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

Data from: 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

Zulliger_etal_MolEcol2013

Data described in the ReadMe file included in the zip archiv

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.ISSN:2045-775

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

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.ISSN:0012-9658ISSN:1939-917

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.ISSN:0038-0717ISSN:1879-342

Current atmospheric nitrogen deposition still exceeds critical loads for sensitive, semi-natural ecosystems in Switzerland

Increased atmospheric nitrogen (N) deposition is driving nutrient imbalances, soil acidification, biodiversity losses and the long-term reduction in stability of sensitive ecosystems which previously had limited N. In this study, we analysed the concentrations of seven different N compounds in precipitation and in the air at 34 sites across Switzerland. We calculated the N deposition by precipitation (bulk deposition) and applied the inferential method to derive dry deposition (gases, aerosols) from air concentrations. We then quantified the total inorganic N deposition by adding together the bulk and dry deposition. Finally, the total inorganic N input into the sensitive ecosystems of the 34 sites was compared to the critical loads of these ecosystems.N deposition by precipitation was the main contributor to the total N load in 16 out of 34 sites, especially into open ecosystems such as alpine/subalpine grassland, mountain hay meadows, and raised bogs. Dry deposition of ammonia (NH3) was the second most important pathway, in particular for forests close to agricultural activities, due to high NH3 concentrations and the higher deposition velocity. The N deposition exceeded the lower limit of the Critical Load of Nitrogen (CLN) range at most sites, and at many sites even surpassed the upper limit of the CLN range. No, or minor, exceedances of the critical loads for N were found only at remote sites at higher elevation in the Central Alps. Annual inorganic N deposition between 2000 and 2017 revealed a significant decline in oxidised N compounds at four of five sites (-1.6-1.8% per year), but reduced compounds only decreased at two sites (-1% and -1.4% per year) and even increased at one site (+1.2% per year), despite adopted abatement strategies for agricultural practices. This emphasises that most sensitive ecosystems in Switzerland continue to be exposed to excessive N loads through atmospheric deposition, with detrimental consequences for the biodiversity and stability of these ecosystems

A miniature world in decline: European Red List of Mosses, Liverworts and Hornworts

This publication has been prepared by IUCN (International Union for Conservation of Nature) as a deliverable of the LIFE European Red Lists project (LIFE14 PRE BE 001). A miniature world in decline: The European Red List of Mosses, Liverworts and Hornworts is, therefore, a part of a series of publications released since 2015, when the project began, that also include: • European Red List of Lycopods and Ferns, 2017 • European Red List of Saproxylic Beetles, 2018 • European Red list of Terrestrial Molluscs: slugs, snails, and semi-slugs, 2019 • European Red list of Trees, 2019 • European Red list of Selected Endemic Shrubs, 2019 Based on other European Red List assessments, 59% of freshwater molluscs, 40% of freshwater fishes, 28% of grasshoppers, crickets and bush-crickets, 23% of amphibians, 20% of reptiles, 20% of ferns and lycopods, 17% of mammals, 16% of dragonflies, 13% of birds, 9% of butterflies and bees, 8% of aquatic plants and 2% of medicinal plants are threatened at the European level (Allen et al., 2014; IUCN, 2015; Hochkirch et al., 2016; García Criado et al., 2017). Additional European Red Lists assessing a selection of species showed that 22% of terrestrial molluscs, 16% of crop wild relatives and 18% of saproxylic beetles are also threatened (Cuttelod et al., 2011; Bilz et al., 2011; Cálix et al., 2018). The findings of this work suggest that 23% of bryophytes are threatened species in Europe, representing the fifth most threatened group of plants assessed so far