Comparison of survey methods for fungi using metabarcoding and fruit body inventories in an altitudinal gradient.

Metabarcoding of environmental samples is nowadays an established method in biodiversity research. When it comes to studying fungal populations in various ecotypes, fruit body inventories are the traditional method to assess the diversity of fungal communities. In this study, both methods-metabarcoding of soil samples and a traditional fruit body inventory-were conducted on 144 sample plots in an altitudinal gradient in the Bavarian Forest (Germany) and the results were compared. Metabarcoding detected significantly more species than the traditional fruit body inventory. The majority of taxa recorded in the fruit body inventory belonged to the Basidiomycota, whereas in the metabarcoding data, the distribution of species between Basidiomycota and Ascomycota was approximately balanced. Species of several orders forming inconspicuous or hypogeous fruit bodies were detected only by metabarcoding, while several wood decomposers were recorded only in the fruit body inventory. The proportion of detected wood-colonising species with melanized spores was considerably higher with metabarcoding than with the fruit body inventory, where more than 70% of recorded wood-colonisers had hyaline spores. Based on the metabarcoding data, a decline of species richness with increasing altitude was evident, but this was not visible in the fruit body inventory data. Detrended correspondence analyses yielded similar results for relative species community similarities with both survey methods.

Microplastics accumulate fungal pathogens in terrestrial ecosystems.

Microplastic (MP) is a pervasive pollutant in nature that is colonised by diverse groups of microbes, including potentially pathogenic species. Fungi have been largely neglected in this context, despite their affinity for plastics and their impact as pathogens. To unravel the role of MP as a carrier of fungal pathogens in terrestrial ecosystems and the immediate human environment, epiplastic mycobiomes from municipal plastic waste from Kenya were deciphered using ITS metabarcoding as well as a comprehensive meta-analysis, and visualised via scanning electron as well as confocal laser scanning microscopy. Metagenomic and microscopic findings provided complementary evidence that the terrestrial plastisphere is a suitable ecological niche for a variety of fungal organisms, including important animal and plant pathogens, which formed the plastisphere core mycobiome. We show that MPs serve as selective artificial microhabitats that not only attract distinct fungal communities, but also accumulate certain opportunistic human pathogens, such as cryptococcal and Phoma-like species. Therefore, MP must be regarded a persistent reservoir and potential vector for fungal pathogens in soil environments. Given the increasing amount of plastic waste in terrestrial ecosystems worldwide, this interrelation may have severe consequences for the trans-kingdom and multi-organismal epidemiology of fungal infections on a global scale.

FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results.

Repeatability of study setups and reproducibility of research results by underlying data are major requirements in science. Until now, abstract models for describing the structural logic of studies in environmental sciences are lacking and tools for data management are insufficient. Mandatory for repeatability and reproducibility is the use of sophisticated data management solutions going beyond data file sharing. Particularly, it implies maintenance of coherent data along workflows. Design data concern elements from elementary domains of operations being transformation, measurement and transaction. Operation design elements and method information are specified for each consecutive workflow segment from field to laboratory campaigns. The strict linkage of operation design element values, operation values and objects is essential. For enabling coherence of corresponding objects along consecutive workflow segments, the assignment of unique identifiers and the specification of their relations are mandatory. The abstract model presented here addresses these aspects, and the software DiversityDescriptions (DWB-DD) facilitates the management of thusly connected digital data objects and structures. DWB-DD allows for an individual specification of operation design elements and their linking to objects. Two workflow design use cases, one for DNA barcoding and another for cultivation of fungal isolates, are given. To publish those structured data, standard schema mapping and XML-provision of digital objects are essential. Schemas useful for this mapping include the Ecological Markup Language, the Schema for Meta-omics Data of Collection Objects and the Standard for Structured Descriptive Data. Data pipelines with DWB-DD include the mapping and conversion between schemas and functions for data publishing and archiving according to the Open Archival Information System standard. The setting allows for repeatability of study setups, reproducibility of study results and for supporting work groups to structure and maintain their data from the beginning of a study. The theory of 'FAIR++' digital objects is introduced.

Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research.

With the advent of advanced molecular meta-omics techniques and methods, a new era commenced for analysing and characterizing historic collection specimens, as well as recently collected environmental samples. Nucleic acid and protein sequencing-based analyses are increasingly applied to determine the origin, identity and traits of environmental (biological) objects and organisms. In this context, the need for new data structures is evident and former approaches for data processing need to be expanded according to the new meta-omics techniques and operational standards. Existing schemas and community standards in the biodiversity and molecular domain concentrate on terms important for data exchange and publication. Detailed operational aspects of origin and laboratory as well as object and data management issues are frequently neglected. Meta-omics Data and Collection Objects (MOD-CO) has therefore been set up as a new schema for meta-omics research, with a hierarchical organization of the concepts describing collection samples, as well as products and data objects being generated during operational workflows. It is focussed on object trait descriptions as well as on operational aspects and thereby may serve as a backbone for R&D laboratory information management systems with functions of an electronic laboratory notebook. The schema in its current version 1.0 includes 653 concepts and 1810 predefined concept values, being equivalent to descriptors and descriptor states, respectively. It is published in several representations, like a Semantic Media Wiki publication with 2463 interlinked Wiki pages for concepts and concept values, being grouped in 37 concept collections and subcollections. The SQL database application DiversityDescriptions, a generic tool for maintaining descriptive data and schemas, has been applied for setting up and testing MOD-CO and for concept mapping on elements of corresponding schemas.

Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49.

The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.