Diversity and ubiquity of thermophilic methanogenic archaea in temperate anoxic soils

Temperate rice field soil from Vercelli (Italy) contains moderately thermophilic methanogens of the yet uncultivated rice cluster I (RC-I), which become prevalent upon incubation at temperatures of 45-50 degrees C. We studied whether such thermophilic methanogens were ubiquitously present in anoxic soils. Incubation of different rice field soils (from Italy, China and the Philippines) and flooded riparian soils (from the Netherlands) at 45 degrees C resulted in vigorous CH(4) production after a lag phase of about 10 days. The archaeal community structure in the soils was analysed by terminal restriction fragment length polymorphism (T-RFLP) targeting the SSU rRNA genes retrieved from the soil, and by cloning and sequencing. Clones of RC-I methanogens mostly exhibited T-RF of 393 bp, but also terminal restriction fragment (T-RF) of 158 and 258 bp length, indicating a larger diversity than previously assumed. No RC-I methanogens were initially found in flooded riparian soils. However, these archaea became abundant upon incubation of the soil at 45 degrees C. Thermophilic RC-I methanogens were also found in the rice field soils from Pavia, Pila and Gapan. However, the archaeal communities in these soils also contained other methanogenic archaea at high temperature. Rice field soil from Buggalon, on the other hand, only contained thermophilic Methanomicrobiales rather than RC-I methanogens, and rice field soil from Jurong mostly Methanomicrobiales and only a few RC-I methanogens. The archaeal community of rice field soil from Zhenjiang almost exclusively consisted of Methanosarcinaceae when incubated at high temperature. Our results show that moderately thermophilic methanogens are common in temperate soils. However, RC-I methanogens are not always dominating or ubiquitous.     

Microbial community analysis of rectal methanogens and sulfate reducing bacteria in two non-human primate species

Background  Methanogenesis by methanogenic Archaea and sulfate reduction by sulfate reducing bacteria (SRB) are the major hydrogenotrophic pathways in the human colon. Methanogenic status of mammals is suggested to be under evolutionary rather than dietary control. However, information is lacking regarding the dynamics of hydrogenotrophic microbial communities among different primate species.
Methods  Rectal swabs were collected from 10 sooty mangabeys ( Cercocebus atys ) and 10 baboons ( Papio hamadryas ). The diversity and abundance of methanogens and SRB were examined using PCR-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (qPCR).
Results  The DGGE results revealed that intestinal Archaea and SRB communities differ between mangabeys and baboons. Phylogenetic analyses of Archaea DGGE bands revealed two distinct clusters with one representing a putative novel order of methanogenic Archaea. The qPCR detected a similar abundance of methanogens and SRB.
Conclusions  Intestinal Archaea and SRB coexist in these primates, and the community patterns are host species-specific.     

Activity and diversity of methanogens in a petroleum hydrocarbon-contaminated aquifer

Methanogenic activity was investigated in a petroleum hydrocarbon-contaminated aquifer by using a series of four push-pull tests with acetate, formate, H(2) plus CO(2), or methanol to target different groups of methanogenic Archaea. Furthermore, the community composition of methanogens in water and aquifer material was explored by molecular analyses, i.e., fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes amplified with the Archaea-specific primer set ARCH915 and UNI-b-rev, and sequencing of DNA from dominant DGGE bands. Molecular analyses were subsequently compared with push-pull test data. Methane was produced in all tests except for a separate test where 2-bromoethanesulfonate, a specific inhibitor of methanogens, was added. Substrate consumption rates were 0.11 mM day(-1) for methanol, 0.38 mM day(-1) for acetate, 0.90 mM day(-1) for H(2), and 1.85 mM day(-1) for formate. Substrate consumption and CH(4) production during all tests suggested that at least three different physiologic types of methanogens were present: H(2) plus CO(2) or formate, acetate, and methanol utilizers. The presence of 15 to 20 bands in DGGE profiles indicated a diverse archaeal population. High H(2) and formate consumption rates agreed with a high diversity of methanogenic Archaea consuming these substrates (16S rRNA gene sequences related to several members of the Methanomicrobiaceae) and the detection of Methanomicrobiaceae by using FISH (1.4% of total DAPI [4',6-diamidino-2-phenylindole]-stained microorganisms in one water sample; probe MG1200). Considerable acetate consumption agreed with the presence of sequences related to the obligate acetate degrader Methanosaeata concilii and the detection of this species by FISH (5 to 22% of total microorganisms; probe Rotcl1). The results suggest that both aceticlastic and CO(2)-type substrate-consuming methanogens are likely involved in the terminal step of hydrocarbon degradation, while methanogenesis from methanol plays a minor role. DGGE profiles further indicate similar archaeal community compositions in water and aquifer material. The combination of hydrogeological and molecular methods employed in this study provide improved information on the community and the potential activity of methanogens in a petroleum hydrocarbon-contaminated aquifer.     

Unexpectedly High Bacterial Diversity in Arctic Tundra Relative to Boreal Forest Soils, Revealed by Serial Analysis of Ribosomal Sequence Tags

Arctic tundra and boreal forest soils have globally relevant functions that affect atmospheric chemistry and climate, yet the bacterial composition and diversity of these soils have received little study. Serial analysis of ribosomal sequence tags (SARST) and denaturing gradient gel electrophoresis (DGGE) were used to compare composite soil samples taken from boreal and arctic biomes. This study comprises an extensive comparison of geographically distant soil bacterial communities, involving the analysis of 12,850 ribosomal sequence tags from six composite soil samples. Bacterial diversity estimates were greater for undisturbed arctic tundra soil samples than for boreal forest soil samples, with the highest diversity associated with a sample from an extreme northern location (82^oN). The lowest diversity estimate was obtained from an arctic soil sample that was disturbed by compaction and sampled from a greater depth. Since samples from the two biomes did not form distinct clusters on the basis of SARST data and DGGE fingerprints, factors other than latitude likely influenced the phylogenetic compositions of these communities. The high number of ribosomal sequences analyzed enabled the identification of possible cosmopolitan and endemic bacterial distributions in particular soils.     

Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags

Arctic tundra and boreal forest soils have globally relevant functions that affect atmospheric chemistry and climate, yet the bacterial composition and diversity of these soils have received little study. Serial analysis of ribosomal sequence tags (SARST) and denaturing gradient gel electrophoresis (DGGE) were used to compare composite soil samples taken from boreal and arctic biomes. This study comprises an extensive comparison of geographically distant soil bacterial communities, involving the analysis of 12,850 ribosomal sequence tags from six composite soil samples. Bacterial diversity estimates were greater for undisturbed arctic tundra soil samples than for boreal forest soil samples, with the highest diversity associated with a sample from an extreme northern location (82(o)N). The lowest diversity estimate was obtained from an arctic soil sample that was disturbed by compaction and sampled from a greater depth. Since samples from the two biomes did not form distinct clusters on the basis of SARST data and DGGE fingerprints, factors other than latitude likely influenced the phylogenetic compositions of these communities. The high number of ribosomal sequences analyzed enabled the identification of possible cosmopolitan and endemic bacterial distributions in particular soils.     

Methanogenic activity and biomass in Holocene permafrost deposits of the Lena Delta, Siberian Arctic and its implication for the global methane budget

Permafrost environments within the Siberian Arctic are natural sources of the climate relevant trace gas methane. In order to improve our understanding of the present and future carbon dynamics in high latitudes, we studied the methane concentration, the quantity and quality of organic matter, and the activity and biomass of the methanogenic community in permafrost deposits. For these investigations a permafrost core of Holocene age was drilled in the Lena Delta (72°22′N, 126°28′E). The organic carbon of the permafrost sediments varied between 0.6% and 4.9% and was characterized by an increasing humification index with permafrost depth. A high CH₄ concentration was found in the upper 4 m of the deposits, which correlates well with the methanogenic activity and archaeal biomass (expressed as PLEL concentration). Even the incubation of core material at −3 and −6°C with and without substrates showed a significant CH₄ production (range: 0.04–0.78 nmol CH₄ h⁻¹ g⁻¹). The results indicated that the methane in Holocene permafrost deposits of the Lena Delta originated from modern methanogenesis by cold‐adapted methanogenic archaea. Microbial generated methane in permafrost sediments is so far an underestimated factor for the future climate development.     

Methane fluxes in permafrost habitats of the Lena Delta: effects of microbial community structure and organic matter quality

For the understanding and assessment of recent and future carbon dynamics of arctic permafrost soils the processes of CH(4) production and oxidation, the community structure and the quality of dissolved organic matter (DOM) were studied in two soils of a polygonal tundra. Activities of methanogens and methanotrophs differed significantly in their rates and distribution patterns among the two investigated profiles. Community structure analysis showed similarities between both soils for ester-linked phospholipid fatty acids (PLFAs) and differences in the fraction of unsaponifiable PLFAs and phospholipid ether lipids. Furthermore, a shift of the overall composition of the microbiota with depth at both sites was indicated by an increasing portion of iso- and anteiso-branched fatty acids related to the amount of straight-chain fatty acids. Although permafrost soils represent a large carbon pool, it was shown that the reduced quality of organic matter leads to a substrate limitation of the microbial metabolism. It can be concluded from our and previous findings first that microbial communities in the active layer of an Arctic polygon tundra are composed by members of all three domains of life, with a total biomass comparable to temperate soil ecosystems, and second that these microorganisms are well adapted to the extreme temperature gradient of their environment.     

Community structure of methanogenic archaea and methane production associated with compost-treated tropical rice-field soil

The diversity and density of methanogenic archaea and methane production were investigated ex situ at different growth stages of rice plant cultivated in compost-treated tropical rice fields. The qPCR analysis revealed variation in methanogens population from 3.40?×?10(6) to 1.11?×?10(7) copies?g(-1) dws, in the year 2009 and 4.37?×?10(6) to 1.36?×?10(7) copies?g(-1) dws in the year 2010. Apart from methanogens, a large number of bacterial (9.60?×?10(9) -1.44?×?10(10) copies?g(-1) dws) and archaeal (7.13?×?10(7) -3.02?×?10(8) copies?g(-1) dws) communities were also associated with methanogenesis. Methanogen population size varied in the order: flowering > ripening > tillering > postharvest > preplantation stage. The RFLP-based 16S rRNA gene-targeted phylogenetic analysis showed that clones were closely related to diverse group of methanogens comprising members of Methanomicrobiaceae, Methanosarcinaceae, Methanosaetaceae and RC I. Laboratory incubation studies revealed higher amount of cumulative CH(4) at the flowering stage. The integration of methanogenic community structure and CH(4) production potential of soil resulted in a better understanding of the dynamics of CH(4) production in organically treated rice-field soil. The hypothesis that the stages of plant development influence the methanogenic community structure leading to temporal variation in the CH(4) production has been successfully tested.     

Heavy-machinery traffic impacts methane emissions as well as methanogen abundance and community structure in oxic forest soils

Temperate forest soils are usually efficient sinks for the greenhouse gas methane, at least in the absence of significant amounts of methanogens. We demonstrate here that trafficking with heavy harvesting machines caused a large reduction in CH(4) consumption and even turned well-aerated forest soils into net methane sources. In addition to studying methane fluxes, we investigated the responses of methanogens after trafficking in two different forest sites. Trafficking generated wheel tracks with different impact (low, moderate, severe, and unaffected). We found that machine passes decreased the soils' macropore space and lowered hydraulic conductivities in wheel tracks. Severely compacted soils yielded high methanogenic abundance, as demonstrated by quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes, whereas these sequences were undetectable in unaffected soils. Even after a year after traffic compression, methanogen abundance in compacted soils did not decline, indicating a stability of methanogens here over time. Compacted wheel tracks exhibited a relatively constant community structure, since we found several persisting mcrA sequence types continuously present at all sampling times. Phylogenetic analysis revealed a rather large methanogen diversity in the compacted soil, and most mcrA gene sequences were mostly similar to known sequences from wetlands. The majority of mcrA gene sequences belonged either to the order Methanosarcinales or Methanomicrobiales, whereas both sites were dominated by members of the families Methanomicrobiaceae Fencluster, with similar sequences obtained from peatland environments. The results show that compacting wet forest soils by heavy machinery causes increases in methane production and release.     

自然湿地土壤产甲烷菌和甲烷氧化菌多样性的分子检测

自然湿地是CH4排放的重要来源之一。产甲烷菌和甲烷氧化菌是介导自然湿地甲烷循环的重要功能菌群。开展产甲烷菌和甲烷氧化菌多样性的检测研究有助于揭示微生物介导的甲烷循环以及自然湿地甲烷排放的时空异质性。传统基于培养的检测方法已被证实无法充分描述产甲烷菌和甲烷氧化菌的多样性,而分子检测方法为自然湿地土壤产甲烷菌和甲烷氧化菌的多样性检测提供了一种更准确和科学的工具。本文综述了自然湿地土壤产甲烷菌和甲烷氧化菌的定性和定量分子检测方法,包括末端限制性片段长度多态性（T-RFLP）、变性梯度凝胶电泳（DGGE）、荧光原位杂交（FISH）和实时定量PCR（real-time qPCR）,重点分析了分子检测中两类重要的标记基因,总结了不同类型自然湿地产甲烷菌和甲烷氧化菌群落多样性的最新成果,提出了我国在该领域今后应深入研究探讨的一些问题及建议。     

Activity, structure and dynamics of the methanogenic archaeal community in a flooded Italian rice field

Methane production was studied in an Italian rice field over two consecutive years (1998, 1999) by measuring the rates of total and acetate-dependent methanogenesis in soil and root samples. Population dynamics of methanogens were followed by terminal restriction fragment length polymorphism and real-time PCR targeting archaeal SSU rRNA genes. Rates of total and acetate-dependent methanogenesis in soil increased during the season, reached a maximum at about 70-80 days after flooding and then decreased again. In contrast, the size of the archaeal community remained relatively constant. Therefore, the seasonal changes in the methanogenic processes were probably not caused by changes in the size of the methanogenic community but in its activity. During the 1998/1999 winter period, a slight decrease in archaeal cell numbers was found. In both years, the dominant groups were methanogens affiliated with Rice cluster I, Methanosaetaceae, Methanosarcinaceae and Methanobacteriaceae. Correspondence analysis showed, however, that the archaeal community structure was different in 1998 and 1999. Methanogens with potential acetoclastic activity made up a larger fraction of the total archaeal community in 1999 (32-53%) than in 1998 (20-32%). Furthermore, the frequency of Methanosaetaceae relative to Methanosarcinaceae was significantly higher in 1999 than in 1998. This difference could be explained by the much lower soil acetate concentrations in 1999, to which Methanosaetaceae are physiologically better adapted than Methanosarcinaceae. Over the season, however, the composition of the archaeal community remained relatively constant and thus did not reflect the observed seasonal change in CH(4) production activity. The analysis of rice root samples in 1999 showed that the archaeal community structure on the roots was similar to that in soil but with acetoclastic methanogens being relatively less common. This observation is in agreement with domination of CH(4) production by H(2)/CO(2)-dependent methanogenesis on roots. Our study provided a link between size, structure and function of the methanogenic community in an Italian rice field.     

Diversity of the particulate methane monooxygenase gene in methanotrophic samples from different rice field soils in China and the Philippines

Methanotrophic bacteria play a crucial role in regulating the emission of CH4 from rice fields into the atmosphere. We investigated the CH4 oxidation activity together with the diversity of methanotrophic bacteria in ten rice field soils from different geographic locations. Upon incubation of aerated soil slurries under 7% CH4, rates of CH4 oxidation increased after a lag phase of 1-4 days and reached values of 3-10 micromol d(-1) g-dw(-1) soil. The methanotrophic community was assayed by retrieval of the pmoA gene which encodes the a subunit of the particulate methane monooxygenase. After extraction of DNA from actively CH4-oxidizing soil samples and PCR-amplification of the pmoA, the community was analyzed by Denaturant Gradient Gel Electrophoresis (DGGE) and Terminal Restriction Fragment Length Polymorphism (T-RFLP). DGGE bands were excised, the pmoA re-amplified, sequenced and the encoded amino acid sequence comparatively analyzed by phylogenetic treeing. The analyses allowed the detection of pmoA sequences related to the following methanotrophic genera: the type-I methanotrophs Methylobacter, Methylomicrobium, Methylococcus and Methylocaldum, and the type-II methanotrophs Methylocystis and Methylosinus. T-RFLP analysis detected a similar diversity, but type-II pmoA more frequently than DGGE. All soils but one contained type-II in addition to type-I methanotrophs. Type-I Methylomonas was not detected at all. Different combinations of methanotrophic genera were detected in the different soils. However, there was no obvious geographic pattern of the distribution of methanotrophs.     

Methanogenic profiles by denaturing gradient gel electrophoresis using order-specific primers in anaerobic sludge digestion

In the present study, the diversity of methanogenic populations was monitored for 25 days, together with the process data for an anaerobic batch reactor treating waste-activated sludge. To understand this microbial diversity and dynamics, 16S rRNA-gene-targeted denaturing gradient gel electrophoresis (DGGE) fingerprinting was conducted at two different taxonomic levels: the domain and order levels. The DGGE profiles of the domain Archaea and the three orders Methanosarcinales, Methanomicrobiales, and Methanobacteriales were comparatively analyzed after each DGGE band was sequenced to enable identification. The DGGE profiles of the three orders showed methanogens belonging to each order that were not detected in the DGGE profile of the Archaea. This discrepancy may have resulted from PCR bias or differences in the abundances of the three microbial orders in the anaerobic bioreactor. In conclusion, to fully understand the detailed methanogenic diversity and dynamics in an anaerobic bioreactor, it is necessary to conduct DGGE analysis with 16S rRNA gene primers that target lower taxonomic groups.     

Genomic suppression subtractive hybridization as a tool to identify differences in mycorrhizal fungal genomes

Understanding the ecology of methanogens in natural and engineered environments is a prerequisite to predicting or managing methane emissions. In this study, a novel high-throughput fingerprint method was developed for determining methanogen diversity and relative abundance within environmental samples. The method described here, designated amplicon length heterogeneity PCR of the mcrA gene (LH-mcrA), is based on the natural length variation in the mcrA gene. The mcrA gene encodes the alpha-subunit of the methyl-coenzyme M reductase, which is involved in the terminal step of methane production by methanogens. The methanogenic communities from stored swine and dairy manures were distinct from each other. To validate the method, methanogenic communities in a plug flow-type bioreactor (PFBR) treating swine manure were characterized using LH-mcrA method and correlated to mcrA gene clone libraries. The diversity and relative abundance of the methanogenic groups were assessed. Methanobrevibacter, Methanosarcinaceae, Methanoculleus, Methanogenium, Methanocorpusculum and one unidentified group were assigned to particular LH-mcrA amplicons. Particular phylotypes related to Methanoculleus were predominant in the last compartment of the PFBR where the bulk of methane was produced. LH-mcrA method was found to be a reliable, fast and cost-effective alternative for diversity assessment of methanogenic communities in microbial systems.     

Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta,Siberia

With this study, we present first data on the diversity of aerobic methanotrophic bacteria (MOB) in an Arctic permafrost active layer soil of the Lena Delta, Siberia. Applying denaturing gradient gel electrophoresis and cloning of 16S ribosomal ribonucleic acid (rRNA) and pmoA gene fragments of active layer samples, we found a general restriction of the methanotrophic diversity to sequences closely related to the genera Methylobacter and Methylosarcina, both type I MOB. In contrast, we revealed a distinct species-level diversity. Based on phylogenetic analysis of the 16S rRNA gene, two new clusters of MOB specific for the permafrost active layer soil of this study were found. In total, 8 out of 13 operational taxonomic units detected belong to these clusters. Members of these clusters were closely related to Methylobacter psychrophilus and Methylobacter tundripaludum, both isolated from Arctic environments. A dominance of MOB closely related to M. psychrophilus and M. tundripaludum was confirmed by an additional pmoA gene analysis. We used diversity indices such as the Shannon diversity index or the Chao1 richness estimator in order to compare the MOB community near the surface and near the permafrost table. We determined a similar diversity of the MOB community in both depths and suggest that it is not influenced by the extreme physical and geochemical gradients in the active layer.     

Effect of inhibition of acetoclastic methanogenesis on growth of archaeal populations in an anoxic model environment

Methyl fluoride is frequently used to specifically inhibit acetoclastic methanogenesis, thus allowing determination of the relative contribution of acetate versus H2/CO2 to total CH4 production in natural environments. However, the effect of the inhibitor on growth of the target archaeal population has not yet been studied. Therefore, we incubated rice roots as an environmental model system under anoxic conditions in the presence and absence of CH3F, measured the activity and Gibbs free energy (DeltaG) of CH4 production, and determined the abundance of individual archaeal populations by using a combination of quantitative (real-time) PCR and analysis of terminal restriction fragment length polymorphism targeting the 16S rRNA gene. It was shown that CH3F specifically inhibited not only acetoclastic methanogenic activity but also the proliferation of Methanosarcina spp, which were the prevalent acetoclastic methanogens in our environmental model system. Therefore, inhibition experiments with CH3F seem to be a suitable method for quantifying acetoclastic CH4 production. It is furthermore shown that the growth and final population size of methanogens were consistent with energetic conditions that at least covered the maintenance requirements of the population.     

Molecular investigations into a globally important carbon pool: permafrost‐protected carbon in Alaskan soils

The fate of carbon (C) contained within permafrost in boreal forest environments is an important consideration for the current and future carbon cycle as soils warm in northern latitudes. Currently, little is known about the microbiology or chemistry of permafrost soils that may affect its decomposition once soils thaw. We tested the hypothesis that low microbial abundances and activities in permafrost soils limit decomposition rates compared with active layer soils. We examined active layer and permafrost soils near Fairbanks, AK, the Yukon River, and the Arctic Circle. Soils were incubated in the lab under aerobic and anaerobic conditions. Gas fluxes at ?5 and 5 °C were measured to calculate temperature response quotients (Q₁₀). The Q₁₀ was lower in permafrost soils (average 2.7) compared with active layer soils (average 7.5). Soil nutrients, leachable dissolved organic C (DOC) quality and quantity, and nuclear magnetic resonance spectroscopy of the soils revealed that the organic matter within permafrost soils is as labile, or even more so, than surface soils. Microbial abundances (fungi, bacteria, and subgroups: methanogens and Basidiomycetes) and exoenzyme activities involved in decomposition were lower in permafrost soils compared with active layer soils, which, together with the chemical data, supports the reduced Q₁₀ values. CH₄ fluxes were correlated with methanogen abundance and the highest CH₄ production came from active layer soils. These results suggest that permafrost soils have high inherent decomposability, but low microbial abundances and activities reduce the temperature sensitivity of C fluxes. Despite these inherent limitations, however, respiration per unit soil C was higher in permafrost soils compared with active layer soils, suggesting that decomposition and heterotrophic respiration may contribute to a positive feedback to warming of this eco region.     

Temperature Dependence of Methane Production in Tropical Rice Soils

Although CH 4 production is sensitive to temperature, it is not clear how temperature controls CH 4 production directly versus the production of organic substrates that methanogens convert into CH 4 . Therefore, this study was done to better understand how CH 4 production in rice paddy soil responded to temperature when the process was not limited by the availability of substrates. In a laboratory-incubation study using three Indian rice soils under flooded conditions, the effect of temperature on CH 4 production was examined. CH 4 production in acid sulphate, laterite, and alluvial soil samples under flooded conditions distinctly increased with increase in temperature from 15°C to 35°C. Laterite and acid sulphate soils produced distinctly less CH 4 than alluvial soils. CO 2 production increased with increase in temperature in all the soils. The readily mineralizable carbon C and Fe 2+ contents in soils were least at 15°C and highest at 35°C, irrespective of soil type. Likewise, a significant correlation existed between microbial population (methanogens and sulphate reducers) and CH 4 production. Comparing the temperature coefficients ( Q 10 ) for methane production within each soil type at low (15°C-25°C) and medium (25°C-35°C) temperature intervals revealed that these values were not uniform for both alluvial and laterite soils. But acid sulphate soil had Q 10 values that were near 2 at both temperature intervals. When these soil samples were amended with substrates (acetate, H 2 -CO 2 , and rice straw), there were stimulatory effects on methane production rates and consequently on the Q 10 values. The pattern of temperature coefficients was characteristic of the soil type and the nature of substrates used for amendment.     

Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO).

Production and consumption processes in soils contribute to the global cycles of many trace gases (CH4, CO, OCS, H2, N2O, and NO) that are relevant for atmospheric chemistry and climate. Soil microbial processes contribute substantially to the budgets of atmospheric trace gases. The flux of trace gases between soil and atmosphere is usually the result of simultaneously operating production and consumption processes in soil: The relevant processes are not yet proven with absolute certainty, but the following are likely for trace gas consumption: H2 oxidation by abiontic soil enzymes; CO cooxidation by the ammonium monooxygenase of nitrifying bacteria; CH4 oxidation by unknown methanotrophic bacteria that utilize CH4 for growth; OCS hydrolysis by bacteria containing carbonic anhydrase; N2O reduction to N2 by denitrifying bacteria; NO consumption by either reduction to N2O in denitrifiers or oxidation to nitrate in heterotrophic bacteria. Wetland soils, in contrast to upland soils are generally anoxic and thus support the production of trace gases (H2, CO, CH4, N2O, and NO) by anaerobic bacteria such as fermenters, methanogens, acetogens, sulfate reducers, and denitrifiers. Methane is the dominant gaseous product of anaerobic degradation of organic matter and is released into the atmosphere, whereas the other trace gases are only intermediates, which are mostly cycled within the anoxic habitat. A significant percentage of the produced methane is oxidized by methanotrophic bacteria at anoxic-oxic interfaces such as the soil surface and the root surface of aquatic plants that serve as conduits for O2 transport into and CH4 transport out of the wetland soils. The dominant production processes in upland soils are different from those in wetland soils and include H2 production by biological N2 fixation, CO production by chemical decomposition of soil organic matter, and NO and N2O production by nitrification and denitrification. The processes responsible for CH4 production in upland soils are completely unclear, as are the OCS production processes in general. A problem for future research is the attribution of trace gas metabolic processes not only to functional groups of microorganisms but also to particular taxa. Thus, it is completely unclear how important microbial diversity is for the control of trace gas flux at the ecosystem level. However, different microbial communities may be part of the reason for differences in trace gas metabolism, e.g., effects of nitrogen fertilizers on CH4 uptake by soil; decrease of CH4 production with decreasing temperature; or different rates and modes of NO and N2O production in different soils and under different conditions.     

Methane Production and Methanogenic Archaea in the Digestive Tracts of Millipedes (Diplopoda)

Methane production by intestinal methanogenic Archaea and their community structure were compared among phylogenetic lineages of millipedes. Tropical and temperate millipedes of 35 species and 17 families were investigated. Species that emitted methane were mostly in the juliform orders Julida, Spirobolida, and Spirostreptida. The irregular phylogenetic distribution of methane production correlated with the presence of the methanogen-specific mcrA gene. The study brings the first detailed survey of methanogens’ diversity in the digestive tract of millipedes. Sequences related to Methanosarcinales, Methanobacteriales, Methanomicrobiales and some unclassified Archaea were detected using molecular profiling (DGGE). The differences in substrate preferences of the main lineages of methanogenic Archaea found in different millipede orders indicate that the composition of methanogen communities may reflect the differences in available substrates for methanogenesis or the presence of symbiotic protozoa in the digestive tract. We conclude that differences in methane production in the millipede gut reflect differences in the activity and proliferation of intestinal methanogens rather than an absolute inability of some millipede taxa to host methanogens. This inference was supported by the general presence of methanogenic activity in millipede faecal pellets and the presence of the 16S rRNA gene of methanogens in all tested taxa in the two main groups of millipedes, the Helminthophora and the Pentazonia.