Arctic permafrost soils store large amounts of soil organic carbon (SOC) that could be released into the atmosphere as methane (CH ₄) in a future warmer climate. How warming affects the complex ...microbial network decomposing SOC is not understood. We studied CH ₄ production of Arctic peat soil microbiota in anoxic microcosms over a temperature gradient from 1 to 30 °C, combining metatranscriptomic, metagenomic, and targeted metabolic profiling. The CH ₄ production rate at 4 °C was 25% of that at 25 °C and increased rapidly with temperature, driven by fast adaptations of microbial community structure, metabolic network of SOC decomposition, and trophic interactions. Below 7 °C, syntrophic propionate oxidation was the rate-limiting step for CH ₄ production; above this threshold temperature, polysaccharide hydrolysis became rate limiting. This change was associated with a shift within the functional guild for syntrophic propionate oxidation, with Firmicutes being replaced by Bacteroidetes. Correspondingly, there was a shift from the formate- and H ₂-using Methanobacteriales to Methanomicrobiales and from the acetotrophic Methanosarcinaceae to Methanosaetaceae . Methanogenesis from methylamines, probably stemming from degradation of bacterial cells, became more important with increasing temperature and corresponded with an increased relative abundance of predatory protists of the phylum Cercozoa. We concluded that Arctic peat microbiota responds rapidly to increased temperatures by modulating metabolic and trophic interactions so that CH ₄ is always highly produced: The microbial community adapts through taxonomic shifts, and cascade effects of substrate availability cause replacement of functional guilds and functional changes within taxa.
Significance Microorganisms are key players in emissions of the greenhouse gas (GHG) methane from anoxic carbon-rich peat soils of the Arctic permafrost region. Although available data and modeling suggest a significant temperature-induced increase of GHG emissions from these regions by the end of this century, the controls of and interactions within the underlying microbial networks are largely unknown. This temperature-gradient study of an Arctic peat soil using integrated omics techniques reveals critical temperatures at which microbial adaptations cause changes in metabolic bottlenecks of anaerobic carbon-degradation pathways. In particular taxonomic shifts within functional guilds at different levels of the carbon degradation cascade enable a fast adaptation of the microbial system resulting in high methane emissions at all temperatures.
Ostracoda (microscopic, aquatic Crustacea) from brackish waters have a great potential for ecological monitoring and palaeoenvironmental analyses in highly variable environments. This has been proven ...in many articles during recent decades but their potential has yet to be fully developed or utilised. The analysis of ostracod assemblage composition, species distributions, eco-phenotypic variability and the analysis of stable isotopes and trace elements in ostracod shells provide valuable information on present and past water salinity, temperature and chemistry, hydrodynamic conditions, substrate characteristics, climate, sea level variations, oxygen and nutrient availability. This article provides an overview on the application of ostracods from brackish waters for palaeoenvironmental reconstruction in the Quaternary and for environmental studies in present day environments.
Nitrogen, one of the limiting factors for the yield of rice, can also have an important function in methane oxidation, thus affecting its global budget. Rice microcosms, planted in the greenhouse, ...were treated with the N-fertilizers urea (UPK) and ammonium sulfate (APK) or were only treated with phosphorous and potassium (PK). Methane oxidation rates in PK and UPK treatments were similar during most of the rice-growing season, revealing no effect of urea. However, ammonium sulfate strongly suppressed methanogenesis providing an unfavorable environment for methanotrophs in APK treatment. Roots and rhizospheric soil samples, collected from six different growth stages of the rice plant, were analyzed by terminal restriction fragment length polymorphism (T-RFLP) of the pmoA gene. Assignment of abundant T-RFs to cloned pmoA sequences indicated that the populations on roots were dominated by type-I methanotrophs, whereas the populations in rhizospheric soil were dominated by type-II methanotrophs irrespectively of growth stages and fertilizer treatments. Non-metric multidimensional scaling ordination analysis of T-RFLP profiles revealed that the methanotrophic community was significantly (P<0.001) affected by the different fertilizer treatments; however, the effect was stronger on the roots than in the rhizospheric soil. Contrary to pmoA gene-based analysis, pmoA transcript-based T-RFLP/cloning/sequencing analysis in rhizospheric soil showed type I as the predominant methanotrophs in both PK and UPK treatments. Collectively, our study showed that type-I methanotrophs were dominant and probably active in rhizospheric soil throughout the season irrespective of nitrogen fertilizer used, whereas type-II methanotrophs were relatively more dominant under unfavorable conditions, such as in APK treatment.
Methane oxidation is a key process controlling methane emission from anoxic habitats into the atmosphere. Methanotrophs, responsible for aerobic methane oxidation, do not only oxidize but also ...assimilate methane. Once assimilated, methane carbon may be utilized by other organisms. Here we report on a microbial food web in a rice field soil driven by methane. A thin layer of water-saturated rice field soil was incubated under opposing gradients of oxygen and ¹³C-labelled methane. Bacterial and eukaryotic communities incorporating methane carbon were analysed by RNA-stable isotope probing (SIP). Terminal restriction fragment length polymorphism (T-RFLP) and cloning showed that methanotrophs were the most prominent group of bacteria incorporating methane carbon. In addition, a few Myxobacteria-related sequences were obtained from the 'heavy' rRNA fraction. Denaturing gradient gel electrophoresis (DGGE) targeting 18S rRNA detected various groups of protists in the 'heavy' rRNA fraction including naked amoeba (Lobosea and Heterolobosea), ciliates (Colpodea) and flagellates (Cercozoa). Incubation of soil under different methane concentrations in air resulted in the development of distinct protozoan communities. These results suggest that methane carbon is incorporated into non-methanotrophic pro- and microeukaryotes probably via grazing, and that methane oxidation is a shaping force of the microeukaryotic community depending on methane availability.
Biological methane oxidation is a key process in the methane cycle of wetland ecosystems. The methanotrophic biomass may be grazed by protozoa, thus linking the methane cycle to the soil microbial ...food web. In the present study, the edibility of different methanotrophs for soil protozoa was compared. The number of methanotroph-feeding protozoa in a rice field soil was estimated by determining the most-probable number (MPN) using methanotrophs as food bacteria; naked amoebae and flagellates were the dominant protozoa. Among ten methanotrophic strains examined as a food source, seven yielded a number of protozoa comparable with the yield with Escherichia coli 10⁴ MPN (g soil dry weight)⁻¹, and three out of four Methylocystis spp. yielded significantly fewer numbers 10²-10³ MPN (g soil dry weight)⁻¹. The lower edibility of the Methylocystis spp. was not explained either by their growth phase or by harmful effects on protozoa. Incubation of the soil under methane resulted in a higher number of protozoa actively grazing on methanotrophs, especially on the less-edible group. Protozoa isolated from the soil demonstrated a grazing preference on the different methanotrophs consistent with the results of MPN counts. The results indicate that selective grazing by protozoa may be a biological factor affecting the methanotrophic community in a wetland soil.
Biodiversity is claimed to be essential for ecosystem functioning, but is threatened by anthropogenic disturbances. Prokaryotes have been assumed to be functionally redundant and virtually ...inextinguishable. However, recent work indicates that microbes may well be sensitive to environmental disturbance. Focusing on methane-oxidizing bacteria as model organisms, we simulated disturbance-induced mortality by mixing native with sterilized paddy soil in two ratios, 1:4 and 1:40, representing moderate and severe die-offs. Disturbed microcosms were compared with an untreated control. Recovery of activity and populations was followed over 4 months by methane uptake measurements, pmoA-qPCR, pmoA-based terminal restriction fragment length polymorphism and a pmoA-based diagnostic microarray. Diversity and evenness of methanotrophs decreased in disturbed microcosms, but functioning was not compromised. We consistently observed distinctive temporal shifts between type I and type II methanotrophs, and a rapid population growth leading to even higher cell numbers comparing disturbed microcosms with the control. Overcompensating mortality suggested that population size in the control was limited by competition with other bacteria. Overall, methanotrophs showed a remarkable ability to compensate for die-offs.
The classification of high-throughput sequencing data of protein-encoding genes is not as well established as for 16S rRNA. The objective of this work was to develop a simple and accurate method of ...classifying large datasets of
pmoA
sequences, a common marker for methanotrophic bacteria. A taxonomic system for
pmoA
was developed based on a phylogenetic analysis of available sequences. The taxonomy incorporates the known diversity of
pmoA
present in public databases, including both sequences from cultivated and uncultivated organisms. Representative sequences from closely related genes, such as those encoding the bacterial ammonia monooxygenase, were also included in the
pmoA
taxonomy. In total, 53 low-level taxa (genus-level) are included. Using previously published datasets of high-throughput
pmoA
amplicon sequence data, we tested two approaches for classifying
pmoA
: a naïve Bayesian classifier and BLAST. Classification of
pmoA
sequences based on BLAST analyses was performed using the lowest common ancestor (LCA) algorithm in MEGAN, a software program commonly used for the analysis of metagenomic data. Both the naïve Bayesian and BLAST methods were able to classify
pmoA
sequences and provided similar classifications; however, the naïve Bayesian classifier was prone to misclassifying contaminant sequences present in the datasets. Another advantage of the BLAST/LCA method was that it provided a user-interpretable output and enabled novelty detection at various levels, from highly divergent
pmoA
sequences to genus-level novelty.
The effects of temperature on rates and pathways of CH₄ production and on the abundance and structure of the archaeal community were investigated in acidic peat from a mire in northern Scandinavia ...(68°N). We monitored the production of CH₄ and CO₂ over time and measured the turnover of Fe(II), ethanol, and organic acids. All experiments were performed with and without specific inhibitors (2-bromoethanesulfonate BES for methanogenesis and CH₃F for acetoclastic methanogenesis). The optimum temperature for methanogenesis was 25°C (2.3 micromol CH₄ · g dry weight⁻¹ · day⁻¹), but the activity was relatively high even at 4°C (0.25 micromol CH₄ · g dry weight⁻¹ · day⁻¹). The theoretical lower limit for methanogenesis was calculated to be at -5°C. The optimum temperature for growth as revealed by real-time PCR was 25°C for both archaea and bacteria. The population structure of archaea was studied by terminal restriction fragment length polymorphism analysis and remained constant over a wide temperature range. Hydrogenotrophic methanogenesis accounted for about 80% of the total methanogenesis. Most 16S rRNA gene sequences that were affiliated with methanogens and all McrA sequences clustered with the exclusively hydrogenotrophic order Methanobacteriales, correlating with the prevalence of hydrogenotrophic methanogenesis. Fe reduction occurred parallel to methanogenesis and was inhibited by BES, suggesting that methanogens were involved in Fe reduction. Based upon the observed balance of substrates and thermodynamic calculations, we concluded that the ethanol pool was oxidized to acetate by the following two processes: syntrophic oxidation with methanogenesis (i) as an H₂ sink and (ii) as a reductant for Fe(III). Acetate accumulated, but a considerable fraction was converted to butyrate, making volatile fatty acids important end products of anaerobic metabolism.
Summary
Cultivation‐independent techniques were applied to assess the succession and phylogenetic composition of bacterial communities in a vertical oxygen gradient in flooded, unplanted paddy soil ...microcosms. Microsensor measurements showed that within 6 h of flooding, oxygen was depleted from 200 µM at the floodwater‐soil interface to undetectable amounts at a depth of approximately 2 mm and below. The gradient was quite stable over time, although the oxygen depletion was less pronounced 84 days than 6 h after flooding. Community fingerprint patterns were obtained by terminal restriction fragment length polymorphism (T‐RFLP) analysis from the oxic, transition, and anoxic zones of triplicate soil microcosms at 0, 1 and 6 h, and 1, 2, 7, 21, 30, 42, 84, and 168 days after flooding. Correspondence analyses revealed that T‐RFLP patterns obtained using either community DNA or RNA were affected by time and oxygen zone, and that there was a significant interaction between the effects of time and oxygen zone. The temporal dynamics of bacterial populations were resolved more clearly using RNA than using DNA. At the RNA level, successional community dynamics were most pronounced from 1 h to 2 days and less pronounced from 2 to 21 days after flooding, for both oxic and anoxic zones. No effect of time or oxygen zone on the community dynamics was observed from 21 to 168 days after flooding. Dominant early successional populations were identified by cloning and comparative sequence analysis of environmental 16S rRNA and 16S rRNA genes as members of the Betaproteobacteria (oxic zone) and the clostridial cluster I (anoxic zone). Dominant late successional populations belonged to the Verrucomicrobia and Nitrospira (detected mainly in the oxic zone), and to the Myxococcales (detected mainly in the anoxic zone). In conclusion, the bacterial community developed through successional stages, leading at the RNA level to almost stable community patterns within 21 days after flooding. This principal finding, in combination with the phylogenetic identity of early‐ and late‐appearing populations, suggests that the community dynamics can be explained by the principles of r‐ and K‐selection.
Summary
We focused on the functional guild of methane oxidizing bacteria (MOB) as model organisms to get deeper insights into microbial biogeography. The pmoA gene was used as a functional and ...phylogenetic marker for MOB in two approaches: (i) a pmoA database (> 4000 sequences) was evaluated to obtain insights into MOB diversity in Italian rice paddies, and paddy fields worldwide. The results show a wide geographical distribution of pmoA genotypes that seem to be specifically adapted to paddy fields (e.g. Rice Paddy Cluster 1 and Rice Paddy Cluster 2). (ii) On the smaller geographical scale, we designed a factorial experiment including three different locations, two rice varieties and two habitats (soil and roots) within each of three rice fields. Multivariate analysis of terminal restriction fragment analysis profiles revealed different community patterns at the three field sites, located 10–20 km apart. Root samples were characterized by high abundance of type I MOB whereas the rice variety had no effect. With the agronomical practice being nearly identical, historical contingencies might be responsible for the field site differences. Considering a large reservoir of viable yet inactive MOB cells acting as a microbial seed bank, environmental conditions might have selected and activated a different subset at a time thereby shaping the community.
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