Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data

An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes), a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficiently identified ITS sequences from the public sequence databases were assigned to the Geoglossomycetes. The association between earth tongues and plants has been hypothesized for a long time, but hard evidence is yet to be collected. The ITS phylogeny showed that four ectomycorrhizal isolates shared a clade with Geoglossum but not with Trichoglossum earth tongues, pointing to the significant potential inherent to ecological data mining of environmental samples. Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se

Using Best–Worst Scaling to Investigate Preferences in Health Care

Introduction Best–worst scaling (BWS) is becoming increasingly popular to elicit preferences in health care. However, little is known about current practice and trends in the use of BWS in health care. This study aimed to identify, review and critically appraise BWS in health care, and to identify trends over time in key aspects of BWS. Methods A systematic review was conducted, using Medline (via Pubmed) and EMBASE to identify all English-language BWS studies published up until April 2016. Using a predefined extraction form, two reviewers independently selected articles and critically appraised the study quality, using the Purpose, Respondents, Explanation, Findings, Significance (PREFS) checklist. Trends over time periods (≤2010, 2011, 2012, 2013, 2014 and 2015) were assessed further. Results A total of 62 BWS studies were identified, of which 26 were BWS object case studies, 29 were BWS profile case studies and seven were BWS multi-profile case studies. About two thirds of the studies were performed in the last 2 years. Decreasing sample sizes and decreasing numbers of factors in BWS object case studies, as well as use of less complicated analytical methods, were observed in recent studies. The quality of the BWS studies was generally acceptable according to the PREFS checklist, except that most studies did not indicate whether the responders were similar to the non-responders. Conclusion Use of BWS object case and BWS profile case has drastically increased in health care, especially in the last 2 years. In contrast with previous discrete-choice experiment reviews, there is increasing use of less sophisticated analytical methods