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Reis PCJ, Tsuji JM, Weiblen C, Schiff SL, Scott M, Stein LY, Neufeld JD. Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats. THE ISME JOURNAL 2024; 18:wrae041. [PMID: 38470309 PMCID: PMC11008690 DOI: 10.1093/ismejo/wrae041] [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: 10/09/2023] [Revised: 01/06/2024] [Accepted: 03/13/2024] [Indexed: 03/13/2024]
Abstract
Methanotrophic bacteria mitigate emissions of the potent greenhouse gas methane (CH4) from a variety of anthropogenic and natural sources, including freshwater lakes, which are large sources of CH4 on a global scale. Despite a dependence on dioxygen (O2) for CH4 oxidation, abundant populations of putatively aerobic methanotrophs have been detected within microoxic and anoxic waters and sediments of lakes. Experimental work has demonstrated active aerobic methanotrophs under those conditions, but how they are able to persist and oxidize CH4 under O2 deficiency remains enigmatic. In this review, we discuss possible mechanisms that underpin the persistence and activity of aerobic methanotrophs under O2-limiting conditions in freshwater habitats, particularly lakes, summarize experimental evidence for microbial oxidation of CH4 by aerobic bacteria under low or no O2, and suggest future research directions to further explore the ecology and metabolism of aerobic methanotrophs in O2-limiting environments.
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Affiliation(s)
- Paula C J Reis
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Jackson M Tsuji
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Cerrise Weiblen
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sherry L Schiff
- Department of Earth & Environmental Sciences, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Matthew Scott
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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2
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Vigderovich H, Eckert W, Elvert M, Gafni A, Rubin-Blum M, Bergman O, Sivan O. Aerobic methanotrophy increases the net iron reduction in methanogenic lake sediments. Front Microbiol 2023; 14:1206414. [PMID: 37577416 PMCID: PMC10415106 DOI: 10.3389/fmicb.2023.1206414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
In methane (CH4) generating sediments, methane oxidation coupled with iron reduction was suggested to be catalyzed by archaea and bacterial methanotrophs of the order Methylococcales. However, the co-existence of these aerobic and anaerobic microbes, the link between the processes, and the oxygen requirement for the bacterial methanotrophs have remained unclear. Here, we show how stimulation of aerobic methane oxidation at an energetically low experimental environment influences net iron reduction, accompanied by distinct microbial community changes and lipid biomarker patterns. We performed incubation experiments (between 30 and 120 days long) with methane generating lake sediments amended with 13C-labeled methane, following the additions of hematite and different oxygen levels in nitrogen headspace, and monitored methane turnover by 13C-DIC measurements. Increasing oxygen exposure (up to 1%) promoted aerobic methanotrophy, considerable net iron reduction, and the increase of microbes, such as Methylomonas, Geobacter, and Desulfuromonas, with the latter two being likely candidates for iron recycling. Amendments of 13C-labeled methanol as a potential substrate for the methanotrophs under hypoxia instead of methane indicate that this substrate primarily fuels methylotrophic methanogenesis, identified by high methane concentrations, strongly positive δ13CDIC values, and archaeal lipid stable isotope data. In contrast, the inhibition of methanogenesis by 2-bromoethanesulfonate (BES) led to increased methanol turnover, as suggested by similar 13C enrichment in DIC and high amounts of newly produced bacterial fatty acids, probably derived from heterotrophic bacteria. Our experiments show a complex link between aerobic methanotrophy and iron reduction, which indicates iron recycling as a survival mechanism for microbes under hypoxia.
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Affiliation(s)
- Hanni Vigderovich
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Werner Eckert
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Marcus Elvert
- MARUM—Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Almog Gafni
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Oded Bergman
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Orit Sivan
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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3
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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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Abstract
Methanobactins (MBs) are small (<1,300-Da) posttranslationally modified copper-binding peptides and represent the extracellular component of a copper acquisition system in some methanotrophs. Interestingly, MBs can bind a range of metal ions, with some being reduced after binding, e.g., Cu2+ reduced to Cu+. Other metal ions, however, are bound but not reduced, e.g., K+. The source of electrons for selective metal ion reduction has been speculated to be water but never empirically shown. Here, using H218O, we show that when MBs from Methylocystis sp. strain SB2 (MB-SB2) and Methylosinus trichosporium OB3b (MB-OB3) were incubated in the presence of either Au3+, Cu2, or Ag+, 18,18O2 and free protons were released. No 18,18O2 production was observed in the presence of either MB-SB2 or MB-OB3b alone, gold alone, copper alone, or silver alone or when K+ or Mo2+ was incubated with MB-SB2. In contrast to MB-OB3b, MB-SB2 binds Fe3+ with an N2S2 coordination and will also reduce Fe3+ to Fe2+. Iron reduction was also found to be coupled to the oxidation of 2H2O and the generation of O2. MB-SB2 will also couple Hg2+, Ni2+, and Co2+ reduction to the oxidation of 2H2O and the generation of O2, but MB-OB3b will not, ostensibly as MB-OB3b binds but does not reduce these metal ions. To determine if the O2 generated during metal ion reduction by MB could be coupled to methane oxidation, 13CH4 oxidation by Methylosinus trichosporium OB3b was monitored under anoxic conditions. The results demonstrate that O2 generation from metal ion reduction by MB-OB3b can support methane oxidation. IMPORTANCE The discovery that MB will couple the oxidation of H2O to metal ion reduction and the release of O2 suggests that methanotrophs expressing MB may be able to maintain their activity under hypoxic/anoxic conditions through the “self-generation” of dioxygen required for the initial oxidation of methane to methanol. Such an ability may be an important factor in enabling methanotrophs to not only colonize the oxic-anoxic interface where methane concentrations are highest but also tolerate significant temporal fluctuations of this interface. Given that genomic surveys often show evidence of aerobic methanotrophs within anoxic zones, the ability to express MB (and thereby generate dioxygen) may be an important parameter in facilitating their ability to remove methane, a potent greenhouse gas, before it enters the atmosphere.
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Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow). Microorganisms 2021; 9:microorganisms9071368. [PMID: 34201891 PMCID: PMC8305228 DOI: 10.3390/microorganisms9071368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/17/2022] Open
Abstract
Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO2 fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace 13CO2 incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6-85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. 13CO2 incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0-5.3% relative 13C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO2 fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.
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Zhou J, Holmes DE, Tang HY, Lovley DR. Correlation of Key Physiological Properties of Methanosarcina Isolates with Environment of Origin. Appl Environ Microbiol 2021; 87:e0073121. [PMID: 33931421 PMCID: PMC8316034 DOI: 10.1128/aem.00731-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/18/2021] [Indexed: 02/06/2023] Open
Abstract
It is known that the physiology of Methanosarcina species can differ significantly, but the ecological impact of these differences is unclear. We recovered two strains of Methanosarcina from two different ecosystems with a similar enrichment and isolation method. Both strains had the same ability to metabolize organic substrates and participate in direct interspecies electron transfer but also had major physiological differences. Strain DH-1, which was isolated from an anaerobic digester, used H2 as an electron donor. Genome analysis indicated that it lacks an Rnf complex and conserves energy from acetate metabolism via intracellular H2 cycling. In contrast, strain DH-2, a subsurface isolate, lacks hydrogenases required for H2 uptake and cycling and has an Rnf complex for energy conservation when growing on acetate. Further analysis of the genomes of previously described isolates, as well as phylogenetic and metagenomic data on uncultured Methanosarcina in anaerobic digesters and diverse soils and sediments, revealed a physiological dichotomy that corresponded with environment of origin. The physiology of type I Methanosarcina revolves around H2 production and consumption. In contrast, type II Methanosarcina species eschew H2 and have genes for an Rnf complex and the multiheme, membrane-bound c-type cytochrome MmcA, shown to be essential for extracellular electron transfer. The distribution of Methanosarcina species in diverse environments suggests that the type I H2-based physiology is well suited for high-energy environments, like anaerobic digesters, whereas type II Rnf/cytochrome-based physiology is an adaptation to the slower, steady-state carbon and electron fluxes common in organic-poor anaerobic soils and sediments. IMPORTANCE Biogenic methane is a significant greenhouse gas, and the conversion of organic wastes to methane is an important bioenergy process. Methanosarcina species play an important role in methane production in many methanogenic soils and sediments as well as anaerobic waste digesters. The studies reported here emphasize that the genus Methanosarcina is composed of two physiologically distinct groups. This is important to recognize when interpreting the role of Methanosarcina in methanogenic environments, especially regarding H2 metabolism. Furthermore, the finding that type I Methanosarcina species predominate in environments with high rates of carbon and electron flux and that type II Methanosarcina species predominate in lower-energy environments suggests that evaluating the relative abundance of type I and type II Methanosarcina may provide further insights into rates of carbon and electron flux in methanogenic environments.
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Affiliation(s)
- Jinjie Zhou
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Dawn E. Holmes
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
- Department of Physical and Biological Science, Western New England University, Springfield, Massachusetts, USA
| | - Hai-Yan Tang
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waster Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
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7
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Biogeochemistry of Mediterranean Wetlands: A Review about the Effects of Water-Level Fluctuations on Phosphorus Cycling and Greenhouse Gas Emissions. WATER 2021. [DOI: 10.3390/w13111510] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Although Mediterranean wetlands are characterized by extreme natural water level fluctuations in response to irregular precipitation patterns, global climate change is expected to amplify this pattern by shortening precipitation seasons and increasing the incidence of summer droughts in this area. As a consequence, a part of the lake sediment will be exposed to air-drying in dry years when the water table becomes low. This periodic sediment exposure to dry/wet cycles will likely affect biogeochemical processes. Unexpectedly, to date, few studies are focused on assessing the effects of water level fluctuations on the biogeochemistry of these ecosystems. In this review, we investigate the potential impacts of water level fluctuations on phosphorus dynamics and on greenhouse gases emissions in Mediterranean wetlands. Major drivers of global change, and specially water level fluctuations, will lead to the degradation of water quality in Mediterranean wetlands by increasing the availability of phosphorus concentration in the water column upon rewetting of dry sediment. CO2 fluxes are likely to be enhanced during desiccation, while inundation is likely to decrease cumulative CO2 emissions, as well as N2O emissions, although increasing CH4 emissions. However, there exists a complete gap of knowledge about the net effect of water level fluctuations induced by global change on greenhouse gases emission. Accordingly, further research is needed to assess whether the periodic exposure to dry–wet cycles, considering the extent and frequency of the cycles, will amplify the role of these especial ecosystems as a source of these gases and thereby act as a feedback mechanism for global warming. To conclude, it is pertinent to consider that a better understanding about the effect of water level fluctuations on the biogeochemistry of Mediterranean wetlands will help to predict how other freshwater ecosystems will respond.
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8
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Roland FAE, Borges AV, Darchambeau F, Llirós M, Descy JP, Morana C. The possible occurrence of iron-dependent anaerobic methane oxidation in an Archean Ocean analogue. Sci Rep 2021; 11:1597. [PMID: 33452366 PMCID: PMC7810693 DOI: 10.1038/s41598-021-81210-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/05/2021] [Indexed: 11/24/2022] Open
Abstract
In the ferruginous and anoxic early Earth oceans, photoferrotrophy drove most of the biological production before the advent of oxygenic photosynthesis, but its association with ferric iron (Fe3+) dependent anaerobic methane (CH4) oxidation (AOM) has been poorly investigated. We studied AOM in Kabuno Bay, a modern analogue to the Archean Ocean (anoxic bottom waters and dissolved Fe concentrations > 600 µmol L-1). Aerobic and anaerobic CH4 oxidation rates up to 0.12 ± 0.03 and 51 ± 1 µmol L-1 d-1, respectively, were put in evidence. In the Fe oxidation-reduction zone, we observed high concentration of Bacteriochlorophyll e (biomarker of the anoxygenic photoautotrophs), which co-occurred with the maximum CH4 oxidation peaks, and a high abundance of Candidatus Methanoperedens, which can couple AOM to Fe3+ reduction. In addition, comparison of measured CH4 oxidation rates with electron acceptor fluxes suggest that AOM could mainly rely on Fe3+ produced by photoferrotrophs. Further experiments specifically targeted to investigate the interactions between photoferrotrophs and AOM would be of considerable interest. Indeed, ferric Fe3+-driven AOM has been poorly envisaged as a possible metabolic process in the Archean ocean, but this can potentially change the conceptualization and modelling of metabolic and geochemical processes controlling climate conditions in the Early Earth.
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Affiliation(s)
- Fleur A E Roland
- Chemical Oceanography Unit, Université de Liège, Liège, Belgium.
| | | | | | - Marc Llirós
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Girona Biomedical Research Institute, Salt, Catalunya, Spain
| | | | - Cédric Morana
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
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9
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Guggenheim C, Freimann R, Mayr MJ, Beck K, Wehrli B, Bürgmann H. Environmental and Microbial Interactions Shape Methane-Oxidizing Bacterial Communities in a Stratified Lake. Front Microbiol 2020; 11:579427. [PMID: 33178162 PMCID: PMC7593551 DOI: 10.3389/fmicb.2020.579427] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/04/2020] [Indexed: 11/13/2022] Open
Abstract
In stratified lakes, methane-oxidizing bacteria (MOB) are strongly mitigating methane fluxes to the atmosphere by consuming methane entering the water column from the sediments. MOB communities in lakes are diverse and vertically structured, but their spatio-temporal dynamics along the water column as well as physico-chemical parameters and interactions with other bacterial species that drive the community assembly have so far not been explored in depth. Here, we present a detailed investigation of the MOB and bacterial community composition and a large set of physico-chemical parameters in a shallow, seasonally stratified, and sub-alpine lake. Four highly resolved vertical profiles were sampled in three different years and during various stages of development of the stratified water column. Non-randomly assembled MOB communities were detected in all compartments. We could identify methane and oxygen gradients and physico-chemical parameters like pH, light, available copper and iron, and total dissolved nitrogen as important drivers of the MOB community structure. In addition, MOB were well-integrated into a bacterial-environmental network. Partial redundancy analysis of the relevance network of physico-chemical variables and bacteria explained up to 84% of the MOB abundances. Spatio-temporal MOB community changes were 51% congruent with shifts in the total bacterial community and 22% of variance in MOB abundances could be explained exclusively by the bacterial community composition. Our results show that microbial interactions may play an important role in structuring the MOB community along the depth gradient of stratified lakes.
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Affiliation(s)
- Carole Guggenheim
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich - Swiss Federal Institute of Technology, Zurich, Switzerland.,Department of Surface Waters - Research and Management, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Remo Freimann
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich - Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Magdalena J Mayr
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich - Swiss Federal Institute of Technology, Zurich, Switzerland.,Department of Surface Waters - Research and Management, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Karin Beck
- Department of Surface Waters - Research and Management, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Bernhard Wehrli
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich - Swiss Federal Institute of Technology, Zurich, Switzerland.,Department of Surface Waters - Research and Management, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Helmut Bürgmann
- Department of Surface Waters - Research and Management, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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10
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Cabrol L, Thalasso F, Gandois L, Sepulveda-Jauregui A, Martinez-Cruz K, Teisserenc R, Tananaev N, Tveit A, Svenning MM, Barret M. Anaerobic oxidation of methane and associated microbiome in anoxic water of Northwestern Siberian lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 736:139588. [PMID: 32497884 DOI: 10.1016/j.scitotenv.2020.139588] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Arctic lakes emit methane (CH4) to the atmosphere. The magnitude of this flux could increase with permafrost thaw but might also be mitigated by microbial CH4 oxidation. Methane oxidation in oxic water has been extensively studied, while the contribution of anaerobic oxidation of methane (AOM) to CH4 mitigation is not fully understood. We have investigated four Northern Siberian stratified lakes in an area of discontinuous permafrost nearby Igarka, Russia. Analyses of CH4 concentrations in the water column demonstrated that 60 to 100% of upward diffusing CH4 was oxidized in the anoxic layers of the four lakes. A combination of pmoA and mcrA gene qPCR and 16S rRNA gene metabarcoding showed that the same taxa, all within Methylomonadaceae and including the predominant genus Methylobacter as well as Crenothrix, could be the major methane-oxidizing bacteria (MOB) in the anoxic water of the four lakes. Correlation between Methylomonadaceae and OTUs within Methylotenera, Geothrix and Geobacter genera indicated that AOM might occur in an interaction between MOB, denitrifiers and iron-cycling partners. We conclude that MOB within Methylomonadaceae could have a crucial impact on CH4 cycling in these Siberian Arctic lakes by mitigating the majority of produced CH4 before it leaves the anoxic zone. This finding emphasizes the importance of AOM by Methylomonadaceae and extends our knowledge about CH4 cycle in lakes, a crucial component of the global CH4 cycle.
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Affiliation(s)
- Léa Cabrol
- Aix-Marseille University, Univ Toulon, CNRS, IRD, M.I.O. UM 110, Mediterranean Institute of Oceanography, Marseille, France; Institute of Ecology and Biodiversity IEB, Faculty of Sciences, Universidad de Chile, Santiago, Chile; Escuela de Ingeniería Bioquímica, Pontificia Universidad de Valparaiso, Av Brasil 2085, Valparaiso, Chile
| | - Frédéric Thalasso
- Biotechnology and Bioengineering Department, Center for Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Laure Gandois
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France
| | - Armando Sepulveda-Jauregui
- ENBEELAB, University of Magallanes, Punta Arenas, Chile; Center for Climate and Resilience Research (CR)2, Santiago, Chile
| | | | - Roman Teisserenc
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France
| | | | - Alexander Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maialen Barret
- Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France.
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11
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Savvichev AS, Kadnikov VV, Rusanov II, Beletsky AV, Krasnova ED, Voronov DA, Kallistova AY, Veslopolova EF, Zakharova EE, Kokryatskaya NM, Losyuk GN, Demidenko NA, Belyaev NA, Sigalevich PA, Mardanov AV, Ravin NV, Pimenov NV. Microbial Processes and Microbial Communities in the Water Column of the Polar Meromictic Lake Bol'shie Khruslomeny at the White Sea Coast. Front Microbiol 2020; 11:1945. [PMID: 32849486 PMCID: PMC7432294 DOI: 10.3389/fmicb.2020.01945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/23/2020] [Indexed: 11/13/2022] Open
Abstract
Microbiological, molecular ecological, biogeochemical, and isotope geochemical research was carried out at the polar Lake Bol'shie Khruslomeny at the coast of the Kandalaksha Bay, White Sea in March and September 2017. The uppermost mixolimnion was oxic, with low salinity (3-5%). The lower chemocline layer was brown-green colored, with very high content of particulate organic matter (up to 11.8 mg C L-1). The lowermost monimolimnion had marine salinity (22-24%) and very high concentrations of sulfide (up to 18 mmol L-1) and CH4 (up to 1.8 mmol L-1). In the chemocline, total microbial abundance and the rate of anoxygenic photosynthesis were 8.8 × 106 cells mL-1 and 34.4 μmol C L-1 day-1, respectively. Both in March and September, sulfate reduction rate increased with depth, peaking (up to 0.6-1.1 μmol S L-1 day-1) in the lower chemocline. Methane oxidation rates in the chemocline were up to 85 and 180 nmol CH4 L-1 day-1 in March and September, respectively; stimulation of this process by light was observed in September. The percentages of cyanobacteria and methanotrophs in the layer where light-induced methane oxidation occurred were similar, ∼2.5% of the microbial community. Light did not stimulate methane oxidation in deeper layers. The carbon isotope composition of particulate organic matter (δ13C-Corg), dissolved carbonates (δ13C-DIC), and methane (δ13C- CH4) indicated high microbial activity in the chemocline. Analysis of the 16S rRNA gene sequences revealed predominance of Cyanobium cyanobacteria (order Synechococcales) in the mixolimnion. Green sulfur bacteria Chlorobium phaeovibrioides capable of anoxygenic photosynthesis constituted ∼20% of the chemocline community both in March and in September. Methyloprofundus gammaptoteobacteria (family Methylomonaceae) were present in the upper chemocline, where active methane oxidation occurred. During winter, cyanobacteria were less abundant in the chemocline, while methanotrophs occurred in higher horizons, including the under-ice layer. Chemolithotrophic gammaproteobacteria of the genus Thiomicrorhabdus, oxidizing reduced sulfur compounds at low oxygen concentrations, were revealed in the chemocline in March. Both in March and September archaea constituted up to 50% of all microorganisms in the hypolimnion. The percentage of putative methanogens in the archaeal community was low, and they occurred mainly in near-bottom horizons.
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Affiliation(s)
- Alexander S. Savvichev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Igor I. Rusanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena D. Krasnova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A. Voronov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Yu. Kallistova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena F. Veslopolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena E. Zakharova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya M. Kokryatskaya
- N. Laverov Federal Center for Integrated Arctic Research, Ural Branch, Russian Academy of Sciences, Moscow, Russia
| | - Galina N. Losyuk
- N. Laverov Federal Center for Integrated Arctic Research, Ural Branch, Russian Academy of Sciences, Moscow, Russia
| | | | - Nikolai A. Belyaev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel A. Sigalevich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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12
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Thalasso F, Sepulveda-Jauregui A, Gandois L, Martinez-Cruz K, Gerardo-Nieto O, Astorga-España MS, Teisserenc R, Lavergne C, Tananaev N, Barret M, Cabrol L. Sub-oxycline methane oxidation can fully uptake CH 4 produced in sediments: case study of a lake in Siberia. Sci Rep 2020; 10:3423. [PMID: 32099029 PMCID: PMC7042212 DOI: 10.1038/s41598-020-60394-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 02/10/2020] [Indexed: 11/09/2022] Open
Abstract
It is commonly assumed that methane (CH4) released by lakes into the atmosphere is mainly produced in anoxic sediment and transported by diffusion or ebullition through the water column to the surface of the lake. In contrast to that prevailing idea, it has been gradually established that the epilimnetic CH4 does not originate exclusively from sediments but is also locally produced or laterally transported from the littoral zone. Therefore, CH4 cycling in the epilimnion and the hypolimnion might not be as closely linked as previously thought. We utilized a high-resolution method used to determine dissolved CH4 concentration to analyze a Siberian lake in which epilimnetic and hypolimnetic CH4 cycles were fully segregated by a section of the water column where CH4 was not detected. This layer, with no detected CH4, was well below the oxycline and the photic zone and thus assumed to be anaerobic. However, on the basis of a diffusion-reaction model, molecular biology, and stable isotope analyses, we determined that this layer takes up all the CH4 produced in the sediments and the deepest section of the hypolimnion. We concluded that there was no CH4 exchange between the hypolimnion (dominated by methanotrophy and methanogenesis) and the epilimnion (dominated by methane lateral transport and/or oxic production), resulting in a vertically segregated lake internal CH4 cycle.
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Affiliation(s)
- Frédéric Thalasso
- Biotechnology and Bioengineering Department, Center for Research and Advanced Studies (Cinvestav), Mexico City, Mexico.,The Environmental Biogeochemistry in Extreme Ecosystems Laboratory (EnBEELab), University of Magallanes, Punta Arenas, Chile
| | - Armando Sepulveda-Jauregui
- The Environmental Biogeochemistry in Extreme Ecosystems Laboratory (EnBEELab), University of Magallanes, Punta Arenas, Chile. .,Center for Climate and Resilience Research (CR)2, Santiago, Chile.
| | - Laure Gandois
- EcoLab, Université de Toulouse, CNRS, Toulouse, France
| | - Karla Martinez-Cruz
- The Environmental Biogeochemistry in Extreme Ecosystems Laboratory (EnBEELab), University of Magallanes, Punta Arenas, Chile
| | - Oscar Gerardo-Nieto
- Biotechnology and Bioengineering Department, Center for Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - María S Astorga-España
- The Environmental Biogeochemistry in Extreme Ecosystems Laboratory (EnBEELab), University of Magallanes, Punta Arenas, Chile
| | | | - Céline Lavergne
- Escuela de Ingeniería Bioquímica, Pontificia Universidad de Valparaiso, Valparaiso, Chile
| | | | | | - Léa Cabrol
- Aix-Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography, Marseille, France
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13
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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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14
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Reis PCJ, Thottathil SD, Ruiz-González C, Prairie YT. Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates. Environ Microbiol 2019; 22:738-751. [PMID: 31769176 DOI: 10.1111/1462-2920.14877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/23/2019] [Accepted: 11/22/2019] [Indexed: 11/30/2022]
Abstract
Lake methane (CH4 ) emissions are largely controlled by aerobic methane-oxidizing bacteria (MOB) which mostly belong to the classes Alpha- and Gammaproteobacteria (Alpha- and Gamma-MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH4 oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD-FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH4 oxidation rates. We found a clear niche separation of Alpha- and Gamma-MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma-MOB appears to dominate methanotrophy throughout the water column, but Alpha-MOB may also be an important player particularly in well-oxygenated bottom waters. The inclusion of Gamma-MOB cell abundance improved environmental models of CH4 oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH4 oxidation rates in lakes and that information on the MOB community can help predict CH4 oxidation rates and thus emissions from lakes.
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Affiliation(s)
- Paula C J Reis
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
| | - Shoji D Thottathil
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), Barcelona, E-08003, Spain
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
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15
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Zakharenko AS, Galachyants YP, Morozov IV, Shubenkova OV, Morozov AA, Ivanov VG, Pimenov NV, Krasnopeev AY, Zemskaya TI. Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal. MICROBIAL ECOLOGY 2019; 78:269-285. [PMID: 30483839 DOI: 10.1007/s00248-018-1299-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.
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Affiliation(s)
- Aleksandra S Zakharenko
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia.
| | - Yuriy P Galachyants
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Igor V Morozov
- Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Olga V Shubenkova
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Alexey A Morozov
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Vyacheslav G Ivanov
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Nikolay V Pimenov
- Research Center of Biotechnology, Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Andrey Y Krasnopeev
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
| | - Tamara I Zemskaya
- Siberian Branch of the Russian Academy of Sciences, Limnological Institute, Ulan-Batorskaya Street 3, 664033, Irkutsk, Russia
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16
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Martinez-Cruz K, Sepulveda-Jauregui A, Casper P, Anthony KW, Smemo KA, Thalasso F. Ubiquitous and significant anaerobic oxidation of methane in freshwater lake sediments. WATER RESEARCH 2018; 144:332-340. [PMID: 30053624 DOI: 10.1016/j.watres.2018.07.053] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
Anaerobic oxidation of methane (AOM) is a microbial process that consumes dissolved methane (CH4) in anoxic sediments and soils and mitigates CH4 release to the atmosphere. The degree to which AOM limits global biospheric CH4 emissions is not fully understood. In marine sediments, where the process was first described, AOM is responsible for oxidizing >90% of the CH4 produced. More recently, AOM has been observed in soils, peatlands, and freshwater ecosystems. In lakes, where sediment anoxia, organic carbon turnover, and CH4 production are common, AOM is not well studied but could represent a significant CH4 sink and constraint on emissions. Here, we present evidence for the occurrence of AOM in the sediment of thirteen lakes that span a global climatic and trophic gradient. We further quantified and modeled AOM patterns and studied potential microbial controls of AOM using laboratory incubations of sediment and stable isotope measurements in three of the thirteen lakes. We demonstrate that AOM is widespread in freshwater lake sediments and accounts for 29%-34% (95% confidence interval) of the mean total CH4 produced in surface and near-surface lake sediments.
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Affiliation(s)
- Karla Martinez-Cruz
- Cinvestav, Department of Biotechnology and Bioengineering, 2508 IPN Ave., San Pedro Zacatenco, 07360, Mexico City, Mexico; Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775, Stechlin, Germany; University of Magallanes, Department of Science and Natural Resources, 01890, Manuel Bulnes Ave., Punta Arenas, Chile
| | - Armando Sepulveda-Jauregui
- Cinvestav, Department of Biotechnology and Bioengineering, 2508 IPN Ave., San Pedro Zacatenco, 07360, Mexico City, Mexico; University of Alaska Fairbanks, Water and Environmental Research Center, 1760 Tanana Loop, Fairbanks, 99775, Alaska, USA
| | - Peter Casper
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775, Stechlin, Germany
| | - Katey Walter Anthony
- University of Alaska Fairbanks, Water and Environmental Research Center, 1760 Tanana Loop, Fairbanks, 99775, Alaska, USA
| | - Kurt A Smemo
- Skidmore College, Environmental Studies and Sciences Program, 815 N. Broadway, Saratoga Springs, 12866, New York, USA
| | - Frederic Thalasso
- Cinvestav, Department of Biotechnology and Bioengineering, 2508 IPN Ave., San Pedro Zacatenco, 07360, Mexico City, Mexico; University of Alaska Fairbanks, Water and Environmental Research Center, 1760 Tanana Loop, Fairbanks, 99775, Alaska, USA.
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17
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Chistoserdova L, Kalyuzhnaya MG. Current Trends in Methylotrophy. Trends Microbiol 2018; 26:703-714. [PMID: 29471983 DOI: 10.1016/j.tim.2018.01.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/18/2018] [Accepted: 01/30/2018] [Indexed: 11/26/2022]
Abstract
Methylotrophy is a field of study dealing with microorganisms capable of utilization of compounds devoid of carbon-carbon bonds (C1 compounds). In this review, we highlight several emerging trends in methylotrophy. First, we discuss the significance of the recent discovery of lanthanide-dependent alcohol dehydrogenases for understanding both the occurrence and the distribution of methylotrophy functions among bacteria, and then we discuss the newly appreciated role of lanthanides in biology. Next, we describe the detection of other methylotrophy pathways across novel bacterial taxa and insights into the evolution of methylotrophy. Further, data are presented on the occurrence and activity of aerobic methylotrophs in hypoxic and anoxic environments, questioning the prior assumptions on niche separation of aerobic and anaerobic methylotrophy. The concept of communal function in aerobic methane oxidation is also briefly discussed. Finally, we review recent research in engineering methylotrophs for biotechnological applications as well as recent progress in engineering synthetic methylotrophy.
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18
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Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry. Sci Rep 2017; 7:46708. [PMID: 28447615 PMCID: PMC5406836 DOI: 10.1038/srep46708] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/23/2017] [Indexed: 01/07/2023] Open
Abstract
Life originated in Archaean oceans, almost 4 billion years ago, in the absence of oxygen and the presence of high dissolved iron concentrations. Early Earth oxidation is marked globally by extensive banded iron formations but the contributing processes and timing remain controversial. Very few aquatic habitats have been discovered that match key physico-chemical parameters of the early Archaean Ocean. All previous whole ecosystem Archaean analogue studies have been confined to rare, low sulfur, and permanently stratified lakes. Here we provide first evidence that millions of Boreal Shield lakes with natural anoxia offer the opportunity to constrain biogeochemical and microbiological aspects of early Archaean life. Specifically, we combined novel isotopic signatures and nucleic acid sequence data to examine processes in the anoxic zone of stratified boreal lakes that are naturally low in sulfur and rich in ferrous iron, hallmark characteristics predicted for the Archaean Ocean. Anoxygenic photosynthesis was prominent in total water column biogeochemistry, marked by distinctive patterns in natural abundance isotopes of carbon, nitrogen, and iron. These processes are robust, returning reproducibly after water column re-oxygenation following lake turnover. Evidence of coupled iron oxidation, iron reduction, and methane oxidation affect current paradigms of both early Earth and modern aquatic ecosystems.
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19
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Camacho A, Walter XA, Picazo A, Zopfi J. Photoferrotrophy: Remains of an Ancient Photosynthesis in Modern Environments. Front Microbiol 2017; 8:323. [PMID: 28377745 PMCID: PMC5359306 DOI: 10.3389/fmicb.2017.00323] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Photoferrotrophy, the process by which inorganic carbon is fixed into organic matter using light as an energy source and reduced iron [Fe(II)] as an electron donor, has been proposed as one of the oldest photoautotrophic metabolisms on Earth. Under the iron-rich (ferruginous) but sulfide poor conditions dominating the Archean ocean, this type of metabolism could have accounted for most of the primary production in the photic zone. Here we review the current knowledge of biogeochemical, microbial and phylogenetic aspects of photoferrotrophy, and evaluate the ecological significance of this process in ancient and modern environments. From the ferruginous conditions that prevailed during most of the Archean, the ancient ocean evolved toward euxinic (anoxic and sulfide rich) conditions and, finally, much after the advent of oxygenic photosynthesis, to a predominantly oxic environment. Under these new conditions photoferrotrophs lost importance as primary producers, and now photoferrotrophy remains as a vestige of a formerly relevant photosynthetic process. Apart from the geological record and other biogeochemical markers, modern environments resembling the redox conditions of these ancient oceans can offer insights into the past significance of photoferrotrophy and help to explain how this metabolism operated as an important source of organic carbon for the early biosphere. Iron-rich meromictic (permanently stratified) lakes can be considered as modern analogs of the ancient Archean ocean, as they present anoxic ferruginous water columns where light can still be available at the chemocline, thus offering suitable niches for photoferrotrophs. A few bacterial strains of purple bacteria as well as of green sulfur bacteria have been shown to possess photoferrotrophic capacities, and hence, could thrive in these modern Archean ocean analogs. Studies addressing the occurrence and the biogeochemical significance of photoferrotrophy in ferruginous environments have been conducted so far in lakes Matano, Pavin, La Cruz, and the Kabuno Bay of Lake Kivu. To date, only in the latter two lakes a biogeochemical role of photoferrotrophs has been confirmed. In this review we critically summarize the current knowledge on iron-driven photosynthesis, as a remains of ancient Earth biogeochemistry.
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Affiliation(s)
- Antonio Camacho
- Cavanilles Institute for Biodiversity and Evolutionary Biology, University of ValenciaBurjassot, Spain
| | - Xavier A. Walter
- Bristol BioEnergy Centre, Bristol Robotics Laboratory, University of the West of EnglandBristol, UK
| | - Antonio Picazo
- Cavanilles Institute for Biodiversity and Evolutionary Biology, University of ValenciaBurjassot, Spain
| | - Jakob Zopfi
- Aquatic and Stable Isotope Biogeochemistry, Department of Environmental Sciences, University of BaselBasel, Switzerland
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