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Background Managed grasslands are global sources of atmospheric methanol, which is one of the most abundant volatile organic compounds in the atmosphere and promotes oxidative capacity for tropospheric and stratospheric ozone depletion. The phyllosphere is a favoured habitat of plant-colonizing methanol-utilizing bacteria. These bacteria also occur in the rhizosphere, but their relevance for methanol consumption and ecosystem fluxes is unclear. Methanol utilizers of the plant-associated microbiota are key for the mitigation of methanol emission through consumption. However, information about grassland plant microbiota members, their biodiversity and metabolic traits, and thus key actors in the global methanol budget is largely lacking. Results We investigated the methanol utilization and consumption potentials of two common plant species (Festuca arundinacea and Taraxacum officinale) in a temperate grassland. The selected grassland exhibited methanol formation. The detection of 13C derived from 13C-methanol in 16S rRNA of the plant microbiota by stable isotope probing (SIP) revealed distinct methanol utilizer communities in the phyllosphere, roots and rhizosphere but not between plant host species. The phyllosphere was colonized by members of Gamma- and Betaproteobacteria. In the rhizosphere, 13C-labelled Bacteria were affiliated with Deltaproteobacteria, Gemmatimonadates, and Verrucomicrobiae. Less-abundant 13C-labelled Bacteria were affiliated with well-known methylotrophs of Alpha-, Gamma-, and Betaproteobacteria. Additional metagenome analyses of both plants were consistent with the SIP results and revealed Bacteria with methanol dehydrogenases (e.g., MxaF1 and XoxF1-5) of known but also unusual genera (i.e., Methylomirabilis, Methylooceanibacter, Gemmatimonas, Verminephrobacter). 14C-methanol tracing of alive plant material revealed divergent potential methanol consumption rates in both plant species but similarly high rates in the rhizosphere and phyllosphere. Conclusions Our study revealed the rhizosphere as an overlooked hotspot for methanol consumption in temperate grasslands. We further identified unusual new but potentially relevant methanol utilizers besides well-known methylotrophs in the phyllosphere and rhizosphere. We did not observe a plant host-specific methanol utilizer community. Our results suggest that our approach using quantitative SIP and metagenomics may be useful in future field studies to link gross methanol consumption rates with the rhizosphere and phyllosphere microbiome.

AimWe investigated how substrate hydraulic properties respond to the presence of arbuscular mycorrhizal fungi (AMF) in root-containing and root-free substrate zones in aMedicago truncatula-Rhizophagus irregularismodel system.MethodsBefore planting, two compartments constructed from standard soil sampling cores (250 cm3) were implanted into non-mycorrhizal and mycorrhizal pots containing a sand-zeolite-soil mix. One compartment allowed root penetration (1 mm mesh cover) and the other only hyphal ingrowth (42 μm mesh cover). After eight weeks of growth under maintenance of moist conditions, the cores were subjected to water retention measurements. Additionally, we measured water retention of bare substrates before and after drying events to check for successful maintenance of moist conditions in pots.ResultsDrying of bare substrates decreased water retention, but planting at least sustained it. The parameters of water retention models responded linearly to root morphological traits across mycorrhizal and non-mycorrhizal substrates. Hyphae-only colonization comparatively affected the course of water retention in ways that suggest increased pore space heterogeneity while maintaining water storage capacity of substrates.ConclusionsHence, water contents corresponded to different substrate matric potentials in non-mycorrhizal and mycorrhizal pots. We conclude that changes to water retention in AMF colonized substrates can contribute to a widely observed phenomenon, i.e. that mycorrhizal plants differ in their moisture stress response from non-mycorrhizal plants.

Oil palm plantations, irreversibly claimed primarily from tropical forest, carpet the landscape in Malaysia and Indonesia, the largest global producers of palm oil. The impact of forest conversion to oil palm agriculture on the plant and animal diversity has gained worldwide attention, but knowledge on the effects on microbially mediated belowground soil processes which drive ecosystem-level responses such as greenhouse gas (GHG) fluxes, particularly methane and nitrous oxide, remain scarce and fragmented. Focusing on the soil microbiome, as well as environmental drivers of soil biogeochemical processes, we synthesize previous research works to provide an overview of the current state of scientific understanding on the effects of deforestation for oil palm agriculture. Forest conversion to oil palm plantations is associated with increased pH, and lowered C and N contents, as typically observed in agricultural soils. Interestingly, in contrast to plant and animal diversity, soil bacterial and functional diversity, as well as fungal abundance, were unaffected or increased. Furthermore, community composition was altered by the land transformation. This indicates the resilience of the microbial diversity to deforestation for oil palm agriculture. However, it remains to be determined whether and how such community resilience would translate to the resilience of soil microbial groups mediating methane- and N-cycling processes central to greenhouse gas turnover.

Background: Managed grasslands are global sources of atmospheric methanol, which is one of the most abundant volatile organic compounds (VOCs) in the atmosphere and promotes oxidative capacity for tropospheric and stratospheric ozone depletion. The phyllosphere is a favoured habitat of plant-colonizing methanol-utilizing bacteria. These bacteria also occur in the rhizosphere, but their relevance for methanol consumption and ecosystem fluxes is unclear. The estimated global methanol emission rate is considerably higher than those escaped into the atmosphere. Thus, methanol utilizers in the plant microbiota might be key for the mitigation of methanol emission through consumption. However, information about grassland plant microbiota members, their biodiversity and metabolic traits, and thus key actors in the global methanol budget is largely lacking.Results: We investigated the methanol utilization and consumption potentials of two common plant species (Festuca arundinacea and Taraxacum officinale) in a temperate and fertilized grassland. The selected grassland exhibited net methanol emission. The detection of 13C derived from 13C-methanol in 16S rRNA of the plant microbiota by stable isotope probing (SIP) revealed distinct methanol utilizer communities in the phyllosphere, roots and rhizosphere but not between plant host species. The phyllosphere was colonized by members of Gamma- and Betaproteobacteria. In the rhizosphere, 13C-labelled Bacteria were affiliated with Deltaproteobacteria, Gemmatimonadates, and Verrucomicrobiae. Less-abundant 13C-labelled Bacteria were affiliated with well-known methylotrophs of Alpha-, Gamma-, and Betaproteobacteria. Additional metagenome analyses of both plants were consistent with the SIP results and revealed Bacteria with methanol dehydrogenases (e.g., MxaF1 and XoxF1-5) of known but also unusual genera (i.e., Methylomirabilis, Methylooceanibacter, Gemmatimonas, Verminephrobacter). 14C-methanol tracing of alive plant material revealed divergent methanol oxidation rates in both plant species but similarly high rates in the rhizosphere and phyllosphere.Conclusions: The rhizosphere has been shown to be an overlooked hotspot for methanol consumption in grasslands. We also identified unusual methanol utilizers in the phyllosphere and rhizosphere. We did not observe a plant host-specific methanol utilizer community. Our results suggest a model for methanol turnover in which both the sources (plants) and sinks (microbiota) of a volatile are separated but in the same ecological unit.

Background: Chloromethane (CH3Cl) is the most abundant chlorinated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH3Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH3Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. Results and Conclusions: We investigated chloromethane-degrading taxa associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with 13C-labelled CH3Cl combined with metagenomic DNA sequencing. Metagenome assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH3Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH3Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH3Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterised methylotrophic cmuA-independent pathway likely drives CH3Cl degradation in the investigated tree ferns.

Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.

A novel strain was isolated from grassland soil that has the potential to assimilate ammonium by the reduction of nitrate in the presence of oxygen. Whole genome sequence analysis revealed the presence of an assimilatory cytoplasmic nitrate reductase gene nasA and the assimilatory nitrite reductase genes nirBD which are involved in the sequential reduction of nitrate to nitrite and further to ammonium, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents a member of the genus Pseudomonas . The closest phylogenetic neighbours based on 16S rRNA gene sequence analysis are the type strains of Pseudomonas peli (98.17%) and Pseudomonas guineae (98.03%). In contrast, phylogenomic analysis revealed a close relationship to Pseudomonas alcaligenes . Computation of the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) with the closest phylogenetic neighbours of S1-A32-2T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. On the basis of these results, it was concluded that the soil isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas campi sp. nov. (type strain S1-A32-2T=LMG 31521T=DSM 110222T) is proposed.

International audience; Chloromethane (CH3 Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH3 Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH3 Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH3 Cl-degrading bacteria associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with 13 C-labelled CH3 Cl combined with metagenomics. Metagenome-assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH3 Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH3 Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH3 Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterized methylotrophic cmuA-independent pathway may drive CH3 Cl degradation in the investigated tree ferns.

German Science Foundation (DFG KE 884/10-1 ; ANR-14-CE35-0005-01) ; French National Research Agency (DFG KE 884/10-1 ; ANR-14-CE35-0005-01); International audience; Chloromethane (CH3Cl, methyl chloride) is the most abundant volatile halocarbon in the atmosphere and involved in stratospheric ozone depletion. The global CH3Cl budget, and especially the CH3Cl sink from microbial degradation in soil, still involves large uncertainties. These may potentially be resolved by a combination of stable isotope analysis and bacterial diversity studies. We determined the stable isotope fractionation of CH3Cl hydrogen and carbon and investigated bacterial diversity during CH3Cl degradation in three soils with different properties (forest, grassland, and agricultural soils) and at different temperatures and headspace mixing ratios of CH3Cl. The extent of chloromethane degradation decreased in the order forest > grassland > agricultural soil. Rates ranged from 0.7 to 2.5 μg g−1 dry wt. d−1 for forest soil, from 0.1 to 0.9 μg g−1 dry wt. d−1 for grassland soil, and from 0.1 to 0.4 μg g−1 dry wt. d−1 for agricultural soil and increased with increasing temperature and CH3Cl supplementation. The measured mean stable hydrogen enrichment factor of CH3Cl of −50 ± 13‰ was unaffected by temperature, mixing ratio, or soil type. In contrast, the stable carbon enrichment factor depended on CH3Cl degradation rates and ranged from −38 to −11‰. Bacterial community composition correlated with soil properties was independent from CH3Cl degradation or isotope enrichment. Nevertheless, increased abundance after CH3Cl incubation was observed in 21 bacterial operational taxonomical units (OTUs at the 97% 16S RNA sequence identity level). This suggests that some of these bacterial taxa, although not previously associated with CH3Cl degradation, may play a role in the microbial CH3Cl sink in soil.

Chitin provides a valuable carbon and nitrogen source for soil microorganisms and is a major component of particulate organic matter in agricultural soils. To date, there is no information on interaction and interdependence in chitin-degrading soil microbiomes. Since microbial chitin degradation occurs under both oxic and anoxic conditions and both conditions occur simultaneously in soil, the comparison of the active microbiome members under both conditions can reveal key players for the overall degradation in aerated soil. A time-resolved 16S rRNA stable isotope probing experiment was conducted with soil material from the top soil layer of a wheat-covered field. [13CU]-chitin was largely mineralized within 20 days under oxic conditions. Cellvibrio, Massilia, and several Bacteroidetes families were identified as initially active chitin degraders. Subsequently, Planctomycetes and Verrucomicrobia were labeled by assimilation of 13C carbon either from [13CU]-chitin or from 13C-enriched components of primary chitin degraders. Bacterial predators (e.g., Bdellovibrio and Bacteriovorax) were labeled, too, and non-labeled microeukaryotic predators (Alveolata) increased their relative abundance toward the end of the experiment (70 days), indicating that chitin degraders were subject to predation. Trophic interactions differed substantially under anoxic and oxic conditions. Various fermentation types occurred along with iron respiration. While Acidobacteria and Chloroflexi were the first taxa to be labeled, although at a low 13C level, Firmicutes and uncultured Bacteroidetes were predominantly labeled at a much higher 13C level during the later stages, suggesting that the latter two bacterial taxa were mainly responsible for the degradation of chitin and also provided substrates for iron reducers. Eventually, our study revealed that (1) hitherto unrecognized Bacteria were involved in a chitin-degrading microbial food web of an agricultural soil, (2) trophic interactions were substantially shaped by the oxygen availability, and (3) detectable predation was restricted to oxic conditions. The gained insights into trophic interactions foster our understanding of microbial chitin degradation, which is in turn crucial for an understanding of soil carbon dynamics.

Microbial degradation of chitin in soil substantially contributes to carbon cycling in terrestrial ecosystems. Chitin is globally the second most abundant biopolymer after cellulose and can be deacetylated to chitosan or can be hydrolyzed to N,N′-diacetylchitobiose and oligomers of N-acetylglucosamine by aerobic and anaerobic microorganisms. Which pathway of chitin hydrolysis is preferred by soil microbial communities is unknown. Supplementation of chitin stimulated microbial activity under oxic and anoxic conditions in agricultural soil slurries, whereas chitosan had no effect. Thus, the soil microbial community likely was more adapted to chitin as a substrate. In addition, this finding suggested that direct hydrolysis of chitin was preferred to the pathway that starts with deacetylation. Chitin was apparently degraded by aerobic respiration, ammonification, and nitrification to carbon dioxide and nitrate under oxic conditions. When oxygen was absent, fermentation products (acetate, butyrate, propionate, hydrogen, and carbon dioxide) and ammonia were detected, suggesting that butyric and propionic acid fermentation, along with ammonification, were likely responsible for anaerobic chitin degradation. In total, 42 different chiA genotypes were detected of which twenty were novel at an amino acid sequence dissimilarity of less than 50%. Various chiA genotypes responded to chitin supplementation and affiliated with a novel deep-branching bacterial chiA genotype (anoxic conditions), genotypes of Beta- and Gammaproteobacteria (oxic and anoxic conditions), and Planctomycetes (oxic conditions). Thus, this study provides evidence that detected chitinolytic bacteria were catabolically diverse and occupied different ecological niches with regard to oxygen availability enabling chitin degradation under various redox conditions on community level.

Editorial on the Research Topic: The Impact of Microorganisms on Consumption of Atmospheric Trace Gases

Methanol is an abundant atmospheric volatile organic compound (VOC) that is released from both living and decaying plant material. In forest and other aerated soils, methanol can be consumed by methanol-utilizing microorganisms that constitute a known terrestrial sink. However, the environmental factors that drive the biodiversity of such methanol-utilizers have been hardly resolved. Soil-derived isolates of methanol-utilizers can also often assimilate multicarbon compounds as alternative substrates. Here, we conducted a comparative DNA stable isotope-probing (SIP) experiment under methylotrophic (only [13C1]-methanol was supplemented) and combined substrate conditions ([12C1]-methanol and alternative multi-carbon [13Cu]-substrates were simultaneously supplemented) to (i) identify methanol-utilizing microorganisms of a deciduous forest soil (European beech dominated temperate forest in Germany), (ii) assess their substrate range in the soil environment and (iii) evaluate their trophic links to other soil microorganisms. The applied multi-carbon substrates represented typical intermediates of organic matter degradation, such as acetate, plant-derived sugars (xylose and glucose), and a lignin-derived aromatic compound (vanillic acid). An experimentally induced pH shift was associated with substantial changes of the diversity of active methanol-utilizers suggesting that soil pH was a niche-defining factor of these microorganisms. The main bacterial methanol-utilizers were members of the Beijerinckiaceae (Bacteria) that played a central role in a detected methanol-based food web. A clear preference for methanol or multi-carbon substrates as carbon source of different Beijerinckiaceae-affiliated phylotypes was observed suggesting a restricted substrate range of the methylotrophic representatives. Apart from Bacteria, we also identified the yeasts Cryptococcus and Trichosporon as methanol-derived carbon-utilizing fungi suggesting that further research is needed to exclude or prove methylotrophy of these fungi.

Novel insights are provided regarding aerobic chemolithotrophic growth of Thermocrinis ruber OC14/7/2 on the electron donors arsenite and monothioarsenate. Thermocrinis ruber is a hyperthermophilic bacterium that thrives in pH-neutral to alkaline hot springs and grows on hydrogen, elemental sulfur, and thiosulfate. Our study showed that T. ruber can also utilize arsenite as sole electron donor producing arsenate. Growth rates of 0.024 h(-1) were lower than for oxidation of thiosulfate to sulfate (μ = 0.247 h(-1)). Fast growth was observed on monothioarsenate (μ = 0.359 h(-1)), comprising different abiotic and biotic redox interactions. The initial dominant process was abiotic transformation of monothioarsenate to arsenate and elemental sulfur, followed by microbial oxidation of sulfur to sulfate. Elevated microbial activity during stationary growth of T. ruber might be explained by microbial oxidation of thiosulfate and arsenite, both also products of abiotic monothioarsenate transformation. However, the observed rapid decrease of monothioarsenate, exceeding concentrations in equilibrium with its products, also indicates direct microbial oxidation of arsenic-bond S(-II) to sulfate. Free sulfide was oxidized abiotically too fast to play a role as electron donor for T. ruber. Our present laboratory and previous field studies suggest that thioarsenates can either indirectly or directly be used by (hyper)thermophiles in arsenic-sulfidic environments.

Summary The impact of temperature on the largely unresolved intermediary ecosystem metabolism and associated unknown microbiota that link cellulose degradation and methane production in soils of a moderately acidic (pH 4.5) fen was investigated. Supplemental [13C]cellulose stimulated the accumulation of propionate, acetate and carbon dioxide as well as initial methane production in anoxic peat soil slurries at 15°C and 5°C. Accumulation of organic acids at 15°C was twice as fast as that at 5°C. 16S rRNA [13C]cellulose stable isotope probing identified novel unclassified Bacteria (79% identity to the next cultured relative Fibrobacter succinogenes), unclassified Bacteroidetes (89% identity to Prolixibacter bellariivorans), Porphyromonadaceae, Acidobacteriaceae and Ruminococcaceae as main anaerobic degraders of cellulose-derived carbon at both 15°C and 5°C. Holophagaceae and Spirochaetaceae were more abundant at 15°C. Clostridiaceae dominated the degradation of cellulose-derived carbon only at 5°C. Methanosarcina was the dominant methanogenic taxa at both 15°C and 5°C. Relative abundance of Methanocella increased at 15°C whereas that of Methanoregula and Methanosaeta increased at 5°C. Thaumarchaeota closely related to Nitrosotalea (presently not known to grow anaerobically) were abundant at 5°C but absent at 15°C indicating that Nitrosotalea sp. might be capable of anaerobic growth at low temperatures in peat.

Light driven primary production by plants is the main source of biomass in terrestrial ecosystems. But also in subsurface habitats like aquifers, life is fueled largely by this plant-derived biomass. Here, we investigate the degradation of plant-derived polysaccharides in a groundwater microbiome to identify the microbial key players involved, and compare them to those from soil of the groundwater recharge area. We quantified the activities of enzymes degrading the abundant plant polymers starch, cellulose and hemicellulose in oligotrophic groundwater samples, despite the low cell numbers present. Normalized to 16S rRNA gene copy numbers, these activities were only one order of magnitude lower than in soil. Stimulation of the groundwater microbiome with either starch or cellulose and hemicellulose led to changes of the enzymatic activity ratios, indicating autochthonous production of enzymes in response to the plant polymers. Furthermore, DNA stable isotope probing with 13C labelled plant polymers allowed us to identify microbes involved in the degradation of these compounds. In (hemi)cellulose microcosms, Bacteroidia and Candidatus Parcubacteria were active, while the active community in starch microcosms mostly comprised Candidatus Saccharibacteria, Cytophagia, and Actinobacteria. Not a single one of the active OTUs was also found to be labelled in soil microcosms. This indicates that the degradation of plant-derived polysaccharides in groundwater is driven by organisms completely distinct from those active in soil. The involvement of members of the candidate phyla Cand. Parcubacteria and Cand. Saccharibacteria, organisms known to be abundant in groundwater, in plant-derived organic matter degradation might strongly impact subsurface carbon cycling.

International audience; Soils, paleosols and terrestrial sediments serve as archives for studying climate change, and represent important terrestrial carbon pools. Archive functioning relies on the chronological integrity of the respective units. Incorporation of younger organic matter (OM) e.g. by plant roots and associated microorganisms into deep subsoil and underlying soil parent material may reduce reliability of paleoenvironmental records and stability of buried OM. Long-term effects of sedimentary characteristics and deep rooting on deep subsoil microbial communities remain largely unknown. We characterized fossil and living microbial communities based on molecular markers in a Central European Late Pleistocene loess-paleosol sequence containing recent and ancient roots with ages of several millenia. The molecular approach, comprising free and phospholipid fatty acids (FAs), core and intact polar glycerol dialkyl glycerol tetraethers (GDGTs), as well as 16S rRNA genes from bacterial DNA, revealed the presence of living microorganisms along the sequence, with bacterial community composition comparable to that of modern topsoils. Up to 88% redundancy between bacterial genetic fingerprint and molecular signature of fossil microorganisms suggested a time-integrated signal of the molecular markers accumulated over a time span potentially lasting from sedimentation over one or more rooting phases until today. Free FAs, core GDGTs and DNA, considered as remains of fossil microorganisms, corresponded with ancient and recent root quantities, whereas phospholipid FAs and intact polar GDGTs, presumably derived from living microorganisms, correlated only with living roots. The biogeochemical and ecological disequilibrium induced by postsedimentary rooting may entail long-term microbial processes like OM mineralization, which may continue even millenia after the lifetime of the root. Deep roots and their fossil remains have been observed in various terrestrial settings, and roots as well as associated microorganisms cause both, OM incorporation and mineralization. Therefore, these findings are crucial for improved understanding of OM dynamics and carbon sequestration potential in deep subsoils.

Aerobic methane (CH(4) ) oxidation reduces the emission of CH(4) from mires and is regulated by various environmental factors. Organic acids and alcohols are intermediates of the anaerobic degradation of organic matter or are released by plant roots. Methanotrophs isolated from mires utilize these compounds preferentially to CH(4) . Thus, the effect of organic acids and ethanol on CH(4) oxidation by methanotrophs of a mire was evaluated. Slurries of mire soil oxidized supplemental CH(4) down to subatmospheric concentrations. The dominant pmoA and mmoX genotypes were affiliated with sequences from Methylocystis species capable of utilization of acetate and atmospheric CH(4) . Soil slurries supplemented with acetate, propionate or ethanol had reduced CH(4) oxidation rates compared with unsupplemented or glucose-supplemented controls. Expression of Methylocystis-affiliated pmoA decreased when CH(4) consumption decreased in response to acetate and was enhanced after acetate was consumed, at which time the consumption of CH(4) reached control levels. The inhibition of methanotroph activity might have been due to either toxicity of organic compounds or their preferred utilization. CH(4) oxidation was reduced at 5 and 0.5 mM of supplemental organic compounds. Acetate concentrations may exceed 3 mM in the investigated mire. Thus, the oxidation of CH(4) might decrease in microzones where organic acids occur.

Cellulose is the most abundant biopolymer in terrestrial ecosystems and is degraded by microbial communities in soils. However, relatively little is known about the diversity and function of soil prokaryotes that might participate in the overall degradation of this biopolymer. The active cellulolytic and saccharolytic Bacteria in an agricultural soil were evaluated by 16S rRNA (13)C-based stable isotope probing. Cellulose, cellobiose and glucose were mineralized under oxic conditions in soil slurries to carbon dioxide. Under anoxic conditions, these substrates were converted primarily to acetate, butyrate, carbon dioxide, hydrogen and traces of propionate and iso-butyrate; the production of these fermentation end-products was concomitant with the apparent reduction of iron(III). [(13)C]-cellulose was mainly degraded under oxic conditions by novel family-level taxa of the Bacteroidetes and Chloroflexi, and a known family-level taxon of Planctomycetes, whereas degradation under anoxic conditions was facilitated by the Kineosporiaceae (Actinobacteria) and cluster III Clostridiaceae and novel clusters within Bacteroidetes. Active aerobic sub-communities in oxic [(13)C]-cellobiose and [(13)C]-glucose treatments were dominated by Intrasporangiaceae and Micrococcaceae (Actinobacteria) whereas active cluster I Clostridiaceae (Firmicutes) were prevalent in anoxic treatments. A very large number (i.e. 28) of the detected taxa did not closely affiliate with known families, and active Archaea were not detected in any of the treatments. These collective findings suggest that: (i) a large uncultured diversity of soil Bacteria was involved in the utilization of cellulose and products of its hydrolysis, (ii) the active saccharolytic community differed phylogenetically from the active cellulolytic community, (iii) oxygen availability impacted differentially on the activity of taxa and (iv) different redox guilds (e.g. fermenters and iron reducers) compete or interact during cellulose degradation in aerated soils.

Coniferous forest soils often consume less of the greenhouse gas methane (CH 4 ) than deciduous forest soils. The reasons for this phenomenon have not been resolved. It might be caused by differences in the diffusive flux of CH 4 through the organic layer, pH or different concentrations of potentially inhibitory compounds. Soil samples were investigated from three adjacent European beech (Fagus sylvatica) and Norway spruce (Picea abies) stands in Germany. Maximal CH 4 oxidation velocities (V max(app) ) and Michaelis Menten constants (K M(app) ), retrieved from intact soil cores at constant CH 4 concentrations, temperature and matric potential, were twice as great in beech as in spruce soils. Also atmospheric CH 4 oxidation rates measured in homogenized soil samples displayed the same trend. Greatest atmospheric CH 4 oxidation rates were detected in the O a horizon or in the upper 5 cm of the mineral soil. In contrast to the beech soils, the O a horizon of the spruce soils consumed no CH 4 . A differential effect due to divergent diffusive flux through the litter layer was not found. pH and ammonium concentration were similar in samples from both forest soil types. Ethylene accumulation in all soils was negligible under oxic conditions. These collective results suggest that the different atmospheric CH 4 uptake by beech and spruce soils is caused by different CH 4 oxidizing capacities of methanotrophic communities in the O a horizon and top mineral soil.

Biological oxidation of atmospheric methane (CH4) in forest soils of the northern hemisphere is an important sink in the global CH4 cycle. The effect of tree species on atmospheric CH4 oxidation is not well understood. Previous studies suggest that soils under European beech (Fagus sylvatica) consume more atmospheric CH4 than soils under Norway spruce (Picea abies). A major difference in the chemical constituents of these tree species is the production of monoterpenes. The objectives of the present study were (i) to quantify monoterpenes in leaves, needles, organic horizons (Oi, Oe, Oa), and mineral soil of a Norway spruce site and an adjacent European beech site of a temperate forest (Steigerwald, Germany) and (ii) to evaluate the potential of abundant monoterpenes to inhibit atmospheric CH4 oxidation. Major compounds were α- and β-pinene, limonene, and camphene. Highest concentrations were measured in Norway spruce samples (up to 63.9 μmol g dw − 1 ). In European beech samples, monoterpene concentrations were close to or below the detection limit (≤0.00015 μmol g dw − 1 ). For limonene, α- and β-pinene, the dose-dependent inhibition on atmospheric CH4 oxidation was determined. β-Pinene had the highest inhibition efficiency, followed by limonene and α-pinene. Norway spruce roots and mineral soil samples displayed similar monoterpene profiles, suggesting that roots can be considered as a source for inhibitory monoterpenes in Norway spruce soils. Monoterpene addition was always coupled to an increased carbon dioxide production. This indicates that monoterpenes may be microbially mineralized in these soils. In summary, the study revealed that the release of monoterpenes by both roots and litter may be sources in soil and that in situ monoterpene concentrations in spruce soil are high enough to explain reduced atmospheric CH4 uptake.

Methanotrophic communities were studied in several periodically water-saturated gleyic soils. When sampled, each soil had an oxic upper layer and consumed methane from the atmosphere (at 1.75 ppmv). In most gleyic soils the K(m(app)) values for methane were between 70 and 800 ppmv. These are higher than most values observed in dry upland soils, but lower than those measured in wetlands. Based on cultivation-independent retrieval of the pmoA-gene and quantification of partial pmoA gene sequences, type II (Alphaproteobacteria) methanotrophs of the genus Methylocystis spp. were abundant (> 10(7) pmoA target molecules per gram of dry soil). Type I (Gammaproteobacteria) methanotrophs related to the genera Methylobacter and Methylocaldum/Methylococcus were detected in some soils. Six pmoA sequence types not closely related to sequences from cultivated methanotrophs were detected as well, indicating that diverse uncultivated methanotrophs were present. Three Gleysols were incubated under different mixing ratios of (13)C-labelled methane to examine (13)C incorporation into phospholipid fatty acids (PLFAs). Phospholipid fatty acids typical of type II methanotrophs, 16:0 and 18:1omega7c, were labelled with (13)C in all soils after incubation under an atmosphere containing 30 ppmv of methane. Incubation under 500 ppmv of methane resulted in labelling of additional PLFAs besides 16:0 and 18:1omega7c, suggesting that the composition of the active methanotrophic community changed in response to increased methane supply. In two soils, 16:1 PLFAs typical of type I methanotrophs were strongly labelled after incubation under the high methane mixing ratio only. Type II methanotrophs are most likely responsible for atmospheric methane uptake in these soils, while type I methanotrophs become active when methane is produced in the soil.

Soil microeukaryotes may trophically benefit from plant biopolymers. However, carbon transfer from cellulose into soil microeukaryotes has not been demonstrated so far. Microeukaryotes assimilating cellulose-derived carbon in oxic and anoxic soil slurries were therefore examined by rRNA-based stable-isotope probing. Bacteriovorous flagellates and ciliates and, likely, mixotrophic algae and saprotrophic fungi incorporated carbon from supplemental [U- 13 C]cellulose under oxic conditions. A previous study using the same soil suggested that cellulolytic Bacteria assimilated 13 C of supplemental cellulose. Thus, it can be assumed that ciliates, cercozoa, and chrysophytes assimilated carbon by grazing upon and utilizing metabolic products of Bacteria that hydrolyzed cellulose in the soil slurries.

The role of soil methylotrophs in methanol exchange with the atmosphere has been widely overlooked. Methanol can be derived from plant polymers and be consumed by soil microbial communities. In the current study, methanol-utilizing methylotrophs of 14 aerated soils were examined to resolve their comparative diversities and capacities to utilize ambient concentrations of methanol. Abundances of cultivable methylotrophs ranged from 10(6)-10(8) gsoilDW(-1). Methanol dissimilation was measured based on conversion of supplemented (14)C-methanol, and occurred at concentrations down to 0.002 μmol methanol gsoilDW(-1). Tested soils exhibited specific affinities to methanol (a(0)s=0.01 d(-1)) that were similar to those of other environments suggesting that methylotrophs with similar affinities were present. Two deep-branching alphaproteobacterial genotypes of mch responded to the addition of ambient concentrations of methanol (0.6 μmol methanol gsoilDW(-1)) in one of these soils. Methylotroph community structures were assessed by amplicon pyrosequencing of genes of mono carbon metabolism (mxaF, mch and fae). Alphaproteobacteria-affiliated genotypes were predominant in all investigated soils, and the occurrence of novel genotypes indicated a hitherto unveiled diversity of methylotrophs. Correlations between vegetation type, soil pH and methylotroph community structure suggested that plant-methylotroph interactions were determinative for soil methylotrophs.

The availability of oxygen (O 2 ) in aerated (i.e., water-unsaturated) soils affects the metabolic activities of aerobic and anaerobic soil prokaryotes that degrade plant-derived saccharides. Fluctuating availabilities of O 2 were imposed on agricultural soil slurries supplemented with cellobiose. Slurries were subjected to oxic conditions (48 h), followed by an anoxic period (120 h) and a final oxic period (24 h). Redox potential was stable at 500 mV during oxic periods but decreased rapidly (within 10 h) under anoxic conditions to −330 mV. The consumption of cellobiose occurred without apparent delay at all redox potentials. The metabolic activities of seven previously identified saccharolytic family-level taxa of the investigated soil were measured with newly designed quantitative PCR assays targeting the 16S rRNA. Four taxa responded to the experimental conditions. The amounts of rRNAs of Micrococcaceae and Cellulomonadaceae ( Actinobacteria ) increased under oxic conditions. In contrast, the RNA contents of Clostridiaceae (cluster I, Firmicutes ) and two uncultured family-level-taxa, i.e., “Cellu” and “Sphingo” (both Bacteroidetes ) increased under anoxic conditions. That the degradation of cellobiose was independent of the availability of O 2 and that redox potentials decreased in response to anaerobic activities indicated that the degradation of cellobiose was linked to functionally redundant cellobiose-degrading taxa capable of altering redox conditions.

Methanogenesis in wetlands is dependent on intermediary substrates derived from the degradation of biopolymers. Formate is one such substrate and is stimulatory to methanogenesis and acetogenesis in anoxic microcosms of soil from the fen Schlöppnerbrunnen. Formate dissimilation also yields CO 2 as a potential secondary substrate. The objective of this study was to resolve potential differences between anaerobic formate- and CO 2 -utilizing prokaryotes of this fen by stable isotope probing. Anoxic soil microcosms were pulsed daily with low concentrations of [ 13 C]formate or 13 CO 2 (i.e., [ 13 C]bicarbonate). Taxa were evaluated by assessment of 16S rRNA genes, mcrA (encoding the alpha-subunit of methyl-coenzyme M reductase), and fhs (encoding formyltetrahydrofolate synthetase). Methanogens, acetogens, and formate-hydrogen lyase-containing taxa appeared to compete for formate. Genes affiliated with Methanocellaceae , Methanobacteriaceae , Acetobacteraceae , and Rhodospirillaceae were 13 C enriched (i.e., labeled) in [ 13 C]formate treatments, whereas genes affiliated with Methanosarcinaceae , Conexibacteraceae , and Solirubrobacteraceae were labeled in 13 CO 2 treatments. [ 13 C]acetate was enriched in [ 13 C]formate treatments, but labeling of known acetogenic taxa was not detected. However, several phylotypes were affiliated with acetogen-containing taxa (e.g., Sporomusa ). Methanosaetaceae -affiliated methanogens appeared to participate in the consumption of acetate. Twelve and 58 family-level archaeal and bacterial 16S rRNA phylotypes, respectively, were detected, approximately half of which had no isolated representatives. Crenarchaeota constituted half of the detected archaeal 16S rRNA phylotypes. The results highlight the unresolved microbial diversity of the fen Schlöppnerbrunnen, suggest that differing taxa competed for the same substrate, and indicate that Methanocellaceae , Methanobacteriaceae , Methanosarcinaceae , and Methanosaetaceae were linked to the production of methane, but they do not clearly resolve the taxa responsible for the apparent conversion of formate to acetate.

Methanol is an atmospheric compound that is primarily released from plant polymers and impacts ozone formation. The global methanol emission rate from terrestrial ecosystems is of the same order of magnitude (4.9 x 10(12) mol year(-1)) as that of methane (10 x 10(12) mol year(-1)). The major proportion of the annual plant-released methanol does not enter the atmosphere, but may be reoxidized by biological methanol oxidation, which is catalyzed by methanol-oxidizing prokaryotes. Fifty-six aerobic methanol-oxidizing species have been isolated from soils. These methylotrophs belong to the Alpha-, Beta-, and Gammaproteobacteria, Verrucomicrobia, Firmicutes, and Actinobacteria. Their ecological niches are determined by oxygen and methanol concentration, temperature, pH, the capability to utilize nitrate as an electron acceptor, and the spectrum of nitrogen sources and utilizable multicarbon substrates. Recently discovered interactions with eukaryotes indicate that their ecological niches may not solely be defined by physicochemical parameters. Nonetheless, there are still gaps in knowledge; based on global methanol budgets, methanol oxidation in soil is important, but has not been addressed adequately by biogeochemical studies. Ratios of above-ground and soil-internal methanol oxidation are not known. The contribution to methanol-oxidation by aerobic and anaerobic methylotrophs in situ also needs further research.