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.

Global fine-resolution data on springtail abundance and community structure

Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.

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.

Measurement(s)	abundances of soil animals
Technology Type(s)	soil samples
Factor Type(s)	NONE
Sample Characteristic - Organism	Lumbricidae • Arthropoda • Mollusca
Sample Characteristic - Environment	Alpine habitats
Sample Characteristic - Location	European Alps

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.

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications.

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.

Global data on earthworm abundance, biomass, diversity and corresponding environmental properties

Earthworms are an important soil taxon as ecosystem engineers, providing a variety of crucial ecosystem functions and services. Little is known about their diversity and distribution at large spatial scales, despite the availability of considerable amounts of local-scale data. Earthworm diversity data, obtained from the primary literature or provided directly by authors, were collated with information on site locations, including coordinates, habitat cover, and soil properties. Datasets were required, at a minimum, to include abundance or biomass of earthworms at a site. Where possible, site-level species lists were included, as well as the abundance and biomass of individual species and ecological groups. This global dataset contains 10,840 sites, with 184 species, from 60 countries and all continents except Antarctica. The data were obtained from 182 published articles, published between 1973 and 2017, and 17 unpublished datasets. Amalgamating data into a single global database will assist researchers in investigating and answering a wide variety of pressing questions, for example, jointly assessing aboveground and belowground biodiversity distributions and drivers of biodiversity change.

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.

Global distribution of earthworm diversity

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

First records of Opetiopalpus sabulosus Motschulsky, 1840 (Coleoptera, Cleridae) for the European Alps

The genus Opetiopalpus from the family of checkered beetles (Coleoptera: Cleridae) is represented by 28 species worldwide, with 11 species found in the Palearctic and only four sparsely in Europe prior to 1998. One species, Opetiopalpussabulosus Motschulsky, 1840, was recently found in Eastern Europe (i.e. Ukraine, Bulgaria, and Moldavia), with the most recent record in 2015 in Eastern Romania; no data are available for Central Europe. During a comprehensive sampling survey in 2016 in the dry inner-Alpine Vinschgau Valley (South Tyrol, Italy), one individual of O.sabulosus was recorded from soil core samples on an extensively managed steppe-like dry pasture at 2000 m a.s.l. This was the first record of O.sabulosus for the European Alps and Central Europe. Further intensive samplings were conducted in 2017 and 2018, in which one additional specimen at a dry pasture at 2500 m confirms the presence of this checkered beetle. Opetiopalpussabulosus seems to have a cryptic lifestyle and therefore a low detection probability. The locations from where the species was recorded, all steppe-like dry grasslands that are part of the LTSER area “Val Mazia/Matschertal” within the LTER-Italia network, are characterized by low precipitation (730 mm at 2000 m a.s.l.) and traditional low input management (grazing cattle, sheep, and horses). Beside O.sabulosus, other rare and new species for South Tyrol and Italy were found at the sampling area. Therefore, our records underline the high biodiversity and the high nature conservational value of these steppe-like dry grasslands and the importance of long-term research to monitor such species.

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.

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.

Application of denaturing gradient gel electrophoresis for analysing the gut microflora of Lumbricus rubellus Hoffmeister under different feeding conditions

The earthworm, Lumbricus rubellus, plays an essential role in soil ecosystems as it affects organic matter decomposition and nutrient cycling. By ingesting a mixture of organic and mineral material, a variety of bacteria and fungi are carried to the intestinal tract of the earthworm. To get a better understanding of the interactions between L. rubellus and the microorganisms ingested, this study tried to reveal if the diet affects the composition of the gut microflora of L. rubellus or if its intestinal tract hosts an indigenous, species-specific microbiota. A feeding experiment with L. rubellus was set up; individuals were collected in the field, transferred to a climate chamber and fed with food sources of different quality (dwarf shrub litter, grass litter or horse dung) for six weeks. DNA was extracted from the guts of the earthworms, as well as from the food sources and the surrounding soil, and further analysed by a molecular fingerprinting method, PCR-DGGE (Polymerase Chain Reaction -- Denaturing Gradient Gel Electrophoresis). We were able to demonstrate that the gut microbiota was strongly influenced by the food source ingested and was considerably different to that of the surrounding soil. Sequencing of dominant bands of the bacterial DGGE fingerprints revealed a strong occurrence of y-Proteobacteria in all gut samples, independent of the food source. A specific microflora in the intestinal tract of L. rubellus, robust against diet changes, could not be found.

Design and implementation of a random neural network routing engine

Random neural network (RNN) is an analytically tractable spiked neural network model that has been implemented in software for a wide range of applications for over a decade. This paper presents the hardware implementation of the RNN model. Recently, cognitive packet networks (CPN) is proposed as an alternative packet network architecture where there is no routing table, instead the RNN based reinforcement learning is used to route packets. Particularly, we describe implementation details for the RNN based routing engine of a CPN network processor chip: the smart packet processor (SPP). The SPP is a dual port device that stores, modifies, and interprets the defining characteristics of multiple RNN models. In addition to hardware design improvements over the software implementation such as the dual access memory, output calculation step, and reduced output calculation module, this paper introduces a major modification to the reinforcement learning algorithm used in the original CPN specification such that the number of weight terms are reduced from 2n/sup 2/ to 2n. This not only yields significant memory savings, but it also simplifies the calculations for the steady state probabilities (neuron outputs in RNN). Simulations have been conducted to confirm the proper functionality for the isolated SPP design as well as for the multiple SPP's in a networked environment.

Fallopian tube cancer associated with paraneoplastic dermatomyositis -- asymptomatic multivisceral exacerbated dermatomyositis mimicking recurrent widespread malignant disease: case report

OBJECTIVE

To report an uncommon case of a recurrent episode of primarily paraneoplastic dermatomyositis which was completely disconnected from the initially triggering malignancy and manifested as a silent pure multivisceral exacerbation.

CASE

A 70-year-old woman presented with a pure multivisceral episode of dermatomyositis without characteristic musculo-cutaneous symptoms one year after successful treatment of fallopian tube carcinoma with complete resolvement of a concomittant paraneoplastic dermatomyositis. The uncommon manifestation of recurrent dermatomyositis involving the lungs, spleen and liver, both adrenal glands and abdominal lymph nodes, mimicked a highly disseminated recurrence of the fallopian tube cancer. Physicians participating in the interdisciplinary tumor board were misled to opt for reinductive chemotherapy. Only histologic diagnosis obtained from multiple biopsies uncovered the inflammatory nature of the disease and spared the patient unneeded chemotherapy.

CONCLUSION

Asymptomatic multivisceral dermatomyositis may mimic metastatic spread of the initially underlying malignancy and may misdirect therapeutic strategies towards inadequate antineoplastic treatment.