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Roland FAE, Borges AV, Bouillon S, Morana C. Nitrate-dependent anaerobic methane oxidation and chemolithotrophic denitrification in a temperate eutrophic lake. FEMS Microbiol Ecol 2021; 97:6360975. [PMID: 34468740 DOI: 10.1093/femsec/fiab124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/30/2021] [Indexed: 11/12/2022] Open
Abstract
While the emissions of methane (CH4) by natural systems have been widely investigated, CH4 aquatic sinks are still poorly constrained. Here, we investigated the CH4 cycle and its interactions with nitrogen (N), iron (Fe) and manganese (Mn) cycles in the oxic-anoxic interface and deep anoxic waters of a small, meromictic and eutrophic lake, during two summertime sampling campaigns. Anaerobic CH4 oxidation (AOM) was measured from the temporal decrease of CH4 concentrations, with the addition of three potential electron acceptors (NO3-, iron oxides (Fe(OH)3) and manganese oxides (MnO2)). Experiments with the addition of either 15N-labeled nitrate (15N-NO3-) or 15N-NO3- combined with sulfide (H2S), to measure denitrification, chemolithotrophic denitrification and anaerobic ammonium oxidation (anammox) rates, were also performed. Measurements showed AOM rates up to 3.8 µmol CH4 L-1 d-1 that strongly increased with the addition of NO3- and moderately increased with the addition of Fe(OH)3. No stimulation was observed with MnO2 added. Potential denitrification and anammox rates up to 63 and 0.27 µmol N2 L-1 d-1, respectively, were measured when only 15N-NO3- was added. When H2S was added, both denitrification and anammox rates increased. Altogether, these results suggest that prokaryote communities in the redoxcline are able to efficiently use the most available substrates.
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Affiliation(s)
- Fleur A E Roland
- Chemical Oceanography Unit, Université de Liège, 4000 Liège, Belgium
| | - Alberto V Borges
- Chemical Oceanography Unit, Université de Liège, 4000 Liège, Belgium
| | - Steven Bouillon
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven (KU Leuven), 3001 Leuven, Belgium
| | - Cédric Morana
- Chemical Oceanography Unit, Université de Liège, 4000 Liège, Belgium
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Wallenius AJ, Dalcin Martins P, Slomp CP, Jetten MSM. Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments. Front Microbiol 2021; 12:631621. [PMID: 33679659 PMCID: PMC7935538 DOI: 10.3389/fmicb.2021.631621] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/29/2021] [Indexed: 12/05/2022] Open
Abstract
Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.
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Affiliation(s)
- Anna J. Wallenius
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Paula Dalcin Martins
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Caroline P. Slomp
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
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Szeinbaum N, Nunn BL, Cavazos AR, Crowe SA, Stewart FJ, DiChristina TJ, Reinhard CT, Glass JB. Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn(III) reduction. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:583-593. [PMID: 32613749 PMCID: PMC7775658 DOI: 10.1111/1758-2229.12867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 05/23/2023]
Abstract
Soluble ligand-bound Mn(III) can support anaerobic microbial respiration in diverse aquatic environments. Thus far, Mn(III) reduction has only been associated with certain Gammaproteobacteria. Here, we characterized microbial communities enriched from Mn-replete sediments of Lake Matano, Indonesia. Our results provide the first evidence for the biological reduction of soluble Mn(III) outside the Gammaproteobacteria. Metagenome assembly and binning revealed a novel betaproteobacterium, which we designate 'Candidatus Dechloromonas occultata.' This organism dominated the enrichment and expressed a porin-cytochrome c complex typically associated with iron-oxidizing Betaproteobacteria and a novel cytochrome c-rich protein cluster (Occ), including an undecaheme putatively involved in extracellular electron transfer. This occ gene cluster was also detected in diverse aquatic bacteria, including uncultivated Betaproteobacteria from the deep subsurface. These observations provide new insight into the taxonomic and functional diversity of microbially driven Mn(III) reduction in natural environments.
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Affiliation(s)
- Nadia Szeinbaum
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- NASA Astrobiology Institute, Alternative Earths Team, Mountain View, CA, USA
| | - Brook L. Nunn
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Amanda R. Cavazos
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sean A. Crowe
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Christopher T. Reinhard
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- NASA Astrobiology Institute, Alternative Earths Team, Mountain View, CA, USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- NASA Astrobiology Institute, Alternative Earths Team, Mountain View, CA, USA
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Lambrecht N, Katsev S, Wittkop C, Hall SJ, Sheik CS, Picard A, Fakhraee M, Swanner ED. Biogeochemical and physical controls on methane fluxes from two ferruginous meromictic lakes. GEOBIOLOGY 2020; 18:54-69. [PMID: 31592570 DOI: 10.1111/gbi.12365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/20/2019] [Accepted: 08/31/2019] [Indexed: 05/28/2023]
Abstract
Meromictic lakes with anoxic bottom waters often have active methane cycles whereby methane is generally produced biogenically under anoxic conditions and oxidized in oxic surface waters prior to reaching the atmosphere. Lakes that contain dissolved ferrous iron in their deep waters (i.e., ferruginous) are rare, but valuable, as geochemical analogues of the conditions that dominated the Earth's oceans during the Precambrian when interactions between the iron and methane cycles could have shaped the greenhouse regulation of the planet's climate. Here, we explored controls on the methane fluxes from Brownie Lake and Canyon Lake, two ferruginous meromictic lakes that contain similar concentrations (max. >1 mM) of dissolved methane in their bottom waters. The order Methanobacteriales was the dominant methanogen detected in both lakes. At Brownie Lake, methanogen abundance, an increase in methane concentration with respect to depths closer to the sediment, and isotopic data suggest methanogenesis is an active process in the anoxic water column. At Canyon Lake, methanogenesis occurred primarily in the sediment. The most abundant aerobic methane-oxidizing bacteria present in both water columns were associated with the Gammaproteobacteria, with little evidence of anaerobic methane oxidizing organisms being present or active. Direct measurements at the surface revealed a methane flux from Brownie Lake that was two orders of magnitude greater than the flux from Canyon Lake. Comparison of measured versus calculated turbulent diffusive fluxes indicates that most of the methane flux at Brownie Lake was non-diffusive. Although the turbulent diffusive methane flux at Canyon Lake was attenuated by methane oxidizing bacteria, dissolved methane was detected in the epilimnion, suggestive of lateral transport of methane from littoral sediments. These results highlight the importance of direct measurements in estimating the total methane flux from water columns, and that non-diffusive transport of methane may be important to consider from other ferruginous systems.
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Affiliation(s)
- Nicholas Lambrecht
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, USA
| | - Sergei Katsev
- Department of Physics, University of Minnesota Duluth, Duluth, MN, USA
- Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, USA
| | - Chad Wittkop
- Department of Chemistry and Geology, Minnesota State University, Mankato, MN, USA
| | - Steven J Hall
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Cody S Sheik
- Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, USA
- Department of Biology, University of Minnesota Duluth, Duluth, MN, USA
| | - Aude Picard
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Mojtaba Fakhraee
- Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, USA
| | - Elizabeth D Swanner
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA, USA
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