Experimental erosion of microbial diversity decreases soil CH4 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 (CH4 ) cycle by removing atmospheric CH4 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 101 -107 -fold, preincubated under a high CH4 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) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH4 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. CH4 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.

Nitrogen concentration in moss compared with N load in precipitation and with total N deposition in Switzerland.

Intensification of farming and an increase in motorised traffic have led to elevated nitrogen (N) emissions and thus to eutrophication of the environment, which threatens the nutrient balance in ecosystems. Earlier studies have demonstrated the suitability of mosses as biomonitors for measuring N deposition by comparing the N concentration in moss with that in precipitation. In our study however, we extended the comparison to the dry deposition of gases (nitrogen dioxide, nitric acid, ammonia) and aerosols (nitrate, ammonium), which, together with the N in precipitation, represent the main contributions to total N deposition. The aim of including several N compounds was to see whether the correlation with the N concentration in moss could be improved. We determined total N input from the atmosphere to the ecosystem at 24 sites in Switzerland and compared this value to the N concentration in two moss species collected <1000 m from these sites. Including the gases and aerosols improved the correlation between the N concentration in moss and N deposition. Ammonia was found to be the most important of the additionally included compounds at these sites. Especially at sites with a relatively high ammonia concentration in the air, the inclusion of ammonia improved the correlation of the comparison. We also demonstrate that the particular moss species tested had no influence on the correlation between N in moss and total N deposition. Our data supports the suitability of mosses as biomonitors for estimating N input into ecosystems.

Positive diversity-functioning relationships in model communities of methanotrophic bacteria.

Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure strains of methanotrophic bacteria, we assembled artificial communities of different diversity levels, with which we inoculated sterile soil microcosms. To assess the functioning of these communities, we measured methane oxidation by gas chromatography throughout the experiment and determined changes in community composition and community size at several time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a positive overyielding effect on methane oxidation, in particular at the beginning of the experiment. This higher assimilation of CH4 at high diversity translated into increased growth and significantly larger communities towards the end of the study. The overyielding of mixtures with respect to CH4 consumption and community size were positively correlated. The temporal CH4 consumption profiles of strain monocultures differed, raising the possibility that temporal complementarity of component strains drove the observed community-level strain richness effects; however, the community niche metric we derived from the temporal activity profiles did not explain the observed strain richness effect. The strain richness effect also was unrelated to both the phylogenetic and functional trait diversity of mixed communities. Overall, our results suggest that positive biodiversity-ecosystem-function relationships show similar patterns across different scales and may be widespread in nature. Additionally, biodiversity is probably also important in natural methanotrophic communities for the ecosystem function methane oxidation. Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help to reduce the emission of the greenhouse gas methane.

Validation of outlier loci through replication in independent data sets: a test on Arabis alpina.

Outlier detection and environmental association analysis are common methods to search for loci or genomic regions exhibiting signals of adaptation to environmental factors. However, a validation of outlier loci and corresponding allele distribution models through functional molecular biology or transplant/common garden experiments is rarely carried out. Here, we employ another method for validation, namely testing outlier loci in specifically designed, independent data sets. Previously, an outlier locus associated with three different habitat types had been detected in Arabis alpina. For the independent validation data set, we sampled 30 populations occurring in these three habitat types across five biogeographic regions of the Swiss Alps. The allele distribution model found in the original study could not be validated in the independent test data set: The outlier locus was no longer indicative of habitat-mediated selection. We propose several potential causes of this failure of validation, of which unaccounted genetic structure and technical issues in the original data set used to detect the outlier locus were most probable. Thus, our study shows that validating outlier loci and allele distribution models in independent data sets is a helpful tool in ecological genomics which, in the case of positive validation, adds confidence to outlier loci and their association with environmental factors or, in the case of failure of validation, helps to explain inconsistencies.

Relationship between site-specific nitrogen concentrations in mosses and measured wet bulk atmospheric nitrogen deposition across Europe.

To assess the relationship between nitrogen concentrations in mosses and wet bulk nitrogen deposition or concentrations in precipitation, moss tissue and deposition were sampled within a distance of 1 km of each other in seven European countries. Relationships for various forms of nitrogen appeared to be asymptotic, with data for different countries being positioned at different locations along the asymptotic relationship and saturation occurring at a wet bulk nitrogen deposition of ca. 20 kg N ha(-1) yr(-1). The asymptotic behaviour was more pronounced for ammonium-N than nitrate-N, with high ammonium deposition at German sites being most influential in providing evidence of the asymptotic behaviour. Within countries, relationships were only significant for Finland and Switzerland and were more or less linear. The results confirm previous relationships described for modelled total deposition. Nitrogen concentration in mosses can be applied to identify areas at risk of high nitrogen deposition at European scale.

Are adaptive loci transferable across genomes of related species? Outlier and environmental association analyses in Alpine Brassicaceae species.

Local adaptation is one possible response of organisms to survive in a changing environment. However, the genetic basis of adaptation is not well understood, especially in nonmodel species. To infer recurrent patterns of local adaptation, we investigated whether the same putative adaptive loci reoccur in related species. We performed genome scans using amplified fragment length polymorphism (AFLP) markers on populations of five Alpine Brassicaceae species sampled across a wide range of environmental conditions. To identify markers potentially under directional selection, we performed outlier and environmental association analyses using a set of topo-climatic variables available as GIS layers. Several AFLP loci showed signatures of adaptation, of which one, found in Cardamine resedifolia (Cre_P1_212.5), was associated with precipitation. We sequence-characterized this candidate locus and genotyped single nucleotide polymorphisms (SNPs) found within this locus for all species. Testing for environmental associations of SNPs revealed the same association of this locus in Arabis alpina but not in other study species. Cumulative statistical evidence indicates that locus Cre_P1_212.5 is environmentally relevant or is linked to a gene under selection in our study range. Furthermore, the locus shows an association to the same potentially selective factor in at least one other related species. These findings help to identify trends in plant adaptation in Alpine ecosystems in response to particular environmental parameters.