Methane Sink Research Articles

Methylobacter couples methane oxidation and N2O production in hypoxic wetland soil

Aerobic methanotrophs differ in metabolic mechanisms under hypoxic environments. Methane oxidation combined with nitrate/nitrite reduction is related to the emissions of greenhouse gases methane and nitrous oxide (N2O). However, the mechanisms underlying methane oxidation and N2O production remain to be elucidated through environmental and pure culture experiments. Here, microcosmic experiments of inhibition of methane oxidation and isotope tracing revealed that methane oxidation coupled to N2O production occurred in hypoxic wetland soil. RNA sequence analysis showed that Methylobacter was the dominant methane oxidizer, and a novel strain Methylobacter sp. YRD-M1 was isolated. Genomic and pure cultured results suggested that nitrite was the electron acceptor of the isolated strain under hypoxic conditions with N2O production. Despite lacking the genetic potential for dissimilatory nitrate reduction, assimilatory nitrate reductase may be involved in incomplete denitrification, leading to N2O production. In addition, strain YRD-M1 consumed dissolved oxygen to below 10 μM, showing a strong oxygen affinity. Furthermore, fermentation was induced with acetate and succinate released during hypoxic incubation. The strain YRD-M1 showed flexible and versatile metabolic processes in oxygen-limited systems. Notably, Methylobacter-like methanotrophs were widely distributed in terrestrial environments. Overall, our findings show that Methylobacter couples methane oxidation and N2O production in hypoxic environments from soil to pure culture, highlighting the potential role of related microbes in linking methane sinks and N2O sources in oxygen-limited environments.

Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China

Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH4). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO3−), sulfate (SO42−), and nitrous oxide (N2O) flux, among them, soil N substances (TN, NO3−, N2O) have essential regulatory roles in the AOM process, while NO3− and N2O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH4 sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH4 biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.

Mining the landfill soil metagenome for denitrifying methanotrophic taxa and validation of methane oxidation in microcosm

In the present study, the microbial community residing at different depths of the landfill was characterized to assess their roles in serving as a methane sink. Physico-chemical characterization revealed the characteristic signatures of anaerobic degradation of organic matter in the bottom soil (50–60 cm) and, active process of aerobic denitrification in the top soil (0–10 cm). This was also reflected from the higher abundance of bacterial domain in the top soil metagenome represented by dominant phyla Proteobacteria and Actinobacteria which are prime decomposers of organic matter in landfill soils. The multiple fold higher relative abundances of the two most abundant genera; Streptomyces and Intrasporangium in the top soil depicted greater denitrifying taxa in top soil than the bottom soil. Amongst the aerobic methanotrophs, the genera Methylomonas, Methylococcus, Methylocella, and Methylacidiphilum were abundantly found in the top soil metagenome that were essential for oxidizing methane generated in the landfill. On the other hand, the dominance of archaeal domain represented by Methanosarcina and Methanoculleus in the bottom soil highlighted the complete anaerobic digestion of organic components via acetoclasty, carboxydotrophy, hydrogenotrophy, methylotrophy. Functional characterization revealed a higher abundance of methane monooxygenase gene in the top soil and methyl coenzyme M reductase gene in the bottom soil that correlated with the higher relative abundance of aerobic methanotrophs in the top soil while methane generation being the active process in the highly anaerobic bottom soil in the landfill. The activity dependent abundance of endogenous microbial communities in the different zones of the landfill was further validated by microcosm studies in serum bottles which established the ability of the methanotrophic community for methane metabolism in the top soil and their potential to serve as sink for methane. The study provides a better understanding about the methanotrophs in correlation with their endogenous environment, so that these bacteria can be used in resolving the environmental issues related to methane and nitrogen management at landfill site.

Atmospheric CO2 and CH4 Fluctuations over the Continent-Sea Interface in the Yenisei River Sector of the Kara Sea

Observations of the atmospheric sources and sinks of carbon dioxide (CO2) and methane (CH4) in the pan-Arctic domain are extremely scarce, limiting our knowledge of carbon turnover in this climatically sensitive environment and the fate of the enormous carbon reservoirs conserved in the permafrost. Especially critical are the gaps in the high latitudes of Siberia, covered by the vast permafrost underlain tundra, where only several atmospheric monitoring sites are operational. This paper presents the first two years (September 2018–January 2021) of accurate continuous observations of atmospheric CO2 and CH4 dry mole fractions at the recently deployed tower-based measurement station “DIAMIS” (73.5068° N, 80.5198° E) located on the southwestern coast of the Taimyr Peninsula, Siberia, at the Gulf of the Yenisei River that opens to the Kara Sea (Arctic Ocean). In this paper, we summarized the scientific rationale of the site, examined the seasonal footprint of the station with an analysis of terrestrial vegetation and maritime sector contributing to the captured atmospheric signal, and illustrated temporal patterns of CO2 and CH4 for the daytime mixed atmospheric layer over the continent–sea interface. Along with the temporal variations reflecting a signal caused pan-Arctic and not very much influenced by the local processes, we analyzed the spatiotemporal distribution of the synoptic anomalies representing the atmospheric signatures of regional sources and sinks of CO2 and CH4 for the studied high-arctic Siberian domain of ~625 thousand km2, with nearly equal capturing the land surface (54%) and the ocean (46%) throughout the year. Both for CO2 and CH4, we have observed a sea–continent declining trend, presuming a larger depletion of trace gases in the maritime air masses compared to the continental domain. So far, over the Kara Sea, we have not detected any prominent signals of CH4 that might have indicated processes of subsea permafrost degradation and occurrence of cold seeps–still mainly observed in the eastern Arctic Seas—The Laptev Sea and the East-Siberian Sea.

Attribution of the 2020 surge in atmospheric methane by inverse analysis of GOSAT observations

Atmospheric methane mixing ratio rose by 15 ppbv between 2019 and 2020, the fastest growth rate on record. We conduct a global inverse analysis of 2019–2020 Greenhouse Gases Observing Satellite observations of atmospheric methane to analyze the combination of sources and sinks driving this surge. The imbalance between sources and sinks of atmospheric methane increased by 31 Tg a−1 from 2019 to 2020, representing a 36 Tg a−1 forcing (direct changes in methane emissions and OH concentrations) on the methane budget away from steady state. 86% of the forcing in the base inversion is from increasing emissions (82 ± 18% in the nine-member inversion ensemble), and only 14% is from decrease in tropospheric OH. Half of the increase in emissions is from Africa (15 Tg a−1) and appears to be driven by wetland inundation. There is also a large relative increase in emissions from Canada and Alaska (4.8 Tg a−1, 24%) that could be driven by temperature sensitivity of boreal wetland emissions.

Unravelling how biochar and dung amendments determine the functional structure and community assembly related to methane metabolisms in grassland soils

Biochar and dung amendments have been extensively employed in soil remediation and fertilization of grasslands, which are the largest terrestrial sinks for methane. However, how these exogenous amendments regulate methane metabolisms at the molecular and community levels remains elusive. In this study, we investigated the functional genes and community assemblies of methanogens and methanotrophs using Geochip 5.0 and high-throughput sequencing to reveal the impacts of biochar and dung on soil methanogenesis and methane oxidation. The interactions between methane metabolic genes and other biogeochemical genes were also examined. According to Geochip microarrays, methanogenic gene mcrA decreased and increased with dung or biochar amendment, respectively; The methanotrophic gene pmoA showed a reverse but not significant tendency. Undominated processes contributed 65.51% to replace homogeneous selections as primary driving forces of methanogen assembly after dung amendment; the contribution of dispersal limitation increased to 46.13% in methanotroph assembly after biochar amendment. The diversity and association of co-occurrence networks for carbon–nitrogen cycling genes decreased after exogenous amendments. These results indicated that biochar and dung amendments prominently regulated the functional genes and community assembly involved in methane metabolisms. The co-existence patterns of methane metabolic genes and other related geochemical genes were also shaped by these amendments. This study provides the scientific reference for the development of grassland management in the context of global warming.Graphical

Occurrence of methane-oxidizing bacteria and methanogenic archaea in earth’s cave systems—A metagenomic analysis

Karst ecosystems represent up to 25% of the land surface and recent studies highlight their potential role as a sink for atmospheric methane. Despite this, there is limited knowledge of the diversity and distribution of methane-oxidizing bacteria (MOB) or methanogens in karst caves and the sub-surface environment in general. Here, we performed a survey of 14 shotgun metagenomes from cave ecosystems covering a broad set of environmental conditions, to compare the relative abundance and phylogenetic diversity of MOB and methanogens, targeting biomarker genes for methane monooxygenase (pmoA and mmoX) and methyl-coenzyme M reductase (mcrA). Taxonomic analysis of metagenomes showed 0.02–1.28% of classified reads were related to known MOB, of which Gammaproteobacterial MOB were the most abundant making up on average 70% of the surveyed caves’ MOB community. Potential for biogenic methane production in caves was also observed, with 0.008–0.39% of reads classified to methanogens and was dominated by sequences related to Methanosarcina. We have also generated a cave ecosystems protein database (CEPD) based on protein level assembly of cave metagenomes that can be used to profile genes of interest.

Diversity and Composition of Methanotroph Communities in Caves.

ABSTRACTMethane oxidizing microorganisms (methanotrophs) are ubiquitous in the environment and represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated methanotrophs are abundant and contribute to CH4 dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of soils collected from > 20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98%) of the samples, including cave sites where CH4 concentrations were at or below detection limits (≤0.3 ppmv). We identified a core methanotroph community among caves comprised of high-affinity methanotrophs. Although associated with local-scale mineralogy, methanotroph composition did not systematically vary between the entrances and interior of caves, where CH4 concentrations varied. We also observed methanotrophs are able to disperse readily between cave systems showing these organisms have low barriers to dispersal. Lastly, the relative abundance of methanotrophs was positively correlated with cave-air CH4 concentrations, suggesting these microorganisms contribute to CH4 flux in subterranean ecosystems.IMPORTANCE Recent observations have shown the atmospheric greenhouse gas methane (CH4) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH4 oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14% of Earth’s land surface area, and therefore may represent a potentially important, but overlooked, CH4 sink. We sampled cave soils to gain a better understand the community composition and structure of cave methanotrophs. Our results show the members of the USC-γ clade are dominant in cave communities and can easily disperse through the environment, methanotroph relative abundance was correlated with local scale mineralogy of soils, and the relative abundance of methanotrophs was positively correlated with CH4 concentrations in cave air.

A novel Methylomirabilota methanotroph potentially couples methane oxidation to iodate reduction.

Methane oxidizing microbes play a key role in reducing the emission of this potent greenhouse gas to the atmosphere. The known versatility of the recently discovered anaerobic Methylomirabilota methanotrophs is limited. Here, we report a novel uncultured Methylomirabilis species, Candidatus Methylomirabilis iodofontis, with the genetic potential of iodate respiration from biofilm in iodine-rich cavern spring water. Star-like cells resembling Methylomirabilis oxyfera were directly observed from the biofilm and a high-quality metagenome-assembled genome (MAG) of Ca. M. iodofontis was assembled. In addition to oxygenic denitrification and aerobic methane oxidation pathways, the M. iodofontis MAG also indicated its iodate-reducing potential, a capability that would enable the bacterium to use iodate other than nitrite as an electron acceptor, a hitherto unrecognized metabolic potential of Methylomirabilota methanotrophs. The results advance the current understanding of the ecophysiology of anaerobic Methylomirabilota methanotrophs and may suggest an additional methane sink, especially in iodate-rich ecosystems.

Prospecting the significance of methane-utilizing bacteria in agriculture.

Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.

Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves.

Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane-oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption, we collected weathered rocks and sediments from three different caves in southwestern China. We determined the potential methane oxidization rates in the range of 1.25 ± 0.08 to 1.87 ± 0.41 ng CH4 g-1 DW h-1 , which are comparable to those reported in forest and grassland soils. Results showed that alkaline oligotrophic caves harbour high numbers of atmMOB, particularly upland soil cluster (USC), which significantly correlated with temperature, CH4 and CO2 concentrations. The absolute abundance of USCγ was higher than that of USCα. USCγ-OPS (open patch soil) and USCγ-SS (subsurface soil) dominated in most samples, whereas USCα-BFS (boreal forest soil) only predominated in the sediments near cave entrances, indicating niche differentiation of atmMOB in caves. Overwhelming dominance of homogenous selection in community assembly resulted in convergence of atmMOB communities. Collectively, our results demonstrated the niche differentiation of USC in subsurface alkaline caves and their non-negligible methane-oxidizing potential, providing brand-new knowledge about atmMOB ecology in subsurface biosphere.

Impact of interannual and multidecadal trends on methane-climate feedbacks and sensitivity

We estimate the causal contributions of spatiotemporal changes in temperature (T) and precipitation (Pr) to changes in Earth’s atmospheric methane concentration (CCH4) and its isotope ratio δ13CH4 over the last four decades. We identify oscillations between positive and negative feedbacks, showing that both contribute to increasing CCH4. Interannually, increased emissions via positive feedbacks (e.g. wetland emissions and wildfires) with higher land surface air temperature (LSAT) are often followed by increasing CCH4 due to weakened methane sink via atmospheric •OH, via negative feedbacks with lowered sea surface temperatures (SST), especially in the tropics. Over decadal time scales, we find alternating rate-limiting factors for methane oxidation: when CCH4 is limiting, positive methane-climate feedback via direct oceanic emissions dominates; when •OH is limiting, negative feedback is favoured. Incorporating the interannually increasing CCH4 via negative feedbacks gives historical methane-climate feedback sensitivity ≈ 0.08 W m−2 °C−1, much higher than the IPCC AR6 estimate.

Genomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soil.

Municipal landfills are known for methane production and a source of nitrate pollution leading to various environmental issues. Therefore, this niche was selected for the isolation of one-carbon (C1) utilizing bacteria with denitrifying capacities using anaerobic enrichment on nitrate mineral salt medium supplemented with methanol as carbon source. Eight axenic cultures were isolated of which, isolate AAK/M5 demonstrated thehighest methanol removal (73.28%) in terms of solublechemical oxygen demand and methane removal (41.27%) at the expense of total nitrate removal of 100% and 33% respectively. The whole genome characterization with phylogenomic approach suggested that the strain AAK/M5 could be assigned to Pseudomonas aeruginosa with close neighbours as type strains DVT779, AES1M, W60856, and LES400. The circular genome annotation showed the presence of complete set of genes essential for methanol utilization and complete denitrification process. The study demonstrates the potential of P. aeruginosa strain AAK/M5 in catalysing methane oxidation thus serving as a methane sink vis-à-vis utilization of nitrate. Considering the existence of such bacteria at landfill site, the study highlights the need to develop strategies for their enrichment and designing of efficient catabolic activity for such environments.

Order of magnitude wall time improvement of variational methane inversions by physical parallelization: a demonstration using TM5-4DVAR

Abstract. Atmospheric inversions are used to constrain emissions of trace gases using atmospheric mole-fraction measurements. The four-dimensional variational (4DVAR) inversion approach allows optimization of emissions at a higher temporal and spatial resolution than ensemble or analytical approaches but provides limited opportunities for scalable parallelization because it is an iterative optimization method. Multidecadal variational inversions are needed to optimally extract information from the long measurement records of long-lived atmospheric trace gases like carbon dioxide and methane. However, the wall time needed – up to months – complicates these multidecadal inversions. The physical parallelization (PP) method introduced by Chevallier (2013) addresses this problem for carbon dioxide inversions by splitting the period of the chemical transport model into blocks and running them in parallel. Here, we present a new implementation of the PP method which is suitable for methane inversions accounting for the chemical sink of methane. The performance of the PP method is tested in an 11-year inversion using a TM5-4DVAR inversion setup that assimilates surface observations to optimize methane emissions at grid scale. Our PP implementation improves the wall time performance by a factor of 5 and shows excellent agreement with a full serial inversion in an identical configuration (global mean emissions difference =0.06 % with an interannual variation correlation R=0.99; regional mean emission difference <5 % and interannual variation R>0.94). The wall time improvement of the PP method increases with the size of the inversion period. The PP method is planned to be used in future releases of the Copernicus Atmosphere Monitoring Service (CAMS) multidecadal methane reanalysis.

Maintaining grass coverage increases methane uptake in Amazonian pastures, with a reduction of methanogenic archaea in the rhizosphere

Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest-to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. We also assessed changes in the soil microbial community structure of both bare (bulk) and rhizospheric pasture soils through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp., Methanocella sp., Methanobacterium sp., and Rice Cluster I. Further, we showed that soil liming to increasing pH compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40–80 days. Liming reduced the relative abundance of Beijerinckiacea family in forest soils, which account for many known methanotrophs. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, compared to bare (bulk) pasture soil.

Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep.

Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b ("Candidatus Methanocomedenaceae") and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. IMPORTANCE Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.

Variations in Concentration and Carbon Isotope Composition of Methanotroph Biomarkers in Sedge Peatlands Along the Altitude Gradient in the Changbai Mountain, China.

Northern peatlands are one of the largest natural sources of atmospheric methane globally. As the only biological sink of methane, different groups of methanotrophs use different carbon sources. However, the variations in microbial biomass and metabolism of different methanotrophic groups in peatlands along the altitude gradient are uncertain. We measured the concentrations and metabolic characteristics of type I (16:1ω7c and 16:1ω5c) and type II (18:1ω7c) methanotroph biomarkers using biomarkers and stable isotopes in eight Carex peatlands along an altitude gradient from 300 to 1,500 m in the Changbai Mountain, China. We found that the trends with altitude in concentrations of the type I and type II methanotroph biomarkers were different. The dominating microbial group changed from type I to type II methanotroph with increasing altitude. The concentrations of type I and type II methanotroph biomarkers were significantly affected by the total phosphorus, total nitrogen, and dissolved organic carbon, respectively. The δ13C values of type II methanotroph biomarkers changed significantly along the altitude gradient, and they were more depleted than type II methanotroph biomarkers, which indicates the difference in carbon source preference between type I and type II methanotrophs. This study highlights the difference in the concentration and carbon source utilization of type I and type II methanotrophic groups along the altitude gradient, and enhances our understanding of the metabolic process of methane mediated by methanotrophs and its impact on carbon-sink function in northern peatlands.

The Proteobacterial Methanotroph Methylosinus trichosporium OB3b Remodels Membrane Lipids in Response to Phosphate Limitation.

ABSTRACTMethane is a potent greenhouse gas in the atmosphere, and its concentration has continued to increase in recent decades. Aerobic methanotrophs, bacteria that use methane as the sole carbon source, are an important biological sink for methane, and they are widely distributed in the natural environment. However, relatively little is known on how methanotroph activity is regulated by nutrients, particularly phosphorus (P). P is the principal nutrient constraining plant and microbial productivity in many ecosystems, ranging from agricultural land to the open ocean. Using a model methanotrophic bacterium, Methylosinus trichosporium OB3b, we demonstrate here that this bacterium can produce P-free glycolipids to replace membrane phospholipids in response to P limitation. The formation of the glycolipid monoglucuronic acid diacylglycerol requires plcP-agt genes since the plcP-agt mutant is unable to produce this glycolipid. This plcP-agt-mediated lipid remodeling pathway appears to be important for M. trichosporium OB3b to cope with P stress, and the mutant grew significantly slower under P limitation. Interestingly, comparative genomics analysis shows that the ability to perform lipid remodeling appears to be a conserved trait in proteobacterial methanotrophs; indeed, plcP is found in all proteobacterial methanotroph genomes, and plcP transcripts from methanotrophs are readily detectable in metatranscriptomics data sets. Together, our study provides new insights into the adaptation to P limitation in this ecologically important group of bacteria.

Gaps in network infrastructure limit our understanding of biogenic methane emissions for the United States

Abstract. Understanding the sources and sinks of methane (CH4) is critical to both predicting and mitigating future climate change. There are large uncertainties in the global budget of atmospheric CH4, but natural emissions are estimated to be of a similar magnitude to anthropogenic emissions. To understand CH4 flux from biogenic sources in the United States (US) of America, a multi-scale CH4 observation network focused on CH4 flux rates, processes, and scaling methods is required. This can be achieved with a network of ground-based observations that are distributed based on climatic regions and land cover. To determine the gaps in physical infrastructure for developing this network, we need to understand the landscape representativeness of the current infrastructure. We focus here on eddy covariance (EC) flux towers because they are essential for a bottom-up framework that bridges the gap between point-based chamber measurements and airborne or satellite platforms that inform policy decisions and global climate agreements. Using dissimilarity, multidimensional scaling, and cluster analysis, the US was divided into 10 clusters distributed across temperature and precipitation gradients. We evaluated dissimilarity within each cluster for research sites with active CH4 EC towers to identify gaps in existing infrastructure that limit our ability to constrain the contribution of US biogenic CH4 emissions to the global budget. Through our analysis using climate, land cover, and location variables, we identified priority areas for research infrastructure to provide a more complete understanding of the CH4 flux potential of ecosystem types across the US. Clusters corresponding to Alaska and the Rocky Mountains, which are inherently difficult to capture, are the most poorly represented, and all clusters require a greater representation of vegetation types.

Greenhouse gas (CO2, CH4, and N2O) emissions after abandonment of agriculture

The GHG (CO2, CH4, N2O) emission potential along a chronosequence of former agricultural soils abandoned for 9 to 32 years were compared to an actively managed (on-going) agricultural soil (reference). The soils were incubated in mesocosms with and without manure amendment, and microbial functional groups involved in nitrous oxide emission were quantitatively assessed. Carbon dioxide emission significantly increased after agriculture abandonment (< 24 years) consistent with higher decomposition rate, but total emission decreased in the long term (> 29 years). With the cessation of agriculture, the abandoned sites generally became a net methane sink. Notably, total nitrous oxide emission showed a significant monotonic decrease over years of abandonment in response to manure amendment, possibly reflecting an altered capacity for (de)nitrification as indicated in the response of the (de)nitrifier abundance. Overall, our findings suggest that the GHG legacy of agriculture diminishes over time (> 29 years), with lowered GHG emissions and global warming potential (GWP) after abandonment of agriculture.