Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem.

Metataxonomic studies of ecosystem microbiotas require the simultaneous processing of samples with contrasting physical and biochemical traits. However, there are no published studies of comparisons of different DNA extraction kits to characterize the microbiotas of the main components of terrestrial ecosystems. Here, and to our knowledge for the first time, five DNA extraction kits were used to investigate the composition and diversity of the microbiota of a subset of samples typically studied in terrestrial ecosystems such as bulk soil, rhizosphere soil, invertebrate taxa and mammalian feces. DNA extraction kit was associated with changes in the relative abundance of hundreds of ASVs, in the same samples, resulting in significant differences in alpha and beta diversity estimates of their microbiotas. Importantly, the impact of DNA extraction kit on sample diversity varies according to sample type, with mammalian feces and soil samples showing the most and least consistent diversity estimates across DNA extraction kits, respectively. We show that the MACHEREY-NAGEL NucleoSpin® Soil kit was associated with the highest alpha diversity estimates, providing the highest contribution to the overall sample diversity, as indicated by comparisons with computationally assembled reference communities, and is recommended to be used for any large-scale microbiota study of terrestrial ecosystems.

Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem.

Metataxonomy has become the standard for characterizing the diversity and composition of microbial communities associated with multicellular organisms and their environment. Currently available protocols for metataxonomy assume a uniform DNA extraction, amplification and sequencing efficiency for all sample types and taxa. It has been suggested that the addition of a mock community (MC) to biological samples before the DNA extraction step could aid identification of technical biases during processing and support direct comparisons of microbiota composition, but the impact of MC on diversity estimates of samples is unknown. Here, large and small aliquots of pulverized bovine fecal samples were extracted with no, low or high doses of MC, characterized using standard Illumina technology for metataxonomics, and analysed with custom bioinformatic pipelines. We demonstrated that sample diversity estimates were distorted only if MC dose was high compared to sample mass (i.e. when MC > 10% of sample reads). We also showed that MC was an informative in situ positive control, permitting an estimation of the sample 16S copy number, and detecting sample outliers. We tested this approach on a range of sample types from a terrestrial ecosystem, including rhizosphere soil, whole invertebrates, and wild vertebrate fecal samples, and discuss possible clinical applications.

Distribution of soil macrofauna across different habitats in the Eastern European Alps.

Macro-invertebrates are important components of soil ecosystems as they provide a wide range of crucial functions and ecosystem services. Knowledge on their distribution in mountain soils is scarce despite the importance of such soils for people living in mountain regions as well as downstream. The present dataset contains records on soil macro-invertebrates belonging to nineteen taxa listed at class or order level and earthworms listed at species level from 22 different habitat types characteristic for the Eastern European Alps. Data were collected over a period of more than 30 years (1987-2020) following a standard protocol. We compiled 1572 single records from 241 unique sampling sites, providing default site parameters (GPS coordinates, habitat type, type of management, elevation, exposition, inclination, bedrock, soil type following WRB classification). Such data are important to analyse global trends and macroecological patterns and to set a basis for tracking long-term changes in macrofauna composition. In addition, this dataset will add to the still sparse knowledge on the occurrence and abundance of alpine soil fauna taxa.

The contribution of landscape features, climate and topography in shaping taxonomical and functional diversity of avian communities in a heterogeneous Alpine region.

Understanding the effects of landscape composition and configuration, climate, and topography on bird diversity is necessary to identify distribution drivers, potential impacts of land use changes, and future conservation strategies. We surveyed bird communities in a study area located in the Central Alps (Autonomous Province of South Tyrol, northeast Italy), by means of point counts and investigated taxonomic and functional diversity at two spatial scales along gradients of land use/land cover (LULC) intensity and elevation. We also explored how environmental variables influence bird traits and red-list categories. Models combining drivers of different types were highly supported, pointing towards synergetic effects of different types of environmental variables on bird communities. The model containing only LULC compositional variables was the most supported one among the single-group models: LULC composition plays a crucial role in shaping local biodiversity and hence bird communities, even across broad landscape gradients. Particularly relevant were wetlands, open habitats, agricultural mosaics made up of small habitat patches and settlements, ecotonal and structural elements in agricultural settings, and continuous forests. To conserve bird diversity in the Alps, planning and management practices promoting and maintaining small fields, structural elements, and a mosaic of different LULC types should be supported, while preserving continuous forests at the same time. Additionally, pastures, extensively used meadows, and wetlands are key to conservation. These strategies might mitigate the impacts of global change on bird diversity in the Alps and in other European mountain areas.

Effects of land use and climate on carbon and nitrogen pool partitioning in European mountain grasslands.

European mountain grasslands are increasingly affected by land-use changes and climate, which have been suggested to exert important controls on grassland carbon (C) and nitrogen (N) pools. However, so far there has been no synthetic study on whether and how land-use changes and climate interactively affect the partitioning of these pools amongst the different grassland compartments. We analyzed the partitioning of C and N pools of 36 European mountain grasslands differing in land-use and climate with respect to above- and belowground phytomass, litter and topsoil (top 23 cm). We found that a reduction of management intensity and the abandonment of hay meadows and pastures increased above-ground phytomass, root mass and litter as well as their respective C and N pools, concurrently decreasing the fractional contribution of the topsoil to the total organic carbon pool. These changes were strongly driven by the cessation of cutting and grazing, a shift in plant functional groups and a related reduction in litter quality. Across all grasslands studied, variation in the impact of land management on the topsoil N pool and C/N-ratio were mainly explained by soil clay content combined with pH. Across the grasslands, below-ground phytomass as well as phytomass- and litter C concentrations were inversely related to the mean annual temperature; furthermore, C/N-ratios of phytomass and litter increased with decreasing mean annual precipitation. Within the topsoil compartment, C concentrations decreased from colder to warmer sites, and increased with increasing precipitation. Climate generally influenced effects of land use on C and N pools mainly through mean annual temperature and less through mean annual precipitation. We conclude that site-specific conditions need to be considered for understanding the effects of land use and of current and future climate changes on grassland C and N pools.

Contribution to the molecular phylogeny of Sciaridae (Diptera) with special attention to the genera emBradysia/em and emCorynoptera/em.

The systematics of the dipteran family Sciaridae is based mainly on morphological characters and has remained quite controversial. In this study, we used two mitochondrial DNA markers (CO1, 16S) and a nuclear one (28S) to take a glimpse into phylogenetic relationships of part of the North and Central European Sciaridae. A total of 91 species from 19 genera were analysed using Maximum Likelihood based phylogenetics (depending on the availability of valid sequences, 50-70 per gene). We strengthen the suggestion of the Chaetosciara group as an independent subfamily. Within the subfamily Megalosphyinae, two separate Bradysia clades were identified, suggesting a close relation between the genera Zygoneura, Austrosciara, and Scatopsciara. The genus Alpinosciara gen. n. is established to place the species of the former Corynoptera crassistylata group inside the subfamily Megalosphyinae. This new genus now includes 22 species.

Species richness and beta diversity patterns of multiple taxa along an elevational gradient in pastured grasslands in the European Alps.

To understand how diversity is distributed in space is a fundamental aim for optimizing future species and community conservation. We examined in parallel species richness and beta diversity components of nine taxonomic groups along a finite space, represented by pastured grasslands along an elevational gradient. Beta diversity, which is assumed to bridge local alpha diversity to regional gamma diversity was partitioned into the two components turnover and nestedness and analyzed at two levels: from the lowest elevation to all other elevations, and between neighboring elevations. Species richness of vascular plants, butterflies, beetles, spiders and earthworms showed a hump-shaped relationship with increasing elevation, while it decreased linearly for grasshoppers and ants, but increased for lichens and bryophytes. For most of the groups, turnover increased with increasing elevational distance along the gradient while nestedness decreased. With regard to step-wise beta diversity, rates of turnover or nestedness did not change notably between neighboring steps for the majority of groups. Our results support the assumption that species communities occupying the same habitat significantly change along elevation, however transition seems to happen continuously and is not detectable between neighboring steps. Our findings, rather than delineating levels of major diversity losses, indicate that conservation actions targeting at a preventive protection for species and their environment in mountainous regions require the consideration of entire spatial settings.

Life-history traits and physiological limits of the alpine fly Drosophila nigrosparsa (Diptera: Drosophilidae): A comparative study.

Interspecific variation in life-history traits and physiological limits can be linked to the environmental conditions species experience, including climatic conditions. As alpine environments are particularly vulnerable under climate change, we focus on the montane-alpine fly Drosophila nigrosparsa. Here, we characterized some of its life-history traits and physiological limits and compared these with those of other drosophilids, namely Drosophila hydei, Drosophila melanogaster, and Drosophila obscura. We assayed oviposition rate, longevity, productivity, development time, larval competitiveness, starvation resistance, and heat and cold tolerance. Compared with the other species assayed, D. nigrosparsa is less fecund, relatively long-living, starvation susceptible, cold adapted, and surprisingly well heat adapted. These life-history characteristics provide insights into invertebrate adaptations to alpine conditions which may evolve under ongoing climate change.

Effects of Alpine land-use changes: Soil macrofauna community revisited.

Although soil invertebrates play a decisive role in maintaining ecosystem functioning, little is known about their structural composition in Alpine soils and how their abundances are affected by the currently ongoing land-use changes. In this study, we re-assessed the soil macrofauna community structure of managed and abandoned Alpine pastureland, which has already been evaluated 14 years earlier. Our results confirm clear shifts in the community composition after abandonment, in that (1) Chilopoda and Diplopoda were recorded almost exclusively on the abandoned sites, (2) Coleoptera larvae and Diptera larvae were more abundant on the abandoned than on the managed sites, whereas (3) Lumbricidae dominated on the managed sites. By revisiting managed and abandoned sites, we infer community patterns caused by abandonment such as changes in the epigeic earthworm community structure, and we discuss seasonal and sampling effects. Our case study improves the still limited understanding of spatio-temporal biodiversity patterns of Alpine soil communities.

Genomic Resources Notes Accepted 1 June 2015-31 July 2015.

This article documents the public availability of (i) microbiomes in diet and gut of larvae from the dipteran Dilophus febrilis using massive parallel sequencing, (ii) SNP and SSR discovery and characterization in the transcriptome of the Atlantic mackerel (Scomber scombrus, L) and (iii) assembled transcriptome for an endangered, endemic Iberian cyprinid fish (Squalius pyrenaicus).

Increased decomposer diversity accelerates and potentially stabilises litter decomposition.

Little is known about the effect of decomposer diversity on litter decomposition in alpine areas. Especially under the premise that alpine ecosystems are very sensitive to global change and are currently undergoing extensive land-use changes, a better understanding is needed to predict how environmental change will affect litter decomposition. A mesocosm experiment was conducted to compare the effects of the most common and functionally diverse invertebrates (earthworms, millipedes and sciarid larvae) found in alpine soils on decomposition rates and to assess how decomposer diversity affects litter decomposition. Experimental and estimated (i.e. projected to field decomposer-biomass) litter mass loss was 13-33% higher in the three-species treatment. Notably, the variability in decomposition was greatly reduced when decomposer diversity was high, indicating a portfolio effect. Our results suggest that invertebrate decomposer diversity is essential for sustaining litter decomposition in alpine areas and for the stability of this service.

Drought-induced reduction in uptake of recently photosynthesized carbon by springtails and mites in alpine grassland.

We tested whether experimental summer drought affects the transfer of recently photosynthesized carbon from plants to soil mesofauna in a subalpine meadow. From day one after (13)CO(2) pulse-labelling of the plant canopy, roots, collembolans and mites were enriched in δ(13)C in control, but not in drought plots. However, as the difference in δ(13)C between roots and soil animals was not affected by the drought treatment, we conclude that drought affects the tight linkage between photosynthesis and soil mesofauna primarily via functional responses of plants rather than via changes in the mesofauna.

Palatability of selected alpine plant litters for the decomposer Lumbricus rubellus (Lumbricidae).

On alpine pastureland the decline in large-bodied earthworm numbers and biomass after abandonment of management might be the result of a shift from highly palatable grass litter to poorly digestible leaf litter of dwarf shrubs. To test this hypothesis, we analysed nitrogen, phosphorous and total phenolic contents of fresh and aged litter of eight commonly occuring alpine plant species and compared consumption rates of these food sources in a controlled feeding experiment with Lumbricus rubellus (Lumbricidae). Furthermore, we analysed the microbial community structure of aged litter materials to check for a relationship between the microbial characteristics of the different plant litter types and the food choice of earthworms. Plant litters differed significantly in their chemical composition, earthworms, however, showed no preference for any litter species, but generally rejected fresh litter material. Microbial community structures of the litter types were significantly different, but we could find no evidence for selective feeding of L. rubellus. We conclude that L. rubellus is a widespread, adaptable ubiquist, which is able to feed on a variety of food sources differing in quality and palatability, as long as they have been exposed to wheathering.

Association of elevated C-reactive protein levels with an impaired prognosis in patients with surgically treated endometrial cancer.

OBJECTIVE: To evaluate whether C-reactive protein (CRP) serum levels are associated with prognosis in surgically treated endometrial cancer. METHODS: In the present multicenter study, CRP serum levels were measured preoperatively in 403 surgically staged patients with endometrioid endometrial cancer. Results were correlated to clinical data. RESULTS: The mean (standard deviation) serum CRP level in patients with endometrial cancer was 1.0 (1.8) mg/dL. Serum CRP levels were associated with tumor stage (P=.01), but not with tumor grade (P=.8), lymph node involvement (P=.8), and age at diagnosis (P=.9). In a univariable survival analysis, serum CRP levels, tumor stage, tumor grade, and age at diagnosis were associated with disease-free and overall survival (all P <.001). In a multivariable Cox regression model, serum CRP levels (P=.001, P=.004), tumor stage (P <.001, P <.001), tumor grade (P=.02, P=.009), and age at diagnosis (P=.002, P=.001) were independent prognostic factors for disease-free and overall survival. CONCLUSION: Our results suggest that elevated serum CRP levels are associated with a less favorable prognosis in patients with surgically treated endometrial cancer. LEVEL OF EVIDENCE: II.