Structure and function of methanotrophic communities in a landfill-cover soil

In landfill-cover soils, aerobic methane-oxidizing bacteria (MOB) convert CH4 to CO2, mitigating emissions of the greenhouse gas CH4 to the atmosphere. We investigated overall MOB community structure and assessed spatial differences in MOB diversity, abundance and activity in a Swiss landfill-cover soil. Molecular cloning, terminal restriction-fragment length polymorphism (T-RFLP) and quantitative PCR of pmoA genes were applied to soil collected from 16 locations at three different depths to study MOB community structure, diversity and abundance; MOB activity was measured in the field using gas push-pull tests. The MOB community was highly diverse but dominated by Type Ia MOB, with novel pmoA sequences present. Type II MOB were detected mainly in deeper soil with lower nutrient and higher CH4 concentrations. Substantial differences in MOB community structure were observed between one high- and one low-activity location. MOB abundance was highly variable across the site [4.0 × 104 to 1.1 × 107 (g soil dry weight)-1]. Potential CH4 oxidation rates were high [1.8-58.2 mmol CH4 (L soil air)-1 day-1] but showed significant lateral variation and were positively correlated with mean CH4 concentrations (P < 0.01), MOB abundance (P < 0.05) and MOB diversity (weak correlation, P < 0.17). Our findings indicate that Methylosarcina and closely related MOB are key players and that MOB abundance and community structure are driving factors in CH4 oxidation at this landfil

Do temporal and spatial heterogeneity modulate biodiversity–functioning relationships in com-munities of methanotrophic bacteria?

Positive relationships between biodiversity functioning have been found in communities of plants but also of soil microbes. The beneficial effects of diversity are thought to be driven by niche partitioning among community members, which leads to more complete or more efficient community-level resource use through various mechanisms. An intriguing related question is whether environmentally more heterogeneous habitats provide a larger total niche space and support stronger diversity—functioning relationships because they harbor more species or allow species to partition the available niche space more efficiently. Here, we tested this hypothesis by assembling communities of 1, 2 or 4 methanotrophic isolates and exposing them to temporally (constant or diurnal temperature cycling) and structurally (one or two aggregate size classes) more heterogeneous conditions. In total, we incubated 396 microcosms for 41 days and found that more biodiverse communities consumed more methane (CH4) and tended to have a larger community size (higher pmoA copy numbers). Diurnal temperature cycling strongly reduced CH4 oxidation and growth, whereas soil aggregate composition and diversity had no detectable effect. Biodiversity effects varied greatly with the identity of the community members that were combined. With respect to community level CH4 consumption, strain interactions were positive or neutral but never negative, and could neither be explained by 14 structural and function traits we collected or by the observed competitive hierarchy among the strains. Overall, our results indicate that methanotrophic diversity promotes methanotrophic community functioning. The strains that performed best varied with environmental conditions, suggesting that a high biodiversity is important for maintaining methanotrophic functioning as environmental conditions fluctuate over time

Experimental erosion of microbial diversity decreases soil CH4_4 consumption rates

Biodiversity‐ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH$_{4}$) cycle by removing atmospheric CH$_{4}$ and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution‐to‐extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 10$^{1}$–10$^{7}$‐fold, preincubated under a high CH$_{4}$ atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH$_{4}$ consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH$_{4}$ consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log‐dilution. CH$_{4}$ consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales

Field-scale labelling and activity quantification of methane-oxidizing bacteria in a landfill-cover soil

Aerobic methane-oxidizing bacteria (MOB) play an important role in soils, mitigating emissions of the greenhouse gas methane (CH4) to the atmosphere. Here, we combined stable isotope probing on MOB-specific phospholipid fatty acids (PLFA-SIP) with field-based gas push-pull tests (GPPTs). This novel approach (SIP-GPPT) was tested in a landfill-cover soil at four locations with different MOB activity. Potential oxidation rates derived from regular- and SIP-GPPTs agreed well and ranged from 0.2 to 52.8 mmol CH4 (L soil air)−1 day−1. PLFA profiles of soil extracts mainly contained C14 to C18 fatty acids (FAs), with a dominance of C16 FAs. Uptake of 13C into MOB biomass during SIP-GPPTs was clearly indicated by increased δ13C values (up to c. 1500‰) of MOB-characteristic FAs. In addition, 13C incorporation increased with CH4 oxidation rates. In general, FAs C14:0, C16:1ω8, C16:1ω7 and C16:1ω6 (type I MOB) showed highest 13C incorporation, while substantial 13C incorporation into FAs C18:1ω8 and C18:1ω7 (type II MOB) was only observed at high-activity locations. Our findings demonstrate the applicability of the SIP-GPPT approach for in situ quantification of potential CH4 oxidation rates and simultaneous labelling of active MOB, suggesting a dominance of type I MOB over type II MOB in the CH4-oxidizing community in this landfill-cover soi

Biochemical characterization of a novel monospecific endo-β-1,4-glucanase belonging to GH Family 5 from a rhizosphere metagenomic library

Cellulases have a broad range of different industrial applications, ranging from food and beverages to pulp and paper and the biofuels area. Here a metagenomics based strategy was used to identify the cellulolytic enzyme CelRH5 from the rhizosphere. CelRH5 is a novel monospecific endo-β-1,4-glucanase belonging to the glycosyl hydrolase family 5 (GH5). Structural based modelling analysis indicated that CelRH5 is related to endo-β-1,4-glucanases derived from thermophilic microorganisms such as Thermotoga maritima, Fervidobacterium nodosum and Ruminiclostridium thermocellum sharing 30-40% amino acid sequence identity. The molecular weight of the enzyme was determined as 40.5 kDa. Biochemical analyses revealed that the enzyme displayed good activity with soluble forms of cellulose as a substrate such as ostazin brilliant red hydroxyethyl cellulose (OBR-HEC), carboxymethylcellulose (CMC), hydroxyethyl cellulose (HEC) and insoluble azurine cross-linked hydroxyethylcellulose (AZCL-HEC). The enzyme shows highest enzymatic activity at pH 6.5 with high pH tolerance, remaining stable in the pH range 4.5 – 8.5. Highest activity was observed at 40 ˚C, but CelRH5 is psychrotolerant being active and stable at temperatures below 30 ˚C. The presence of final products of cellulose hydrolysis (glucose and cellobiose) or metal ions such as Na+, K+, Li+ and Mg2+, as well as ethylenediaminetetraacetic acid (EDTA), urea, dithiothreitol (DTT), dimethyl sulfoxide (DMSO), 2-mercaptoethanol (2-ME) or glycerol, did not have a marked effect on CelRH5 activity. However, the enzyme is quite sensitive in presence of 10 mM ions Zn2+, Ni2+, Co2+, Fe3+ and reagents such as 1 M guanidine HCl, 0.1% sodium dodecyl sulphate (SDS) and 20% ethanol. Given that it is psychrotolerant and retains activity in the presence of final cellulose degradation products, metal ions and various reagents, which are common in many technological processes; CelRH5 may be potential suitability for a variety of different biotechnological applications

A radon-resistant microbial community

The Paralana hot spring is an intriguing site with astrobiological implications as an analogue for conditions on the early Earth. The research conducted thus far has identified a diverse community of mostly thermophilic microbes. Whilst it is possible that the resident microbial community is unaffected by the radon, we consider this the least likely possibility. More probable is that the microbes have adapted to the environment, having evolved mechanisms that allow them to survive in the presence of ionising radiation. If this is the case, then the NASA collaborative study has a good chance of identifying a highly radiationresistant microbe. So, remember to occasionally look up into the heavens over the next few years – that bright streak might just be carrying Australia’s first official ‘micronauts’.3 page(s

Thermophilic bacteria from an Australian geothermal aquifer-A culture-independent analysis

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Extraction of DNA from acidic, hydrothermally modified volcanic soils

Acidic soils for microbial diversity studies were collected from Devil’s Kitchen, a fumarolic field on Mt Hood, USA. The very dense soils, which contain clay and other minerals, are derived from andesitic and dacitic rocks altered by volcanic heat and acidic, sulfur-rich hydrothermal steam. An initial attempt to extract biomass DNA using a mechanical-based cell lysis protocol was ineffective. However, by using various other protocols, DNA was successfully extracted, leading to the identification of several acidophilic Mt Hood extremophiles. The results emphasise the importance of testing different extraction procedures when dealing with apparently intractable samples.5 page(s

Structure and function of methanotrophic communities in a landfill-cover soil

ISSN:0168-6496ISSN:1574-694

Methane and Carbon Dioxide Fluxes from a European Alpine Fen Over the Snow-Free Period

Wetlands play an important role in the global carbon cycle and are sources and sinks for the greenhouse gases methane (CH4) and carbon dioxide (CO2). We provide an in situ study on variability of daytime CH4 emissions and net ecosystem CO2 exchange (NEE) from a permanently submerged, Carex rostrata dominated Swiss alpine fen over the snow-free period (June-October). Flux chamber measurements were combined with analyses of above-ground biomass and physico-chemical pore water properties. The fen was a net daytime CH4 source throughout the snow-free period, and emissions varied significantly between the sampling dates, ranging from 3.1 ± 0.9mg CH4 m−2 h−1 in October to 8.0 ± 2.9mg CH4 m−2 h−1 in August. The fen was generally a daytime sink for CO2, and net CO2 emission was only observed in late October. Variations in NEE were more pronounced than variations in CH4 emissions, but both fluxes correlated with changes in green C. rostrata biomass and subsurface temperatures. Methane and CO2 pore water concentrations also varied significantly over the snow-free period, decreasing and increasing, respectively. These variations were linked to the development of biomass, but CH4 emissions and NEE were not correlated with the respective pore water concentrations