Lower functional redundancy in “narrow” than “broad” functions in global soil metagenomics

Understanding the relationship between soil microbial taxonomic compositions and functional profiles is essential for predicting ecosystem functions under various environmental disturbances. However, even though microbial communities are sensitive to disturbance, ecosystem functions remain relatively stable, as soil microbes are likely to be functionally redundant. Microbial functional redundancy may be more associated with “broad” functions carried out by a wide range of microbes, than with “narrow” functions specialized by specific microorganisms. Thus, a comprehensive study to evaluate how microbial taxonomic compositions correlate with “broad” and “narrow” functional profiles is necessary. Here, we evaluated soil metagenomes worldwide to assess whether functional and taxonomic diversities differ significantly between the five “broad” and the five “narrow” functions that we chose. Our results revealed that compared with the five “broad” functions, soil microbes capable of performing the five “narrow” functions were more taxonomically diverse, and thus their functional diversity was more dependent on taxonomic diversity, implying lower levels of functional redundancy in “narrow” functions. Co-occurrence networks indicated that microorganisms conducting “broad” functions were positively related, but microbes specializing “narrow” functions were interacting mostly negatively. Our study provides strong evidence to support our hypothesis that functional redundancy is significantly different between “broad” and “narrow” functions in soil microbes, as the association of functional diversity with taxonomy were greater in the five “narrow” rather than the five “broad” functions.

Plant occurrences on the Rybachy and the Sredny Peninsulas, Murmansk Region, Russia: a dataset

The Rybachy and the Sredny Peninsulas are the northernmost part of Murmansk Region in the European part of Russia. While the most part of the Region is covered by boreal forest, the Peninsulas are covered by tundra. The vegetation and flora of Murmansk Region are well studied at present. The Peninsulas were first studied in 1829 by a Finnish botanist Jacob Fellman. The most comprehensive research was conducted in the late 19th - early 20th century. Nevertheless, the species composition of the Peninsulas' flora has changed significantly over the past 100 years due to land use and climate change. The aim of this dataset is to make the data on species occurrences for this territory digitally available via GBIF. To date, more or less complete digital floristic data were provided only by the project for digitising the book "Flora of Murmansk Region" (1953–1966). The present dataset is a part of the project studying the vegetation of the territory. We recorded the information about species frequency and distribution using the relevé method. We present a dataset based on 991 relevés from all vegetation types, which includes 16,289 records of georeferenced plant occurrences that belong to 568 species. There are 23 species of lichens (Ascomycota), 142 species of mosses (Bryophyta), three species of liverworts (Marchantiophyta) and 400 species of vascular plants (Tracheophyta) in the present dataset. The taxonomic diversity and unevenness result from the vegetation sampling. The data were collected in 2008, 2009, 2011, 2014 and 2015. The dataset cannot be considered as a complete vegetation database or a flora checklist, but it contains the occurrences and frequencies of the species from all the vegetation types.

Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome

Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.

Systematic whole-genome sequencing reveals an unexpected diversity among actinomycetoma pathogens and provides insights into their antibacterial susceptibilities

Mycetoma is a neglected tropical chronic granulomatous inflammatory disease of the skin and subcutaneous tissues. More than 70 species with a broad taxonomic diversity have been implicated as agents of mycetoma. Understanding the full range of causative organisms and their antibiotic sensitivity profiles are essential for the appropriate treatment of infections. The present study focuses on the analysis of full genome sequences and antibiotic resistance profiles of actinomycetoma strains from patients seen at the Mycetoma Research Centre in Sudan with a view to developing rapid diagnostic tests. Seventeen pathogenic isolates obtained by surgical biopsies were sequenced using MinION and Illumina methods, and their antibiotic resistance profiles determined. The results highlight an unexpected diversity of actinomycetoma causing pathogens, including three Streptomyces isolates assigned to species not previously associated with human actinomycetoma and one new Streptomyces species. Thus, current approaches for clinical and histopathological classification of mycetoma may need to be updated. The standard treatment for actinomycetoma is a combination of sulfamethoxazole/trimethoprim and amoxicillin/clavulanic acid. Most tested isolates were not susceptible to sulfamethoxazole/trimethoprim or to amoxicillin alone. However, the addition of the β-lactamase inhibitor clavulanic acid to amoxicillin increased susceptibility, particularly for Streptomyces somaliensis and Streptomyces sudanensis . Actinomadura madurae isolates appear to be particularly resistant under laboratory conditions, suggesting that alternative agents, such as amikacin, should be considered for more effective treatment. The results obtained will inform future diagnostic methods for the identification of actinomycetoma and treatment.

CATALOGUE OF AQUATIC MITES FROM THE MINHO RIVER (NW IBERIAN PENINSULA)

Acari are a subclass of chelicerate arthropods that includes mites and ticks. The present study focuses on the taxonomic diversity of aquatic mites in the Portuguese territory of the Minho Region. Our aim was to compile all available information and thus generate a list of species linking them to the site where they were recorded. Aquatic species were all those that live exclusively in the marine environment, deep sea, intertidal, freshwater, brackish water or in transitional environments with the terrestrial environment if their lifestyle is associated with the aquatic environment. Since the first records of Portuguese endemic mites by Lunblad in the 1950s several authors have contributed to accurately catalogue, record, and redescribe this vast group in Portugal and Minho consecutively. In our review in this work, we used the Global Biodiversity Information Facility (GBIF) to obtain previous occurrences supplemented by an extensive literature review and the book collection Süßwasserfauna von Mitteleuropa, among others. Additionally, we resorted to active sampling and by-catch sampling in the Portuguese section of the Rio Minho catchment area. The collected organisms represent 12 new records for the Minho River and among them 10 are new records for Portugal, which were deposited in the Natural History Museum of the Iberian Peninsula - NatMIP (“Museu de História Natural da Península Ibérica”), Vila Nova de Cerveira, Portugal.

Optimizing mangrove conservation efforts with improved understanding of phytosociology-ecology synergy in Sri Lanka

The study aimed to understand the forest structure and ecological factors influencing mangrove distribution in eight mangrove forests across three climatic zones in Sri Lanka. We studied mangrove diversity and vegetation structure with 10m wide belt transects laid of different lengths (n=96) across the land-water gradient. Mangroves along the transect were identified, enumerated, and measured diameter at breast height (DBH). Subsurface water samples were taken in the adjoining lagoon/estuary to assess the environmental parameters (n=144), and water quality parameters were measured. Site-dependent spatial changes in the community structure were depicted through cluster analysis (CA). The forest survey revealed a heterogeneous mixture of 20 true mangrove species across the sites dominated by Avicennia, Rhizophora, and Sonneratia spp. Among the several environmental parameters analyzed by the distance-based redundancy ordination analysis (dbRDA), salinity, dissolved oxygen, and precipitation were found to be controlling factors in mangrove community structure. In addition, discriminant analysis confirmed the presence of ecological-phytosociological influence on mangrove assemblages identified through CA. The significant structural parameters tree density, and taxonomic diversity when tested using the canonical analysis of principal coordinates (CAP), altered the species abundance across the sites surveyed. The results suggest that there is a strong linkage between phytosociology and ecology with the mangrove forest distribution and this relationship needs to be considered wisely to fortify successful restoration practices.