production. Strains H2 and A1 had at least five and two phylogenetically different hydA genes, respectively. The relative abundances of their hydA transcripts differed among the paralogs and H2 production activity changed in a manner that depended on the growth phase and conditions. Increases or decreases in the relative abundances of the transcripts of two out of five hydA genes in strain H2 correlated with changes in H2 production rates, whereas those of the others remained unchanged or decreased. In strain A1, the relative abundances of the transcripts of two hydA genes differed between monoculture, sulfate-reducing, and syntrophic, methanogenic conditions. The relative abundance of the transcripts of one hydA gene, predicted to encode a cytosolic [FeFe]-hydrogenase, was higher under syntrophic, methanogenic conditions than sulfate-reducing conditions, while that of the transcripts of the other hydA gene decreased with time under both conditions. This study showed that the transcription of the hydA gene during growth with active H2 production was differently regulated among the paralogs in H2 producers isolated from paddy field soil.
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Affiliation(s)
- Ryuko Baba
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Mayumi Morita
- Laboratory of Soil Biology and Chemistry, School of Agricultural Sciences, Nagoya University
| | - Susumu Asakawa
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Takeshi Watanabe
- Laboratory of Soil Biology and Chemistry, Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University
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34
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Thompson AW, Turkarslan S, Arens CE, López García de Lomana A, Raman AV, Stahl DA, Baliga NS. Robustness of a model microbial community emerges from population structure among single cells of a clonal population. Environ Microbiol 2017; 19:3059-3069. [PMID: 28419704 DOI: 10.1111/1462-2920.13764] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 03/15/2017] [Accepted: 04/10/2017] [Indexed: 01/12/2023]
Abstract
Microbial populations can withstand, overcome and persist in the face of environmental fluctuation. Previously, we demonstrated how conditional gene regulation in a fluctuating environment drives dilution of condition-specific transcripts, causing a population of Desulfovibrio vulgaris Hildenborough (DvH) to collapse after repeatedly transitioning from sulfate respiration to syntrophic conditions with the methanogen Methanococcus maripaludis. Failure of the DvH to successfully transition contributed to the collapse of this model community. We investigated the mechanistic basis for loss of robustness by examining whether conditional gene regulation altered heterogeneity in gene expression across individual DvH cells. We discovered that robustness of a microbial population across environmental transitions was attributable to the retention of cells in two states that exhibited different condition-specific gene expression patterns. In our experiments, a population with disrupted conditional regulation successfully alternated between cell states. Meanwhile, a population with intact conditional regulation successfully switched between cell states initially, but collapsed after repeated transitions, possibly due to the high energy requirements of regulation. These results demonstrate that the survival of this entire model microbial community is dependent on the regulatory system's influence on the distribution of distinct cell states among individual cells within a clonal population.
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Affiliation(s)
| | | | | | | | | | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
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Turkarslan S, Raman AV, Thompson AW, Arens CE, Gillespie MA, von Netzer F, Hillesland KL, Stolyar S, López García de Lomana A, Reiss DJ, Gorman-Lewis D, Zane GM, Ranish JA, Wall JD, Stahl DA, Baliga NS. Mechanism for microbial population collapse in a fluctuating resource environment. Mol Syst Biol 2017; 13:919. [PMID: 28320772 PMCID: PMC5371734 DOI: 10.15252/msb.20167058] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Managing trade-offs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. To investigate this hypothesis, we imposed a fluctuating environment that required the sulfate-reducer Desulfovibrio vulgaris to undergo repeated ecologically relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen-consuming Methanococcus maripaludis Strikingly, the microbial community became progressively less proficient at restoring the environmentally relevant physiological state after each perturbation and most cultures collapsed within 3-7 shifts. Counterintuitively, the collapse phenomenon was prevented by a single regulatory mutation. We have characterized the mechanism for collapse by conducting RNA-seq analysis, proteomics, microcalorimetry, and single-cell transcriptome analysis. We demonstrate that the collapse was caused by conditional gene regulation, which drove precipitous decline in intracellular abundance of essential transcripts and proteins, imposing greater energetic burden of regulation to restore function in a fluctuating environment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Drew Gorman-Lewis
- Earth and Space Sciences, University of Washington, Seattle, WA, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | | | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
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Velázquez-Sánchez HI, Puebla-Nuñez HF, Aguilar-López R. Novel Feedback Control to Improve Biohydrogen Production by Desulfovibrio alaskensis. INTERNATIONAL JOURNAL OF CHEMICAL REACTOR ENGINEERING 2016. [DOI: 10.1515/ijcre-2016-0044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Abstract
In this paper, a novel control algorithm to increase biohydrogen production in a continuous reactor using the sulphate-reducing bacteria Desulfovibrio alaskensis with lactate as carbon source is proposed. This work was conducted via numerical simulations, based on an experimentally corroborated kinetic model, considered as a benchmark of the system. A bifurcation analysis to identify the reactor’s steady-state performance was done in order to identify feasible operating regions. The proposed controller cancels the upper bounds of the reactor, imposing a finite-time convergence to the selected set point. The closed-loop stability of the reactor is analysed via the dynamic of the regulation error. Finally, numerical experiments were conducted in order to compare the dynamic behaviour of the proposed closed-loop system versus its open-loop counterpart and a well-tuned classical PI controller one. The proposed methodology increases the hydrogen productivity controlling with a satisfactory performance the biomass concentration, which is considered as the control output.
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Großkopf T, Zenobi S, Alston M, Folkes L, Swarbreck D, Soyer OS. A stable genetic polymorphism underpinning microbial syntrophy. THE ISME JOURNAL 2016; 10:2844-2853. [PMID: 27258948 PMCID: PMC5042321 DOI: 10.1038/ismej.2016.80] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 03/28/2016] [Accepted: 04/01/2016] [Indexed: 12/22/2022]
Abstract
Syntrophies are metabolic cooperations, whereby two organisms co-metabolize a substrate in an interdependent manner. Many of the observed natural syntrophic interactions are mandatory in the absence of strong electron acceptors, such that one species in the syntrophy has to assume the role of electron sink for the other. While this presents an ecological setting for syntrophy to be beneficial, the potential genetic drivers of syntrophy remain unknown to date. Here, we show that the syntrophic sulfate-reducing species Desulfovibrio vulgaris displays a stable genetic polymorphism, where only a specific genotype is able to engage in syntrophy with the hydrogenotrophic methanogen Methanococcus maripaludis. This 'syntrophic' genotype is characterized by two genetic alterations, one of which is an in-frame deletion in the gene encoding for the ion-translocating subunit cooK of the membrane-bound COO hydrogenase. We show that this genotype presents a specific physiology, in which reshaping of energy conservation in the lactate oxidation pathway enables it to produce sufficient intermediate hydrogen for sustained M. maripaludis growth and thus, syntrophy. To our knowledge, these findings provide for the first time a genetic basis for syntrophy in nature and bring us closer to the rational engineering of syntrophy in synthetic microbial communities.
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Affiliation(s)
- Tobias Großkopf
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Simone Zenobi
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Mark Alston
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - Leighton Folkes
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - David Swarbreck
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - Orkun S Soyer
- School of Life Sciences, The University of Warwick, Coventry, UK
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38
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Zhao Z, Zhang Y, Yu Q, Dang Y, Li Y, Quan X. Communities stimulated with ethanol to perform direct interspecies electron transfer for syntrophic metabolism of propionate and butyrate. WATER RESEARCH 2016; 102:475-484. [PMID: 27403870 DOI: 10.1016/j.watres.2016.07.005] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/18/2016] [Accepted: 07/03/2016] [Indexed: 05/28/2023]
Abstract
Direct interspecies electron transfer (DIET) has been considered as an alternative to interspecies H2 transfer (IHT) for syntrophic metabolism, but the microorganisms capable of metabolizing the key intermediates, such as propionate and butyrate, via DIET have yet to be described. A strategy of culturing the enrichments with ethanol as a DIET substrate to stimulate the communities for the syntrophic metabolism of propionate and/or butyrate was proposed in this study. The results showed that the syntrophic propionate and/or butyrate degradation was significantly improved in the ethanol-stimulated reactor when propionate/butyrate was the sole carbon source. The conductivity of the ethanol-stimulated enrichments was as 5 folds (for propionate)/76 folds (for butyrate) as that of the traditional enrichments (never ethanol fed). Microbial community analysis revealed that Geobacter species known to proceed DIET were only detected in the ethanol-stimulated enrichments. Together with the significant increase of Methanosaeta and Methanosarcina species in these enrichments, the potential DIET between Geobacter and Methanosaeta or Methanosarcina species might be established to improve the syntrophic propionate and/or butyrate degradation. Further experiments demonstrated that granular activated carbon (GAC) could improve the syntrophic metabolism of propionate and/or butyrate of the ethanol-stimulated enrichments, while almost no effects on the traditional enrichments. Also, the high H2 partial pressure could inhibit the syntrophic propionate and/or butyrate degradation of the traditional enrichments, but its effect on that of the ethanol-stimulated enrichments was negligible.
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Affiliation(s)
- Zhiqiang Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Qilin Yu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yan Dang
- Beijing Key Lab for Source Control Technology of Water Pollution, Beijing Forestry University, 35 Tsinghua East Road, Beijing, 100083, China; Department of Microbiology, University of Massachusetts, Amherst, MA, 01003-9298, USA
| | - Yang Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xie Quan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
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Microbe-microbe interactions trigger Mn(II)-oxidizing gene expression. ISME JOURNAL 2016; 11:67-77. [PMID: 27518809 DOI: 10.1038/ismej.2016.106] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 11/08/2022]
Abstract
Manganese (Mn) is an important metal in geochemical cycles. Some microorganisms can oxidize Mn(II) to Mn oxides, which can, in turn, affect the global cycles of other elements by strong sorption and oxidation effects. Microbe-microbe interactions have important roles in a number of biological processes. However, how microbial interactions affect Mn(II) oxidation still remains unknown. Here, we investigated the interactions between two bacteria (Arthrobacter sp. and Sphingopyxis sp.) in a co-culture, which exhibited Mn(II)-oxidizing activity, although neither were able to oxidize Mn(II) in isolation. We demonstrated that the Mn(II)-oxidizing activity in co-culture was most likely induced via contact-dependent interactions. The expressed Mn(II)-oxidizing protein in the co-culture was purified and identified as a bilirubin oxidase belonging to strain Arthrobacter. Full sequencing of the bilirubin oxidase-encoding gene (boxA) was performed. The Mn(II)-oxidizing protein and the transcripts of boxA were detected in the co-culture, but not in either of the isolated cultures. This indicate that boxA was silent in Arthrobacter monoculture, and was activated in response to presence of Sphingopyxis in the co-culture. Further, transcriptomic analysis by RNA-Seq, extracellular superoxide detection and cell density quantification by flow cytometry indicate induction of boxA gene expression in Arthrobacter was co-incident with a stress response triggered by co-cultivation with Sphingopyxis. Our findings suggest the potential roles of microbial physiological responses to stress induced by other microbes in Mn(II) oxidation and extracellular superoxide production.
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40
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Treu L, Campanaro S, Kougias PG, Zhu X, Angelidaki I. Untangling the Effect of Fatty Acid Addition at Species Level Revealed Different Transcriptional Responses of the Biogas Microbial Community Members. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6079-90. [PMID: 27154312 DOI: 10.1021/acs.est.6b00296] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In the present study, RNA-sequencing was used to elucidate the change of anaerobic digestion metatranscriptome after long chain fatty acids (oleate) exposure. To explore the general transcriptional behavior of the microbiome, the analysis was first performed on shotgun reads without considering a reference metagenome. As a second step, RNA reads were aligned on the genes encoded by the microbial community, revealing the expression of more than 51 000 different transcripts. The present study is the first research which was able to dissect the transcriptional behavior at a single species level by considering the 106 microbial genomes previously identified. The exploration of the metabolic pathways confirmed the importance of Syntrophomonas species in fatty acids degradation, and also highlighted the presence of protective mechanisms toward the long chain fatty acid effects in bacteria belonging to Clostridiales, Rykenellaceae, and in species of the genera Halothermothrix and Anaerobaculum. Additionally, an interesting transcriptional activation of the chemotaxis genes was evidenced in seven species belonging to Clostridia, Halothermothrix, and Tepidanaerobacter. Surprisingly, methanogens revealed a very versatile behavior different from each other, even among similar species of the Methanoculleus genus, while a strong increase of the expression level in Methanosarcina sp. was evidenced after oleate addition.
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Affiliation(s)
- Laura Treu
- Department of Environmental Engineering, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova , Viale dell'Università 16, Legnaro, PD 35020, Italy
| | - Stefano Campanaro
- Department of Biology, University of Padova , Via U. Bassi 58/b, 35121, Padova Italy
| | - Panagiotis G Kougias
- Department of Environmental Engineering, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - Xinyu Zhu
- Department of Environmental Engineering, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
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41
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Electron transfer pathways of formate-driven H2 production in Desulfovibrio. Appl Microbiol Biotechnol 2016; 100:8135-46. [DOI: 10.1007/s00253-016-7649-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/12/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
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42
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Jia X, Liu C, Song H, Ding M, Du J, Ma Q, Yuan Y. Design, analysis and application of synthetic microbial consortia. Synth Syst Biotechnol 2016; 1:109-117. [PMID: 29062933 PMCID: PMC5640696 DOI: 10.1016/j.synbio.2016.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 01/28/2016] [Accepted: 02/12/2016] [Indexed: 12/17/2022] Open
Abstract
The rapid development of synthetic biology has conferred almost perfect modification on single cells, and provided methodological support for synthesizing microbial consortia, which have a much wider application potential than synthetic single cells. Co-cultivating multiple cell populations with rational strategies based on interacting relationships within natural microbial consortia provides theoretical as well as experimental support for the successful obtaining of synthetic microbial consortia, promoting it into extensive research on both industrial applications in plenty of areas and also better understanding of natural microbial consortia. According to their composition complexity, synthetic microbial consortia are summarized in three aspects in this review and are discussed in principles of design and construction, insights and methods for analysis, and applications in energy, healthcare, etc.
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Affiliation(s)
- Xiaoqiang Jia
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Chang Liu
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Hao Song
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Mingzhu Ding
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Jin Du
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Qian Ma
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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43
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Microbial diversity arising from thermodynamic constraints. ISME JOURNAL 2016; 10:2725-2733. [PMID: 27035705 PMCID: PMC5042319 DOI: 10.1038/ismej.2016.49] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 02/25/2016] [Accepted: 03/01/2016] [Indexed: 01/15/2023]
Abstract
The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments.
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44
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Yang H, Gandhi H, Cornish AJ, Moran JJ, Kreuzer HW, Ostrom NE, Hegg EL. Isotopic fractionation associated with [NiFe]- and [FeFe]-hydrogenases. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:285-292. [PMID: 27071219 DOI: 10.1002/rcm.7432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
RATIONALE Hydrogenases catalyze the reversible formation of H2 from electrons and protons with high efficiency. Understanding the relationships between H2 production, H2 uptake, and H2-H2O exchange can provide insight into the metabolism of microbial communities in which H2 is an essential component in energy cycling. METHODS We used stable H isotopes (1H and 2H) to probe the isotope effects associated with three [FeFe]-hydrogenases and three [NiFe]-hydrogenases. RESULTS All six hydrogenases displayed fractionation factors for H2 formation that were significantly less than 1, producing H2 that was severely depleted in 2H relative to the substrate, water. Consistent with differences in their active site structure, the fractionation factors for each class appear to cluster, with the three [NiFe]-hydrogenases (α = 0.27–0.40) generally having smaller values than the three [FeFe]-hydrogenases (α = 0.41–0.55). We also obtained isotopic fractionation factors associated with H2 uptake and H2-H2O exchange under conditions similar to those utilized for H2 production, providing a more complete picture of the reactions catalyzed by hydrogenases. CONCLUSIONS The fractionation factors determined in our studies can be used as signatures for different hydrogenases to probe their activity under different growth conditions and to ascertain which hydrogenases are most responsible for H2 production and/or uptake in complex microbial communities.
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45
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Koch S, Benndorf D, Fronk K, Reichl U, Klamt S. Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:17. [PMID: 26807149 PMCID: PMC4724120 DOI: 10.1186/s13068-016-0429-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/07/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Microbial communities are ubiquitous in nature and play a major role in ecology, medicine, and various industrial processes. In this study, we used stoichiometric metabolic modeling to investigate a community of three species, Desulfovibrio vulgaris, Methanococcus maripaludis, and Methanosarcina barkeri, which are involved in acetogenesis and methanogenesis in anaerobic digestion for biogas production. RESULTS We first constructed and validated stoichiometric models of the core metabolism of the three species which were then assembled to community models. The community was simulated by applying the previously described concept of balanced growth demanding that all organisms of the community grow with equal specific growth rate. For predicting community compositions, we propose a novel hierarchical optimization approach: first, similar to other studies, a maximization of the specific community growth rate is performed which, however, often leads to a wide range of optimal community compositions. In a secondary optimization, we therefore also demand that all organisms must grow with maximum biomass yield (optimal substrate usage) reducing the range of predicted optimal community compositions. Simulating two-species as well as three-species communities of the three representative organisms, we gained several important insights. First, using our new optimization approach we obtained predictions on optimal community compositions for different substrates which agree well with measured data. Second, we found that the ATP maintenance coefficient influences significantly the predicted community composition, especially for small growth rates. Third, we observed that maximum methane production rates are reached under high-specific community growth rates and if at least one of the organisms converts its substrate(s) with suboptimal biomass yield. On the other hand, the maximum methane yield is obtained at low community growth rates and, again, when one of the organisms converts its substrates suboptimally and thus wastes energy. Finally, simulations in the three-species community clarify exchangeability and essentiality of the methanogens in case of alternative substrate usage and competition scenarios. CONCLUSIONS In summary, our study presents new methods for stoichiometric modeling of microbial communities in general and provides valuable insights in interdependencies of bacterial species involved in the biogas process.
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Affiliation(s)
- Sabine Koch
- />Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106 Magdeburg, Germany
| | - Dirk Benndorf
- />Otto-von-Guericke-University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Karen Fronk
- />Harz University of Applied Sciences, Friedrichstrasse 57-59, 38855 Wernigerode, Germany
| | - Udo Reichl
- />Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106 Magdeburg, Germany
- />Otto-von-Guericke-University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Steffen Klamt
- />Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106 Magdeburg, Germany
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46
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Tan B, Jane Fowler S, Laban NA, Dong X, Sensen CW, Foght J, Gieg LM. Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples. THE ISME JOURNAL 2015; 9:2028-45. [PMID: 25734684 PMCID: PMC4542035 DOI: 10.1038/ismej.2015.22] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 11/09/2022]
Abstract
Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate- and H2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities.
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Affiliation(s)
- Boonfei Tan
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - S Jane Fowler
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Nidal Abu Laban
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Xiaoli Dong
- Visual Genomics Centre, Faculty of Medicine, Calgary, Alberta, Canada
| | | | - Julia Foght
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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47
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Thompson AW, Crow MJ, Wadey B, Arens C, Turkarslan S, Stolyar S, Elliott N, Petersen TW, van den Engh G, Stahl DA, Baliga NS. A method to analyze, sort, and retain viability of obligate anaerobic microorganisms from complex microbial communities. J Microbiol Methods 2015; 117:74-7. [PMID: 26187776 DOI: 10.1016/j.mimet.2015.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/08/2015] [Accepted: 07/09/2015] [Indexed: 10/23/2022]
Abstract
A high speed flow cytometric cell sorter was modified to maintain a controlled anaerobic environment. This technology enabled coupling of the precise high-throughput analytical and cell separation capabilities of flow cytometry to the assessment of cell viability of evolved lineages of obligate anaerobic organisms from cocultures.
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Affiliation(s)
| | | | - Brian Wadey
- BD Biosciences, Advanced Cytometry Group, Seattle, USA
| | | | | | | | - Nicholas Elliott
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | | | | | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, USA; Departments of Biology and Microbiology, University of Washington, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA; Lawrence Berkeley National Lab, Berkeley, CA, USA
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48
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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49
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Metabolite-enabled mutualistic interaction between Shewanella oneidensis and Escherichia coli in a co-culture using an electrode as electron acceptor. Sci Rep 2015; 5:11222. [PMID: 26061569 PMCID: PMC4462164 DOI: 10.1038/srep11222] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 05/19/2015] [Indexed: 01/26/2023] Open
Abstract
Mutualistic interactions in planktonic microbial communities have been extensively studied. However, our understanding on mutualistic communities consisting of co-existing planktonic cells and biofilms is limited. Here, we report a planktonic cells-biofilm mutualistic system established by the fermentative bacterium Escherichia coli and the dissimilatory metal-reducing bacterium Shewanella oneidensis in a bioelectrochemical device, where planktonic cells in the anode media interact with the biofilms on the electrode. Our results show that the transfer of formate is the key mechanism in this mutualistic system. More importantly, we demonstrate that the relative distribution of E. coli and S. oneidensis in the liquid media and biofilm is likely driven by their metabolic functions towards an optimum communal metabolism in the bioelectrochemical device. RNA sequencing-based transcriptomic analyses of the interacting organisms in the mutualistic system potentially reveal differential expression of genes involved in extracellular electron transfer pathways in both species in the planktonic cultures and biofilms.
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Benomar S, Ranava D, Cárdenas ML, Trably E, Rafrafi Y, Ducret A, Hamelin J, Lojou E, Steyer JP, Giudici-Orticoni MT. Nutritional stress induces exchange of cell material and energetic coupling between bacterial species. Nat Commun 2015; 6:6283. [PMID: 25704114 DOI: 10.1038/ncomms7283] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 01/12/2015] [Indexed: 12/24/2022] Open
Abstract
Knowledge of the behaviour of bacterial communities is crucial for understanding biogeochemical cycles and developing environmental biotechnology. Here we demonstrate the formation of an artificial consortium between two anaerobic bacteria, Clostridium acetobutylicum (Gram-positive) and Desulfovibrio vulgaris Hildenborough (Gram-negative, sulfate-reducing) in which physical interactions between the two partners induce emergent properties. Molecular and cellular approaches show that tight cell-cell interactions are associated with an exchange of molecules, including proteins, which allows the growth of one partner (D. vulgaris) in spite of the shortage of nutrients. This physical interaction induces changes in expression of two genes encoding enzymes at the pyruvate crossroads, with concomitant changes in the distribution of metabolic fluxes, and allows a substantial increase in hydrogen production without requiring genetic engineering. The stress induced by the shortage of nutrients of D. vulgaris appears to trigger the interaction.
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Affiliation(s)
- Saida Benomar
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - David Ranava
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - María Luz Cárdenas
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Eric Trably
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Yan Rafrafi
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Adrien Ducret
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 13009 Marseille, France
| | - Jérôme Hamelin
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Jean-Philippe Steyer
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
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