scholarly journals Multiple groups of methanotrophic bacteria mediate methane oxidation in anoxic lake sediments

2021 ◽  
Author(s):  
Guangyi Su ◽  
Jakob Zopfi ◽  
Moritz F. Lehmann
Keyword(s):  
Lake Sediments ◽  
Methane Oxidation ◽  
Methane Emissions ◽  
Type I ◽  
Methanotrophic Bacteria ◽  
Anoxic Sediments ◽  
Anoxic Conditions ◽  
Aerobic Methanotrophs ◽  
Multiple Groups ◽  
Lake Sempach

Freshwater lakes represent an important source of the potent greenhouse gas methane (CH4) to the atmosphere. Methane emissions are regulated to large parts by aerobic (MOx) and anaerobic (AOM) oxidation of methane that are important sinks in lakes. In contrast to marine benthic environments, our knowledge about the modes of AOM and the related methanotrophic microorganisms in anoxic lake sediments is still rudimentary. Here we demonstrate the occurrence of AOM in the anoxic sediments of Lake Sempach (Switzerland), with maximum in situ AOM rates observed within the surface sediment layers in presence of multiple groups of methanotrophic bacteria and various oxidants known to support AOM. However, substrate-amended incubations (with NO2-, NO3-, SO42-, Fe3+ and Mn4+) revealed that none of the electron acceptors previously reported to support AOM enhanced methane turnover in Lake Sempach sediments under anoxic conditions. In contrast, the addition of oxygen to the anoxic sediments resulted in an approximately tenfold increase in methane oxidation relative to the anoxic incubations. Phylogenetic and isotopic evidence indicate that both Type I and Type II aerobic methanotrophs were growing on methane under both oxic and anoxic conditions, although methane assimilation rates were an order of magnitude higher under oxic conditions. While the anaerobic electron acceptor responsible for AOM could not be identified, these findings expand our understanding of the metabolic versatility of canonically aerobic methanotrophs under anoxic conditions, with important implications for future investigations to identify methane oxidation processes. Bacterial AOM by facultative aerobic methane oxidizers might be of much larger environmental significance in reducing methane emissions than previously thought.

scholarly journals Modification of methane oxidation pathways during long-term incubations of methanic lake sediments

2021 ◽  
Author(s):  
Hanni Vigderovich ◽  
Werner Eckert ◽  
Michal Elul ◽  
Maxim Rubin-Blum ◽  
Marcus Elvert ◽  
...  
Keyword(s):  
Lake Sediments ◽  
Carbon Isotope ◽  
Iron Oxides ◽  
Methane Oxidation ◽  
Electron Acceptors ◽  
Anaerobic Oxidation Of Methane ◽  
Methanotrophic Bacteria ◽  
Oxidation Of Methane ◽  
Isotope Measurements

Abstract. Anaerobic oxidation of methane (AOM) is one of the major processes limiting the release of the greenhouse gas methane from natural environments. In Lake Kinneret sediments, iron-coupled AOM (Fe-AOM) was suggested to play a substantial role (10–15 % relative to methanogenesis) in the methanic zone (> 20 cm sediment depth), based on geochemical profiles and experiments on fresh sediments. Apparently, the oxidation of methane is mediated by a combination of mcr gene bearing archaea and aerobic bacterial methanotrophs. Here we aimed to investigate the survival of this complex microbial interplay under controlled conditions. We followed the AOM process during long-term (~18 months) anaerobic slurry experiments of these methanic sediments with two stages of incubations and additions of 13C-labeled methane, multiple electron acceptors and inhibitors. After these incubation stages carbon isotope measurements in the dissolved inorganic pool still showed considerable AOM (3–8 % relative to methanogenesis). Specific lipid carbon isotope measurements and metagenomic analyses indicate that after the prolonged incubation aerobic methanotrophic bacteria were no longer involved in the oxidation process, whereas mcr gene bearing archaea were most likely responsible for oxidizing the methane. Humic substances and iron oxides are likely electron acceptors to support this oxidation, whereas sulfate, manganese, nitrate, and nitrite did not support the AOM in these methanic sediments. Our results suggest in the natural lake sediments methanotrophic bacteria are responsible for part of the methane oxidation by the reduction of combined micro levels of oxygen and iron oxides in a cryptic cycle, while the rest of the methane is converted by reverse methanogenesis. After long-term incubation, the latter prevails without bacterial methanotropic activity and with a different iron reduction pathway.

scholarly journals Effect of Afforestation and Reforestation of Pastures on the Activity and Population Dynamics of Methanotrophic Bacteria

2007 ◽  
Vol 73 (16) ◽  
pp. 5153-5161 ◽  
Author(s):  
Brajesh K. Singh ◽  
Kevin R. Tate ◽  
Gokul Kolipaka ◽  
Carolyn B. Hedley ◽  
Catriona A. Macdonald ◽  
...  
Keyword(s):  
Community Structure ◽  
Methane Oxidation ◽  
Phospholipid Fatty Acid ◽  
Pine Forest ◽  
Polymorphism Analysis ◽  
Type I ◽  
Methanotrophic Bacteria ◽  
Type Ii ◽  
Methylococcus Capsulatus ◽  
Methanotrophic Communities

ABSTRACT We investigated the effect of afforestation and reforestation of pastures on methane oxidation and the methanotrophic communities in soils from three different New Zealand sites. Methane oxidation was measured in soils from two pine (Pinus radiata) forests and one shrubland (mainly Kunzea ericoides var. ericoides) and three adjacent permanent pastures. The methane oxidation rate was consistently higher in the pine forest or shrubland soils than in the adjacent pasture soils. A combination of phospholipid fatty acid (PLFA) and stable isotope probing (SIP) analyses of these soils revealed that different methanotrophic communities were active in soils under the different vegetations. The C18 PLFAs (signature of type II methanotrophs) predominated under pine and shrublands, and C16 PLFAs (type I methanotrophs) predominated under pastures. Analysis of the methanotrophs by molecular methods revealed further differences in methanotrophic community structure under the different vegetation types. Cloning and sequencing and terminal-restriction fragment length polymorphism analysis of the particulate methane oxygenase gene (pmoA) from different samples confirmed the PLFA-SIP results that methanotrophic bacteria related to type II methanotrophs were dominant in pine forest and shrubland, and type I methanotrophs (related to Methylococcus capsulatus) were dominant in all pasture soils. We report that afforestation and reforestation of pastures caused changes in methane oxidation by altering the community structure of methanotrophic bacteria in these soils.

scholarly journals Complete and Draft Genome Sequences of Aerobic Methanotrophs Isolated from a Riparian Wetland

2021 ◽  
Vol 10 (9) ◽  
Author(s):  
Ohana Yonara de Assis Costa ◽  
Marion Meima-Franke ◽  
Paul L. E. Bodelier
Keyword(s):  
Draft Genome ◽  
Methane Emissions ◽  
Methanotrophic Bacteria ◽  
Genome Sequences ◽  
Riparian Wetland ◽  
Aerobic Methanotrophs

ABSTRACT Wetlands are important sources of methane emissions, and the impacts of these emissions can be mitigated by methanotrophic bacteria. The genomes of methanotrophs Methylomonas sp. strain LL1 and Methylosinus sp. strain H3A, as well as Methylocystis sp. strains H4A, H15, H62, and L43, were sequenced and are reported here.

scholarly journals Methanotrophic Community Detected by DNA-SIP at Bertioga’s Mangrove Area, Southeast Brazil

2020 ◽  
Author(s):  
Débora do Carmo Linhares ◽  
Flávia Talarico Saia ◽  
Rubens Tadeu Delgado Duarte ◽  
Cristina Rossi Nakayama ◽  
Itamar Soares de Melo ◽  
...  
Keyword(s):  
Methane Oxidation ◽  
Nitrate Reduction ◽  
Taxonomic Diversity ◽  
Stable Isotope Probing ◽  
Methanotrophic Bacteria ◽  
Mangrove Area ◽  
Oxygen Starvation ◽  
Aerobic Methanotrophs ◽  
Oxygen Tensions ◽  
Bacterial Groups

AbstractMethanotrophic bacteria can use methane as sole carbon and energy source. Its importance in the environment is related to the mitigation of methane emissions from soil and water to the atmosphere. Brazilian mangroves are highly productive, have potential to methane production, and it is inferred that methanotrophic community is of great importance for this ecosystem. The scope of this study was to investigate the functional and taxonomic diversity of methanotrophic bacteria present in the anthropogenic impacted sediments from Bertioga’s mangrove (SP, Brazil). Sediment sample was cultivated with methane and the microbiota actively involved in methane oxidation was identified by DNA-based stable isotope probing (DNA-SIP) using methane as a labeled substrate. After 4 days of incubation and consumption of 0.7 mmol of methane, the most active microorganisms were related to methanotrophs Methylomonas and Methylobacter as well as to methylotrophic Methylotenera, indicating a possible association of these bacterial groups within a methane derived food chain in the Bertioga mangrove. The abundance of genera Methylomonas, able to couple methane oxidation to nitrate reduction, may indicate that under low dissolved oxygen tensions some aerobic methanotrophs could shift to intraerobic methane oxidation to avoid oxygen starvation.

scholarly journals Metabolic flexibility of aerobic methanotrophs under anoxic conditions in Arctic lake sediments

2021 ◽  
Author(s):  
Ruo He ◽  
Jing Wang ◽  
John W. Pohlman ◽  
Zhongjun Jia ◽  
Yi-Xuan Chu ◽  
...  
Keyword(s):  
Lake Sediments ◽  
Metabolic Flexibility ◽  
Anoxic Conditions ◽  
Arctic Lake ◽  
Aerobic Methanotrophs

A membrane biofilm reactor achieves aerobic methane oxidation coupled to denitrification (AME-D) with high efficiency

2008 ◽  
Vol 58 (1) ◽  
pp. 83-87 ◽  
Author(s):  
O. Modin ◽  
K. Fukushi ◽  
F. Nakajima ◽  
K. Yamamoto
Keyword(s):  
Methane Oxidation ◽  
High Efficiency ◽  
Biofilm Reactor ◽  
Practical Application ◽  
Suspended Culture ◽  
Consumption Ratio ◽  
Membrane Biofilm Reactor ◽  
Nitrate Consumption ◽  
Attached Culture ◽  
Aerobic Methanotrophs

Methane would potentially be an inexpensive, widely available electron donor for denitrification of wastewaters poor in organics. Currently, no methanotrophic microbe is known to denitrify. However, aerobic methane oxidation coupled to denitrification (AME-D) has been observed in several laboratory studies. In the AME-D process, aerobic methanotrophs oxidise methane and release organic metabolites and lysis products, which are used by coexisting denitrifiers as electron donors for denitrification. Due to the presence of oxygen, the denitrification efficiency in terms of methane-to-nitrate consumption is usually low. To improve this efficiency the use of a membrane biofilm reactor was investigated. The denitrification efficiency of an AME-D culture in (1) a suspended growth reactor, and (2) a membrane biofilm reactor was studied. The methane-to-nitrate consumption ratio for the suspended culture was 8.7. For the membrane-attached culture the ratio was 2.2. The results clearly indicated that the membrane-attached biofilm was superior to the suspended culture in terms of denitrification efficiency. This study showed that for practical application of the AME-D process, focus should be placed on development of a biofilm reactor.

scholarly journals Methylocella Species Are Facultatively Methanotrophic

2005 ◽  
Vol 187 (13) ◽  
pp. 4665-4670 ◽  
Author(s):  
Svetlana N. Dedysh ◽  
Claudia Knief ◽  
Peter F. Dunfield
Keyword(s):  
Methane Oxidation ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Methanotrophic Bacteria ◽  
Soluble Methane Monooxygenase ◽  
Cell Counts ◽  
Carbon Compounds ◽  
Methane Fluxes ◽  
The One ◽  
Pcr Targeting

ABSTRACT All aerobic methanotrophic bacteria described to date are unable to grow on substrates containing carbon-carbon bonds. Here we demonstrate that members of the recently discovered genus Methylocella are an exception to this. These bacteria are able to use as their sole energy source the one-carbon compounds methane and methanol, as well as the multicarbon compounds acetate, pyruvate, succinate, malate, and ethanol. To conclusively verify facultative growth, acetate and methane were used as model substrates in growth experiments with the type strain Methylocella silvestris BL2. Quantitative real-time PCR targeting the mmoX gene, which encodes a subunit of soluble methane monooxygenase, showed that copies of this gene increased in parallel with cell counts during growth on either acetate or methane as the sole substrate. This verified that cells possessing the genetic basis of methane oxidation grew on acetate as well as methane. Cloning of 16S rRNA genes and fluorescence in situ hybridization with strain-specific and genus-specific oligonucleotide probes detected no contaminants in cultures. The growth rate and carbon conversion efficiency were higher on acetate than on methane, and when both substrates were provided in excess, acetate was preferably used and methane oxidation was shut down. Our data demonstrate that not all methanotrophic bacteria are limited to growing on one-carbon compounds. This could have major implications for understanding the factors controlling methane fluxes in the environment.

scholarly journals Diploptene <i>δ</i><sup>13</sup>C values from contemporary thermokarst lake sediments show complex spatial variation

2016 ◽  
Vol 13 (8) ◽  
pp. 2611-2621 ◽  
Author(s):  
Kimberley L. Davies ◽  
Richard D. Pancost ◽  
Mary E. Edwards ◽  
Katey M. Walter Anthony ◽  
Peter G. Langdon ◽  
...  
Keyword(s):  
Spatial Variation ◽  
Lake Sediments ◽  
Methane Oxidation ◽  
Methane Production ◽  
Small Scale ◽  
Δ13c Values ◽  
Thermokarst Lakes ◽  
Methane Ebullition ◽  
Methane Efflux ◽  
Isotopic Signal

Abstract. Cryospheric changes in northern high latitudes are linked to significant greenhouse gas flux to the atmosphere, for example, methane that originates from organic matter decomposition in thermokarst lakes. The set of pathways that link methane production in sediments, via oxidation in the lake system, to the flux of residual methane to the atmosphere is complex and exhibits temporal and spatial variation. The isotopic signal of bacterial biomarkers (hopanoids, e.g. diploptene) in sediments has been used to identify contemporary ocean-floor methane seeps and, in the geological record, periods of enhanced methane production (e.g. the PETM). The biomarker approach could potentially be used to assess temporal changes in lake emissions through the Holocene via the sedimentary biomarker record. However, there are no data on the consistency of the signal of isotopic depletion in relation to source or on the amount of noise (unexplained variation) in biomarker values from modern lake sediments. We assessed methane oxidation as represented by the isotopic signal of biomarkers from methane oxidising bacteria (MOB) in multiple surface sediment samples in three distinct areas known to emit varying levels of methane in two shallow Alaskan thermokarst lakes. Diploptene was present and had δ13C values lower than −38 ‰ in all sediments analysed, suggesting methane oxidation was widespread. However, there was considerable variation in δ13C values within each area. The most 13C-depleted diploptene was found in an area of high methane ebullition in Ace Lake (diploptene δ13C values between −68.2 and −50.1 ‰). In contrast, significantly higher diploptene δ13C values (between −42.9 and −38.8 ‰) were found in an area of methane ebullition in Smith Lake. δ13C values of diploptene between −56.8 and −46.9 ‰ were found in the centre of Smith Lake, where ebullition rates are low but diffusive methane efflux occurs. The small-scale heterogeneity of the samples may reflect patchy distribution of substrate and/or MOB within the sediments. The two ebullition areas differ in age and type of organic carbon substrate, which may affect methane production, transport, and subsequent oxidation. Given the high amount of variation in surface samples, a more extensive calibration of modern sediment properties, within and among lakes, is required before down-core records of hopanoid isotopic signatures are developed.

UK landfill methane emissions: Use of mobile plume measurements and carbon isotopic characterisation to reassess oxidation rates for open and closed sites 

2021 ◽  
Author(s):  
Semra Bakkaloglu ◽  
Dave Lowry ◽  
Rebecca Fisher ◽  
James France ◽  
Euan Nisbet
Keyword(s):  
Methane Oxidation ◽  
Mole Fraction ◽  
Oxidation Rate ◽  
Methane Emissions ◽  
Isotopic Signature ◽  
Oxidation Rates ◽  
Landfill Cover ◽  
Carbon Isotopic ◽  
Landfill Sites ◽  
The Impact

&lt;p&gt;Biological methane oxidation in landfill cover material can be characterised using stable isotopes. Methane oxidation fraction is calculated from the carbon isotopic signature of emitted CH&lt;sub&gt;4&lt;/sub&gt;, with enhanced microbial consumption of methane in the aerobic portion of the landfill cover indicated by a shift to less depleted isotopic values in the residual methane emitted to air. This study was performed at four southwest England landfill sites. Mobile mole fraction measurement at the four sites was coupled with Flexfoil bag sampling of air for high-precision isotope analysis. Gas well samples collected from the pipeline systems and downwind plume air samples were utilized to estimate methane oxidation rate for whole sites. This work was designed to assess the impact on carbon isotopic signature and oxidation rate as UK landfill practice and waste streams have changed in recent years.&lt;/p&gt;&lt;p&gt;The landfill status such as closed and active, seasonal variation, cap stripping and site closure impact on landfill isotopic signature and oxidation rate were evaluated. The isotopic signature of &lt;sup&gt;13&lt;/sup&gt;C-CH&lt;sub&gt;4&lt;/sub&gt; values of emissions varied between -60 and -54&amp;#8240;, with an averaged value of -57 +- 2&amp;#8240; for methane from closed and active landfill sites. Methane emissions from older, closed landfill sites were typically more enriched in &lt;sup&gt;13&lt;/sup&gt;C than emissions from active sites. This study found that the isotopic signature of &lt;sup&gt;13&lt;/sup&gt;C-CH&lt;sub&gt;4&lt;/sub&gt; of fugitive methane did not show a seasonal trend, and there was no plume observed from a partial cap stripping process to assess changes in &lt;sup&gt;13&lt;/sup&gt;C-CH&lt;sub&gt;4&lt;/sub&gt;&amp;#160;&amp;#160;isotopic signatures of emitted methane. Also, the closure of an active landfill cell caused a significant decrease in mole fraction of measured CH&lt;sub&gt;4&lt;/sub&gt;, which was less depleted &lt;sup&gt;13&lt;/sup&gt;C in the emitted plume due to a higher oxidation rate. Methane oxidation, estimated from the isotope fractionation, ranged from 3 to 27%, with mean values of 7% and 15% for active and closed landfills, respectively. These results indicate that the oxidation rate is highly site specific.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;

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