1
|
Osorio-Rodriguez D, Metcalfe KS, McGlynn SE, Yu H, Dekas AE, Ellisman M, Deerinck T, Aristilde L, Grotzinger JP, Orphan VJ. Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation. Proc Natl Acad Sci U S A 2023; 120:e2302156120. [PMID: 38079551 PMCID: PMC10743459 DOI: 10.1073/pnas.2302156120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Authigenic carbonate minerals can preserve biosignatures of microbial anaerobic oxidation of methane (AOM) in the rock record. It is not currently known whether the microorganisms that mediate sulfate-coupled AOM-often occurring as multicelled consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB)-are preserved as microfossils. Electron microscopy of ANME-SRB consortia in methane seep sediments has shown that these microorganisms can be associated with silicate minerals such as clays [Chen et al., Sci. Rep. 4, 1-9 (2014)], but the biogenicity of these phases, their geochemical composition, and their potential preservation in the rock record is poorly constrained. Long-term laboratory AOM enrichment cultures in sediment-free artificial seawater [Yu et al., Appl. Environ. Microbiol. 88, e02109-21 (2022)] resulted in precipitation of amorphous silicate particles (~200 nm) within clusters of exopolymer-rich AOM consortia from media undersaturated with respect to silica, suggestive of a microbially mediated process. The use of techniques like correlative fluorescence in situ hybridization (FISH), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), and nanoscale secondary ion mass spectrometry (nanoSIMS) on AOM consortia from methane seep authigenic carbonates and sediments further revealed that they are enveloped in a silica-rich phase similar to the mineral phase on ANME-SRB consortia in enrichment cultures. Like in cyanobacteria [Moore et al., Geology 48, 862-866 (2020)], the Si-rich phases on ANME-SRB consortia identified here may enhance their preservation as microfossils. The morphology of these silica-rich precipitates, consistent with amorphous-type clay-like spheroids formed within organic assemblages, provides an additional mineralogical signature that may assist in the search for structural remnants of microbial consortia in rocks which formed in methane-rich environments from Earth and other planetary bodies.
Collapse
Affiliation(s)
- Daniela Osorio-Rodriguez
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Kyle S. Metcalfe
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Shawn E. McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo152-8550, Japan
| | - Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- College of Urban and Environmental Sciences, Peking University, Beijing100871, China
| | - Anne E. Dekas
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
- Department of Earth System Science, Stanford University, Stanford, CA94305
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, School of Medicine, La Jolla, CA92093
| | - Tom Deerinck
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, School of Medicine, La Jolla, CA92093
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL60208
| | - John P. Grotzinger
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| |
Collapse
|
2
|
Dal Co A, Ackermann M, van Vliet S. Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals. Cell Syst 2023; 14:98-108. [PMID: 36796335 DOI: 10.1016/j.cels.2022.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/14/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
Most bacteria live in dense, spatially structured communities such as biofilms. The high density allows cells to alter the local microenvironment, whereas the limited mobility can cause species to become spatially organized. Together, these factors can spatially organize metabolic processes within microbial communities so that cells in different locations perform different metabolic reactions. The overall metabolic activity of a community depends both on how metabolic reactions are arranged in space and on how they are coupled, i.e., how cells in different regions exchange metabolites. Here, we review mechanisms that lead to the spatial organization of metabolic processes in microbial systems. We discuss factors that determine the length scales over which metabolic activities are arranged in space and highlight how the spatial organization of metabolic processes affects the ecology and evolution of microbial communities. Finally, we define key open questions that we believe should be the main focus of future research.
Collapse
Affiliation(s)
- Alma Dal Co
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland; Department of Environmental Microbiology, Eawag, 8600 Duebendorf, Switzerland.
| | | |
Collapse
|
3
|
Wu L, Jin T, Chen H, Shen Z, Zhou Y. Conductive materials as fantastic toolkits to stimulate direct interspecies electron transfer in anaerobic digestion: new insights into methanogenesis contribution, characterization technology, and downstream treatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 326:116732. [PMID: 36402020 DOI: 10.1016/j.jenvman.2022.116732] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/29/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Direct interspecies electron transfer (DIET) stimulated by conductive materials (CMs) enables intercellular metabolic coupling that can address the unfavorable thermodynamical dilemma inherent in anaerobic digestion (AD). Although the DIET mechanism and stimulation have been extensively summarized, the methanogenesis contribution, characterization techniques, and downstream processes of CMs-led DIET in AD are surprisingly under-reviewed. Therefore, this review aimed to address these gaps. First, the contribution of CMs-led DIET to methanogenesis was re-evaluated by comparing the effect of various factors, including volatile fatty acids, free ammonia, and functional enzymes. It was revealed that AD systems are usually intricate and cannot allow the methanogenesis stimulation to be singularly attributed to the establishment of DIET. Additionally, considerable attention has been attached to the characterization of DIET occurrence, involving species identification, gene expression, electrical properties, cellular features, and syntrophic metabolism, suggesting the significance of accurate characterization methods for identifying the syntrophic metabolism interactions. Moreover, the type of CMs has a significant impact on AD downstream processes involving biogas purity, sludge dewaterability, and biosolids management. Finally, the central bottleneck consists in building a mathematical model of DIET to explain the mechanism of DIET in a deeper level from kinetics and thermodynamics.
Collapse
Affiliation(s)
- Linjun Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environment Sciences, Beijing 100012, PR China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Tao Jin
- China Construction Eco-environmental Group CO.,LTD, Beijing 100037, PR China
| | - Hong Chen
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic Engineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Zhiqiang Shen
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environment Sciences, Beijing 100012, PR China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China.
| | - Yuexi Zhou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environment Sciences, Beijing 100012, PR China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China.
| |
Collapse
|
4
|
Wegener G, Laso-Pérez R, Orphan VJ, Boetius A. Anaerobic Degradation of Alkanes by Marine Archaea. Annu Rev Microbiol 2022; 76:553-577. [PMID: 35917471 DOI: 10.1146/annurev-micro-111021-045911] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alkanes are saturated apolar hydrocarbons that range from its simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Current affiliation: Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Victoria J Orphan
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Division of Geological and Planetary Sciences and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Antje Boetius
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany;
| |
Collapse
|
5
|
Gupta D, Shalvarjian KE, Nayak DD. An archaea-specific c-type cytochrome maturation machinery is crucial for methanogenesis in Methanosarcina acetivorans. eLife 2022; 11:76970. [PMID: 35380107 PMCID: PMC9084895 DOI: 10.7554/elife.76970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
c-Type cytochromes (cyt c) are proteins that undergo post-translational modification to covalently bind heme, which allows them to facilitate redox reactions in electron transport chains across all domains of life. Genomic evidence suggests that cyt c are involved in electron transfer processes among the Archaea, especially in members that produce or consume the potent greenhouse gas methane. However, neither the maturation machinery for cyt c in Archaea nor their role in methane metabolism has ever been functionally characterized. Here, we have used CRISPR-Cas9 genome editing tools to map a distinct pathway for cyt c biogenesis in the model methanogenic archaeon Methanosarcina acetivorans, and have also identified substrate-specific functional roles for cyt c during methanogenesis. Although the cyt c maturation machinery from M. acetivorans is universally conserved in the Archaea, our evolutionary analyses indicate that different clades of Archaea acquired this machinery through multiple independent horizontal gene transfer events from different groups of Bacteria. Overall, we demonstrate the convergent evolution of a novel Archaea-specific cyt c maturation machinery and its physiological role during methanogenesis, a process which contributes substantially to global methane emissions. Archaea are single-celled organisms that were discovered over half a century ago. Recently, there has been a renewed interest in these microbes because theyplay a key role in climate change by controlling greenhouse gas emissions, like methane. Indeed, methane-producing Archaea generate nearly 70% of the methane gas released into the atmosphere. A group of proteins called c-type cytochromes are essential to energy generation in several methane-producing archaea. However, it is a mystery how Archaea assemble their c-type cytochromes. In fact, genomic studies suggest that Archaea are missing some of the c-type cytochrome assembly machinery that bacteria use. This has led scientists to suspect that Archaea have an alternate mechanism for building these essential components. To solve this mystery, Gupta, Shalvarjian, and Nayak used CRISPR-Cas9 gene-editing tools to characterize which proteins are essential for c-type cytochrome production in Methanosarcina acetivorans, a species of Archaea that produces methane. These experiments showed that M. acetivorans discarded a few parts of the process used by bacteria to generate c-type cytochromes, streamlining the assembly of these proteins. By comparing the genes of different Archaeal species, Gupta, Shalvarjian and Nayak were able to determine that Archaea acquired the genes for producing c-type cytochromes from bacteria via horizontal gene transfer, a process in which genes move directly from one organism into another. The streamlining of the process took place later, as different Archaeal species evolved independently, but losing the same parts of the process. Gupta Shalvajiran and Nayak’s experiments also showed that c-type cytochromes are essential for the growth and fitness of methane-producing Archaea like M. acetivorans. The role of c-type cytochromes in methane production varies in different species of Archaea depending on their growth substrate or where they live. These results provide vital information about how Archaea produce methane, and the tools and techniques developed will aid further investigation of the role of Archaea in climate change.
Collapse
Affiliation(s)
- Dinesh Gupta
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Katie E Shalvarjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Dipti D Nayak
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| |
Collapse
|
6
|
Vavilin VA, Lokshina LY, Rytov SV. Anaerobic oxidation of methane coupled with sulphate reduction: high concentration of methanotrophic archaea might be responsible for low stable isotope fractionation factors in methane. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2022; 58:44-59. [PMID: 34846953 DOI: 10.1080/10256016.2021.2000405] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
The changes in δ13CH4 and δ12C1H32H during sulphate-dependent anaerobic oxidation of methane (AOM) were described using dynamic modelling. The batch sulphate-dependent AOM at the nearly linear dynamics of methane oxidation with different enriched cultures originating from three marine sediments was simulated. The traditional Rayleigh equation for carbon and hydrogen stable isotopes in methane was derived from the basic dynamic isotope equation. The general and reduced models, taking into account the reaction stoichiometry and based on balances of chemical elements and their isotopes, describes a redistribution of stable isotope values in the sulphate-dependent AOM process. It was shown that AOM is the first and rate-limiting step in the whole AOM + SR (sulphate reduction) process. The different fractionation factors of carbon and hydrogen isotopes in methane were obtained for three marine sediments. It was concluded that during incubation the highest concentration of methanotrophic archaea might be responsible for the lowest fractionation factors of stable isotopes of carbon and hydrogen in methane. The interpretation of this phenomenon was suggested. Different concentrations of methanotrophic archaea can lead to variations of isotope fractionation factors.
Collapse
Affiliation(s)
- Vasily A Vavilin
- Water Problems Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | - Lyudmila Y Lokshina
- Water Problems Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | - Sergey V Rytov
- Water Problems Institute, Russian Academy of Sciences, Moscow, Russian Federation
| |
Collapse
|
7
|
Controls on Interspecies Electron Transport and Size Limitation of Anaerobically Methane-Oxidizing Microbial Consortia. mBio 2021; 12:mBio.03620-20. [PMID: 33975943 PMCID: PMC8263020 DOI: 10.1128/mbio.03620-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
About 382 Tg yr−1 of methane rising through the seafloor is oxidized anaerobically (W. S. Reeburgh, Chem Rev 107:486–513, 2007, https://doi.org/10.1021/cr050362v), preventing it from reaching the atmosphere, where it acts as a strong greenhouse gas. Microbial consortia composed of anaerobic methanotrophic archaea and sulfate-reducing bacteria couple the oxidation of methane to the reduction of sulfate under anaerobic conditions via a syntrophic process. Recent experimental studies and modeling efforts indicate that direct interspecies electron transfer (DIET) is involved in this syntrophy. Here, we explore a fluorescent in situ hybridization-nanoscale secondary ion mass spectrometry data set of large, segregated anaerobic oxidation of methane (AOM) consortia that reveal a decline in metabolic activity away from the archaeal-bacterial interface and use a process-based model to identify the physiological controls on rates of AOM. Simulations reproducing the observational data reveal that ohmic resistance and activation loss are the two main factors causing the declining metabolic activity, where activation loss dominated at a distance of <8 μm. These voltage losses limit the maximum spatial distance between syntrophic partners with model simulations, indicating that sulfate-reducing bacterial cells can remain metabolically active up to ∼30 μm away from the archaeal-bacterial interface. Model simulations further predict that a hybrid metabolism that combines DIET with a small contribution of diffusive exchange of electron donors can offer energetic advantages for syntrophic consortia.
Collapse
|
8
|
He X, Chadwick G, Jiménez Otero F, Orphan V, Meile C. Spatially Resolved Electron Transport through Anode‐Respiring
Geobacter sulfurreducens
Biofilms: Controls and Constraints. ChemElectroChem 2021. [DOI: 10.1002/celc.202100111] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaojia He
- Department of Marine Sciences University of Georgia Athens GA USA
| | - Grayson Chadwick
- Division of Geological and Planetary Sciences California Institute of Technology Pasadena CA USA
| | | | - Victoria Orphan
- Division of Geological and Planetary Sciences California Institute of Technology Pasadena CA USA
| | - Christof Meile
- Department of Marine Sciences University of Georgia Athens GA USA
| |
Collapse
|
9
|
Dynamic modeling of anaerobic methane oxidation coupled to sulfate reduction: role of elemental sulfur as intermediate. Bioprocess Biosyst Eng 2021; 44:855-874. [PMID: 33566183 DOI: 10.1007/s00449-020-02495-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
The process dynamics of anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR), and the potential role of elemental sulfur as intermediate are presented in this paper. Thermodynamic screening and experimental evidence from the literature conclude that a prominent model to describe AOM-SR is based on the concept that anaerobic methane oxidation proceeds through the production of the intermediate elemental sulfur. Two microbial groups are involved in the process: (a) anaerobic methanotrophs (ANME-2) and (b) Desulfosarcina/Desulfococcus sulfur reducers cluster (DSS). In this work, a dynamic model was developed to explore the interactions between biotic and abiotic processes to simulate the microbial activity, the chemical composition and speciation of the liquid phase, and the gas phase composition in the reactor headspace. The model includes the microbial kinetics for the symbiotic growth of ANME-2 and DSS, mass transfer phenomena between the gas and liquid phase for methane, hydrogen sulfide, and carbon dioxide and acid-base reactions for bicarbonate, sulfide, and ammonium. A data set from batch experiments, running for 250 days in artificial seawater inoculated with sediment from Marine Lake Grevelingen (The Netherlands) was used to calibrate the model. The inherent characteristics of AOM-SR make the identification of the kinetic parameters difficult due to the high correlation between them. However, by meaningfully selecting a set of kinetic parameters, the model simulates successfully the experimental data for sulfate reduction and sulfide production. The model can be considered as the basic structure for simulating continuous flow three-phase engineered systems based on AOM-SR.
Collapse
|
10
|
Rotaru AE, Yee MO, Musat F. Microbes trading electricity in consortia of environmental and biotechnological significance. Curr Opin Biotechnol 2021; 67:119-129. [PMID: 33540362 DOI: 10.1016/j.copbio.2021.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 02/08/2023]
Abstract
Favorable interspecies associations prevail in natural microbial assemblages. Some of these favorable associations are co-metabolic dependent partnerships in which extracellular electrons are exchanged between species. For such electron exchange to occur, the cells must exhibit electroactive interfaces and get involved in direct cell-to-cell contact (Direct Interspecies Electron Transfer/DIET) or use available conductive mineral grains from their environment (Conductive-particle-mediated Interspecies Electron Transfer/CIET). This review will highlight recent discoveries and knowledge gaps regarding DIET and CIET interspecies associations in artificial co-cultures and consortia from natural and man-made environments and emphasize approaches to validate DIET and CIET. Additionally, we acknowledge the initiation of a movement towards applying electric syntrophies in biotechnology, bioremediation and geoengineering for natural attenuation of toxic compounds. Next, we have highlighted the urgent research needs that must be met to develop such technologies.
Collapse
Affiliation(s)
| | - Mon Oo Yee
- Lawrence Berkley National Laboratories, Cyclotron Rd. 1, Berkeley, CA, United States
| | - Florin Musat
- Helmholtz Center for Environmental Research, Permoserstraße 15, Leipzig, Germany
| |
Collapse
|
11
|
Ruby E. Getting to know our microbial friends by dropping into their neighbourhood. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:27-30. [PMID: 33047473 DOI: 10.1111/1758-2229.12895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Edward Ruby
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| |
Collapse
|
12
|
Desmond-Le Quéméner E, Moscoviz R, Bernet N, Marcus A. Modeling of interspecies electron transfer in anaerobic microbial communities. Curr Opin Biotechnol 2021; 67:49-57. [PMID: 33465544 DOI: 10.1016/j.copbio.2020.12.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/19/2020] [Accepted: 12/23/2020] [Indexed: 12/14/2022]
Abstract
Interspecies electron transfer (IET) is a key phenomenon in anaerobic ecosystems, which is traditionally modeled as hydrogen transfer. Recently discovered alternative mediated IET (MIET) or direct IET (DIET) offer exciting alternative mechanisms of microbial partnerships that could lead to new strategies for the improvement of biotechnologies. Here, we analyze mathematical modeling of DIET and MIET in anaerobic ecosystems. Bioenergetics approaches already enable the evaluation of different energy sharing scenarios between microorganisms and give interesting clues on redox mediators and on possible ways of driving microbial communities relying on IET. The modeling of DIET kinetics however is currently only in its infancy. Recent concepts introduced for the modeling of electroactive biofilms should be further exploited. Recent modeling examples confirms the potential of DIET to increase the IET rates compared to H2-MIET, but also point out the need for additional characterizations of biological components supporting IET to improve predictions.
Collapse
Affiliation(s)
| | - Roman Moscoviz
- SUEZ, Centre International de Recherche Sur l'Eau et l'Environnement (CIRSEE), Le Pecq, France
| | - Nicolas Bernet
- INRAE, Univ Montpellier, LBE, 102 avenue des Etangs, 11100, Narbonne, France
| | - Andrew Marcus
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA
| |
Collapse
|
13
|
Short-range interactions govern the dynamics and functions of microbial communities. Nat Ecol Evol 2020; 4:366-375. [DOI: 10.1038/s41559-019-1080-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/02/2019] [Indexed: 11/08/2022]
|
14
|
Vavilin V, Lokshina L, Rytov S. Using kinetic isotope effect to evaluate the significance of the sequential and parallel steps: formation of microbial consortium during reversible anaerobic methane oxidation coupled with sulfate reduction. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 79:2056-2067. [PMID: 31318343 DOI: 10.2166/wst.2019.201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The purpose of this study was to describe the dynamics of anaerobic oxidation of methane (AOM) coupled with sulfate reduction (SR) using experimental data from a continuous incubation experiments published earlier in order to show that formation of consortia of anaerobic archaea (ANME) and Desulfosarcina-like bacteria (DSS) may have a significant effect on sulfur isotope fractionation. The dynamic simulation of reversible AOM by ANME coupled with SR by DSS was performed. This simulation took into account biomass growth and fractionation of stable isotopes of sulfur. Two kinetic schemes with and without ANME + DSS consortium formation were tested. The respective models were applied at five influent methane concentrations. A good fit to experimental data was obtained only when assuming active ANME and DSS biomass accumulation. The assumption about incorporation of reversibility of anaerobic methane oxidation and sulfate reduction did not improve the model's fit to experimental data. In accordance with both the models, sulfur isotope fractionation was smallest for the highest influent methane concentration. The model considering the formation of consortia of ANME + DSS is proved to be more appropriate.
Collapse
Affiliation(s)
- Vasily Vavilin
- Water Problems Institute, Russian Academy of Sciences, 3 Gubkina str., Moscow 119333, Russian Federation E-mail:
| | - Lyudmila Lokshina
- Water Problems Institute, Russian Academy of Sciences, 3 Gubkina str., Moscow 119333, Russian Federation E-mail:
| | - Sergey Rytov
- Water Problems Institute, Russian Academy of Sciences, 3 Gubkina str., Moscow 119333, Russian Federation E-mail:
| |
Collapse
|