Depth related diversity of methanogen Archaea in Finnish oligotrophic fen

Anaerobic methane oxidation is quantitatively important in deeper peat layers of boreal peatlands: Evidence from anaerobic incubations, in situ stable isotopes depth profiles, and microbial communities

Boreal peatlands store most of their carbon in layers deeper than 0.5 m under anaerobic conditions, where carbon dioxide and methane are produced as terminal products of organic matter degradation. Since the global warming potential of methane is much greater than that of carbon dioxide, the balance between the production rates of these gases is important for future climate predictions. Herein, we aimed to understand whether anaerobic methane oxidation (AMO) could explain the high CO2/CH4 anaerobic production ratios that are widely observed for the deeper peat layers of boreal peatlands. Furthermore, we quantified the metabolic pathways of methanogenesis to examine whether hydrogenotrophic methanogenesis is a dominant methane production pathway for the presumably recalcitrant deeper peat. To assess the CH4 cycling in deeper peat, we combined laboratory anaerobic incubations with a pathway-specific inhibitor, in situ depth patterns of stable isotopes in CH4, and 16S rRNA gene amplicon sequencing for three representative boreal peatlands in Western Siberia. We found up to a 69 % reduction in CH4 production due to AMO, which largely explained the high CO2/CH4 anaerobic production ratios and the in situ depth-related patterns of δ13C and δD in methane. The absence of acetate accumulation after inhibiting acetotrophic methanogenesis and the presence of sulfate- and nitrate-reducing anaerobic acetate oxidizers in the deeper peat indicated that these microorganisms use SO42- and NO3- as electron acceptors. Acetotrophic methanogenesis dominated net CH4 production in the deeper peat, accounting for 81 ± 13 %. Overall, anaerobic oxidation is quantitatively important for the methane cycle in the deeper layers of boreal peatlands, affecting both methane and its main precursor concentrations.

Do the Culturable Microbial Groups Present in Cutaway Bogs Change According to Temporal Variation? Pilot Study Based on the Midlands in the Republic of Ireland

Cutaway peatlands in the midlands of the Republic of Ireland are rarely the focus of scientific studies. The soil quality and related microenvironment have been severely impacted by peat extraction. Returning them to a ‘near-natural state’ would require greater insights into this ecological niche. The current research took the initiative to study the microbiology of vast cutaway sites in the midlands of Ireland. Peat was collected over two seasons in January, February and April. Homogenised peat was aseptically cultured on a range of specific and non-specific culture media. Microbial enumeration, Gram staining and other microscopic observations of morphologically distinct microorganisms were performed. The total viable bacterial and fungal numbers were highest in February (1.33 × 105 CFU ml−1 and 5.93 × 106 CFU ml−1, respectively) and were lowest in April (1.14 × 103 CFU ml−1 and 5.57 × 106 CFU ml−1). Penicillium spp. and Trichoderma spp. were common in all the sites. The highest values of phosphate solubilisation index were recorded in peat collected in April (SI = 3.167 & 3.000). Overall, there is a statistically significant difference (p ≤ 0.0001) among the microbial numbers across the three months. This variation could be due to the temperature and pH differences across peat soil.

Effect of short-term warming and drought on the methanogenic communities in degraded peatlands in Zoige Plateau

Peatlands in Qinghai-Tibetan are degrading with climate change and human activities. Peatland degradation and climate change affect methane emissions. Methanogens are key functional microbes during methane production; however, knowledge of methanogens in degraded peatlands is lacking. Here, we investigated the effects of short-term (1 year) warming (OTC), drought (20%), and their combination on methanogens in the degraded peatlands on the Zoige Plateau of China via qPCR and clone library analysis. The results showed that Methanomicrobiales and Methanobacteriales were predominant in all the treatments. Non-metric multidimensional scaling (NMDS) and PERMANOVA analyses showed that the methanogenic community structure among the climate change treatments was not significantly different. The relative abundance of methanogen communities showed insignificant variation among the climate change treatments. The copy number and Shannon diversity of methanogens were significantly different within the climate change treatments, and drought significantly decreased the copy number of methanogens when compared to the control. The Redundancy analysis (RDA) results and correlation analysis showed that the environmental variables measured had no significant effect on methanogenic community structure and Shannon diversity. These results indicate that methanogens are insensitive to short-term climate change in degraded peatlands. This study provides insight into methane emissions from the Zoige Plateau peatlands by focusing on the possible responses of the methanogens to climate-driven changes.

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.

Recovery of fen peatland microbiomes and predicted functional profiles after rewetting

Many of the world's peatlands have been affected by water table drawdown and subsequent loss of organic matter. Rewetting has been proposed as a measure to restore peatland functioning and to halt carbon loss, but its effectiveness is subject to debate. An important prerequisite for peatland recovery is a return of typical microbial communities, which drive key processes. To evaluate the effect of rewetting, we investigated 13 fen peatland areas across a wide (>1500 km) longitudinal gradient in Europe, in which we compared microbial communities between drained, undrained, and rewetted sites. There was a clear difference in microbial communities between drained and undrained fens, regardless of location. Community recovery upon rewetting was substantial in the majority of sites, and predictive functional profiling suggested a concomitant recovery of biogeochemical peatland functioning. However, communities in rewetted sites were only similar to those of undrained sites when soil organic matter quality (as expressed by cellulose fractions) and quantity were still sufficiently high. We estimate that a minimum organic matter content of ca. 70% is required to enable microbial recovery. We conclude that peatland recovery after rewetting is conditional on the level of drainage-induced degradation: severely altered physicochemical peat properties may preclude complete recovery for decades.

Diversity and Distribution of Methanogenic Community Between Two Typical Alpine Ecosystems on the Qinghai-Tibetan Plateau

Alpine permafrost regions are important sources of biogenic CH₄ and methanogens play an important role in the methane-producing process. The alpine permafrost on the Qinghai-Tibetan plateau comprises about one-sixth of China's land area, and there are various types of alpine ecosystems. However, the methanogenic communities in the typical alpine ecosystems are poorly understood. In this study, the active layers and permafrost layers of the natural ecosystem of alpine grassland (DZ2-1) and alpine swamp meadow (DZ2-5) were selected to investigate the diversity and abundance of methanogenic communities. Methanobacterium (63.65%) are overwhelmingly dominant in the active layer of the alpine grassland (DZ2-1A). ZC-I cluster (26.13%), RC-I cluster (19.56%), and Methanobacterium (15.02%) are the dominant groups in the permafrost layer of the alpine grassland (DZ2-1P). Methanosaeta (32.92%), Fen cluster (29.59%), Methanosarcina (16.33%), and Methanobacterium (13.95%) are the dominant groups in the active layer of the alpine swamp meadow (DZ2-5A), whereas the Fen cluster (50.85%), ZC-I cluster (27.63%), and RC-I cluster (14.15%) are relatively abundant in the permafrost layer of the alpine swamp meadow (DZ2-5P). qPCR data showed that the abundance of methanogens was higher in the natural ecosystem of alpine swamp meadow than in alpine grassland. We found that the community characteristics of methanogens were related to environmental factors. Pearson correlation analyses indicated that the relative abundance of Methanobacterium had a significantly positive correlation with hydrogen concentration (P < 0.01), while the relative abundances of Methanosaeta and Methanosarcina were positively correlated with acetate concentration (P < 0.05). This study will help us to understand the methanogenic communities and their surrounding environments in alpine ecosystems.

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.

Modelling the specific pathway of CH4 and CO2 formation using carbon isotope fractionation: an example for a boreal mesotrophic fen

We described mathematically the process of peat methanization in a boreal mesotrophic fen. Gaseous and dissolved CH₄ and CO₂ as well as their δ¹³C signatures were considered in the dynamic equations for incubation bottles. In accordance with the model, acetate, H₂, and CO₂ were produced during cellulose hydrolysis and acidogenesis. ¹³C/¹²C in CO₂ was a key variable reflecting dynamic changes in the rates of cellulose hydrolysis and acidogenesis, acetoclastic and hydrogenotrophic methanogenesis. As CO₂ is the substrate in hydrogenotrophic methanogenesis, δ¹³C-CO₂ increased from the start till the dissolved hydrogen concentration became very low. Thereafter, the rate of acetoclastic methanogenesis with the significant current acetate concentration dominated over the rate of hydrogenotrophic methanogenesis leading to the decreasing δ¹³C-CO₂ and the increasing δ¹³C-CH₄. The model was validated by describing the system's dynamics under strong and weak inhibition of acetoclastic and hydrogenotrophic methanogenesis by methyl fluoride, respectively. During peat methanization at the lowered temperature of 10 °C, the processes of hydrogenotrophic methanogenesis and homoacetogenesis competing for H₂ may occur. However, based on dynamics of the carbon isotope signatures, especially on dynamics of δ¹³C-CO₂, the model showed no significant contribution of homoacetogens in peat methanization.

Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems

About half of the global methane (CH₄ ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH₄ emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.

Methanogenic Community Was Stable in Two Contrasting Freshwater Marshes Exposed to Elevated Atmospheric CO2

The effects of elevated atmospheric CO₂ concentration on soil microbial communities have been previously recorded. However, limited information is available regarding the response of methanogenic communities to elevated CO₂ in freshwater marshes. Using high-throughput sequencing and real-time quantitative PCR, we compared the abundance and community structure of methanogens in different compartments (bulk soil, rhizosphere soil, and roots) of Calamagrostis angustifolia and Carex lasiocarpa growing marshes under ambient (380 ppm) and elevated CO₂ (700 ppm) atmospheres. C. lasiocarpa rhizosphere was a hotspot for potential methane production, based on the 10-fold higher abundance of the mcrA genes per dry weight. The two marshes and their compartments were occupied by different methanogenic communities. In the C. lasiocarpa marsh, archaeal family Methanobacteriaceae, Rice Cluster II, and Methanosaetaceae co-dominated in the bulk soil, while Methanobacteriaceae was the exclusively dominant methanogen in the rhizosphere soil and roots. Families Methanosarcinaceae and Methanocellaceae dominated in the bulk soil of C. angustifolia marsh. Conversely, Methanosarcinaceae and Methanocellaceae together with Methanobacteriaceae dominated in the rhizosphere soil and roots, respectively, in the C. angustifolia marsh. Elevated atmospheric CO₂ increased plant photosynthesis and belowground biomass of C. lasiocarpa and C. angustifolia marshes. However, it did not significantly change the abundance (based on mcrA qPCR), diversity, or community structure (based on high-throughput sequencing) of methanogens in any of the compartments, irrespective of plant type. Our findings suggest that the population and species of the dominant methanogens had weak responses to elevated atmospheric CO₂. However, minor changes in specific methanogenic taxa occurred under elevated atmospheric CO₂. Despite minor changes, methanogenic communities in different compartments of two contrasting freshwater marshes were rather stable under elevated atmospheric CO₂.

CH4 and CO2 production below two contrasting peatland micro-relief forms: An inhibitor and δ13C study

Two peatland micro-relief forms (microforms) - hummocks and hollows - differ by their hydrological characteristics (water table level, i.e. oxic-anoxic conditions) and vegetation communities. We studied the CH₄ and CO₂ production potential and the localization of methanogenic pathways in both hummocks and hollows at depths of 15, 50, 100, 150 and 200cm in a laboratory incubation experiment. For this purpose, we measured CH₄ and CO₂ production rates, peat elemental composition, as well as δ¹³C values of gases and solids; the specific inhibitor of methanogenesis BES (2-bromo-ethane sulfonate, 1mM) was aimed to preferentially block the acetoclastic pathway. The cumulative CH₄ production of all depths was almost one fold higher in hollows than in hummocks, with no differences in CO₂. With depth, CO₂ and CH₄ production decreased, and the relative contribution of the hydrogenotrophic pathway of methanogenesis increased. The highest methanogenic activity among all depths and both microforms was measured at 15cm of hollows (91%) at which the highest relative contribution of acetoclastic vs. hydrogenotrophic pathway (92 and 8%, respectively) was detected. For hummocks, the CH₄ production was the highest at 50cm (82%), where relative contribution of acetoclastic methanogenesis comprised 89%. The addition of 1mM BES was not selective and inhibited both methanogenic pathways in the soil. Thus, BES was less efficient in partitioning the pathways compared with the δ¹³C signature. We conclude that the peat microforms - dry hummocks and wet hollows - play an important role for CH₄ but not for CO₂ production when the effects of living vegetation are excluded.

Incubation of innovative methanogenic communities to seed anaerobic digesters

The methanogenic communities in alternative inocula and their potential to increase CH₄ production in mesophilic and psychrophilic dairy manure-based anaerobic digesters were examined. Quantitative-PCR and terminal restriction fragment length polymorphism (T-RFLP) profiles were used to determine archaeal and methanogenic community changes when three inocula (wetland sediment (WS), landfill leachate (LL), and mesophilic digestate (MD)) were incubated at 15, 25, and 35 °C for 91 and 196 days. After each incubation period, the inocula were used in biochemical methane potential (BMP) tests at the incubation temperatures. There was no significant correlation between inoculum mcrA gene copy numbers and CH₄ produced in BMP tests, suggesting that population size was not a distinguishing characteristic for predicting CH₄ production. Archaeal composition in LL and WS reactors generally converged with MD reactors after incubation at 25 and 35 °C for 196 days. These MD reactors had high relative abundance of TRF 302, likely Methanosaetaceae, and low acetic acid (0.62-1.61 mM). At 15 °C incubation, most reactors were associated with high acetic acid (1.61-133.6 mM) and dominated by TRF 199, likely Methanosarcinaceae. The LL reactor incubated at 25 °C for 91 days had higher relative abundance of TRF 199 and produced significantly higher CH₄ than WS and MD reactors in BMP test. In the future, it may be possible to create enrichment cultures that favor particular methanogens and use them as inoculum to benefit digesters at low mesophilic temperatures. Our data provides evidence that tailoring the archaeal community could benefit digesters operating under different conditions.

Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences

Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However, their distribution in other methanogenic environments has not been addressed systematically. Here, we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal faeces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems.

Distribution, activities, and interactions of methanogens and sulfate-reducing prokaryotes in the Florida Everglades

To gain insight into the mechanisms controlling methanogenic pathways in the Florida Everglades, the distribution and functional activities of methanogens and sulfate-reducing prokaryotes (SRPs) were investigated in soils (0 to 2 or 0 to 4 cm depth) across the well-documented nutrient gradient in the water conservation areas (WCAs) caused by runoff from the adjacent Everglades Agricultural Area. The methyl coenzyme M reductase gene (mcrA) sequences that were retrieved from WCA-2A, an area with relatively high concentrations of SO4 (2-) (≥39 μM), indicated that methanogens inhabiting this area were broadly distributed within the orders Methanomicrobiales, Methanosarcinales, Methanocellales, Methanobacteriales, and Methanomassiliicoccales. In more than 3 years of monitoring, quantitative PCR (qPCR) using newly designed group-specific primers revealed that the hydrogenotrophic Methanomicrobiales were more numerous than the Methanosaetaceae obligatory acetotrophs in SO4 (2-)-rich areas of WCA-2A, while the Methanosaetaceae were dominant over the Methanomicrobiales in WCA-3A (with relatively low SO4 (2-) concentrations; ≤4 μM). qPCR of dsrB sequences also indicated that SRPs are present at greater numbers than methanogens in the WCAs. In an incubation study with WCA-2A soils, addition of MoO4 (2-) (a specific inhibitor of SRP activity) resulted in increased methane production rates, lower apparent fractionation factors [αapp; defined as (amount of δ(13)CO2 + 1,000)/(amount of δ(13)CH4 + 1,000)], and higher Methanosaetaceae mcrA transcript levels compared to those for the controls without MoO4 (2-). These results indicate that SRPs play crucial roles in controlling methanogenic pathways and in shaping the structures of methanogen assemblages as a function of position along the nutrient gradient.

Snapshot of methanogen sensitivity to temperature in Zoige wetland from Tibetan plateau

Zoige wetland in Tibetan plateau represents a cold environment at high altitude where significant methane emission has been observed. However, it remains unknown how the production and emission of CH₄ from Zoige wetland will respond to a warming climate. Here we investigated the temperature sensitivity of methanogen community in a Zoige wetland soil under the laboratory incubation conditions. One soil sample was collected and the temperature sensitivity of the methanogenic activity, the structure of methanogen community and the methanogenic pathways were determined. We found that the response of methanogenesis to temperature could be separated into two phases, a high sensitivity in the low temperature range and a modest sensitivity under mesophilic conditions, respectively. The aceticlastic methanogens Methanosarcinaceae were the main methanogens at low temperatures, while hydrogenotrophic Methanobacteriales, Methanomicrobiales, and Methanocellales were more abundant at higher temperatures. The total abundance of mcrA genes increased with temperature indicating that the growth of methanogens was stimulated. The growth of hydrogenotrophic methanogens, however, was faster than aceticlastic ones resulting in the shift of methanogen community. Determination of carbon isotopic signatures indicated that methanogenic pathway was also shifted from mainly aceticlastic methanogenesis to a mixture of hydrogenotrophic and aceticlastic methanogenesis with the increase of temperature. Collectively, the shift of temperature responses of methanogenesis was in accordance with the changes in methanogen composition and methanogenic pathway in this wetland sample. It appears that the aceticlastic methanogenesis dominating at low temperatures is more sensitive than the hydrogenotrophic one at higher temperatures.

Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes

Communities of methanogens, anaerobic methanotrophic archaea and aerobic methanotrophic bacteria (MOB) were compared by profiling polymerase chain reaction (PCR)-amplified products of mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS) and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clades 1,2, and Methanomassiliicoccus-like groups of methanogens were the most abundant groups in nSCS sediment samples. Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was updated. Quantitative polymerase chain reaction was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4∼3.9 × 10⁶ copies per gram dry weight) and of intertidal mudflat (5.5∼5.8 × 10⁶ copies per gram dry weight) was observed, but higher abundance (6.9 × 10⁶ to 1.02 × 10⁸ copies per gram dry weight) was found in subsurface samples of both sediment types. Aerobic MOB were more abundant in surface layers (6.7∼11.1 × 10⁵ copies per gram dry weight) than the subsurface layers (1.2∼5.9 × 10⁵ copies per gram dry weight) based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal mudflat, but less pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51 × 10⁸ copies per gram dry weight) and pmoA gene (1.56 × 10⁷ copies per gram dry weight). This study investigated the prokaryotic communities responsible for methane cycling in both marine and coastal wetland ecosystems, showing the distribution characteristics of mcrA gene-harboring communities in nSCS and stratification of mcrA and pmoA gene diversity and abundance in the Mai Po Nature Reserve.

Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments

Archaea are widespread in marine sediments, but their occurrence and relationship with natural salinity gradients in estuarine sediments is not well understood. This study investigated the abundance and diversity of Archaea in sediments at three sites [Brightlingsea (BR), Alresford (AR) and Hythe (HY)] along the Colne Estuary, using quantitative real-time PCR (qPCR) of 16S rRNA genes, DNA hybridization, Archaea 16S rRNA and mcrA gene phylogenetic analyses. Total archaeal 16S rRNA abundance in sediments were higher in the low-salinity brackish sediments from HY (2-8 × 10(7) 16S rRNA gene copies cm(-3)) than the high-salinity marine sites from BR and AR (2 × 10(4)-2 × 10(7) and 4 × 10(6)-2 × 10(7) 16S rRNA gene copies cm(-3), respectively), although as a proportion of the total prokaryotes Archaea were higher at BR than at AR or HY. Phylogenetic analysis showed that members of the 'Bathyarchaeota' (MCG), Thaumarchaeota and methanogenic Euryarchaeota were the dominant groups of Archaea. The composition of Thaumarchaeota varied with salinity, as only 'marine' group I.1a was present in marine sediments (BR). Methanogen 16S rRNA genes from low-salinity sediments at HY were dominated by acetotrophic Methanosaeta and putatively hydrogentrophic Methanomicrobiales, whereas the marine site (BR) was dominated by mcrA genes belonging to methylotrophic Methanococcoides, versatile Methanosarcina and methanotrophic ANME-2a. Overall, the results indicate that salinity and associated factors play a role in controlling diversity and distribution of Archaea in estuarine sediments.

Microbial trophic interactions and mcrA gene expression in monitoring of anaerobic digesters

Anaerobic digestion (AD) is a biological process where different trophic groups of microorganisms break down biodegradable organic materials in the absence of oxygen. A wide range of AD technologies is being used to convert livestock manure, municipal and industrial wastewaters, and solid organic wastes into biogas. AD gains importance not only because of its relevance in waste treatment but also because of the recovery of carbon in the form of methane, which is a renewable energy and is used to generate electricity and heat. Despite the advances on the engineering and design of new bioreactors for AD, the microbiology component always poses challenges. Microbiology of AD processes is complicated as the efficiency of the process depends on the interactions of various trophic groups involved. Due to the complex interdependence of microbial activities for the functionality of the anaerobic bioreactors, the genetic expression of mcrA, which encodes a key enzyme in methane formation, is proposed as a parameter to monitor the process performance in real time. This review evaluates the current knowledge on microbial groups, their interactions, and their relationship to the performance of anaerobic biodigesters with a focus on using mcrA gene expression as a tool to monitor the process.

Metatranscriptomic analysis of arctic peat soil microbiota

Recent advances in meta-omics and particularly metatranscriptomic approaches have enabled detailed studies of the structure and function of microbial communities in many ecosystems. Molecular analyses of peat soils, ecosystems important to the global carbon balance, are still challenging due to the presence of coextracted substances that inhibit enzymes used in downstream applications. We sampled layers at different depths from two high-Arctic peat soils in Svalbard for metatranscriptome preparation. Here we show that enzyme inhibition in the preparation of metatranscriptomic libraries can be circumvented by linear amplification of diluted template RNA. A comparative analysis of mRNA-enriched and nonenriched metatranscriptomes showed that mRNA enrichment resulted in a 2-fold increase in the relative abundance of mRNA but biased the relative distribution of mRNA. The relative abundance of transcripts for cellulose degradation decreased with depth, while the transcripts for hemicellulose debranching increased, indicating that the polysaccharide composition of the peat was different in the deeper and older layers. Taxonomic annotation revealed that Actinobacteria and Bacteroidetes were the dominating polysaccharide decomposers. The relative abundances of 16S rRNA and mRNA transcripts of methanogenic Archaea increased substantially with depth. Acetoclastic methanogenesis was the dominating pathway, followed by methanogenesis from formate. The relative abundances of 16S rRNA and mRNA assigned to the methanotrophic Methylococcaceae, primarily Methylobacter, increased with depth. In conclusion, linear amplification of total RNA and deep sequencing constituted the preferred method for metatranscriptomic preparation to enable high-resolution functional and taxonomic analyses of the active microbiota in Arctic peat soil.

Isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a Sphagnum peat bog

Two dense and highly enriched (up to 10(9) cells ml(-1), <10% of bacterial satellites) acido-tolerant (pH 4.0-6.5) methanogenic consortia, '26' and 'K', were isolated from the peat beneath a Sphagnum-Eriophorum-Carex community in West Siberia. Both consortia produced methane from CO2:H2 on chemically defined, diluted N-free media containing Ti(III)citrate as reducing agent. The phylogenetic analysis of 16S ribosomal DNA revealed three archaeal and nine bacterial sequence types. Consortium '26' contained single archaea Methanobacterium sp., represented by rods of 1.5-10x0.5-1.0 microm. In consortium 'K', there were two archaeal phylotypes, the respective methanogens were further differentiated morphologically with the fluorescence in situ hybridization technique: one less abundant (<2%) population of the long-curved rods (50-100x0.3-0.4 microm) fell into the order of Methanomicrobiales, while the dominant organism ( approximately 98%), represented by straight rods with abrupt rectangular ends (3-9x0.5 microm), was affiliated with earlier uncultured 'Rice cluster I'. The main bacterial satellite used citrate as a single carbon and energy source; it was similar in both consortia, and after isolation in pure culture, it was identified as a new member of the alpha-subclass of Proteobacteria. The other bacterial satellites were distributed among four taxonomic groups: the delta-subclass of Proteobacteria, the Flavobacterium-Bacteroides-Cytophaga line of descent, the Acidobacterium-Fibrobacter line of descent and the Green non-sulfur bacteria line of descent. At least 11 out of 12 components of acido-tolerant consortia are new to science at the species, genus and order levels; their existence until now was evident only from environmental gene retrievals. The Sphagnum wetlands, attracting attention only recently because of their global environmental role, are shown to be an especially valuable source of novel prokaryotic organisms.

Cross-site soil microbial communities under tillage regimes: fungistasis and microbial biomarkers

The exploitation of soil ecosystem services by agricultural management strategies requires knowledge of microbial communities in different management regimes. Crop cover by no-till management protects the soil surface, reducing the risk of erosion and nutrient leaching, but might increase straw residue-borne and soilborne plant-pathogenic fungi. A cross-site study of soil microbial communities and Fusarium fungistasis was conducted on six long-term agricultural fields with no-till and moldboard-plowed treatments. Microbial communities were studied at the topsoil surface (0 to 5 cm) and bottom (10 to 20 cm) by general bacterial and actinobacterial terminal restriction fragment length polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) analyses. Fusarium culmorum soil fungistasis describing soil receptivity to plant-pathogenic fungi was explored by using the surface layer method. Soil depth had a significant impact on general bacterial as well as actinobacterial communities and PLFA profiles in no-till treatment, with a clear spatial distinction of communities (P < 0.05), whereas the depth-related separation of microbial communities was not observed in plowed fields. The fungal biomass was higher in no-till surface soil than in plowed soil (P < 0.07). Soil total microbial biomass and fungal biomass correlated with fungistasis (P < 0.02 for the sum of PLFAs; P < 0.001 for PLFA 18:2ω6). Our cross-site study demonstrated that agricultural management strategies can have a major impact on soil microbial community structures, indicating that it is possible to influence the soil processes with management decisions. The interactions between plant-pathogenic fungi and soil microbial communities are multifaceted, and a high level of fungistasis could be linked to the high microbial biomass in soil but not to the specific management strategy.

Prokaryotic communities of acidic peatlands from the southern Brazilian Atlantic Forest

The acidic peatlands of southern Brazil are ecosystems essential for the maintenance of the Atlantic Forest, one of the 25 hot-spots of biodiversity in the world. In this work, we investigated the composition of prokaryotic communities in four histosols of three acidic peatland regions by constructing small-subunit (SSU) rRNA gene libraries and sequencing. SSU rRNA gene sequence analysis showed the prevalence of Acidobacteria (38.8%) and Proteobacteria (27.4%) of the Bacteria domain and Miscellaneous (58%) and Terrestrial (24%) groups of Crenarchaeota of the Archaea domain. As observed in other ecosystems, archaeal communities showed lower richness than bacterial communities. We also found a limited number of Euryarchaeota and of known methanotrophic bacteria in the clone libraries.

Methanolinea mesophila sp. nov., a hydrogenotrophic methanogen isolated from rice field soil, and proposal of the archaeal family Methanoregulaceae fam. nov. within the order Methanomicrobiales

A novel mesophilic, hydrogenotrophic methanogen, designated strain TNRT, was isolated from an anaerobic, propionate-degradation enrichment culture that was originally established from a rice field soil sample from Taiwan. Cells were non-motile rods, 2.0–6.5 µm long by 0.3 µm wide. Filamentous (up to about 100 µm) and coccoid (about 1 µm in diameter) cells were also observed in cultures in the late exponential phase of growth. Strain TNRT grew at 20–40 °C (optimally at 37 °C), at pH 6.5–7.4 (optimally at pH 7.0) and in the presence of 0–25 g NaCl l−1 (optimally at 0 g NaCl l−1). The strain utilized H2/CO2 and formate for growth and produced methane. The G+C content of the genomic DNA was 56.4 mol%. Based on sequences of both the 16S rRNA gene and the methanogen-specific marker gene mcrA, strain TNRT was related most closely to Methanolinea tarda NOBI-1T; levels of sequence similarities were 94.8 and 86.4 %, respectively. The 16S rRNA gene sequence similarity indicates that strain TNRT and M. tarda NOBI-1T represent different species within the same genus. This is supported by shared phenotypic properties, including substrate usage and cell morphology, and differences in growth temperature. Based on these genetic and phenotypic properties, strain TNRT is considered to represent a novel species of the genus Methanolinea , for which the name Methanolinea mesophila sp. nov. is proposed; the type strain is TNRT ( = NBRC 105659T = DSM 23604T). In addition, we also suggest family status for the E1/E2 group within the order Methanomicrobiales , for which the name Methanoregulaceae fam. nov. is proposed; the type genus of family is Methanoregula.

Bromeliad catchments as habitats for methanogenesis in tropical rainforest canopies

Tropical epiphytic plants within the family Bromeliaceae are unusual in that they possess foliage capable of retaining water and impounded material. This creates an acidic (pH 3.5-6.5) and anaerobic (<1 ppm O(2)) environment suspended in the canopy. Results from a Costa Rican rainforest show that most bromeliads (n = 75/86) greater than ~20 cm in plant height or ~4-5 cm tank depth, showed presence of methanogens within the lower anoxic horizon of the tank. Archaea were dominated by methanogens (77-90% of recovered ribotypes) and community structure, although variable, was generally comprised of a single type, closely related to either hydrogenotrophic Methanoregula or Methanocella, a specific clade of aceticlastic Methanosaeta, or Methanosarcina. Juvenile bromeliads, or those species, such as Guzmania, with shallow tanks, generally did not possess methanogens, as assayed by polymerase chain reaction specific for methanogen 16S rRNA genes, nor did artificial catchments (~100 ml volume), in place 6-12 months prior to sample collection. Methanogens were not detected in soil (n = 20), except in one case, in which the dominant ribotype was different from nearby bromeliads. Recovery of methyl coenzyme M reductase genes supported the occurrence of hydrogenotrophic and aceticlastic methanogens within bromeliad tanks, as well as the trend, via QPCR analysis of mcrA, of increased methanogenic capacity with increased plant height. Methane production rates of up to 300 nmol CH(4) ml tank water(-1) day(-1) were measured in microcosm experiments. These results suggest that bromeliad-associated archaeal communities may play an important role in the cycling of carbon in neotropical forests.

Methanogen community structure-activity relationship and bioaugmentation of overloaded anaerobic digesters

Accumulation of acids in anaerobic digesters after organic overload can inhibit or stop CH4 production. Therefore, methods to reduce acid concentrations would be helpful. One potential method to improve recovery involves bioaugmentation, addition of specific microorganisms to improve performance. In this study, transiently overloaded digesters were bioaugmented with a propionate-degrading enrichment culture in an effort to decrease recovery time. Biomass samples from 14 different, full-scale anaerobic digesters were screened for specific methanogenic activity (SMA) against propionate; the microbial communities were also compared. SMA values spanned two orders of magnitude. Principal component analysis of denaturing gradient gel electrophoresis (DGGE) banding patterns for a functional gene (mcrA) suggested an underlying community structure-activity relationship; the presence of hydrogenotrophic methanogens closely related to Methanospirillum hungatei and Methanobacterium beijingense was associated with high propionate SMA values. The biomass sample demonstrating the highest SMA was enriched for propionate degrading activity and then used to bioaugment overloaded digesters. Bioaugmented digesters recovered more rapidly following the organic overload, requiring approximately 25 days (2.5 solids retention times (SRTs)) less to recover compared to non-bioaugmented digesters. Benefits of bioaugmentation continued for more than 12 SRTs after organic overload. Bioaugmentation is a promising approach to decrease recovery time after organic overload.

Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea

For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α-subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers.

Methanogen diversity in the rumen of Indian Surti buffalo (Bubalus bubalis), assessed by 16S rDNA analysis

The methanogenic communities in buffalo rumen were characterized using a culture-independent approach of a pooled sample of rumen fluid from three adult Surti buffaloes. Buffalo rumen is likely to include species of various methanogens, so 16S rDNA sequences were amplified and cloned from the sample. A total of 171 clones were sequenced to examine 16S rDNA sequence similarity. About 52.63% sequences (90 clones) had ≥ 90% similarity, whereas, 46.78% of the sequences (81 clones) were 75-89% similar to 16S rDNA database sequences, respectively. Phylogenetic analyses were also used to infer the makeup of methanogenic communities in the rumen of Surti buffalo. As a result, we distinguished 23 operational taxonomic units (OTUs) based on unique 16S rDNA sequences: 12 OTUs (52.17%) affiliated to Methanomicrobiales order, 10 OTUs (43.47%) of the order Methanobacteriales and one OTU (4.34%) of Methanosarcina barkeri like clone, respectively. In addition, the population of Methanomicrobiales and Methabacteriales orders were also observed, accounting 4% and 2.17% of total archea. This study has revealed the largest assortment of hydrogenotrophic methanogens phylotypes ever identified from rumen of Surti buffaloes.

Effect of spatial differences in microbial activity, pH, and substrate levels on methanogenesis initiation in refuse

The initiation of methanogenesis in refuse occurs under high volatile fatty acid (VFA) concentration and low pH (5.5 to 6.25), which generally are reported to inhibit methanogenic Archaea. One hypothesized mechanism for the initiation of methanogenesis in refuse decomposition is the presence of pH-neutral niches within the refuse that act as methanogenesis initiation centers. To provide experimental support for this mechanism, laboratory-scale landfill reactors were operated and destructively sampled when methanogenesis initiation was observed. The active bacterial and archaeal populations were evaluated using RNA clone libraries, RNA terminal restriction fragment length polymorphism (T-RFLP), and reverse transcription-quantitative PCR (RT-qPCR). Measurements from 81 core samples from vertical and horizontal sections of each reactor showed large spatial differences in refuse pH, moisture content, and VFA concentrations. No pH-neutral niches were observed prior to methanogenesis. RNA clone library results showed that active bacterial populations belonged mostly to Clostridiales, and that methanogenic Archaea activity at low pH was attributable to Methanosarcina barkeri. After methanogenesis began, pH-neutral conditions developed in high-moisture-content areas containing substantial populations of M. barkeri. These areas expanded with increasing methane production, forming a reaction front that advanced to low-pH areas. Despite low-pH conditions in >50% of the samples within the reactors, the leachate pH was neutral, indicating that it is not an accurate indicator of landfill microbial conditions. In the absence of pH-neutral niches, this study suggests that methanogens tolerant to low pH, such as M. barkeri, are required to overcome the low-pH, high-VFA conditions present during the anaerobic acid phase of refuse decomposition.

Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge

A novel methane-producing archaeon, strain SMSPT, was isolated from an anaerobic, propionate-degrading enrichment culture that was originally obtained from granular sludge in a mesophilic upflow anaerobic sludge blanket (UASB) reactor used to treat a beer brewery effluent. Cells were non-motile, blunt-ended, straight rods, 1.0–2.6 μm long by 0.5 μm wide; cells were sometimes up to 7 μm long. Asymmetrical cell division was observed in rod-shaped cells. Coccoid cells (0.5–1.0 μm in diameter) were also observed in mid- to late-exponential phase cultures. Growth was observed between 10 and 40 °C (optimum, 30–33 °C) and pH 7.0 and 7.6 (optimum, pH 7.4). The G+C content of the genomic DNA was 56.2 mol%. The strain utilized formate and hydrogen for growth and methane production. Based on comparative sequence analyses of the 16S rRNA and mcrA (encoding the alpha subunit of methyl-coenzyme M reductase, a key enzyme in the methane-producing pathway) genes, strain SMSPT was affiliated with group E1/E2 within the order Methanomicrobiales. The closest relative based on both 16S rRNA and mcrA gene sequences was Methanoregula boonei 6A8T (96.3 % 16S rRNA gene sequence similarity, 85.4 % deduced McrA amino acid sequence similarity). The percentage of 16S rRNA gene sequence similarity indicates that strain SMSPT and Methanoregula boonei 6A8T represent different species within the same genus. This is supported by our findings of shared phenotypic properties, including cell morphology and growth temperature range, and phenotypic differences in substrate usage and pH range. Based on these genetic and phenotypic properties, we propose that strain SMSPT represents a novel species of the genus Methanoregula, for which we propose the name Methanoregula formicica sp. nov., with the type strain SMSPT (=NBRC 105244T =DSM 22288T).

Molecular identification of methanogenic archaea from surti buffaloes (bubalus bubalis), reveals more hydrogenotrophic methanogens phylotypes

Methane emissions from ruminant livestock are considered to be one of the more potent forms of greenhouses gases contributing to global warming. Many strategies to reduce emissions are targeting the methanogens that inhabit the rumen, but such an approach can only be successful if it targets all the major groups of ruminant methanogens. Therefore, a thorough knowledge of the diversity of these microbes in breeds of buffaloes, as well as in response to geographical location and different diets, is required. Therefore, molecular diversity of rumen methanogens in Surti buffaloes was investigated using 16S rRNA gene libraries prepared from pooled rumen contents from three Surti buffaloes. A total of 171 clones were identified revealing 23 different sequences (phylotypes). Of these 23 sequences, twelve sequences (12 OTUs, 83 clones) and 10 sequences (10 OTUs, 83 clones) were similar to methanogens belonging to the orders Methanomicrobiales and Methanobacteriales, and the remaining 1 phylotype (5 clones) were similar to Methanosarcina barkeri. These unique sequences clustered within a distinct and strongly supported phylogenetic group. Further studies and effective strategies can be made to inhibit the growth of Methanomicrobiales and Methanobacteriales phylotypes to reduce the methane emission from rumen and thus help in preventing global warming.

Links between methane flux and transcriptional activities of methanogens and methane oxidizers in a blanket peat bog

The relationship between biogeochemical process rates and microbial functional activity was investigated by analysis of the transcriptional dynamics of the key functional genes for methanogenesis (methyl coenzyme M reductase; mcrA) and methane oxidation (particulate methane monooxygenase; pmoA) and in situ methane flux at two peat soil field sites with contrasting net methane-emitting and -oxidizing characteristics. qPCR was used to quantify the abundances of mcrA and pmoA genes and transcripts at two soil depths. Total methanogen and methanotroph transcriptional dynamics, calculated from mcrA and pmoA gene : transcript abundance ratios, were similar at both sites and depths. However, a linear relationship was demonstrated between surface mcrA and pmoA transcript dynamics and surface flux rates at the methane-emitting and methane-oxidizing sites, respectively. Results indicate that methanotroph activity was at least partially substrate-limited at the methane-emitting site and by other factors at the methane-oxidizing site. Soil depth also contributed to the control of surface methane fluxes, but to a lesser extent. Small differences in the soil water content may have contributed to differences in methanogen and methanotroph activities. This study therefore provides a first insight into the regulation of in situ, field-level surface CH(4) flux at the molecular level by an accurate reflection of gene : transcript abundance ratios for the key genes in methane generation and consumption.

Spatial structure and persistence of methanogen populations in humic bog lakes

Patterns of diversity within methanogenic archaea in humic bog lakes are quantified over time and space to determine the roles that spatial isolation and seasonal mixing play in structuring microbial populations. The protein encoding gene mcrA is used as a molecular marker for the detection of fine-scale differences between methanogens in four dimictic bog lakes in which the water column is mixed twice a year and one meromictic lake that is permanently stratified. Although similar sequences are observed in each bog lake, each lake has its own characteristic set of persisting sequence types, indicating that methanogen populations are delimited either by low migration between the anaerobic hypolimnia or by lake-specific selection. The meromictic lake is differentiated from all other lakes and contains sequences with a higher degree of microdiversity than the dimictic lakes. By relating the structure of diversity to the depth of each bog lake, we propose the hypothesis that the deeper parts of the water column favor microdiversification of methanogens, whereas the periodically disturbed water column of shallower dimictic lakes promote genetically more diverse methanogen communities.

Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog

A novel acidiphilic, hydrogenotrophic methanogen, designated strain 6A8(T), was isolated from an acidic (pH 4.0-4.5) and ombrotrophic (rain-fed) bog located near Ithaca, NY, USA. Cultures were dimorphic, containing thin rods (0.2-0.3 μm in diameter and 0.8-3.0 μm long) and irregular cocci (0.2-0.8 μm in diameter). The culture utilized H(2)/CO(2) to produce methane but did not utilize formate, acetate, methanol, ethanol, 2-propanol, butanol or trimethylamine. Optimal growth conditions were near pH 5.1 and 35 °C. The culture grew in basal medium containing as little as 0.43 mM Na(+) and growth was inhibited completely by 50 mM NaCl. To our knowledge, strain 6A8(T) is one of the most acidiphilic (lowest pH optimum) and salt-sensitive methanogens in pure culture. Acetate, coenzyme M, vitamins and yeast extract were required for growth. It is proposed that a new genus and species be established for this organism, Methanoregula boonei gen. nov., sp. nov. The type strain of Methanoregula boonei is 6A8(T) (=DSM 21154(T) =JCM 14090(T)).

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.

Correlation of methane production and functional gene transcriptional activity in a peat soil

The transcription dynamics of subunit A of the key gene in methanogenesis (methyl coenzyme M reductase; mcrA) was studied to evaluate the relationship between process rate (methanogenesis) and gene transcription dynamics in a peat soil ecosystem. Soil methanogen process rates were determined during incubation of peat slurries at temperatures from 4 to 37 degrees C, and real-time quantitative PCR was applied to quantify the abundances of mcrA genes and transcripts; corresponding transcriptional dynamics were calculated from mcrA transcript/gene ratios. Internal standards suggested unbiased recovery of mRNA abundances in comparison to DNA levels. In comparison to those in pure-culture studies, mcrA transcript/gene ratios indicated underestimation by 1 order of magnitude, possibly due to high proportions of inactive or dead methanogens. Methane production rates were temperature dependent, with maxima at 25 degrees C, but changes in abundance and transcription of the mcrA gene showed no correlation with temperature. However, mcrA transcript/gene ratios correlated weakly (regression coefficient = 0.76) with rates of methanogenesis. Methanogen process rates increased over 3 orders of magnitude, while the corresponding maximum transcript/gene ratio increase was only 18-fold. mcrA transcript dynamics suggested steady-state expression in peat soil after incubation for 24 and 48 h, similar to that in stationary-phase cultures. mcrA transcript/gene ratios are therefore potential in situ indicators of methanogen process rate changes in complex soil systems.

mcrA-targeted real-time quantitative PCR method to examine methanogen communities

Methanogens are of great importance in carbon cycling and alternative energy production, but quantitation with culture-based methods is time-consuming and biased against methanogen groups that are difficult to cultivate in a laboratory. For these reasons, methanogens are typically studied through culture-independent molecular techniques. We developed a SYBR green I quantitative PCR (qPCR) assay to quantify total numbers of methyl coenzyme M reductase alpha-subunit (mcrA) genes. TaqMan probes were also designed to target nine different phylogenetic groups of methanogens in qPCR assays. Total mcrA and mcrA levels of different methanogen phylogenetic groups were determined from six samples: four samples from anaerobic digesters used to treat either primarily cow or pig manure and two aliquots from an acidic peat sample stored at 4 degrees C or 20 degrees C. Only members of the Methanosaetaceae, Methanosarcina, Methanobacteriaceae, and Methanocorpusculaceae and Fen cluster were detected in the environmental samples. The three samples obtained from cow manure digesters were dominated by members of the genus Methanosarcina, whereas the sample from the pig manure digester contained detectable levels of only members of the Methanobacteriaceae. The acidic peat samples were dominated by both Methanosarcina spp. and members of the Fen cluster. In two of the manure digester samples only one methanogen group was detected, but in both of the acidic peat samples and two of the manure digester samples, multiple methanogen groups were detected. The TaqMan qPCR assays were successfully able to determine the environmental abundance of different phylogenetic groups of methanogens, including several groups with few or no cultivated members.