Methanotrophic populations in estuarine sediment from Newport Bay, California

High methane concentrations in tidal salt marsh soils: Where does the methane go?

Tidal salt marshes produce and emit CH4 . Therefore, it is critical to understand the biogeochemical controls that regulate CH4 spatial and temporal dynamics in wetlands. The prevailing paradigm assumes that acetoclastic methanogenesis is the dominant pathway for CH4 production, and higher salinity concentrations inhibit CH4 production in salt marshes. Recent evidence shows that CH4 is produced within salt marshes via methylotrophic methanogenesis, a process not inhibited by sulfate reduction. To further explore this conundrum, we performed measurements of soil-atmosphere CH4 and CO2 fluxes coupled with depth profiles of soil CH4 and CO2 pore water gas concentrations, stable and radioisotopes, pore water chemistry, and microbial community composition to assess CH4 production and fate within a temperate tidal salt marsh. We found unexpectedly high CH4 concentrations up to 145,000 μmol mol-1 positively correlated with S2- (salinity range: 6.6-14.5 ppt). Despite large CH4 production within the soil, soil-atmosphere CH4 fluxes were low but with higher emissions and extreme variability during plant senescence (84.3 ± 684.4 nmol m-2  s-1 ). CH4 and CO2 within the soil pore water were produced from young carbon, with most Δ14 C-CH4 and Δ14 C-CO2 values at or above modern. We found evidence that CH4 within soils was produced by methylotrophic and hydrogenotrophic methanogenesis. Several pathways exist after CH4 is produced, including diffusion into the atmosphere, CH4 oxidation, and lateral export to adjacent tidal creeks; the latter being the most likely dominant flux. Our findings demonstrate that CH4 production and fluxes are biogeochemically heterogeneous, with multiple processes and pathways that can co-occur and vary in importance over the year. This study highlights the potential for high CH4 production, the need to understand the underlying biogeochemical controls, and the challenges of evaluating CH4 budgets and blue carbon in salt marshes.

Sulfate concentrations affect sulfate reduction pathways and methane consumption in coastal wetlands

Coastal wetlands are an important source of methane emissions, and understanding the mechanisms that control methane emissions from coastal wetlands is of great significance to global warming. Anaerobic oxidation of methane driven by sulfate is an important process to prevent methane emissions from coastal wetlands. The effects of environmental changes on this process and the function of the sulfate-methane transition zone (SMTZ) are poorly understood. In this study, spatiotemporal variations in pore-water geochemistry (concentrations of SO₄^2-, CH₄ and DIC as well as δ¹³C-DIC and δ¹³C-CH₄) in the Beidagang wetland, Tianjin, China, were investigated to unravel factors controlling the role of anaerobic oxidation of methane in coastal wetlands. Results show that the geochemical profile of pore-water is characterized by significant spatial and temporal variability, which may be related to changes in sulfate concentration, temperature and dissolved oxygen. The carbon isotope fractionation factors (ε_C) during methane oxidation range from 8.9‰ to 12.5‰, indicating that the sulfate-driven anaerobic oxidation of methane (S-AOM) dominates the methane oxidation in the Beidagang coastal wetland in both winter and summer, in both high and low salinity wetlands, and in both open water and littoral areas. However, sulfate concentration has a strong influence on the sulfate reduction pathways and methane consumption. The consumption of methane and sulfate by S-AOM is more significant in coastal wetlands with high sulfate concentrations, with S-AOM consuming nearly all of the upward-diffusing methane (96%) and downward-diffusing sulfate (96%). In addition, the dissolved inorganic carbon (DIC) produced in the pore-water mainly comes from methanogenesis, accounting for more than 80% of the total DIC pool, but in the areas with high sulfate concentrations in water column, the contribution of S-AOM to the DIC pool is greater, although only a small fraction of the total DIC pool (9%). The depth and width of the SMTZ show a clear spatial and temporal pattern, with active methanogenesis activity and upward high methane flux shoaling the SMTZ and increasing the risk of high methane emissions from coastal wetlands with low sulfate concentrations. Our findings highlight the importance of sulfate-driven anaerobic oxidation of methane in coastal wetlands and the effect of sulfate concentration on it. It contributes to our understanding of the mechanism of methane production and emissions from the coastal wetland system, particularly in light of the increased demand for coastal wetland restoration under global warming.

USCγ Dominated Community Composition and Cooccurrence Network of Methanotrophs and Bacteria in Subterranean Karst Caves

Karst caves have recently been demonstrated to act as a sink for atmospheric methane, due in part to consumption by microbes residing in caves that can oxidize methane at atmospheric levels. However, our knowledge about the responsible atmospheric methane-oxidizing bacteria (atmMOB) in this vast habitat remains limited to date. To address this issue, weathered rock samples from three karst caves were collected in Guilin City and subjected to high-throughput sequencing of pmoA and 16S rRNA genes. The results showed that members of the high-affinity upland soil cluster (USC), especially upland soil cluster gamma (USCγ), with absolute abundances of 104 to 109 copies · g-1 dry sample, dominated the atmMOB communities, while Proteobacteria and Actinobacteria dominated the overall bacterial communities. Moreover, USCγ was a keystone taxon in cooccurrence networks of both the atmMOB and the total bacterial community, whereas keystone taxa in the bacterial network also included Gaiella and Aciditerrimonas. Positive links overwhelmingly dominated the cooccurrence networks of both atmMOB and the total bacterial community, indicating a consistent response to environmental disturbances. Our study shed new insights on the diversity and abundances underlining atmMOB and total bacterial communities and on microbial interactions in subterranean karst caves, which increased our understanding about USC and supported karst caves as a methane sink. IMPORTANCE Karst caves have recently been demonstrated to be a potential atmospheric methane sink, presumably due to consumption by methane-oxidizing bacteria. However, the sparse knowledge about the diversity, distribution, and community interactions of methanotrophs requires us to seek further understanding of the ecological significance of methane oxidation in these ecosystems. Our pmoA high-throughput results from weathered rock samples from three karst caves in Guilin City confirm the wide occurrence of atmospheric methane-oxidizing bacteria in this habitat, especially those affiliated with the upland soil cluster, with a gene copy number of 104 to 109 copies per gram dry sample. Methanotrophs and the total bacterial communities had more positive than negative interactions with each other as indicated by the cooccurrence network, suggesting their consistent response to environmental disturbance. Our results solidly support caves as an atmospheric methane sink, and they contribute to a comprehensive understanding of the diversity, distribution, and interactions of microbial communities in subsurface karst caves.

Simultaneous Denitrification and Bio-Methanol Production for Sustainable Operation of Biogas Plants

This study was conducted to secure the sustainability of biogas plants for generating resources from food waste (FW) leachates, which are prohibited from marine dumping and have been obligated to be completely treated on land since 2013 in South Korea. The aim of this study is to reduce the nitrogen load of the treatment process while producing bio-methanol using digested FW leachate diverted into wastewater treatment plants. By using biogas in conditions where methylobacter (M. marinus 88.2%) with strong tolerance to highly chlorinated FW leachate dominated, 3.82 mM of methanol production and 56.1% of total nitrogen (TN) removal were possible. Therefore, the proposed method can contribute to improving the treatment efficiency by accommodating twice the current carried-in FW leachate amount based on TN or by significantly reducing the nitrogen load in the subsequent wastewater treatment process. Moreover, the produced methanol can be an effective alternative for carbon source supply for denitrification in the subsequent process.

Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic-Anoxic Interface of the Congo Deep-Sea Fan

Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3-5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic-anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase (pmoA) genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs.

The Bacteriohopanepolyol Inventory of Novel Aerobic Methane Oxidising Bacteria Reveals New Biomarker Signatures of Aerobic Methanotrophy in Marine Systems

Aerobic methane oxidation (AMO) is one of the primary biologic pathways regulating the amount of methane (CH4) released into the environment. AMO acts as a sink of CH4, converting it into carbon dioxide before it reaches the atmosphere. It is of interest for (paleo)climate and carbon cycling studies to identify lipid biomarkers that can be used to trace AMO events, especially at times when the role of methane in the carbon cycle was more pronounced than today. AMO bacteria are known to synthesise bacteriohopanepolyol (BHP) lipids. Preliminary evidence pointed towards 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol) being a characteristic biomarker for Type I methanotrophs. Here, the BHP compositions were examined for species of the recently described novel Type I methanotroph bacterial genera Methylomarinum and Methylomarinovum, as well as for a novel species of a Type I Methylomicrobium. Aminopentol was the most abundant BHP only in Methylomarinovum caldicuralii, while Methylomicrobium did not produce aminopentol at all. In addition to the expected regular aminotriol and aminotetrol BHPs, novel structures tentatively identified as methylcarbamate lipids related to C-35 amino-BHPs (MC-BHPs) were found to be synthesised in significant amounts by some AMO cultures. Subsequently, sediments and authigenic carbonates from methane-influenced marine environments were analysed. Most samples also did not contain significant amounts of aminopentol, indicating that aminopentol is not a useful biomarker for marine aerobic methanotophic bacteria. However, the BHP composition of the marine samples do point toward the novel MC-BHPs components being potential new biomarkers for AMO.

New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase

Marine methylotrophs play a key role in the global carbon cycle by metabolizing reduced one-carbon compounds that are found in high concentrations in marine environments. Genome, physiology and diversity studies have been greatly facilitated by the numerous model organisms brought into culture. However, the availability of marine representatives remains poor. Here, we report the isolation of four novel species from North Sea sediment enrichments closely related to the Alphaproteobacterium Methyloceanibacter caenitepidi. Each of the newly isolated Methyloceanibacter species exhibited a clear genome sequence divergence which was reflected in physiological differences. Notably one strain R-67174 was capable of oxidizing methane as sole source of carbon and energy using solely a soluble methane monooxygenase and represents the first marine Alphaproteobacterial methanotroph brought into culture. Differences in maximum cell density of >1.5 orders of magnitude were observed. Furthermore, three strains were capable of producing nitrous oxide from nitrate. Together, these findings highlight the metabolic and physiologic variability within closely related Methyloceanibacter species and provide a new understanding of the physiological basis of marine methylotrophy.

A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity

River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane-oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4-30°C, pH 6-8, 1-15 g l(-1) NaCl), communities were enriched by sequences affiliated with Methylobacter and Methylomonas spp. and specifically a Methylobacter psychrophilus-related species at 4-21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l(-1) selected for putative thermophiles (Methylocaldum), acidophiles (Methylosoma) and haloalkaliphiles (Methylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary.

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.

Molecular diversity of the methanotrophic bacteria communities associated with disused tin-mining ponds in Kampar, Perak, Malaysia

In a previous study, notable differences of several physicochemical properties, as well as the community structure of ammonia oxidizing bacteria as judged by 16S rRNA gene analysis, were observed among several disused tin-mining ponds located in the town of Kampar, Malaysia. These variations were associated with the presence of aquatic vegetation as well as past secondary activities that occurred at the ponds. Here, methane oxidizing bacteria (MOB), which are direct participants in the nutrient cycles of aquatic environments and biological indicators of environmental variations, have been characterised via analysis of pmoA functional genes in the same environments. The MOB communities associated with disused tin-mining ponds that were exposed to varying secondary activities were examined in comparison to those in ponds that were left to nature. Comparing the sequence and phylogenetic analysis of the pmoA clone libraries at the different ponds (idle, lotus-cultivated and post-aquaculture), we found pmoA genes indicating the presence of type I and type II MOB at all study sites, but type Ib sequences affiliated with the Methylococcus/Methylocaldum lineage were most ubiquitous (46.7 % of clones). Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture was observed to harbor the highest richness of MOB. However, varying secondary activity or sample type did not show a strong variation in community patterns as compared to the ammonia oxidizers in our previous study.

The effect of nitrogen enrichment on c(1)-cycling microorganisms and methane flux in salt marsh sediments

Methane (CH₄) flux from ecosystems is driven by C₁-cycling microorganisms – the methanogens and the methylotrophs. Little is understood about what regulates these communities, complicating predictions about how global change drivers such as nitrogen enrichment will affect methane cycling. Using a nitrogen addition gradient experiment in three Southern California salt marshes, we show that sediment CH₄ flux increased linearly with increasing nitrogen addition (1.23 μg CH₄ m⁻² day⁻¹ for each g N m⁻² year⁻¹ applied) after 7 months of fertilization. To test the reason behind this increased CH₄ flux, we conducted a microcosm experiment altering both nitrogen and carbon availability under aerobic and anaerobic conditions. Methanogenesis appeared to be both nitrogen and carbon (acetate) limited. N and C each increased methanogenesis by 18%, and together by 44%. In contrast, methanotrophy was stimulated by carbon (methane) addition (830%), but was unchanged by nitrogen addition. Sequence analysis of the sediment methylotroph community with the methanol dehydrogenase gene (mxaF) revealed three distinct clades that fall outside of known lineages. However, in agreement with the microcosm results, methylotroph abundance (assayed by qPCR) and composition (assayed by terminal restriction fragment length polymorphism analysis) did not vary across the experimental nitrogen gradient in the field. Together, these results suggest that nitrogen enrichment to salt marsh sediments increases methane flux by stimulating the methanogen community.

Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09

Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria, isolated from coastal seawater. Here we present the complete genome sequence of this strain, the first available from an aerobic marine methanotroph.

Emerging topics in marine methane biogeochemistry

Our knowledge of physical, chemical, geological and biological processes affecting methane in the ocean and in underlying sediments is expanding at a rapid pace. On first inspection, marine methane biogeochemistry appears simple: Methane distribution in sediment is set by the deposition pattern of organic material, and the balance of sources and sinks keeps its concentration low in most waters. However, recent research reveals that methane is affected by complex biogeochemical processes whose interactions are understood only at a superficial level. Such processes span the deep-subsurface, near subsurface, and ocean waters, and relate primarily to the production, consumption, and transport of methane. The purpose of this synthesis is to examine select processes within the framework of methane biogeochemistry, to formulate hypotheses on how they might operate and interact with one another, and to consider their controls.

Methane assimilation and trophic interactions with marine Methylomicrobium in deep-water coral reef sediment off the coast of Norway

Deep-water coral reefs are seafloor environments with diverse biological communities surrounded by cold permanent darkness. Sources of energy and carbon for the nourishment of these reefs are presently unclear. We investigated one aspect of the food web using DNA stable-isotope probing (DNA-SIP). Sediment from beneath a Lophelia pertusa reef off the coast of Norway was incubated until assimilation of 5 micromol 13CH4 g(-1) wet weight occurred. Extracted DNA was separated into 'light' and 'heavy' fractions for analysis of labelling. Bacterial community fingerprinting of PCR-amplified 16S rRNA gene fragments revealed two predominant 13C-specific bands. Sequencing of these bands indicated that carbon from 13CH4 had been assimilated by a Methylomicrobium and an uncultivated member of the Gammaproteobacteria. Cloning and sequencing of 16S rRNA genes from the heavy DNA, in addition to genes encoding particulate methane monooxygenase and methanol dehydrogenase, all linked Methylomicrobium with methane metabolism. Putative cross-feeders were affiliated with Methylophaga (Gammaproteobacteria), Hyphomicrobium (Alphaproteobacteria) and previously unrecognized methylotrophs of the Gammaproteobacteria, Alphaproteobacteria, Deferribacteres and Bacteroidetes. This first marine methane SIP study provides evidence for the presence of methylotrophs that participate in sediment food webs associated with deep-water coral reefs.

Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin

Methane vents are of significant geochemical and ecological importance. Notable progress has been made toward understanding anaerobic methane oxidation in marine sediments; however, the diversity and distribution of aerobic methanotrophs in the water column are poorly characterized. Both environments play an essential role in regulating methane release from the oceans to the atmosphere. In this study, the diversity of particulate methane monooxygenase (pmoA) and 16S rRNA genes from two methane vent environments along the California continental margin was characterized. The pmoA phylotypes recovered from methane-rich sediments and the overlying water column differed. Sediments harbored the greatest number of unique pmoA phylotypes broadly affiliated with the Methylococcaceae family, whereas planktonic pmoA phylotypes formed three clades that were distinct from the sediment-hosted methanotrophs and distantly related to established methanotrophic clades. Water column-associated phylotypes were highly similar between field sites, suggesting that planktonic methanotroph diversity is controlled primarily by environmental factors rather than geographical proximity. Analysis of 16S rRNA genes from methane-rich waters did not readily recover known methanotrophic lineages, with only a few phylotypes demonstrating distant relatedness to Methylococcus. The development of new pmo primers increased the recovery of monooxygenase genes from the water column and led to the discovery of a highly diverged monooxygenase sequence which is phylogenetically intermediate to Amo and pMMO. This sequence potentiates insight into the amo/pmo superfamily. Together, these findings lend perspective into the diversity and segregation of aerobic methanotrophs within different methane-rich habitats in the marine environment.

Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary

The surface microlayer (SML) is the thin biogenic film found at the surface of a water body. The SML is poorly understood but has been shown to be important in biogeochemical cycling and sea-air gas exchange. We sampled the SML of the Blyth estuary at two sites (salinities 21 and 31 psu) using 47 mm polycarbonate membranes. DNA was extracted from the SML and corresponding subsurface water (0.4 m depth) and microbial (bacteria and archaea) community analysis was performed using denaturing gradient gel electrophoresis of 16S rRNA gene PCR amplicons. The diversity of bacterial functional genes that encode enzyme subunits for methane monooxygenase (pmoA and mmoX) and carbon monoxide dehydrogenase (coxL) was assessed using PCR, clone library construction and restriction fragment length polymorphism (RFLP) analysis. Methanotroph genes were present only in low copy numbers and pmoA was detected only in subsurface samples. Diversity of mmoX genes was low and most of the clone sequences detected were similar to those of mmoX from Methylomonas spp. Interestingly, some sequences detected in the SML were different from those detected in the subsurface. RFLP analysis of coxL clone libraries indicated a high diversity of carbon monoxide (CO)-utilizing bacteria in the estuary. The habitats of the closely related coxL sequences suggest that CO-utilizing bacteria in the estuary are recruited from both marine and freshwater/terrestrial inputs. In contrast, methanotroph recruitment appears to occur solely from freshwater input into the estuary.

Methylosoma difficile gen. nov., sp. nov., a novel methanotroph enriched by gradient cultivation from littoral sediment of Lake Constance

A novel methanotroph, strain LC 2(T), was isolated from the littoral sediment of Lake Constance by enrichment in opposing gradients of methane and oxygen, followed by traditional isolation methods. Strain LC 2(T) grows on methane or methanol as its sole carbon and energy source. It is a Gram-negative, non-motile, pale-pink-coloured methanotroph showing typical intracytoplasmic membranes arranged in stacks. Cells are coccoid, elliptical or rod-shaped and occur often in pairs. Strain LC 2(T) grows at low oxygen concentrations and in counter-gradients of methane and oxygen. It can grow on medium free of bound nitrogen, possesses the nifH gene and fixes atmospheric nitrogen at low oxygen pressure. It grows at neutral pH and at temperatures between 10 and 30 degrees C. Phylogenetically, it is most closely related to the genus Methylobacter, with the type strains of Methylobacter tundripaludum and Methylobacter psychrophilus showing 94 and 93.4 % 16S rRNA gene sequence similarity, respectively. Furthermore, the pmoA gene sequence of strain LC 2(T) is most closely related to pmoA gene sequences of Methylobacter strains (92 % similar to Methylobacter sp. LW 12 by deduced amino acid sequence identity). The DNA G+C content is 49.9 mol% and the major cellular fatty acid is 16 : 1omega7c (60 %). Strain LC 2(T) (=JCM 14076(T)=DSM 18750(T)) is described as the type strain of a novel species within a new genus, Methylosoma difficile gen. nov., sp. nov.