Links between archaeal community structure, vegetation type and methanogenic pathway in Alaskan peatlands

Microbial activity contributes to spatial heterogeneity of wetland methane fluxes

The emission of methane from wetlands is spatially heterogeneous, as concurrently measured surface fluxes can vary by orders of magnitude within the span of a few meters. Despite extensive study and the climatic significance of these emissions, it remains unclear what drives large, within-site variations. While geophysical factors (e.g., soil temperature) are known to correlate with methane (CH4) flux, measurable variance in these parameters often declines as spatial and temporal scales become finer. As methane emitted from wetlands is the direct, net product of microbial metabolisms which both produce and degrade CH4, it stands to reason that characterizing the spatial variability of microbial communities within a wetland-both horizontally and vertically-may help explain observed variances in flux. To that end, we surveyed microbial communities to a depth of 1 m across an ombrotrophic peat bog in Maine, USA using amplicon sequencing and gene expression techniques. Surface methane fluxes and geophysical factors were concurrently measured. Across the first meter of peat at the site, we observed significant changes in the abundance and composition of methanogenic taxa at every depth sampled, with variance in methanogen abundance explaining 70% of flux heterogeneity at a subset of plots. Among measured environmental factors, only peat depth emerged as correlated with flux, and had significant impact on the abundance and composition of methane-cycling communities. These conclusions suggest that a heightened awareness of how microbial communities are structured and spatially distributed within wetlands could offer improved insights into predicting CH4 flux dynamics. IMPORTANCE Globally, wetlands are one of the largest sources of methane (CH4), a greenhouse gas with a warming impact significantly greater than CO2. Methane produced in wetlands is the byproduct of a group of microorganisms which convert organic carbon into CH4. Despite our knowledge of how this process works, it is still unclear what drives dramatic, localized (<10 m) variance in emission rates from the surface of wetlands. While environmental conditions, like soil temperature or water table depth, correlate with methane flux when variance in these factors is large (e.g., spring vs fall), the explanatory power of these variables decline when spatial and temporal scales become smaller. As methane fluxes are the direct product of microbial activity, we profiled how the microbial community varied, both horizontally and vertically, across a peat bog in Maine, USA, finding that variance in microbial communities was likely contributing to much of the observed variance in flux.

Winter drainage and film mulching cultivation mitigated CH4 emission by regulating the function and structure of methanogenic archaeal and fermenting bacterial communities in paddy soil

Winter flooding of harvested rice fields is a typical cropping system in mountainous areas, which emits considerable amounts of CH₄. Plastic film mulching cultivation is recognized as an important rice cultivation practice in paddy field for water-saving irrigation. However, the effects of these managements on CH₄ emissions in paddy soil and the underlying microbial mechanism are unclear. A field experiment was carried out with the application of winter drainage followed by traditional rice cultivation (WD), winter drainage followed by plastic film mulching cultivation (MC), as well as winter flooding followed by traditional rice cultivation (WF) as control in hilly paddy fields. We investigated the CH₄ emissions, functional (CH₄ production rate, ¹³C isotope) and structural (abundance, structure) responses of soil methanogenic archaeal and fermenting bacterial communities during rice season. Shifting the fields from WF into WD and MC substantially mitigated CH₄ emissions by 62.3% and 59.2%, respectively, paralleled with the enhancement of soil Eh and the reductions of soil DOC content. Compared with WF, WD and MC both significantly decreased CH₄ production rates and the copy numbers of mcrA gene. Moreover, an increasing contribution of hydrogenotrophic methanogenesis (from 30.7% to 50.0%) to total CH₄ production was observed during the conversion from WF to MC under an anaerobic incubation, paralleled with the decreased acetate content and increased δ¹³C values of acetate-methyl and total acetate. The communities of methanogenic archaea and fermenting bacteria strongly responded to the shift from WF to WD, while MC only showed significant effects on the methanogenic archaeal communities. Compared with WF, WD and MC significantly increased the relative abundance of Methanothrix, Methanosarcina and Methanocella, while those of Methanoregula, Massilia and Geobacter were decreased. The co-occurrence networks showed that WD and MC induced the loss of mixed methanogenic fermentation modules, indicating the decrease in functional biodiversity and redundancy of fermenting bacterial and methanogenic archaeal communities.The findings suggest that WD and MC approach mitigate CH₄ emission by regulating the function and structure of methanogenic archaeal and fermenting bacterial communities in paddy soil, which represent the effective management strategies considering the water availability and CH₄ mitigation in paddy-field agriculture.

Metagenomic evidence of suppressed methanogenic pathways along soil profile after wetland conversion to cropland

Wetland conversion to cropland substantially suppresses methane (CH4) emissions due to the strong suppression of methanogenesis, which consists of various pathways. In this study, we evaluated the cultivation impacts on four predominant CH4 production pathways, including acetate, carbon dioxide (CO2), methylamines, and methanol, in a wetland and cultivated cropland in northeastern China. The results showed significant suppression of CH4 production potential and the abundance of genes for all four methanogenic pathways in cropland. The consistency between CH4 production and methanogenesis genes indicates the robustness of genomic genes in analyzing methanogenesis. The suppression effects varied across seasons and along soil profiles, most evident in spring and 0 to 30 cm layers. The acetate pathway accounted for 55% in wetland vs. 70% in the cropland of all functional genes for CH4 production; while the other three pathways were stronger in response to cultivation, which presented as stronger suppressions in both abundance of functional genes (declines are 52% of CO2 pathway, 68% of methanol pathway, and 62% of methylamines pathway, vs. 19% of acetate pathway) and their percentages in four pathways (from 20 to 15% for CO2, 15 to 9% for methylamines, and 10 to 6% for methanol pathway vs. 55 to 70% for acetate pathway). The structural equation models showed that substrate availability was most correlated with CH4 production potential in the wetland, while the positive correlations of acetate, CO2, and methylamine pathways with CH4 production potential were significant in the cropland. The quantitative responses of four CH4 production pathways to land conversion reported in this study provide benchmark information for validating the CH4 model in simulating CH4 cycling under land use and land cover change.

Effects of agricultural land use on the differentiation of nitrifier communities and functional patterns from natural terrestrial ecosystems

Human activities severely affect the global nitrogen (N) cycle. Croplands receive intensive N fertilization; consequently, cropland and natural ecosystem differentiation often results in community and functional variation in N-transforming microbes, including nitrifiers, which perform nitrification central to N cycle. However, evidence of such variation is mostly limited to ammonia oxidizers (AO) in local fields, excluding soil heterogeneity and nitrite-oxidizing bacteria (NOB); the variation under diverse climatic and soil conditions is not comprehensively understood. We conducted a large-scale survey of 131 cropland and natural sites in China. The community patterns of ammonia-oxidizing bacteria (AOB) and NOB differed significantly between croplands and some natural ecosystems, whereas ammonia-oxidizing archaea (AOA) were not affected by ecosystem type. The AOB population and nitrification potential (NP) were significantly higher in agroecosystems than in natural systems except wetlands. Fewer co-occurrence interactions involving nitrifiers were observed in croplands than in natural ecosystems except forests, systematically indicating the ecological diversification of nitrifiers in potential microbial associations among these habitats. Ecosystem type, pH, organic matter (OM), total phosphorus (TP), mean annual temperature (MAT) and mean annual precipitation (MAP) were primary drivers of nitrifier community and functional shifts. This study provides the first large-scale evidence of overall nitrifier community (i.e., AOA, AOB and NOB) and potential functional shifts between agroecosystems and natural environments, enabling predictions of terrestrial N cycle under foreseeable natural land use conversions and global climate change.

Microbial Community Structures and Methanogenic Functions in Wetland Peat Soils

Methane metabolism in wetlands involves diverse groups of bacteria and archaea, which are responsible for the biological decomposition of organic matter under certain anoxic conditions. Recent advances in environmental omics revealed the phylogenetic diversity of novel microbial lineages, which have not been previously placed in the traditional tree of life. The present study aimed to verify the key players in methane production, either well-known archaeal members or recently identified lineages, in peat soils collected from wetland areas in Japan. Based on an ana­lysis of microbial communities using 16S rRNA gene sequencing and the mole­cular cloning of the functional gene, mcrA, a marker gene for methanogenesis, methanogenic archaea belonging to Methanomicrobiales, Methanosarcinales, Methanobacteriales, and Methanomassiliicoccales were detected in anoxic peat soils, suggesting the potential of CH₄ production in this natural wetland. “Candidatus Bathyarchaeia”, archaea with vast metabolic capabilities that is widespread in anoxic environments, was abundant in subsurface peat soils (up to 96% of the archaeal community) based on microbial gene quantification by qPCR. These results emphasize the importance of discovering archaea members outside of traditional methanogenic lineages that may have significant functions in the wetland biogeochemical cycle.

Impact of climate change-induced alterations in peatland vegetation phenology and composition on carbon balance

Global climate is changing faster than humankind has ever experienced. Model-based predictions of future climate are becoming more complex and precise, but they still lack crucial information about the reaction of some important ecosystems, such as peatlands. Peatlands belong to one of the largest carbon stores on the Earth. They are mostly distributed in high latitudes, where the temperature rises faster than in the other parts of the planet. Warmer climate and changes in precipitation patterns cause changes in the composition and phenology of peatland vegetation. Peat mosses are becoming less abundant, vascular plants cover is increasing, and the vegetation season and phenophases of vascular plants start sooner. The alterations in vegetation cause changes in the carbon assimilation and release of greenhouse gases. Therefore, this article reviews the impact of climate change-induced alterations in peatland vegetation phenology and composition on future climate and the uncertainties that need to be addressed for more accurate climate prediction.

Variations in bacterial and archaeal community structure and diversity along the soil profiles of a peatland in Southwest China

As bacteria and archaea are key components in the ecosystem, information on their dynamics in soil profiles is important for understanding the biogeochemical cycles in peatlands. However, little is known about the vertical distribution patterns of bacteria and archaea in the Bitahai peatland, or about their relationships with soil chemical properties. Here, bacterial and archaeal abundance, diversity, and composition of the Bitahai peatlands at 0-100 cm soil depths were analyzed by sequencing of 16S rRNA genes (Illumina, MiSeq). Soil pH, total C, N, and P concentrations and stoichiometric ratios were also estimated. The results revealed that total C and total N contents, as well as C:P and N:P ratios, significantly increased with increasing peatland soil depths, while total P decreased. The top three dominant phyla were Proteobacteria (39.64%), Acidobacteria (12.93%), and Chloroflexi (12.81%) in bacterial communities, and were Crenarchaeota (58.67%), Thaumarchaeota (14.34%), and Euryarchaeota (10.82%) in archaeal communities in the Bitahai peatland, respectively. The total relative abundance of methanogenic groups and ammonia-oxidizing microorganisms all significantly decreased with soil depth. Both bacterial and archaeal diversities were significantly affected by the soil depth. Soil C, N, and P concentrations and stoichiometric ratios markedly impacted the community structure and diversity in archaea, but not in bacteria. Therefore, these results highlighted that the microbial community structure and diversity depended on soil depth for the Bitahai peatlands, and the factors affecting bacteria and archaea in the Bitahai peatlands were different.

The role of oxygen in stimulating methane production in wetlands

Methane (CH4 ), a potent greenhouse gas, is the second most important greenhouse gas contributor to climate change after carbon dioxide (CO2 ). The biological emissions of CH4 from wetlands are a major uncertainty in CH4 budgets. Microbial methanogenesis by Archaea is an anaerobic process accounting for most biological CH4 production in nature, yet recent observations indicate that large emissions can originate from oxygenated or frequently oxygenated wetland soil layers. To determine how oxygen (O2 ) can stimulate CH4 emissions, we used incubations of Sphagnum peat to demonstrate that the temporary exposure of peat to O2 can increase CH4 yields up to 2000-fold during subsequent anoxic conditions relative to peat without O2 exposure. Geochemical (including ion cyclotron resonance mass spectrometry, X-ray absorbance spectroscopy) and microbiome (16S rDNA amplicons, metagenomics) analyses of peat showed that higher CH4 yields of redox-oscillated peat were due to functional shifts in the peat microbiome arising during redox oscillation that enhanced peat carbon (C) degradation. Novosphingobium species with O2 -dependent aromatic oxygenase genes increased greatly in relative abundance during the oxygenation period in redox-oscillated peat compared to anoxic controls. Acidobacteria species were particularly important for anaerobic processing of peat C, including in the production of methanogenic substrates H2 and CO2 . Higher CO2 production during the anoxic phase of redox-oscillated peat stimulated hydrogenotrophic CH4 production by Methanobacterium species. The persistence of reduced iron (Fe(II)) during prolonged oxygenation in redox-oscillated peat may further enhance C degradation through abiotic mechanisms (e.g., Fenton reactions). The results indicate that specific functional shifts in the peat microbiome underlie O2 enhancement of CH4 production in acidic, Sphagnum-rich wetland soils. They also imply that understanding microbial dynamics spanning temporal and spatial redox transitions in peatlands is critical for constraining CH4 budgets; predicting feedbacks between climate change, hydrologic variability, and wetland CH4 emissions; and guiding wetland C management strategies.

Methanogenic archaea in peatlands

Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.

Changes in Methane Emission and Community Composition of Methane-Cycling Microorganisms Along an Elevation Gradient in the Dongting Lake Floodplain, China

Methane (CH4) emission and environmental controls of CH4-cycling microorganisms are unclear in inland floodplains. Here, we examined soil CH4 emissions and the community composition of CH4-cycling microorganisms under three vegetation types—mudflat (MF, no vegetation cover), Carex meadow (CM, mainly Carex brevicuspis), and reed land (RL, mainly Miscanthus sacchariflorus)—from water-adjacent areas to higher-elevation land in the Dongting Lake floodplain, China. The results showed that CH4 emission is the highest in CM, while significant absorption was observed in the RL site. The abundance ratio of methanogen/methanotroph was the highest in CM, intermediate in MF, and lowest in RL. The Methanosarcinaceae family represented the dominant methanogens in the three sampling sites (41.32–75.25%). The genus Methylocystis (60.85%, type II methanotrophs) was dominant in CM, while Methylobacter and Methylosarcina (type I methanotrophs) were the dominant genera in MF (51.00%) and RL (50.24%), respectively. Structural equation model analysis showed that methanogen and methanotroph abundance were affected by water table depth, soil water content, and pH indirectly through soil organic content, total nitrogen, microbial biomass carbon, and microbial biomass nitrogen. These results indicated that the Dongting Lake floodplain may change from a CH4 source to a CH4 sink with vegetation succession with an increase in elevation, and the methanogen/methanotroph ratio can be used as a proxy for CH4 emission in wetland soils. The continuous increase in reed area combined with the decrease in Carex meadow may mitigate CH4 emission and enhance the CH4 sink function during the non-flood season in the Dongting Lake floodplain.

Effects of soil properties, heavy metals, and PBDEs on microbial community of e-waste contaminated soil

Heavy metals and polybrominated diphenyl ethers (PBDEs) are ubiquitous pollutants at electronic waste (e-waste) contaminated sites, their individual impacts on soil microbial community has attracted wide attention, however, limited research is available on the combined effects of heavy metals and PBDEs on microbial community of e-waste contaminated. Therefore, combined effects of heavy metals and PBDEs on the microbial community in the e-waste contaminated soil were investigated in this study. Samples were collected from Ziya e-waste recycling area in Tianjin, northern China, and the soil microbial communities were then analyzed by the high-throughput MiSeq 16S rRNA sequencing to assess the effects of soil properties, heavy metals, and PBDEs on the soil microbial community. Candidatus Nitrososphaera, Steroidobacter and Kaistobacter were the dominant microbial species in the soils. Similar microbial metabolic functions, including amino acid metabolism, carbohydrate metabolism and membrane transport, were found in all soil samples. Redundancy analysis and variation partition analysis revealed that the microbial community was mainly influenced by PBDEs (including BDE 183, BDE 99, BDE 100 and BDE 154) in horizontal soil samples. However, TN, biomass, BDE 100, BDE 99 and BDE 66 were the major drivers shaping the microbial community in vertical soil samples.

The acetotrophic pathway dominates methane production in Zoige alpine wetland coexisting with hydrogenotrophic pathway

As a typical alpine wetland on the Tibetan Plateau, the Zoige wetland processes a large carbon stock and is a hotspot of methane emission. To date, many studies have investigated the methane flux in this wetland; however, the research on the source of methane in the soils of Zoige wetland is not clear enough. In this study, we determined the dynamic characteristics of the stable carbon isotopes during the methanogenesis of Zoige wetland soil and the corresponding microbial changes. The results showed that the δ¹³CH₄ varied between −19.86‰ and −28.32‰ and the α_C ranged from 1.0029 to 1.0104 in the methanogenesis process, which suggests the dominance of acetotrophic methanogenesis. And among the increased methanogens, acetotrophic methanogens multiplied more obviously than hydrogenotrophic menthanogens. In addition, the results of structural equation models showed that the variations in stable carbon isotopes during the process were mainly affected by acetotrophic methanogens. Although the acetotrophic pathway was dominate, the varied isotope characteristics, increased methanogens and ratio of carbon dioxide to methane all showed that hydrogenotrophic and acetotrophic methanogenesis coexisted in the Zoige wetland. Overall, our study provided a detailed and definitive information to the source of methane in the soil of the Zoige wetland and laid a foundation of mechanism to the research of greenhouse gas in this alpine wetland.

Microbial Community Structure in a Malaysian Tropical Peat Swamp Forest: The Influence of Tree Species and Depth

Tropical peat swamp forests sequester globally significant stores of carbon in deep layers of waterlogged, anoxic, acidic and nutrient-depleted peat. The roles of microbes in supporting these forests through the formation of peat, carbon sequestration and nutrient cycling are virtually unknown. This study investigated physicochemical peat properties and microbial diversity between three dominant tree species: Shorea uliginosa (Dipterocarpaceae), Koompassia malaccensis (legumes associated with nitrogen-fixing bacteria), Eleiodoxa conferta (palm) and depths (surface, 45 and 90 cm) using microbial 16S rRNA gene amplicon sequencing. Water pH, oxygen, nitrogen, phosphorus, total phenolic contents and C/N ratio differed significantly between depths, but not tree species. Depth also strongly influenced microbial diversity and composition, while both depth and tree species exhibited significant impact on the archaeal communities. Microbial diversity was highest at the surface, where fresh leaf litter accumulates, and nutrient supply is guaranteed. Nitrogen was the core parameter correlating to microbial communities, but the interactive effects from various environmental variables displayed significant correlation to relative abundance of major microbial groups. Proteobacteria was the dominant phylum and the most abundant genus, Rhodoplanes, might be involved in nitrogen fixation. The most abundant methanogens and methanotrophs affiliated, respectively, to families Methanomassiliicoccaceae and Methylocystaceae. Our results demonstrated diverse microbial communities and provide valuable insights on microbial ecology in these extreme ecosystems.

Effects of transgenic Bt rice on the active rhizospheric methanogenic archaeal community as revealed by DNA-based stable isotope probing

AIMS

This study aimed to investigate the influence of planting Cry1Ab/Cry1Ac gene expressing rice (Bt rice) on rhizospheric active methanogenic archaeal communities.

METHODS AND RESULTS

The nontransgenic parental line was used as the control (Ck rice). DNA-based stable isotope probing (DNA-SIP) technology traced the rhizospheric active methanogens at the tillering stage. The results revealed significantly lower CH₄ emission flux from Bt soil than that from Ck soil during the whole growth period. The active methanogenic community composition remained stable. The RC-I lineage (77·9-79·8%) and Methanosaetaceae (13·9-15·1%) were the predominant active methanogens in Bt and Ck rice rhizospheres. However, the abundance of functionally active methanogens in the Bt rice rhizosphere was significantly reduced. Lower levels of root exudates (that included carbohydrate and organic acids) from Bt rice were also detected at the tillering stage.

CONCLUSION

This study found that the genetic modification of rice reduced the potential methanogenic substrates came from plant-derived root exudates, which represented an important factor in reducing CH₄ generation and active methanogenic archaeal abundance in Bt rhizosphere soil.

SIGNIFICANCE AND IMPACT OF THE STUDY

The effect of genetically modified (GM) insect-resistant crops on soil micro-organisms has become an issue of public concern, especially the indirect effect of plant metabolisms caused by the insertion of foreign genes. Methanogenesis, which is regarded as a critical ecological process in paddy soil, is influenced by plant root exudates; these are mainly derived from photosynthesis. The variations in root exudates across the Bt and Ck rice suggested the indirect influence of foreign gene insertion. DNA-SIP successfully traced the active methanogenic archaeal populations assimilating ¹³ C-labelled photosynthetic carbon and found a strong influence of planting Bt rice on active methanogens. As a consequence, we proposed that analysis of functionally active micro-organisms is more suitable for monitoring and predicting the environmental influence of GM plants.

Temporal and spatial impact of Spartina alterniflora invasion on methanogens community in Chongming Island, China

Methane production by methanogens in wetland is recognized as a significant contributor to global warming. Spartina alterniflora (S. alterniflora), which is an invasion plant in China's wetland, was reported to have enormous effects on methane production. But studies on shifts in the methanogen community in response to S. alterniflora invasion at temporal and spatial scales in the initial invasion years are rare. Sediments derived from the invasive species S. alterniflora and the native species Phragmites australis (P. australis) in pairwise sites and an invasion chronosequence patch (4 years) were analyzed to investigate the abundance and community structure of methanogens using quantitative real-time PCR (qPCR) and Denaturing gradient gel electrophoresis (DGGE) cloning of the methyl-coenzyme M reductase A (mcrA) gene. For the pairwise sites, the abundance of methanogens in S. alterniflora soils was lower than that of P. australis soils. For the chronosequence patch, the abundance and diversity of methanogens was highest in the soil subjected to two years invasion, in which we detected some rare groups including Methanocellales and Methanococcales. These results indicated a priming effect at the initial invasion stages of S. alterniflora for microorganisms in the soil, which was also supported by the diverse root exudates. The shifts of methanogen communities after S. alterniflora invasion were due to changes in pH, salinity and sulfate. The results indicate that root exudates from S. alterniflora have a priming effect on methanogens in the initial years after invasion, and the predominate methylotrophic groups (Methanosarcinales) may adapt to the availability of diverse substrates and reflects the potential for high methane production after invasion by S. alterniflora.

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

Archaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress.

The Archaea represent a significant component of the plant microbiome, whereas their function is still unclear. Different plant species representing the natural vegetation of alpine bogs harbor a substantial archaeal community originating from five phyla, 60 genera, and 334 operational taxonomic units (OTUs). We identified a core archaeome for all bog plants and ecosystem-specific, so far unclassified Archaea. In the metagenomic data set, Archaea were found to have the potential to interact with plants by (i) possible plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic (especially oxidative and osmotic) stress. The unexpectedly high degree of plant specificity supports plant-archaeon interactions. Moreover, functional signatures of Archaea reveal genetic capacity for the interplay with fungi and an important role in the carbon and nitrogen cycle: e.g., CO₂ and N₂ fixation. These facts reveal an important, yet unobserved role of the Archaea for plants as well as for the bog ecosystem.

IMPORTANCEArchaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress.

Biogeographic distribution of bacterial, archaeal and methanogenic communities and their associations with methanogenic capacity in Chinese wetlands

Natural wetlands and anthropogenic paddy fields are the dominant biogenic sources of atmospheric methane emission which have been speculated as the most probable sources for the increase of post-2006 atmospheric methane. Regional differences in CH₄ emission is possibly due to microbial biogeographic distribution. Here we collected soils from 19 wetlands from different regions in China. The methane production capacity (MPC) was measured for each soil samples and varied from 1.11 to 841.94mg/kg dry soil. High throughput sequencing was employed to investigate the diversity and composition of bacterial, archaeal and methanogenic communities. Similar biogeographic patterns for bacterial, archaeal and methanogenic communities along the latitudinal gradient were observed, and the biogeographic assemblies of different microbial groups were driven by concurrent factors, including edaphic variables (total organic carbon, total phosphorus and pH) and climatic variables (annual frost days, mean annual temperature, direct solar radiation and mean annual precipitation). MPC was significantly correlated with TOC concentration, and in addition, various functional taxa were positively correlated with MPC (P<0.05), for example, Sphingomonas, Syntrophomonas, Methanospirillum and Methanoregula, indicating their potential contributions in the methanogenic process, and many of them were fermentative bacteria and methanogens. Network analysis showed that some syntrophs, sulfate-reducers and methanogens were tightly co-occurred in one module, suggesting their involvements in cross-linked functional processes. Our study implicated both temperature and substrate availability altered the biogeographic patterns of microbial community as well as methane production potential in Chinese wetlands.

Global Biogeographic Analysis of Methanogenic Archaea Identifies Community-Shaping Environmental Factors of Natural Environments

Methanogenic archaea are important for the global greenhouse gas budget since they produce methane under anoxic conditions in numerous natural environments such as oceans, estuaries, soils, and lakes. Whether and how environmental change will propagate into methanogenic assemblages of natural environments remains largely unknown owing to a poor understanding of global distribution patterns and environmental drivers of this specific group of microorganisms. In this study, we performed a meta-analysis targeting the biogeographic patterns and environmental controls of methanogenic communities using 94 public mcrA gene datasets. We show a global pattern of methanogenic archaea that is more associated with habitat filtering than with geographical dispersal. We identify salinity as the control on methanogenic community composition at global scale whereas pH and temperature are the major controls in non-saline soils and lakes. The importance of salinity for structuring methanogenic community composition is also reflected in the biogeography of methanogenic lineages and the physiological properties of methanogenic isolates. Linking methanogenic alpha-diversity with reported values of methane emission identifies estuaries as the most diverse methanogenic habitats with, however, minor contribution to the global methane budget. With salinity, temperature and pH our study identifies environmental drivers of methanogenic community composition facing drastic changes in many natural environments at the moment. However, consequences of this for the production of methane remain elusive owing to a lack of studies that combine methane production rate with community analysis.

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios

Northern peatlands in general have high methane (CH₄) emissions, but individual peatlands show considerable variation as CH₄ sources. Particularly in nutrient-poor peatlands, CH₄ production can be low and exceeded by carbon dioxide (CO₂) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO₂ to CH₄ produced. After [¹³C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH₄ and CO₂ The oligotrophic fen had lower CH₄ production but produced 3 to 59 times more CO₂ than CH₄ RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH₄ production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO₂ production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH₄ production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO₂ production in peatlands.

IMPORTANCE

Peatlands are major sources of the greenhouse gas methane (CH₄), yet in many peatlands, CO₂ production from unresolved anaerobic processes exceeds CH₄ production. Anaerobic degradation produces the precursors of CH₄ production but also represents competing processes. We show that anaerobic degradation leading to high or low CH₄ production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH₄ production, while novel and unconventional degraders could be identified in a site where CO₂ production greatly exceeds CH₄ production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH₄ production and reveal bacteria potentially producing the excess CO₂ in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH₄ emission from peatlands.

Shifts in methanogen community structure and function across a coastal marsh transect: effects of exotic Spartina alterniflora invasion

Invasion of Spartina alterniflora in coastal areas of China increased methane (CH4) emissions. To elucidate the underlying mechanisms, we measured CH4 production potential, methanogen community structure and biogeochemical factors along a coastal wetland transect comprised of five habitat regions: open water, bare tidal flat, invasive S. alterniflora marsh and native Suaeda salsa and Phragmites australis marshes. CH4 production potential in S. alterniflora marsh was 10 times higher than that in other regions, and it was significantly correlated with soil organic carbon, dissolved organic carbon and trimethylamine concentrations, but was not correlated with acetate or formate concentrations. Although the diversity of methanogens was lowest in S. alterniflora marsh, invasion increased methanogen abundance by 3.48-fold, compared with native S. salsa and P. australis marshes due to increase of facultative Methanosarcinaceae rather than acetotrophic and hydrogenotrophic methanogens. Ordination analyses suggested that trimethylamine was the primary factor regulating shift in methanogen community structure. Addition of trimethylamine increased CH4 production rates by 1255-fold but only by 5.61- and 11.4-fold for acetate and H2/CO2, respectively. S. alterniflora invasion elevated concentration of non-competitive trimethylamine, and shifted methanogen community from acetotrophic to facultative methanogens, which together facilitated increased CH4 production potential.

Bacterial Community Features Are Shaped by Geographic Location, Physicochemical Properties, and Oil Contamination of Soil in Main Oil Fields of China

Geographic location and physicochemical properties are thought to represent major factors that shape soil bacterial community abundance and diversity. Crude oil contamination is becoming a notable concern with respect to soil property variation; however, the quantifiable influences of geographic location, physicochemical properties, and oil contamination are still poorly understood. In this study, the 16S ribosomal RNA genes of bacteria in the four oil fields in China were analyzed by using pyrosequencing. Results showed that physicochemical properties were the most dominant factor of bacterial community distribution, followed by geographical location. Oil contamination was a driving factor whose indirect influence was stronger than its direct influence. Under the impact of these three factors, different oil fields presented diversified and distinguishable bacterial community features. The soil of sites with the highest total petroleum hydrocarbon content (HB), nitrogen content (DQ), and phosphorus content (XJ) contained the largest proportion of functional groups participating in hydrocarbon degradation, nitrogen turnover, and phosphorus turnover, respectively. The first dominant phylum of the site with loam soil texture (HB) was Actinobacteria instead of Proteobacteria in other sites with sandy or sandy loam soil texture (DQ, SL, XJ). The site with the highest salinization and alkalization (SL) exhibited the largest proportion of unique local bacteria. The site that was located in the desert with extremely low precipitation (XJ) had the most diversified bacteria distribution. The bacterial community diversity was strongly influenced by soil physicochemical properties.

Microform-related community patterns of methane-cycling microbes in boreal Sphagnum bogs are site specific

Vegetation and water table are important regulators of methane emission in peatlands. Microform variation encompasses these factors in small-scale topographic gradients of dry hummocks, intermediate lawns and wet hollows. We examined methane production and oxidization among microforms in four boreal bogs that showed more variation of vegetation within a bog with microform than between the bogs. Potential methane production was low and differed among bogs but not consistently with microform. Methane oxidation followed water table position with microform, showing higher rates closer to surface in lawns and hollows than in hummocks. Methanogen community, analysed by mcrA terminal restriction fragment length polymorphism and dominated by Methanoregulaceae or 'Methanoflorentaceae', varied strongly with bog. The extent of microform-related variation of methanogens depended on the bog. Methanotrophs identified as Methylocystis spp. in pmoA denaturing gradient gel electrophoresis similarly showed effect of bog, and microform patterns were stronger within individual bogs. Our results suggest that methane-cycling microbes in boreal Sphagnum bogs with seemingly uniform environmental conditions may show strong site-dependent variation. The bog-intrinsic factor may be related to carbon availability but contrary to expectations appears to be unrelated to current surface vegetation, calling attention to the origin of carbon substrates for microbes in bogs.

Warmer temperature accelerates methane emissions from the Zoige wetland on the Tibetan Plateau without changing methanogenic community composition

Zoige wetland, locating on the Tibet Plateau, accounts for 6.2% of organic carbon storage in China. However, the fate of the organic carbon storage in the Zoige wetland remains poorly understood despite the Tibetan Plateau is very sensitive to global climate change. As methane is an important greenhouse gas and methanogenesis is the terminal step in the decomposition of organic matter, understanding how methane emissions from the Zoige wetland is fundamental to elucidate the carbon cycle in alpine wetlands responding to global warming. In this study, microcosms were performed to investigate the effects of temperature and vegetation on methane emissions and microbial processes in the Zoige wetland soil. A positive correlation was observed between temperature and methane emissions. However, temperature had no effect on the main methanogenic pathway--acetotrophic methanogenesis. Moreover, methanogenic community composition was not related to temperature, but was associated with vegetation, which was also involved in methane emissions. Taken together, these results indicate temperature increases methane emissions in alpine wetlands, while vegetation contributes significantly to methanogenic community composition and is associated with methane emissions. These findings suggest that in alpine wetlands temperature and vegetation act together to affect methane emissions, which furthers a global warming feedback loop.

Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost

The response of methanogens to thawing permafrost is an important factor for the global greenhouse gas budget. We tracked methanogenic community structure, activity, and abundance along the degradation of sub-Arctic palsa peatland permafrost. We observed the development of pronounced methane production, release, and abundance of functional (mcrA) methanogenic gene numbers following the transitions from permafrost (palsa) to thaw pond structures. This was associated with the establishment of a methanogenic community consisting both of hydrogenotrophic (Methanobacterium, Methanocellales), and potential acetoclastic (Methanosarcina) members and their activity. While peat bog development was not reflected in significant changes of mcrA copy numbers, potential methane production, and rates of methane release decreased. This was primarily linked to a decline of potential acetoclastic in favor of hydrogenotrophic methanogens. Although palsa peatland succession offers similarities with typical transitions from fen to bog ecosystems, the observed dynamics in methane fluxes and methanogenic communities are primarily attributed to changes within the dominant Bryophyta and Cyperaceae taxa rather than to changes in peat moss and sedge coverage, pH and nutrient regime. Overall, the palsa peatland methanogenic community was characterized by a few dominant operational taxonomic units (OTUs). These OTUs seem to be indicative for methanogenic species that thrive in terrestrial organic rich environments. In summary, our study shows that after an initial stage of high methane emissions following permafrost thaw, methane fluxes, and methanogenic communities establish that are typical for northern peat bogs.

Site history and edaphic features override the influence of plant species on microbial communities in restored tidal freshwater wetlands

Restored wetland soils differ significantly in physical and chemical properties from their natural counterparts even when plant community compositions are similar, but effects of restoration on microbial community composition and function are not well understood. Here, we investigate plant-microbe relationships in restored and natural tidal freshwater wetlands from two subestuaries of the Chesapeake Bay. Soil samples were collected from the root zone of Typha latifolia, Phragmites australis, Peltandra virginica, and Lythrum salicaria. Soil microbial composition was assessed using 454 pyrosequencing, and genes representing bacteria, archaea, denitrification, methanogenesis, and methane oxidation were quantified. Our analysis revealed variation in some functional gene copy numbers between plant species within sites, but intersite comparisons did not reveal consistent plant-microbe trends. We observed more microbial variations between plant species in natural wetlands, where plants have been established for a long period of time. In the largest natural wetland site, sequences putatively matching methanogens accounted for ∼17% of all sequences, and the same wetland had the highest numbers of genes coding for methane coenzyme A reductase (mcrA). Sequences putatively matching aerobic methanotrophic bacteria and anaerobic methane-oxidizing archaea (ANME) were detected in all sites, suggesting that both aerobic and anaerobic methane oxidation are possible in these systems. Our data suggest that site history and edaphic features override the influence of plant species on microbial communities in restored wetlands.

Microbial community composition and in silico predicted metabolic potential reflect biogeochemical gradients between distinct peatland types

It is not well understood how the ecological status and microbial community composition of spruce swamp forests (SSF) relate to those found in bogs and fens. To clarify this, we investigated biogeochemical parameters and microbial community composition in a bog, a fen and two SSF using high throughput barcoded sequencing of the small ribosomal subunit (SSU) variable region V4. The results demonstrated that the microbial community of SSF is positioned between those of bogs and fens, and this was confirmed by in silico predicted metabolic potentials. This corresponds well with the position of SSF on the trophic gradient and reflects distinct responses of microbial communities to environmental variables. Species richness and microbial diversity increased significantly from bog to fen, with SSF in between, reflecting the variation in pH, nutrient availability and peat decomposability. The archaeal community, dominated by hydrogenotrophic methanogens, was more similar in SSF and the bog compared with the fen. The composition of the bacterial community of SSF was intermediate between those of bog and fen. However, the production of CO2 (an indicator of peat decomposability) did not differ between SSF and bog, suggesting the limiting effect of low pH and poor litter quality on the functioning of the bacterial community in SSF. These results help to clarify the transitional position of SSF between bogs and fens and showed the strong effect of environmental conditions on microbial community composition and functioning.

Southern Appalachian peatlands support high archaeal diversity

Mid-latitude peatlands with a temperate climate are sparsely studied and as such represent a gap in the current knowledge base regarding archaeal populations present and their roles in these environments. Phylogenetic analysis of the archaeal populations among three peatlands in the Southern Appalachians reveal not only methanogenic species but also significant populations of thaumarchaeal and crenarchaeal-related organisms of the uncultured miscellaneous crenarchaeotal group (MCG) and the terrestrial group 1.1c, as well as deep-branching Euryarchaeota primarily within the Lake Dagow sediment and rice cluster V lineages. The Thaum/Crenarchaea and deep-branching Euryarchaea represented approximately 24-83% and 2-18%, respectively, of the total SSU rRNA clones retrieved in each library, and methanogens represented approximately 14-72% of the clones retrieved. Several taxa that are either rare or novel to acidic peatlands were detected including the euryarchaeal SM1K20 cluster and thaumarchaeal/crenarchaeal-related clusters 1.1a, C3, SAGMCG-1, pSL12, and AK59. All three major groups (methanogens, Thaumarchaea/Crenarchaea, and deep-branching Euryarchaea) were detected in the RNA library, suggesting at least a minimum level of maintenance activity. Compared to their northern counterparts, Southern Appalachian peatlands appear to harbor a relatively high diversity of Archaea and exhibit a high level of intra-site heterogeneity.

Substrate and/or substrate-driven changes in the abundance of methanogenic archaea cause seasonal variation of methane production potential in species-specific freshwater wetlands

There are large temporal and spatial variations of methane (CH4) emissions from natural wetlands. To understand temporal changes of CH4 production potential (MPP), soil samples were collected from a permanently inundated Carex lasiocarpa marsh and a summer inundated Calamagrostis angustifolia marsh over the period from June to October of 2011. MPP, dissolved organic carbon (DOC) concentration, abundance and community structure of methanogenic archaea were assessed. In the C. lasiocarpa marsh, DOC concentration, MPP and the methanogen population showed similar seasonal variations and maximal values in September. MPP and DOC in the C. angustifolia marsh exhibited seasonal variations and values peaked during August, while the methanogen population decreased with plant growth. Methanogen abundance correlated significantly (P = 0.02) with DOC only for the C. lasiocarpa marsh. During the sampling period, the dominant methanogens were the Methanosaetaceae and Zoige cluster I (ZC-Ι) in the C. angustifolia marsh, and Methanomicrobiales and ZC-Ι in the C. lasiocarpa marsh. MPP correlated significantly (P = 0.04) with DOC and methanogen population in the C. lasiocarpa marsh but only with DOC in the C. angustifolia marsh. Addition of C. lasiocarpa litter enhanced MPP more effectively than addition of C. angustifolia litter, indicating that temporal variation of substrates is controlled by litter deposition in the C. lasiocarpa marsh while living plant matter is more important in the C. angustifolia marsh. This study indicated that there was no apparent shift in the dominant types of methanogen during the growth season in the species-specific freshwater wetlands. Temporal variation of MPP is controlled by substrates and substrate-driven changes in the abundance of methanogenic archaea in the C. lasiocarpa marsh, while MPP depends only on substrate availability derived from root exudates or soil organic matter in the C. angustifolia marsh.

Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands

Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide (CO₂) and methane (CH₄) production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between natural, mined, and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and CH₄ or CO₂ production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought about by these land uses.

Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales

Understanding the dynamics of methane (CH4 ) emissions is of paramount importance because CH4 has 25 times the global warming potential of carbon dioxide (CO2 ) and is currently the second most important anthropogenic greenhouse gas. Wetlands are the single largest natural CH4 source with median emissions from published studies of 164 Tg yr(-1) , which is about a third of total global emissions. We provide a perspective on important new frontiers in obtaining a better understanding of CH4 dynamics in natural systems, with a focus on wetlands. One of the most exciting recent developments in this field is the attempt to integrate the different methodologies and spatial scales of biogeochemistry, molecular microbiology, and modeling, and thus this is a major focus of this review. Our specific objectives are to provide an up-to-date synthesis of estimates of global CH4 emissions from wetlands and other freshwater aquatic ecosystems, briefly summarize major biogeophysical controls over CH4 emissions from wetlands, suggest new frontiers in CH4 biogeochemistry, examine relationships between methanogen community structure and CH4 dynamics in situ, and to review the current generation of CH4 models. We highlight throughout some of the most pressing issues concerning global change and feedbacks on CH4 emissions from natural ecosystems. Major uncertainties in estimating current and future CH4 emissions from natural ecosystems include the following: (i) A number of important controls over CH4 production, consumption, and transport have not been, or are inadequately, incorporated into existing CH4 biogeochemistry models. (ii) Significant errors in regional and global emission estimates are derived from large spatial-scale extrapolations from highly heterogeneous and often poorly mapped wetland complexes. (iii) The limited number of observations of CH4 fluxes and their associated environmental variables loosely constrains the parameterization of process-based biogeochemistry models.

Effect of soil properties and hydrology on archaeal community composition in three temperate grasslands on peat

Grasslands established on drained peat soils are regarded as negligible methane (CH4 ) sources; however, they can still exhibit considerable soil CH4 dynamics. We investigated archaeal community composition in two different fen peat soils and one bog peat soil under permanent grassland in Denmark. We used terminal restriction fragment length polymorphism (T-RFLP) fingerprinting and clone libraries to characterize the soils' archaeal community composition to gain a better understanding of relationships between peat properties and land use, respectively, and CH4 dynamics. Samples were taken at three different depths and at four different seasons. Archaeal community composition varied considerably between the three peatlands and, to a certain degree, also with peat depth, but seemed to be quite stable at individual sampling depths throughout the year. Archaeal community composition was mainly linked to soil pH. No methanogens were detected at one fen site with soil pH ranging from 3.2 to 4.4. The methanogenic community of the bog (soil pH 3.9-4.6) was dominated by hydrogenotrophs, whereas the second fen site (soil pH 5.0-5.3) comprised both aceticlastic and hydrogenotrophic methanogens. Overall, there seemed to be a significant coupling between peat type and archaeal community composition, with local hydrology modifying the strength of this coupling.

Microbial community structure and activity linked to contrasting biogeochemical gradients in bog and fen environments of the Glacial Lake Agassiz Peatland

The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites.

Predominance of thaumarchaeal ammonia oxidizer abundance and transcriptional activity in an acidic fen

We investigated the abundance, community composition and transcriptional activity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the acidic fen Schlöppnerbrunnen (Germany) that was subjected to water table manipulations. Quantitative PCR targeting amoA gene copies and transcripts showed that AOA dominated the ammonia-oxidizing community in the upper 20 cm of the peat soil. Numbers of archaeal amoA gene copies and transcripts as well as the relative fraction of AOA of the total archaea decreased with depth. AOA-AmoA sequences were 96.2-98.9% identical to that of Candidatus Nitrosotalea devanaterra while bacterial AmoA sequences affiliated with Nitrosospira clusters 2 and 4. Archaeal but not bacterial amoA transcripts were detected in short-term laboratory incubations of peat that showed nitrifying activity. Nitrate accumulated in the peat pore water after 6 weeks of induced drought during a field experiment. Subsequent rewetting resulted in a significant decrease of AOA transcriptional activity, indicating that AOA responded to water table fluctuations on the transcriptional level. Our results suggest that nitrification in this fen is primarily linked to archaeal ammonia oxidation. pH and anoxia appear to be key factors regulating AOA community composition, vertical distribution and activity in acidic fens.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

Microbial community analysis of anodes from sediment microbial fuel cells powered by rhizodeposits of living rice plants

By placing the anode of a sediment microbial fuel cell (SMFC) in the rhizosphere of a rice plant, root-excreted rhizodeposits can be microbially oxidized with concomitant current generation. Here, various molecular techniques were used to characterize the composition of bacterial and archaeal communities on such anodes, as influenced by electrical circuitry, sediment matrix, and the presence of plants. Closed-circuit anodes in potting soil were enriched with Desulfobulbus-like species, members of the family Geobacteraceae, and as yet uncultured representatives of the domain Archaea.

Intermediary ecosystem metabolism as a main driver of methanogenesis in acidic wetland soil

Methanogens have a very limited substrate range, and their in situ activities are thus linked to 'intermediary ecosystem metabolism', i.e. complex trophic interactions with other microorganisms catalysing essential intermediary processes that ultimately drive methanogenesis. However, information on intermediary ecosystem metabolism and associated biota is fragmented and often conceptualized rather than resolved. The main objective of this review is to evaluate the concept of intermediary ecosystem metabolism in context with recent work aimed at resolving the complex trophic interactions of a methane-emitting peatland.