EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.

Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.

Matching the puzzle piece to a new jigsaw: The effect of surrounding environments on plants and invertebrates in the translocated wet meadow.

Habitat translocation is a method of habitat salvation conducted in cases of its inevitable destruction during construction projects. To evaluate the large-scale turf translocation of wet meadows to derelict land, with consideration of the possible impact of the surrounding area on the translocated habitat, salvaged Molinion meadows were compared to reference meadows near the donor site and to varied plots in the receptor area. The study included the soil, vegetation and selected groups of invertebrates at different motility and food levels. Pollinators (wild bees, butterflies), grasshoppers, ants and soil mesofauna, with emphasis on springtails, were counted and identified to the species level. Lower numbers of springtails and higher numbers of grasshoppers were observed in the translocated plots than in the reference plots. For springtails, the decreased soil porosity was a clear disadvantage. Mobile animals with a high food specificity responded dynamically to the habitat translocation. The translocated plots maintained their biodiversity. However, an influx of cosmopolitan species was noticeable, especially for the plants and pollinators. A few vulnerable species declined in number. The habitat translocation to derelict land was associated with a deterioration of the ecological condition of the habitat; thus, natural habitats should be preserved where they are if possible. However, in the case of their inevitable destruction, translocation is better than nothing. Revitalised areas can be a valuable spot for local pollinators, as well as for other animals, as far as their biodiversity is maintained. Caring for pollinators, which are under threat on a global scale, should be a particular concern for the safety of crops and phytocoenoses.

Drivers of systematic bias in alien plant species distribution data.

Among the main challenges in modelling biological invasion is a lack of valid data on the absence of invasive species. Absence data are important for assessing the reliability of models, but multiple surveys at a location are needed. In practice, omission errors are more frequent than commission errors. We therefore quantified how eliminating potentially biased areas from invasive species distribution models (iSDMs) affected the models' performance, and we assessed how the distribution of biased areas correlated with environmental factors. We hypothesized that for neophytes, the distribution of biased areas corresponds to specific land relief and/or particular landscape and land use, but not the density of roads and urbanized areas. The data on neophytes were obtained from a distribution atlas covering approximately 31,000 km2 in Central Europe overlaid with a 2 × 2 km square grid. One hundred fifty-three species were used for modelling neophyte richness, and negative residuals from the model were assumed to indicate biased squares. Twenty invasive species were used as an independent dataset for testing the effect of excluding the biased squares on iSDM performance. The exclusion of biased squares increased the iSDM performance from an area under the curve value of 0.73 to 0.78. The best results were obtained by excluding 30 % of the squares from the original dataset. The presence of damp sites explained the distribution of biased squares; the density of roads and urbanized areas had no impact. The applied method allows distinguishing biased, plausibly undersampled squares in a species distribution atlas, the exclusion of which significantly improves iSDM performance. The results suggest that the commonly observed low sampling effort in areas distant from communication routes and urbanized areas was not crucial in modelling invasive species distribution, which can be related to smaller neophyte richness in remote areas resulting from low propagule pressure.

Towards a better understanding of linear species distribution in river valleys: The abundance of river corridor plants is linked to soil exchangeable potassium and pH.

The phenomenon that some vascular plant species grow mainly or exclusively in the large river valleys of Central Europe constitutes a long-standing distribution puzzle. In our study, we focused on determining which physicochemical properties of soil affect the distribution of river corridor plant (RCP) species. Research that included RCP coverage, the physicochemical properties of soil as well as several topographic and spatial variables were conducted in 10 transects perpendicular to the San River (SE Poland). The sampled plots were located both in close proximity to the river, where the greatest number of RCP populations are concentrated, and along anthropogenic linear landscape elements which have proven to be important for RCP occurrence in areas located away from the riverbed. Spearman rank correlation matrices were constructed to observe the general relationships between particular variables and Boosted Regression Tree models were used for explaining RCP coverage. Our study indicated that in the case of plots located in proximity to the river, the expected coverage of RCP species was highest in plots characterized by a higher soil exchangeable potassium (K) content, as well as in those located closer to the San River and at lower altitudes. In plots situated along anthropogenic linear landscape elements, the expected coverage of RCPs was highest in plots with a high soil exchangeable K content and in those with a high soil pH. The analyses clearly showed that the physicochemical properties of soils indeed affect RCP species occurrence and they require soils with a high exchangeable K content and a high pH. Since these two soil parameters are closely related to soil fertility, and additionally K enhances root development, we suppose that both factors strengthen the competitiveness of RCPs in floodplain ecosystems.

Drivers of Solidago species invasion in Central Europe-Case study in the landscape of the Carpathian Mountains and their foreground.

AIM: The invasion process is a complex, context-dependent phenomenon; nevertheless, it can be described using the PAB framework. This framework encompasses the joint effect of propagule pressure (P), abiotic characteristics of the environment (A), and biotic characteristics of both the invader and recipient vegetation (B). We analyzed the effectiveness of proxies of PAB factors to explain the spatial pattern of Solidago canadensis and S. gigantea invasion using invasive species distribution models. LOCATION: Carpathian Mountains and their foreground, Central Europe. METHODS: The data on species presence or absence were from an atlas of neophyte distribution based on a 2 × 2 km grid, covering approximately 31,200 km2 (7,752 grid cells). Proxies of PAB factors, along with data on historical distribution of invaders, were used as explanatory variables in Boosted Regression Trees models to explain the distribution of invasive Solidago. The areas with potentially lower sampling effort were excluded from analysis based on a target species approach. RESULTS: Proxies of the PAB factors helped to explain the distribution of both S. canadensis and S. gigantea. Distributions of both species were limited climatically because a mountain climate is not conducive to their growth; however, the S. canadensis distribution pattern was correlated with proxies of human pressure, whereas S. gigantea distribution was connected with environmental characteristics. The varied responses of species with regard to distance from their historical distribution sites indicated differences in their invasion drivers. MAIN CONCLUSIONS: Proxies of PAB are helpful in the choice of explanatory variables as well as the ecological interpretation of species distribution models. The results underline that human activity can cause variation in the invasion of ecologically similar species.

Monitoring of fungal root colonisation, arbuscular mycorrhizal fungi diversity and soil microbial processes to assess the success of ecosystem translocation.

To compensate for an airport expansion, including construction on valuable wet meadows of a Natura 2000 system, 1.3 ha of turf, cut into blocks, were transferred to artificial basins in a habitat garden. To evaluate the impact of translocation on this ecosystem, and thus the success of its preservation, we monitored fungal root colonisation of Molinia caerulea, the diagnostic plant species for wet meadows, along with arbuscular mycorrhizal fungi (AMF) species richness and composition in soils and soil microbial processes for three seasons: prior to the transfer (2013) and the two following years (2014-15). We observed few changes in the fungal colonisation of M. caerulea, suggesting that the fungal associations of this species were unaffected. The number of AMF species declined directly after the translocation; however, in 2015, an increased number of species was recorded. There were no differences in AMF species composition, nor did soil basal respiration rate, substrate-induced respiration (SIR), or substrate-active biomass (Cmic) change over the years. Only metabolic coefficient (qCO2) decreased after the transfer. The small number of effects in fungal root colonisation, AMF diversity, and microbial processes following the translocation of the ecosystem prove its success. This can be attributed to the deep turf translocation that kept the relevant microbial communities almost unaffected.

Functioning grouped soil microbial communities according to ecosystem type, based on comparison of fallows and meadows in the same region.

Predicting the composition and function of microbial communities at a bio-geographical scale, across ecosystems, is challenging. We compared six abandoned fields to six meadows to see whether soil microbial community structure and activity are more similar within the ecosystem type than between the types. We implemented bacteria and fungi phylogenetic markers profiling, phospholipids analysis, fluorescence counts of total bacteria and algae and microscopy of arbuscular mycorrhizal fungi (AMF). The functional performance of microbial communities was assessed using enzymes activity measurements as well as culturing and incubation experiments. The studied fallows and meadows had similar biomass and general structure of soil microbial communities. However, the AMF root colonization frequency was higher in the meadows than in the fallows. The AMF colonization was promoted in meadows characterised by lower availability of NO3-, P and K as well as higher soil pH, which additionally hampered plant acquisition of P at the P-limited ecosystem. Fallow and meadow microbial communities showed characteristic functional traits. Meadow soils exhibited higher basal respiration rate, while cellulose decomposition and nitrogen mineralization were faster in fallows. Even when no major differences in community structure could have been detected soil microbial communities adapted to local and/or instantaneous environmental conditions and formed functionally-specific ecotypes. This work points out the relevance of preserving meadows as reservoirs of plant diversity, which cope excellent in nutrient depleted conditions and in mountain regions thanks to microbial components of ecosystem.

Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes.

Soda lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. This makes them valuable model systems for studying the connection between community structure and abiotic parameters such as pH and salinity. For the first time, we apply high-throughput sequencing to accurately estimate phylogenetic richness and composition in five soda lakes, located in the Ethiopian Rift Valley. The lakes were selected for their contrasting pH, salinities and stratification and several depths or spatial positions were covered in each lake. DNA was extracted and analyzed from all lakes at various depths and RNA extracted from two of the lakes, analyzed using both amplicon- and shotgun sequencing. We reveal a surprisingly high biodiversity in all of the studied lakes, similar to that of freshwater lakes. Interestingly, diversity appeared uncorrelated or positively correlated to pH and salinity, with the most "extreme" lakes showing the highest richness. Together, pH, dissolved oxygen, sodium- and potassium concentration explained approximately 30% of the compositional variation between samples. A diversity of prokaryotic and eukaryotic taxa could be identified, including several putatively involved in carbon-, sulfur- or nitrogen cycling. Key processes like methane oxidation, ammonia oxidation and 'nitrifier denitrification' were also confirmed by mRNA transcript analyses.