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Omics approaches (e.g., transcriptomics, metabolomics) are promising for ecological risk assessment (ERA) since they provide mechanistic information and early warning signals. A crucial step in the analysis of omics data is the modeling of concentration-dependency which may have different trends including monotonic (e.g., linear, exponential) or biphasic (e.g., U shape, bell shape) forms. The diversity of responses raises challenges concerning detection and modeling of significant responses and effect concentration (EC) derivation. Furthermore, handling high-throughput data sets is time-consuming and requires effective and automated processing routines. Thus, we developed an open source tool (DRomics, available as an R-package and as a web-based service) which, after elimination of molecular responses (e.g., gene expressions from microarrays) with no concentration-dependency and/or high variability, identifies the best model for concentration–response curve description. Subsequently, an EC (e.g., a benchmark dose) is estimated from each curve, and curves are classified based on their model parameters. This tool is especially dedicated to manage data obtained from an experimental design favoring a great number of tested doses rather than a great number of replicates and also to handle properly monotonic and biphasic trends. The tool finally provides restitution for a table of results that can be directly used to perform ERA approaches.

Wood-inhabiting fungi have essential roles in the regulation of carbon stocks and nutrient cycling in forest ecosystems. However, knowledge pertaining to wood-inhabiting fungi is only fragmentary and controversial. Here we established a large-scale deadwood experiment with 11 tree species to investigate diversity and tree species preferences of wood-inhabiting fungi using next-generation sequencing. Our results contradict existing knowledge based on sporocarp surveys and challenge current views on their distribution and diversity in temperate forests. Analyzing α-, β- and γ-diversity, we show that diverse fungi colonize deadwood at different spatial scales. Specifically, coniferous species have higher α- and γ-diversity than the majority of analyzed broadleaf species, but two broadleaf species showed the highest β-diversity. Surprisingly, we found nonrandom co-occurrence (P<0.001) and strong tree species preferences of wood-inhabiting fungi, especially in broadleaf trees (P<0.01). Our results indicate that the saprotrophic fungal community is more specific to tree species than previously thought.

Wood-inhabiting fungi have essential roles in the regulation of carbon stocks and nutrient cycling in forest ecosystems. However, knowledge pertaining to wood-inhabiting fungi is only fragmentary and controversial. Here we established a large-scale deadwood experiment with 11 tree species to investigate diversity and tree species preferences of wood-inhabiting fungi using next-generation sequencing. Our results contradict existing knowledge based on sporocarp surveys and challenge current views on their distribution and diversity in temperate forests. Analyzing a-, ß- and ?-diversity, we show that diverse fungi colonize deadwood at different spatial scales. Specifically, coniferous species have higher a- and ?-diversity than the majority of analyzed broadleaf species, but two broadleaf species showed the highest ß-diversity. Surprisingly, we found nonrandom co-occurrence (P<0.001) and strong tree species preferences of wood-inhabiting fungi, especially in broadleaf trees (P<0.01). Our results indicate that the saprotrophic fungal community is more specific to tree species than previously thought.

Land-use intensification is a major driver of biodiversity loss. Alongside reductions in local species diversity, biotic homogenization at larger spatial scales is of great concern for conservation. Biotic homogenization means a decrease in β-diversity (the compositional dissimilarity between sites). Most studies have investigated losses in local (α)-diversity and neglected biodiversity loss at larger spatial scales. Studies addressing β-diversity have focused on single or a few organism groups (for example, ref. 4), and it is thus unknown whether land-use intensification homogenizes communities at different trophic levels, above- and belowground. Here we show that even moderate increases in local land-use intensity (LUI) cause biotic homogenization across microbial, plant and animal groups, both above- and belowground, and that this is largely independent of changes in α-diversity. We analysed a unique grassland biodiversity dataset, with abundances of more than 4,000 species belonging to 12 trophic groups. LUI, and, in particular, high mowing intensity, had consistent effects on β-diversity across groups, causing a homogenization of soil microbial, fungal pathogen, plant and arthropod communities. These effects were nonlinear and the strongest declines in β-diversity occurred in the transition from extensively managed to intermediate intensity grassland. LUI tended to reduce local α-diversity in aboveground groups, whereas the α-diversity increased in belowground groups. Correlations between the β-diversity of different groups, particularly between plants and their consumers, became weaker at high LUI. This suggests a loss of specialist species and is further evidence for biotic homogenization. The consistently negative effects of LUI on landscape-scale biodiversity underscore the high value of extensively managed grasslands for conserving multitrophic biodiversity and ecosystem service provision. Indeed, biotic homogenization rather than local diversity loss could prove to be the most substantial consequence of land-use intensification.

Many experiments have shown that loss of biodiversity reduces the capacity of ecosystems to provide the multiple services on which humans depend. However, experiments necessarily simplify the complexity of natural ecosystems and will normally control for other important drivers of ecosystem functioning, such as the environment or land use. In addition, existing studies typically focus on the diversity of single trophic groups, neglecting the fact that biodiversity loss occurs across many taxa and that the functional effects of any trophic group may depend on the abundance and diversity of others. Here we report analysis of the relationships between the species richness and abundance of nine trophic groups, including 4,600 above- and below-ground taxa, and 14 ecosystem services and functions and with their simultaneous provision (or multifunctionality) in 150 grasslands. We show that high species richness in multiple trophic groups (multitrophic richness) had stronger positive effects on ecosystem services than richness in any individual trophic group; this includes plant species richness, the most widely used measure of biodiversity. On average, three trophic groups influenced each ecosystem service, with each trophic group influencing at least one service. Multitrophic richness was particularly beneficial for ‘regulating’ and ‘cultural’ services, and for multifunctionality, whereas a change in the total abundance of species or biomass in multiple trophic groups (the multitrophic abundance) positively affected supporting services. Multitrophic richness and abundance drove ecosystem functioning as strongly as abiotic conditions and land-use intensity, extending previous experimental results to real-world ecosystems. Primary producers, herbivorous insects and microbial decomposers seem to be particularly important drivers of ecosystem functioning, as shown by the strong and frequent positive associations of their richness or abundance with multiple ecosystem services. Our results show that multitrophic richness and abundance support ecosystem functioning, and demonstrate that a focus on single groups has led to researchers to greatly underestimate the functional importance of biodiversity.

Two new arbuscular mycorrhizal fungal species, (Glomeromycota) Septoglomus fuscumand S. furcatum, are described and illustrated. Spores of S. fuscumusually occur in loose hypogeous clusters, rarely singly in soil or inside roots, and S. furcatumforms only single spores in soil. Spores of S. fuscumare brownish orange to dark brown, globose to subglobose, (20–)47(–90) μm diam, rarely ovoid, 21–50 × 23–60 μm. Their spore wall consists of a semi-persistent, semi-flexible, orange white to golden yellow, rarely hyaline, outer layer, easily separating from a laminate, smooth, brownish orange to dark brown inner layer. Spores of S. furcatumare reddish brown to dark brown, globose to subglobose, (106–) 138(–167) μm diam, rarely ovoid, 108–127 × 135–160 μm, usually with one subtending hypha that is frequently branched below the spore base, or occasionally with two subtending hyphae located close together. Spore walls consists of a semipermanent, hyaline to light orange outermost layer, a semipermanent, hyaline to golden yellow middle layer, and a laminate, smooth, reddish brown to dark brown innermost layer. None of the spore-wall layers of S. fuscumand S. furcatumstain in Melzer’s reagent. In the field, S. fuscumwas associated with roots of Arctotheca populifoliacolonizing maritime dunes located near Strand in South Africa and S. furcatumwas associated with Cordia oncocalyxgrowing in a dry forest in the Ceará State, Brazil. In single-species cultures with Plantago lanceolataas host plant, S. fuscumand S. furcatumformed arbuscular mycorrhizae. Phylogenetic analyses of the SSU, ITS and LSU nrDNA sequences placed the two new species in genus Septoglomusand both new taxa were separated from described Septoglomusspecies.

Two new arbuscular mycorrhizal fungal species (Glomeromycota) of genus Glomus, G. africanumand G. iranicum, are described and illustrated. Both species formed spores in loose clusters and singly in soil and G. iranicumsometimes inside roots. G. africanumspores are pale yellow to brownish yellow, globose to subglobose, (60–)87(−125) μm diam, sometimes ovoid to irregular, 80–110 × 90–140 μm. The spore wall consists of a semipermanent, hyaline, outer layer and a laminate, smooth, pale yellow to brownish yellow, inner layer, which always is markedly thinner than the outer layer. G. iranicumspores are hyaline to pastel yellow, globose to subglobose, (13–)40(−56) μm diam, rarely egg-shaped, prolate to irregular, 39–54 × 48–65 μm. The spore wall consists of three smooth layers: one mucilaginous, short-lived, hyaline, outermost; one permanent, semirigid, hyaline, middle; and one laminate, hyaline to pastel yellow, innermost. Only the outermost spore wall layer of G. iranicumstains red in Melzer’s reagent. In the field G. africanumwas associated with roots of five plant species and an unrecognized shrub colonizing maritime sand dunes of two countries in Europe and two in Africa, and G. iranicumwas associated with Triticum aestivumcultivated in southwestern Iran. In one-species cultures with Plantago lanceolataas the host plant G. africanumand G. iranicumformed arbuscular mycorrhizae. Phylogenetic analyses of partial SSU sequences of nrDNA placed the two new species in Glomusgroup A. Both species were distinctly separated from sequences of described Glomusspecies.

Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland. Sequencing of 16S rRNA genes showed that only a few surface soil-inhabiting Archaea were present in the groundwater suggesting a restricted input from the surface. Dominant groups in the groundwater belonged to the marine group I (MG-I) Thaumarchaeota and the Woesearchaeota. Most of the groups detected in the aquitard and aquifer rock samples belonged to either cultured or predicted lithoautotrophs (e.g., Thaumarchaeota or Hadesarchaea). Furthermore, to target autotrophs, a series of 13CO2 stable isotope-probing experiments were conducted using filter pieces obtained after filtration of 10,000 L of groundwater to concentrate cells. These incubations identified the SAGMCG Thaumarchaeota and Bathyarchaeota as groundwater autotrophs. Overall, the results suggest that the majority of Archaea on rocks are fixing CO2, while archaeal autotrophy seems to be limited in the groundwater.