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Löffler M, Schwab L, Dethlefsen F, Lagmöller L, Vogt C, Richnow HH. Anaerobic dihydrogen consumption of nutrient-limited aquifer sediment microbial communities examined by stable isotope analysis. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2024; 60:103-121. [PMID: 38344763 DOI: 10.1080/10256016.2024.2306146] [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: 03/27/2023] [Accepted: 12/21/2023] [Indexed: 03/20/2024]
Abstract
The biogeochemical consequences of dihydrogen (H2) underground storage in porous aquifers are poorly understood. Here, the effects of nutrient limitations on anaerobic H2 oxidation of an aquifer microbial community in sediment microcosms were determined in order to evaluate possible responses to high H2 partial pressures. Hydrogen isotope analyses of H2 yielded isotope depletion in all biotic setups indicating microbial H2 consumption. Carbon isotope analyses of carbon dioxide (CO2) showed isotope enrichment in all H2-supplemented biotic setups indicating H2-dependent consumption of CO2 by methanogens or homoacetogens. Homoacetogenesis was indicated by the detection of acetate and formate. Consumption of CO2 and H2 varied along the differently nutrient-amended setups, as did the onset of methane production. Plotting carbon against hydrogen isotope signatures of CH4 indicated that CH4 was produced hydrogenotrophically and fermentatively. The putative hydrogenotrophic Methanobacterium sp. was the dominant methanogen. Most abundant phylotypes belonged to typical ferric iron reducers, indicating that besides CO2, Fe(III) was an important electron acceptor. In summary, our study provides evidence for the adaptability of subsurface microbial communities under different nutrient-deficient conditions to elevated H2 partial pressures.
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Affiliation(s)
- Michaela Löffler
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Laura Schwab
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Frank Dethlefsen
- Department of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy (KGE), University of Kiel, Kiel, Germany
| | - Louisa Lagmöller
- Department of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy (KGE), University of Kiel, Kiel, Germany
| | - Carsten Vogt
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hans-Hermann Richnow
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Isodetect GmbH, Leipzig, Germany
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2
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Li Q, Ma Z, Huo J, Zhang X, Wang R, Zhang S, Jiao J, Dong X, Janssen PH, Ungerfeld EM, Greening C, Tan Z, Wang M. Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield. THE ISME JOURNAL 2024; 18:wrad016. [PMID: 38365243 PMCID: PMC10811737 DOI: 10.1093/ismejo/wrad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 02/18/2024]
Abstract
Ruminants are essential for global food security, but these are major sources of the greenhouse gas methane. Methane yield is controlled by the cycling of molecular hydrogen (H2), which is produced during carbohydrate fermentation and is consumed by methanogenic, acetogenic, and respiratory microorganisms. However, we lack a holistic understanding of the mediators and pathways of H2 metabolism and how this varies between ruminants with different methane-emitting phenotypes. Here, we used metagenomic, metatranscriptomic, metabolomics, and biochemical approaches to compare H2 cycling and reductant disposal pathways between low-methane-emitting Holstein and high-methane-emitting Jersey dairy cattle. The Holstein rumen microbiota had a greater capacity for reductant disposal via electron transfer for amino acid synthesis and propionate production, catalyzed by enzymes such as glutamate synthase and lactate dehydrogenase, and expressed uptake [NiFe]-hydrogenases to use H2 to support sulfate and nitrate respiration, leading to enhanced coupling of H2 cycling with less expelled methane. The Jersey rumen microbiome had a greater proportion of reductant disposal via H2 production catalyzed by fermentative hydrogenases encoded by Clostridia, with H2 mainly taken up through methanogenesis via methanogenic [NiFe]-hydrogenases and acetogenesis via [FeFe]-hydrogenases, resulting in enhanced methane and acetate production. Such enhancement of electron incorporation for metabolite synthesis with reduced methanogenesis was further supported by two in vitro measurements of microbiome activities, metabolites, and public global microbiome data of low- and high-methane-emitting beef cattle and sheep. Overall, this study highlights the importance of promoting alternative H2 consumption and reductant disposal pathways for synthesizing host-beneficial metabolites and reducing methane production in ruminants.
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Affiliation(s)
- Qiushuang Li
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyuan Ma
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Jiabin Huo
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Xiumin Zhang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Rong Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Shizhe Zhang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Jinzhen Jiao
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Peter H Janssen
- AgResearch Limited, Grasslands Research Centre, Palmerston North, Private Bag 11008, New Zealand
| | - Emilio M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias (INIA), Temuco, Vilcún 4880000, Chile
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Zhiliang Tan
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Lever MA, Alperin MJ, Hinrichs KU, Teske A. Zonation of the active methane-cycling community in deep subsurface sediments of the Peru trench. Front Microbiol 2023; 14:1192029. [PMID: 37250063 PMCID: PMC10213550 DOI: 10.3389/fmicb.2023.1192029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
The production and anaerobic oxidation of methane (AOM) by microorganisms is widespread in organic-rich deep subseafloor sediments. Yet, the organisms that carry out these processes remain largely unknown. Here we identify members of the methane-cycling microbial community in deep subsurface, hydrate-containing sediments of the Peru Trench by targeting functional genes of the alpha subunit of methyl coenzyme M reductase (mcrA). The mcrA profile reveals a distinct community zonation that partially matches the zonation of methane oxidizing and -producing activity inferred from sulfate and methane concentrations and carbon-isotopic compositions of methane and dissolved inorganic carbon (DIC). McrA appears absent from sulfate-rich sediments that are devoid of methane, but mcrA sequences belonging to putatively methane-oxidizing ANME-1a-b occur from the zone of methane oxidation to several meters into the methanogenesis zone. A sister group of ANME-1a-b, referred to as ANME-1d, and members of putatively aceticlastic Methanothrix (formerly Methanosaeta) occur throughout the remaining methanogenesis zone. Analyses of 16S rRNA and mcrA-mRNA indicate that the methane-cycling community is alive throughout (rRNA to 230 mbsf) and active in at least parts of the sediment column (mRNA at 44 mbsf). Carbon-isotopic depletions of methane relative to DIC (-80 to -86‰) suggest mostly methane production by CO2 reduction and thus seem at odds with the widespread detection of ANME-1 and Methanothrix. We explain this apparent contradiction based on recent insights into the metabolisms of both ANME-1 and Methanothricaceae, which indicate the potential for methanogenetic growth by CO2 reduction in both groups.
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Affiliation(s)
- Mark A. Lever
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, United States
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Marc J. Alperin
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Kawagucci S, Sakai S, Tasumi E, Hirai M, Takaki Y, Nunoura T, Saitoh M, Ueno Y, Yoshida N, Shibuya T, Clifford Sample J, Okumura T, Takai K. Deep Subseafloor Biogeochemical Processes and Microbial Populations Potentially Associated with the 2011 Tohoku-oki Earthquake at the Japan Trench Accretionary Wedge (IODP Expedition 343). Microbes Environ 2023; 38:n/a. [PMID: 37331792 DOI: 10.1264/jsme2.me22108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023] Open
Abstract
Post-mega-earthquake geochemical and microbiological properties in subseafloor sediments of the Japan Trench accretionary wedge were investigated using core samples from Hole C0019E, which was drilled down to 851 m below seafloor (mbsf) at a water depth of 6,890 m. Methane was abundant throughout accretionary prism sediments; however, its concentration decreased close to the plate boundary decollement. Methane isotope systematics indicated a biogenic origin. The content of mole-cular hydrogen (H2) was low throughout core samples, but markedly increased at specific depths that were close to potential faults predicted by logging-while-drilling ana-lyses. Based on isotopic systematics, H2 appeared to have been abundantly produced via a low-temperature interaction between pore water and the fresh surface of crushed rock induced by earthquakes. Subseafloor microbial cell density remained constant at approximately 105 cells mL-1. Amplicon sequences revealed that predominant members at the phylum level were common throughout the units tested, which also included members frequently found in anoxic subseafloor sediments. Metabolic potential assays using radioactive isotopes as tracers revealed homoacetogenic activity in H2-enriched core samples collected near the fault. Furthermore, homoacetogenic bacteria, including Acetobacterium carbinolicum, were isolated from similar samples. Therefore, post-earthquake subseafloor microbial communities in the Japan Trench accretionary prism appear to be episodically dominated by homoacetogenic populations and potentially function due to the earthquake-induced low-temperature generation of H2. These post-earthquake microbial communities may eventually return to the steady-state communities dominated by oligotrophic heterotrophs and hydrogenotrophic and methylotrophic methanogens that are dependent on refractory organic matter in the sediment.
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Affiliation(s)
- Shinsuke Kawagucci
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Sanae Sakai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Eiji Tasumi
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Yuichiro Ueno
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology
- Earth-Life Science Institute, Tokyo Institute of Technology
| | - Naohiro Yoshida
- Earth-Life Science Institute, Tokyo Institute of Technology
- National Institute of Information and Communications Technology
| | - Takazo Shibuya
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Tomoyo Okumura
- Center for Advanced Marine Core Research, Kochi University
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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5
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Chimeric inheritance and crown-group acquisitions of carbon fixation genes within Chlorobiales: Origins of autotrophy in Chlorobiales and implication for geological biomarkers. PLoS One 2022; 17:e0275539. [PMID: 36227849 PMCID: PMC9560492 DOI: 10.1371/journal.pone.0275539] [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] [Received: 03/21/2022] [Accepted: 09/16/2022] [Indexed: 11/21/2022] Open
Abstract
The geological record of microbial metabolisms and ecologies primarily consists of stable isotope fractionations and the diagenetic products of biogenic lipids. Carotenoid lipid biomarkers are particularly useful proxies for reconstructing this record, providing information on microbial phototroph primary productivity, redox couples, and oxygenation. The biomarkers okenane, chlorobactane, and isorenieratene are generally considered to be evidence of anoxygenic phototrophs, and provide a record that extends to 1.64 Ga. The utility of the carotenoid biomarker record may be enhanced by examining the carbon isotopic ratios in these products, which are diagnostic for specific pathways of biological carbon fixation found today within different microbial groups. However, this joint inference assumes that microbes have conserved these pathways across the duration of the preserved biomarker record. Testing this hypothesis, we performed phylogenetic analyses of the enzymes constituting the reductive tricarboxylic acid (rTCA) cycle in Chlorobiales, the group of anoxygenic phototrophic bacteria usually implicated in the deposition of chlorobactane and isorenieretane. We find phylogenetically incongruent patterns of inheritance across all enzymes, indicative of horizontal gene transfers to both stem and crown Chlorobiales from multiple potential donor lineages. This indicates that a complete rTCA cycle was independently acquired at least twice within Chlorobiales and was not present in the last common ancestor. When combined with recent molecular clock analyses, these results predict that the Mesoproterzoic lipid biomarker record diagnostic for Chlorobiales should not preserve isotopic fractionations indicative of a full rTCA cycle. Furthermore, we conclude that coupling isotopic and biomarker records is insufficient for reliably reconstructing microbial paleoecologies in the absence of a complementary and consistent phylogenomic narrative.
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6
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Natural Source Zone Depletion (NSZD) Quantification Techniques: Innovations and Future Directions. SUSTAINABILITY 2022. [DOI: 10.3390/su14127027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Natural source zone depletion (NSZD) is an emerging technique for sustainable and cost-effective bioremediation of light non-aqueous phase liquid (LNAPL) in oil spill sites. Depending on regulatory objectives, NSZD has the potential to be used as either the primary or sole LNAPL management technique. To achieve this goal, NSZD rate (i.e., rate of bulk LNAPL mass depletion) should be quantified accurately and precisely. NSZD has certain characteristic features that have been used as surrogates to quantify the NSZD rates. This review highlights the most recent trends in technology development for NSZD data collection and rate estimation, with a focus on the operational and technical advantages and limitations of the associated techniques. So far, four principal techniques are developed, including concentration gradient (CG), dynamic closed chamber (DCC), CO2 trap and thermal monitoring. Discussions revolving around two techniques, “CO2 trap” and “thermal monitoring”, are expanded due to the particular attention to them in the current industry. The gaps of knowledge relevant to the NSZD monitoring techniques are identified and the issues which merit further research are outlined. It is hoped that this review can provide researchers and practitioners with sufficient information to opt the best practice for the research and application of NSZD for the management of LNAPL impacted sites.
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7
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Garcia AK, Cavanaugh CM, Kacar B. The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution. THE ISME JOURNAL 2021; 15:2183-2194. [PMID: 33846565 PMCID: PMC8319343 DOI: 10.1038/s41396-021-00971-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/12/2021] [Accepted: 03/25/2021] [Indexed: 11/09/2022]
Abstract
The oldest and most wide-ranging signal of biological activity (biosignature) on our planet is the carbon isotope composition of organic materials preserved in rocks. These biosignatures preserve the long-term evolution of the microorganism-hosted metabolic machinery responsible for producing deviations in the isotopic compositions of inorganic and organic carbon. Despite billions of years of ecosystem turnover, evolutionary innovation, organismic complexification, and geological events, the organic carbon that is a residuum of the global marine biosphere in the rock record tells an essentially static story. The ~25‰ mean deviation between inorganic and organic 13C/12C values has remained remarkably unchanged over >3.5 billion years. The bulk of this record is conventionally attributed to early-evolved, RuBisCO-mediated CO2 fixation that, in extant oxygenic phototrophs, produces comparable isotopic effects and dominates modern primary production. However, billions of years of environmental transition, for example, in the progressive oxygenation of the Earth's atmosphere, would be expected to have accompanied shifts in the predominant RuBisCO forms as well as enzyme-level adaptive responses in RuBisCO CO2-specificity. These factors would also be expected to result in preserved isotopic signatures deviating from those produced by extant RuBisCO in oxygenic phototrophs. Why does the bulk carbon isotope record not reflect these expected environmental transitions and evolutionary innovations? Here, we discuss this apparent discrepancy and highlight the need for greater quantitative understanding of carbon isotope fractionation behavior in extant metabolic pathways. We propose novel, laboratory-based approaches to reconstructing ancestral states of carbon metabolisms and associated enzymes that can constrain isotopic biosignature production in ancient biological systems. Together, these strategies are crucial for integrating the complementary toolsets of biological and geological sciences and for interpretation of the oldest record of life on Earth.
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Affiliation(s)
- Amanda K Garcia
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Colleen M Cavanaugh
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Betul Kacar
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.
- Lunar and Planetary Laboratory and Steward Observatory, University of Arizona, Tucson, AZ, USA.
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8
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Kanaparthi D, Reim A, Martinson GO, Pommerenke B, Conrad R. Methane emission from feather moss stands. GLOBAL CHANGE BIOLOGY 2017; 23:4884-4895. [PMID: 28514080 DOI: 10.1111/gcb.13764] [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: 02/21/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
Data from remote sensing and Eddy towers indicate that forests are not always net sinks for atmospheric CH4 . However, studies describing specific sources within forests and functional analysis of microorganisms on sites with CH4 turnover are scarce. Feather moss stands were considered to be net sinks for carbon dioxide, but received little attention to their role in CH4 cycling. Therefore, we investigated methanogenic rates and pathways together with the methanogenic microbial community composition in feather moss stands from temperate and boreal forests. Potential rates of CH4 emission from intact moss stands (n = 60) under aerobic conditions ranged between 19 and 133 pmol CH4 h-1 gdw-1 . Temperature and water content positively influenced CH4 emission. Methanogenic potentials determined under N2 atmosphere in darkness ranged between 22 and 157 pmol CH4 h-1 gdw-1 . Methane production was strongly inhibited by bromoethane sulfonate or chloroform, showing that CH4 was of microbial origin. The moss samples tested contained fluorescent microbial cells and between 104 and 105 copies per gram dry weight moss of the mcrA gene coding for a subunit of the methyl CoM reductase. Archaeal 16S rRNA and mcrA gene sequences in the moss stands were characteristic for the archaeal families Methanobacteriaceae and Methanosarcinaceae. The potential methanogenic rates were similar in incubations with and without methyl fluoride, indicating that the CH4 was produced by the hydrogenotrophic rather than aceticlastic pathway. Consistently, the CH4 produced was depleted in 13 C in comparison with the moss biomass carbon and acetate accumulated to rather high concentrations (3-62 mM). The δ13 C of acetate was similar to that of the moss biomass, indicating acetate production by fermentation. Our study showed that the feather moss stands contained active methanogenic microbial communities producing CH4 by hydrogenotrophic methanogenesis and causing net emission of CH4 under ambient conditions, albeit at low rates.
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Affiliation(s)
- Dheeraj Kanaparthi
- Department of Biogeochemistry, Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
| | - Andreas Reim
- Department of Biogeochemistry, Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
| | - Guntars O Martinson
- Department of Biogeochemistry, Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
| | - Bianca Pommerenke
- Department of Biogeochemistry, Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
| | - Ralf Conrad
- Department of Biogeochemistry, Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
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Freude C, Blaser M. Carbon Isotope Fractionation during Catabolism and Anabolism in Acetogenic Bacteria Growing on Different Substrates. Appl Environ Microbiol 2016; 82:2728-2737. [PMID: 26921422 PMCID: PMC4836411 DOI: 10.1128/aem.03502-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/21/2016] [Indexed: 11/20/2022] Open
Abstract
Homoacetogenic bacteria are versatile microbes that use the acetyl coenzyme A (acetyl-CoA) pathway to synthesize acetate from CO2 and hydrogen. Likewise, the acetyl-CoA pathway may be used to incorporate other 1-carbon substrates (e.g., methanol or formate) into acetate or to homoferment monosaccharides completely to acetate. In this study, we analyzed the fractionation of pure acetogenic cultures grown on different carbon substrates. While the fractionation of Sporomusa sphaeroides grown on C1 compounds was strong (εC1, -49‰ to -64‰), the fractionation of Moorella thermoacetica and Thermoanaerobacter kivui using glucose (εGlu= -14.1‰) was roughly one-third as strong, suggesting a contribution of less-depleted acetate from fermentative processes. ForM. thermoacetica, this could indeed be validated by the addition of nitrate, which inhibited the acetyl-CoA pathway, resulting in fractionation during fermentation (εferm= -0.4‰). In addition, we determined the fractionation into microbial biomass of T. kivui grown on H2/CO2(εanabol.= -28.6‰) as well as on glucose (εanabol.= +2.9‰).
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Affiliation(s)
- Christoph Freude
- Department of Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Martin Blaser
- Department of Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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10
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Mach V, Blaser MB, Claus P, Chaudhary PP, Rulík M. Methane production potentials, pathways, and communities of methanogens in vertical sediment profiles of river Sitka. Front Microbiol 2015; 6:506. [PMID: 26052322 PMCID: PMC4440369 DOI: 10.3389/fmicb.2015.00506] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/07/2015] [Indexed: 11/13/2022] Open
Abstract
Biological methanogenesis is linked to permanent water logged systems, e.g., rice field soils or lake sediments. In these systems the methanogenic community as well as the pathway of methane formation are well-described. By contrast, the methanogenic potential of river sediments is so far not well-investigated. Therefore, we analyzed (a) the methanogenic potential (incubation experiments), (b) the pathway of methane production (stable carbon isotopes and inhibitor studies), and (c) the methanogenic community composition (terminal restriction length polymorphism of mcrA) in depth profiles of sediment cores of River Sitka, Czech Republic. We found two depth-related distinct maxima for the methanogenic potentials (a) The pathway of methane production was dominated by hydrogenotrophic methanogenesis (b) The methanogenic community composition was similar in all depth layers (c) The main TRFs were representative for Methanosarcina, Methanosaeta, Methanobacterium, and Methanomicrobium species. The isotopic signals of acetate indicated a relative high contribution of chemolithotrophic acetogenesis to the acetate pool.
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Affiliation(s)
- Václav Mach
- Department of Ecology and Environmental Science, Faculty of Science, Palacky University Olomouc, Czech Republic
| | - Martin B Blaser
- Department of Ecology and Environmental Science, Faculty of Science, Palacky University Olomouc, Czech Republic
| | - Peter Claus
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Prem P Chaudhary
- Department of Ecology and Environmental Science, Faculty of Science, Palacky University Olomouc, Czech Republic
| | - Martin Rulík
- Department of Ecology and Environmental Science, Faculty of Science, Palacky University Olomouc, Czech Republic
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11
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Beulig F, Heuer VB, Akob DM, Viehweger B, Elvert M, Herrmann M, Hinrichs KU, Küsel K. Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette. ISME JOURNAL 2014; 9:746-59. [PMID: 25216086 DOI: 10.1038/ismej.2014.148] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 12/13/2022]
Abstract
Effects of extremely high carbon dioxide (CO2) concentrations on soil microbial communities and associated processes are largely unknown. We studied a wetland area affected by spots of subcrustal CO2 degassing (mofettes) with focus on anaerobic autotrophic methanogenesis and acetogenesis because the pore gas phase was largely hypoxic. Compared with a reference soil, the mofette was more acidic (ΔpH ∼0.8), strongly enriched in organic carbon (up to 10 times), and exhibited lower prokaryotic diversity. It was dominated by methanogens and subdivision 1 Acidobacteria, which likely thrived under stable hypoxia and acidic pH. Anoxic incubations revealed enhanced formation of acetate and methane (CH4) from hydrogen (H2) and CO2 consistent with elevated CH4 and acetate levels in the mofette soil. (13)CO2 mofette soil incubations showed high label incorporations with ∼512 ng (13)C g (dry weight (dw)) soil(-1) d(-1) into the bulk soil and up to 10.7 ng (13)C g (dw) soil(-1) d(-1) into almost all analyzed bacterial lipids. Incorporation of CO2-derived carbon into archaeal lipids was much lower and restricted to the first 10 cm of the soil. DNA-SIP analysis revealed that acidophilic methanogens affiliated with Methanoregulaceae and hitherto unknown acetogens appeared to be involved in the chemolithoautotrophic utilization of (13)CO2. Subdivision 1 Acidobacteriaceae assimilated (13)CO2 likely via anaplerotic reactions because Acidobacteriaceae are not known to harbor enzymatic pathways for autotrophic CO2 assimilation. We conclude that CO2-induced geochemical changes promoted anaerobic and acidophilic organisms and altered carbon turnover in affected soils.
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Affiliation(s)
- Felix Beulig
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Verena B Heuer
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Denise M Akob
- 1] Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany [2] U.S. Geological Survey, Reston, VA, USA
| | - Bernhard Viehweger
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Martina Herrmann
- 1] Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany [2] German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, Dept. of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kirsten Küsel
- 1] Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany [2] German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, Germany
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Blaser MB, Dreisbach LK, Conrad R. Carbon isotope fractionation of 11 acetogenic strains grown on H2 and CO2. Appl Environ Microbiol 2013; 79:1787-94. [PMID: 23275504 PMCID: PMC3592252 DOI: 10.1128/aem.03203-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 12/22/2012] [Indexed: 11/20/2022] Open
Abstract
Acetogenic bacteria are able to grow autotrophically on hydrogen and carbon dioxide by using the acetyl coenzyme A (acetyl-CoA) pathway. Acetate is the end product of this reaction. In contrast to the fermentative route of acetate production, which shows almost no fractionation of carbon isotopes, the acetyl-CoA pathway has been reported to exhibit a preference for light carbon. In Acetobacterium woodii the isotope fractionation factor (ε) for (13)C and (12)C has previously been reported to be ε = -58.6‰. To investigate whether such a strong fractionation is a general feature of acetogenic bacteria, we measured the stable carbon isotope fractionation factor of 10 acetogenic strains grown on H(2) and CO(2). The average fractionation factor was ε(TIC) = -57.2‰ for utilization of total inorganic carbon and ε(acetate) = -54.6‰ for the production of acetate. The strongest fractionation was found for Sporomusa sphaeroides (ε(TIC) = -68.3‰), the lowest fractionation for Morella thermoacetica (ε(TIC) = -38.2‰). To investigate the reproducibility of our measurements, we determined the fractionation factor of 21 biological replicates of Thermoanaerobacter kivui. In general, our study confirmed the strong fractionation of stable carbon during chemolithotrophic acetate formation in acetogenic bacteria. However, the specific characteristics of the bacterial strain, as well as the cultural conditions, may have a moderate influence on the overall fractionation.
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Affiliation(s)
- Martin B Blaser
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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13
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Daebeler A, Gansen M, Frenzel P. Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil. PLoS One 2013; 8:e53656. [PMID: 23341965 PMCID: PMC3544908 DOI: 10.1371/journal.pone.0053656] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 12/04/2012] [Indexed: 11/19/2022] Open
Abstract
The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH3F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH3F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH3F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH3F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH3F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens.
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Affiliation(s)
- Anne Daebeler
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Martina Gansen
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Peter Frenzel
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- * E-mail:
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14
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Hädrich A, Heuer VB, Herrmann M, Hinrichs KU, Küsel K. Origin and fate of acetate in an acidic fen. FEMS Microbiol Ecol 2012; 81:339-54. [DOI: 10.1111/j.1574-6941.2012.01352.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 02/16/2012] [Accepted: 02/26/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Anke Hädrich
- Aquatic Geomicrobiology Group; Institute of Ecology; Friedrich Schiller University Jena; Jena; Germany
| | - Verena B. Heuer
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; Bremen; Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology Group; Institute of Ecology; Friedrich Schiller University Jena; Jena; Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; Bremen; Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology Group; Institute of Ecology; Friedrich Schiller University Jena; Jena; Germany
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15
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Pasche N, Schmid M, Vazquez F, Schubert CJ, Wüest A, Kessler JD, Pack MA, Reeburgh WS, Bürgmann H. Methane sources and sinks in Lake Kivu. ACTA ACUST UNITED AC 2011. [DOI: 10.1029/2011jg001690] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Freitas JG, Fletcher B, Aravena R, Barker JF. Methane production and isotopic fingerprinting in ethanol fuel contaminated sites. GROUND WATER 2010; 48:844-857. [PMID: 20070380 DOI: 10.1111/j.1745-6584.2009.00665.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Biodegradation of organic compounds in groundwater can be a significant source of methane in contaminated sites. Methane might accumulate in indoor spaces posing a hazard. The increasing use of ethanol as a gasoline additive is a concern with respect to methane production since it is easily biodegraded and has a high oxygen demand, favoring the development of anaerobic conditions. This study evaluated the use of stable carbon isotopes to distinguish the methane origin between gasoline and ethanol biodegradation, and assessed the occurrence of methane in ethanol fuel contaminated sites. Two microcosm tests were performed under anaerobic conditions: one test using ethanol and the other using toluene as the sole carbon source. The isotopic tool was then applied to seven field sites known to be impacted by ethanol fuels. In the microcosm tests, it was verified that methane from ethanol (δ¹³C = -11.1‰) is more enriched in ¹³C, with δ¹³C values ranging from -20‰ to -30‰, while the methane from toluene (δ¹³C = -28.5‰) had a carbon isotopic signature of -55‰. The field samples had δ¹³C values varying over a wide range (-10‰ to -80‰), and the δ¹³C values allowed the methane source to be clearly identified in five of the seven ethanol/gasoline sites. In the other two sites, methane appears to have been produced from both sources. Both gasoline and ethanol were sources of methane in potentially hazardous concentrations and methane could be produced from organic acids originating from ethanol along the groundwater flow system even after all the ethanol has been completed biodegraded.
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Affiliation(s)
- Juliana G Freitas
- Department of Earth and Environmental Sciences, University of Waterloo, 200 University Ave. W., Waterloo, Ontario, Canada N2L 3G1.
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Valentine DL, Kessler JD, Redmond MC, Mendes SD, Heintz MB, Farwell C, Hu L, Kinnaman FS, Yvon-Lewis S, Du M, Chan EW, Garcia Tigreros F, Villanueva CJ. Propane respiration jump-starts microbial response to a deep oil spill. Science 2010; 330:208-11. [PMID: 20847236 DOI: 10.1126/science.1196830] [Citation(s) in RCA: 206] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The Deepwater Horizon event resulted in suspension of oil in the Gulf of Mexico water column because the leakage occurred at great depth. The distribution and fate of other abundant hydrocarbon constituents, such as natural gases, are also important in determining the impact of the leakage but are not yet well understood. From 11 to 21 June 2010, we investigated dissolved hydrocarbon gases at depth using chemical and isotopic surveys and on-site biodegradation studies. Propane and ethane were the primary drivers of microbial respiration, accounting for up to 70% of the observed oxygen depletion in fresh plumes. Propane and ethane trapped in the deep water may therefore promote rapid hydrocarbon respiration by low-diversity bacterial blooms, priming bacterial populations for degradation of other hydrocarbons in the aging plume.
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Affiliation(s)
- David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
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18
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Kelley CA, Prufert-Bebout LE, Bebout BM. Changes in carbon cycling ascertained by stable isotopic analyses in a hypersaline microbial mat. ACTA ACUST UNITED AC 2006. [DOI: 10.1029/2006jg000212] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cheryl A. Kelley
- Department of Geological Sciences; University of Missouri-Columbia; Columbia Missouri USA
| | | | - Brad M. Bebout
- Exobiology Branch; NASA Ames Research Center; Moffett Field California USA
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19
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Eigenbrode JL, Freeman KH. Late Archean rise of aerobic microbial ecosystems. Proc Natl Acad Sci U S A 2006; 103:15759-64. [PMID: 17043234 PMCID: PMC1635076 DOI: 10.1073/pnas.0607540103] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Indexed: 11/18/2022] Open
Abstract
We report the (13)C content of preserved organic carbon for a 150 million-year section of late Archean shallow and deepwater sediments of the Hamersley Province in Western Australia. We find a (13)C enrichment of approximately 10 per thousand in organic carbon of post-2.7-billion-year-old shallow-water carbonate rocks relative to deepwater sediments. The shallow-water organic-carbon (13)C content has a 29 per thousand range in values (-57 to -28 per thousand), and it contrasts with the less variable but strongly (13)C-depleted (-40 to -45 per thousand) organic carbon in deepwater sediments. The (13)C enrichment likely represents microbial habitats not as strongly influenced by assimilation of methane or other (13)C-depleted substrates. We propose that continued oxidation of shallow settings favored the expansion of aerobic ecosystems and respiring organisms, and, as a result, isotopic signatures of preserved organic carbon in shallow settings approached that of photosynthetic biomass. Facies analysis of published carbon-isotopic records indicates that the Hamersley shallow-water signal may be representative of a late Archean global signature and that it preceded a similar, but delayed, (13)C enrichment of deepwater deposits. The data suggest that a global-scale expansion of oxygenated habitats accompanied the progression away from anaerobic ecosystems toward respiring microbial communities fueled by oxygenic photosynthesis before the oxygenation of the atmosphere after 2.45 billion years ago.
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Affiliation(s)
- Jennifer L Eigenbrode
- Department of Geosciences and Penn State Astrobiology Research Center, Pennsylvania State University, University Park, PA 16802, USA.
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20
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Hinrichs KU, Hayes JM, Bach W, Spivack AJ, Hmelo LR, Holm NG, Johnson CG, Sylva SP. Biological formation of ethane and propane in the deep marine subsurface. Proc Natl Acad Sci U S A 2006; 103:14684-9. [PMID: 16990430 PMCID: PMC1595412 DOI: 10.1073/pnas.0606535103] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Concentrations and isotopic compositions of ethane and propane in cold, deeply buried sediments from the southeastern Pacific are best explained by microbial production of these gases in situ. Reduction of acetate to ethane provides one feasible mechanism. Propane is enriched in (13)C relative to ethane. The amount is consistent with derivation of the third C from inorganic carbon dissolved in sedimentary pore waters. At typical sedimentary conditions, the reactions yield free energy sufficient for growth. Relationships with competing processes are governed mainly by the abundance of H(2). Production of C(2) and C(3) hydrocarbons in this way provides a sink for acetate and hydrogen but upsets the general belief that hydrocarbons larger than methane derive only from thermal degradation of fossil organic material.
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Affiliation(s)
- Kai-Uwe Hinrichs
- Deutsche Forschungsgemeinschaft–Research Center Ocean Margins, Department of Geosciences, University of Bremen, P.O. Box 330440, 28334 Bremen, Germany
- Departments of Geology and Geophysics and
| | | | - Wolfgang Bach
- Deutsche Forschungsgemeinschaft–Research Center Ocean Margins, Department of Geosciences, University of Bremen, P.O. Box 330440, 28334 Bremen, Germany
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institute, Woods Hole, MA 02543
| | - Arthur J. Spivack
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882; and
| | - Laura R. Hmelo
- Deutsche Forschungsgemeinschaft–Research Center Ocean Margins, Department of Geosciences, University of Bremen, P.O. Box 330440, 28334 Bremen, Germany
- Departments of Geology and Geophysics and
| | - Nils G. Holm
- Department of Geology and Geochemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Carl G. Johnson
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institute, Woods Hole, MA 02543
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21
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Cavalier-Smith T. Cell evolution and Earth history: stasis and revolution. Philos Trans R Soc Lond B Biol Sci 2006; 361:969-1006. [PMID: 16754610 PMCID: PMC1578732 DOI: 10.1098/rstb.2006.1842] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This synthesis has three main parts. The first discusses the overall tree of life and nature of the last common ancestor (cenancestor). I emphasize key steps in cellular evolution important for ordering and timing the major evolutionary innovations in the history of the biosphere, explaining especially the origins of the eukaryote cell and of bacterial flagella and cell envelope novelties. Second, I map the tree onto the fossil record and discuss dates of key events and their biogeochemical impact. Finally, I present a broad synthesis, discussing evidence for a three-phase history of life. The first phase began perhaps ca 3.5 Gyr ago, when the origin of cells and anoxic photosynthesis generated the arguably most primitive prokaryote phylum, Chlorobacteria (= Chloroflexi), the first negibacteria with cells bounded by two acyl ester phospholipid membranes. After this 'chlorobacterial age' of benthic anaerobic evolution protected from UV radiation by mineral grains, two momentous quantum evolutionary episodes of cellular innovation and microbial radiation dramatically transformed the Earth's surface: the glycobacterial revolution initiated an oxygenic 'age of cyanobacteria' and, as the ozone layer grew, the rise of plankton; immensely later, probably as recently as ca 0.9 Gyr ago, the neomuran revolution ushered in the 'age of eukaryotes', Archaebacteria (arguably the youngest bacterial phylum), and morphological complexity. Diversification of glycobacteria ca 2.8 Gyr ago, predominantly inhabiting stratified benthic mats, I suggest caused serial depletion of 13C by ribulose 1,5-bis-phosphate caboxylase/oxygenase (Rubisco) to yield ultralight late Archaean organic carbon formerly attributed to methanogenesis plus methanotrophy. The late origin of archaebacterial methanogenesis ca 720 Myr ago perhaps triggered snowball Earth episodes by slight global warming increasing weathering and reducing CO2 levels, to yield runaway cooling; the origin of anaerobic methane oxidation ca 570 Myr ago reduced methane flux at source, stabilizing Phanerozoic climates. I argue that the major cellular innovations exhibit a pattern of quantum evolution followed by very rapid radiation and then substantial stasis, as described by Simpson. They yielded organisms that are a mosaic of extremely conservative and radically novel features, as characterized by De Beer's phrase 'mosaic evolution'. Evolution is not evenly paced and there are no real molecular clocks.
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22
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Eller G, Deines P, Grey J, Richnow HH, Krüger M. Methane cycling in lake sediments and its influence on chironomid larval delta13C. FEMS Microbiol Ecol 2006; 54:339-50. [PMID: 16332332 DOI: 10.1016/j.femsec.2005.04.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Revised: 04/19/2005] [Accepted: 04/20/2005] [Indexed: 11/29/2022] Open
Abstract
Stable carbon isotope analysis of chironomid larvae gave rise to the hypothesis that methane-oxidizing bacteria can provide an important food source for higher trophic levels in lakes. To investigate the importance of the methane cycle for the larval stable carbon signatures, isotope analysis and microbiological and biogeochemical investigations were combined. The study was based on comparison of a dimictic lake (Holzsee) and a polymictic, shallow lake (Grosser Binnensee), both located in northern Germany. Both lakes are inhabited by Chironomus plumosus larvae, which exhibited a stronger (13)C-depletion in Holzsee than in Grosser Binnensee, indicating a greater contribution of methane-carbon in the former. Indeed, the processes involved in the microbial methane cycle were found to be more active in Holzsee, showing higher potential methane production and methane oxidation rates. Consistently, cell numbers of methane-oxidizing bacteria were with 0.5 - 1.7 x 10(6) cells g(dw)(-1) about one order of magnitude higher in Holzsee than in Grosser Binnensee. Molecular analysis of the microbial community structure revealed no differences in the methanotrophic community between the two lakes, with a clear dominance of type I methanotrophs. The methanogenic population seemed to be adapted to the prevailing substrate in the respective lake (H(2)/CO(2) in Holzsee and acetate in Grosser Binnensee), even though differences were minor. In conclusion, the stronger larval (13)C-depletion in Holzsee was not reflected in differences in the microbial community structure, but in the activity and size of the methanogenic and methanotrophic populations in the lake sediment.
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Affiliation(s)
- Gundula Eller
- Max Planck Institute for Limnology, August-Thienemann-Strasse 2, 24306 Plön, Germany.
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23
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Londry KL, Des Marais DJ. Stable carbon isotope fractionation by sulfate-reducing bacteria. Appl Environ Microbiol 2003; 69:2942-9. [PMID: 12732570 PMCID: PMC154509 DOI: 10.1128/aem.69.5.2942-2949.2003] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biogeochemical transformations occurring in the anoxic zones of stratified sedimentary microbial communities can profoundly influence the isotopic and organic signatures preserved in the fossil record. Accordingly, we have determined carbon isotope discrimination that is associated with both heterotrophic and lithotrophic growth of pure cultures of sulfate-reducing bacteria (SRB). For heterotrophic-growth experiments, substrate consumption was monitored to completion. Sealed vessels containing SRB cultures were harvested at different time intervals, and delta(13)C values were determined for gaseous CO(2), organic substrates, and products such as biomass. For three of the four SRB, carbon isotope effects between the substrates, acetate or lactate and CO(2), and the cell biomass were small, ranging from 0 to 2 per thousand. However, for Desulfotomaculum acetoxidans, the carbon incorporated into biomass was isotopically heavier than the available substrates by 8 to 9 per thousand. SRB grown lithoautotrophically consumed less than 3% of the available CO(2) and exhibited substantial discrimination (calculated as isotope fractionation factors [alpha]), as follows: for Desulfobacterium autotrophicum, alpha values ranged from 1.0100 to 1.0123; for Desulfobacter hydrogenophilus, the alpha value was 0.0138, and for Desulfotomaculum acetoxidans, the alpha value was 1.0310. Mixotrophic growth of Desulfovibrio desulfuricans on acetate and CO(2) resulted in biomass with a delta(13)C composition intermediate to that of the substrates. The extent of fractionation depended on which enzymatic pathways were used, the direction in which the pathways operated, and the growth rate, but fractionation was not dependent on the growth phase. To the extent that environmental conditions affect the availability of organic substrates (e.g., acetate) and reducing power (e.g., H(2)), ecological forces can also influence carbon isotope discrimination by SRB.
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Affiliation(s)
- Kathleen L Londry
- Exobiology Branch, NASA Ames Research Center, Moffett Field, California, USA.
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24
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Conrad R, Klose M, Claus P. Pathway of CH4 formation in anoxic rice field soil and rice roots determined by 13C-stable isotope fractionation. CHEMOSPHERE 2002; 47:797-806. [PMID: 12079075 DOI: 10.1016/s0045-6535(02)00120-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In anoxic rice fields methane is produced by either reduction of CO2 or cleavage of acetate. We measured the delta 13C-values of CH4 and CO2, acetate and organic carbon during time course experiments with anoxic methanogenic soil and root samples and used these values to calculate the fractions of CH4 (and acetate) produced from CO2 reduction. Comparison with radiotracer and/or inhibitor studies constrained the kinetic fractionation factors used for calculation. The fractionation factors for the conversion of CO2 to CH4 and of acetate to CH4 were on the order of alpha = 1.07 (epsilon = -70%) and epsilon > or = - 20%, respectively. The pathway of CH4 production changed with time of anoxic incubation. Anoxic slurries of rice field soil first produced CH4 predominantly (>50%) from CO2, then predominantly (>80%) from acetate and finally (after about one month) according to the theoretically expected ratio (33% CO2 and 67% acetate). Anoxic rice roots, on the other hand, initially produced CH4 exclusively from CO2, followed by contribution of acetate of about 40-60%. Rice roots also produced acetate that partially originated (< or = 1 30%) from reduction of CO2 as determined by calculation of isotopic fractionation using fractionation factors from the literature. The results demonstrate that there is quite some variability in pathways of CH4 production, and also indicate that isotopic fractionation factors may be different in different habitats and change with time.
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Affiliation(s)
- Ralf Conrad
- Biogeochemistry Department, Max-Planck-Institut für Terrestrische Mikrobiologie, Marburg, Lahn, Germany.
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26
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Hornibrook ER, Longstaffe FJ, Fyfe WS. Factors influencing stable isotope ratios in CH4 and CO2 within subenvironments of freshwater wetlands: implications for delta-signatures of emissions. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2000; 36:151-176. [PMID: 11077929 DOI: 10.1080/10256010008032940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Much uncertainty still exists regarding spatial and temporal variability of stable isotope ratios (13C/12C and D/H) in different CH4-emission sources. Such variability is especially prevalent in freshwater wetlands where a range of processes can influence stable isotope compositions, resulting in variations of up to approximately 50% for delta13C-CH4 and approximately 50% for deltaD-CH4 values. Within a temperate-zone bog and marsh situated in southwestern Ontario, Canada, gas bubbles in pond sediments exhibit only minor seasonal and spatial variation in delta13C-CH4, deltaD-CH4 and delta13C-CO2 values. In pond sediments, CO2 appears to be the main source of carbon during methanogenesis either directly via CO2 reduction or indirectly through dissimilation of autotrophic acetate. In contrast, CH4 production occurs primarily via acetate fermentation at shallow depths in peat soils adjacent to ponds at each wetland. At greater depths within soils, sigmaCO2 and H2O increasingly exert an influence on delta13C- and deltaD-CH4 values. Secondary alteration processes (e.g., methanotrophy or diffusive transport) are unlikely to be responsible for depth-related changes in stable isotope values of CH4. Recent models that attempt to predict deltaD-CH4 values in freshwater environments from D/H ratios in local precipitation do not adequately account for such changes with depth. Subenvironments (i.e., soil-forming and open water areas) in wetlands should be considered separately with respect to stable isotope signatures in CH4 emission models.
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Affiliation(s)
- E R Hornibrook
- Department of Earth Sciences, The University of Western Ontario, London, Ontario, Canada.
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Gelwicks JT, Risatti JB, Hayes JM. Carbon isotope effects associated with aceticlastic methanogenesis. Appl Environ Microbiol 1994; 60:467-72. [PMID: 11536629 PMCID: PMC201335 DOI: 10.1128/aem.60.2.467-472.1994] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The carbon isotope effects associated with synthesis of methane from acetate have been determined for Methanosarcina barkeri 227 and for methanogenic archaea in sediments of Wintergreen Lake, Michigan. At 37 degrees C, the 13C isotope effect for the reaction acetate (methyl carbon) --> methane, as measured in replicate experiments with M. barkeri, was - 21.3% +/- 0.3%. The isotope effect at the carboxyl portion of acetate was essentially equal, indicating participation of both positions in the rate-determining step, as expected for reactions catalyzed by carbon monoxide dehydrogenase. A similar isotope effect, - 19.2% +/- 0.3% was found for this reaction in the natural community (temperature = 20 degrees C). Given these observations, it has been possible to model the flow of carbon to methane within lake sediment communities and to account for carbon isotope compositions of evolving methane. Extension of the model allows interpretation of seasonal fluctuations in 13C contents of methane in other systems.
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Affiliation(s)
- J T Gelwicks
- Departments of Chemistry and Geological Sciences, Indiana University, Bloomington 47405, USA
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