Alien and native plants show contrasting responses to climate and land use in Europe

Aim We tested whether the distribution and cover of alien plant species in Europe was related to human disturbance and microclimate. Location Surveys were conducted at 13 sites across Europe, each containing a pair of landscapes with different land‐use intensities. Methods Sampling locations were chosen based on land use and microclimate at two scales: land use was characterized at the patch and landscape scale; climate was expressed as regional and local temperature. The slope of each sample location was derived from a digital elevation model. Cover of plant species was measured using point counts and analysed using mixed effect models. Species were classified as native, archaeophytes and neophytes (pre‐ versus post‐ad 1500 immigrants). Due to the zero inflation observed in the alien groups, their cover was analysed conditional on their presence. Results Anthropogenic disturbance was a significant explanatory variable, increasing the presence and cover of alien species and decreasing the cover of native species. Alien presence was increased in sites under agricultural management, while their cover responded to land use at both local and landscape scales (and to their interaction), such that only natural habitats in semi‐natural landscapes had low alien cover. Microclimate was important for neophytes, with presence concentrated around mesic conditions. Slope was relevant for archaeophytes and native species, suppressing the former group and promoting the latter one. Main conclusions We found that, at the European scale, the distribution of alien plants is related to anthropogenic disturbance more than to microclimatic differences. The presence of neophytes, however, was influenced by climate at local and regional scales, with the highest incidence under mesic conditions. The different patterns observed for the presence and cover of alien species suggest different mechanisms acting during their establishment and spread. They also suggest that to counteract the expansion of alien species natural habitats may need to be maintained at landscape scales.     

Effects of OTU Clustering and PCR Artifacts on Microbial Diversity Estimates

Next-generation sequencing has increased the coverage of microbial diversity surveys by orders of magnitude, but differentiating artifacts from rare environmental sequences remains a challenge. Clustering 16S rRNA sequences into operational taxonomic units (OTUs) organizes sequence data into groups of 97 % identity, helping to reduce data volumes and avoid analyzing sequencing artifacts by grouping them with real sequences. Here, we analyze sequence abundance distributions across environmental samples and show that 16S rRNA sequences of >99 % identity can represent functionally distinct microorganisms, rendering OTU clustering problematic when the goal is an accurate analysis of organism distribution. Strict postsequencing quality control (QC) filters eliminated the most prevalent artifacts without clustering. Further experiments proved that DNA polymerase errors in polymerase chain reaction (PCR) generate a significant number of substitution errors, most of which pass QC filters. Based on our findings, we recommend minimizing the number of PCR cycles in DNA library preparation and applying strict postsequencing QC filters to reduce the most prevalent artifacts while maintaining a high level of accuracy in diversity estimates. We further recommend correlating rare and abundant sequences across environmental samples, rather than clustering into OTUs, to identify remaining sequence artifacts without losing the resolution afforded by high-throughput sequencing.     

The composition of the gut microbiota shapes the colon mucus barrier

Two C57BL/6 mice colonies maintained in two rooms of the same specific pathogen-free (SPF) facility were found to have different gut microbiota and a mucus phenotype that was specific for each colony. The thickness and growth of the colon mucus were similar in the two colonies. However, one colony had mucus that was impenetrable to bacteria or beads the size of bacteria—which is comparable to what we observed in free-living wild mice—whereas the other colony had an inner mucus layer penetrable to bacteria and beads. The different properties of the mucus depended on the microbiota, as they were transmissible by transfer of caecal microbiota to germ-free mice. Mice with an impenetrable mucus layer had increased amounts of Erysipelotrichi, whereas mice with a penetrable mucus layer had higher levels of Proteobacteria and TM7 bacteria in the distal colon mucus. Thus, our study shows that bacteria and their community structure affect mucus barrier properties in ways that can have implications for health and disease. It also highlights that genetically identical animals housed in the same facility can have rather distinct microbiotas and barrier structures.     

Classification schemes for protein structure and function

We examine the structural and functional classifications of the protein universe, providing an overview of the existing classification schemes, their features and inter-relationships. We argue that a unified scheme should be based on a natural classification approach and that more comparative analyses of the present schemes are required both to understand their limitations and to help delimit the number of known protein folds and their corresponding functional roles in cells.     

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, "Candidatus Accumulibacter phosphatis." The analysis sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of A. phosphatis in this habitat, its lifestyle outside EBPR and probable cultivation requirements. Comparison of the same species from different EBPR sludges highlights recent evolutionary dynamics in the A. phosphatis genome that could be linked to mechanisms for environmental adaptation. In spite of an apparent lack of phylogenetic overlap in the flanking communities of the two sludges studied, common functional themes were found, at least one of them complementary to the inferred metabolism of the dominant organism. The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems.