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High-throughput sequencing (HTS) of soil environmental DNA (eDNA) allows assessing the full diversity of soil micro-eukaryotes. The resulting operational taxonomic units (OTUs) can be assigned to potential taxonomic and functional identities using increasingly complete reference databases. HTS of soil eDNA is revealing a high diversity and abundance of potential eukaryovorous protists, thus challenging the paradigm of the predominantly bacterivorous function of soil phagotrophic protists (i.e. microbial loop).

Using Illumina sequencing of soil eDNA and targeting the V9 region of the SSU rRNA gene, we investigated the taxonomic and functional diversities, distribution and co-occurrence patterns of soil micro-eukaryotes in three land-use categories: forests, meadows and croplands located in Switzerland. Each OTU was assigned to a broad functional category (phototrophs, phagotrophs, osmotrophs, or parasites).

Total OTU richness was similar in the three land-use categories, but community composition differed significantly between forests and other land-uses. The proportion of fungal sequences (especially Basidiomycota) was highest, and phototroph (i.e. soil microalgae) sequences least abundant in forests. Seven OTUs representing phagotrophic protists, together accounting for >25% of all phagotroph sequences, were significantly correlated to the total number of phototroph sequences, thus suggesting algivory. At least three of these OTUs corresponded to known algal predators.

These results suggest that beyond plants, soil microalgae represent a functionally significant but rarely considered input of carbon in soils that should be taken into account when modelling soil nutrient cycling.

Seppey, C. V. W., Singer, D., Dumack, K., Fournier, B., Belbahri, L., Mitchell, E. A. D., & Lara, E. (2017). Distribution patterns of soil microbial eukaryotes suggests widespread algivory by phagotrophic protists as an alternative pathway for nutrient cycling. Soil Biology and Biochemistry, 112, 68–76. https://doi.org/10.1016/j.soilbio.2017.05.002

Human-driven environmental changes can induce marked shifts in the functional structure of biological communities with possible repercussion on important ecosystem functions and services. At the same time it remains unclear to which extent these changes may differently affect various types of organisms. We investigated species richness and community functional structure of species assemblages at the landscape scale (1 km² plots) for two contrasting model taxa, i.e. plants (producers and sessile organisms) and birds (consumers and mobile organisms), along topography, climate, landscape heterogeneity, and land-use (agriculture and urbanization) gradients in a densely populated region of Switzerland. Our study revealed that agricultural and urban land uses drove marked shifts in the functional structure of biological communities compared to changes along climate and topography gradients, especially for plants, while for birds these changes were comparable. Agricultural and urban land uses enhanced divergence in traits related to resource use for birds (diet and nesting), growth forms, dispersal, and reproductive traits for plants, while it induced convergence in vegetative plant traits (plant height and leaf dry matter content). These results suggest that contrasting assembly patterns may arise within and across taxonomic groups along the same environmental gradients as result of distinct underlying processes and ‘organism-specific’ environmental perceptions. Our results further suggest a potential homogenization of biological communities, as well as low functional diversity and redundancy levels of bird assemblages in our human-dominated study region. This might potentially compromise the maintenance of key ecological processes under future environmental changes.

Concepción, E. D., Götzenberger, L., Nobis, M. P., de Bello, F., Obrist, M. K., & Moretti, M. (2017). Contrasting trait assembly patterns in plant and bird communities along environmental and human-induced land-use gradients. Ecography, 40(6), 753–763. https://doi.org/10.1111/ecog.02121

The biodiversity of agricultural land is usually measured via indicator species that can be recorded time- and cost-efficiently. Behind this approach lies the seldom-questioned assumption that these groups of organisms are good at reflecting the overall species diversity of a habitat. We tested this assumption by comparing the diversity of cow-dung insects with that of grasshopper, butterfly, vascular plant and nearby moss and snail communities on 24 pastures on the Swiss Central Plateau. The diversity of the vascular plants and mosses increased with that of the (often herbivorous) butterflies, grasshoppers and snails, both on the sites examined in our study and on those in the wider vicinity. By contrast, the diversity of the dung insects (flies and parasitic wasps) did not correlate with other groups of organisms. Consequently, vascular plants, grasshoppers, butterflies, mosses and snails can represent one another well. This is not, however, the case for dung insects: they, and hence most likely their functions in decomposing dung, are scarcely represented by the commonly used indicators.

Blanckenhorn, W, Jochmann, R., & Walter, T. (2018). Biodiversität von Kuhdunginsekten und anderen Weidebewohnern nicht korreliert. Agrarfroschung Schweiz 9(1): 20-25.

Although today there is ample evidence that biodiversity is affected by agricultural land use intensification, little is known about how species respond to different land use intensity gradients at landscape scale. To properly describe the relationship between biodiversity and land use intensity, intensity indicators need to account for land cover, management intensity, and be assessed at landscape scale. The study was conducted in 91 landscapes of 1 km² in Switzerland. Three different land use intensity indicators were calculated: indicator 1 was defined as the ratio between agricultural and natural area; indicator 2 as the ratio between arable land and permanent grassland; and indicator 3 as the ratio between agricultural area and biodiversity promotion areas (BPA, i.e. wildlife-friendly managed areas under Swiss agri-environment schemes). Species richness and abundance of birds and butterflies were used as biodiversity indicators and trait-based community indices were used to describe bird community changes. Overall, we found that birds were affected by landscape composition and agricultural management, while butterflies were mainly affected by agricultural management. Specifically, from natural (e.g. forest dominated) to agriculture-dominated landscape, bird species richness showed a sharp decrease when 80% or more of the landscape was farmed. Butterfly species richness followed a hump-shaped curve. None of the species groups was significantly correlated with the proportion of arable land versus permanent grassland. Yet species richness of birds and butterflies significantly changed with the proportion of BPA: the lower the proportion of BPA, the lower the observed richness. Finally, when the proportion of agricultural land increased, populations of migratory birds and hedge/tree breeders decreased. We conclude that to further promote farmland biodiversity, natural areas, such as forests, hedges and waterbodies, should cover at least 20% of the agricultural landscapes and the proportion of BPA should be increased.

Zingg, S., Grenz, J., & Humbert, J.-Y. (2018). Landscape-scale effects of land use intensity on birds and butterflies. Agriculture, Ecosystems & Environment, 267, 119–128. https://doi.org/10.1016/j.agee.2018.08.014