Lichens and their importance for the monitoring of environmental changes in Southern Africa : with special reference to soil-inhabiting lichens.

Lichens are the object of investigation within the framework of the BIOTA Southern Africa project, subproject S04 (http://www.biota-africa.org). This interdisciplinary research project, installed in 2000, focuses on the analysis of biodiversity and its changes along climatic and vegetation gradients (transects) in Namibia and in the Republic of South Africa. In the context of this project, studies on the diversity of lichens are carriedout. Special reference is given to the monitoring of lichens growing on soil, which form the so called biological soil crusts.Lichen diversity is assessed and analysed with respect to its spatial and temporal changes. These are related to various abioticand biotic factors such as climate, soil features and land use. The indicator value of certain terricolouslichen taxaand/or lichen groups (communities) is investigated for the study area, and it is intended to use itin a future long-term monitoring programme in the region. In this brochure, we whish to explain what lichens are, how do they live and where do they grow, and why they are so important as bioindicatorsin arid and semi-arid areas of the world. The activities of the S04 subproject along the BIOTA transect are described, as well as the methods used for monitoring environmental changes in Southern Africa using soil-inhabiting lichens

Types of identification keys

A number of terms related to identification tools are introduced and the advantages of selected types of identification keys are compared

Plastiphily is linked to generic virulence traits of important human pathogenic fungi

Fungi comprise relevant human pathogens, causing over a billion infections each year. Plastic pollution alters niches of fungi by providing trillions of artificial microhabitats, mostly in the form of microplastics, where pathogens might accumulate, thrive, and evolve. However, interactions between fungi and microplastics in nature are largely unexplored. To address this knowledge gap, we investigated the assembly, architecture, and ecology of mycobiomes in soil (micro)plastispheres near human dwellings in a model- and network-based metagenome study combined with a global-scale trait data annotation. Our results reveal a strong selection of important human pathogens, in an idiosyncratic, otherwise predominantly neutrally assembled plastisphere, which is strongly linked to generic fungal virulence traits. These findings substantiate our niche expansion postulate, demonstrate the emergence of plastiphily among fungal pathogens and imply the existence of a plastisphere virulence school, underpinning the need to declare microplastics as a factor of global health

Fungal plastiphily and its link to generic virulence traits makes environmental microplastics a global health factor

Fungi comprise significant human pathogens, causing over a billion infections each year. Plastic pollution alters niches of fungi by providing trillions of artificial microhabitats, mostly in the form of microplastics, where pathogens might accumulate, thrive, and evolve. However, interactions between fungi and microplastics in nature are largely unexplored. To address this knowledge gap, we investigated the assembly, architecture, and ecology of mycobiomes in soil (micro)plastispheres near human dwellings in a model- and network-based metagenome study combined with a global-scale meta-analysis. Our results reveal a strong selection of important human pathogens, in an idiosyncratic, otherwise predominantly neutrally assembled plastisphere, which is strongly linked to generic fungal virulence traits. These findings substantiate our niche expansion postulate, demonstrate the emergence of plastiphily among fungal pathogens and imply the existence of a ‘plastisphere virulence school’, underpinning the need to declare microplastics as a factor of global health

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

Managing and publishing fungal community barcoding data by use of the process-oriented schema MOD-CO and a GFBio data publication pipeline

The need to fulfil FAIR guiding principles for data management and publication [1] directly affects researchers, i.e., data producers as well as data managers. Data management has to be set up well already at an early stage of the data life cycle. This is demonstrated by a best practice work- and dataflow 'Fungal community barcoding data', which has been established as side product in the context of the project 'GBOL 2 Mycology‘, German Barcode of Life initiative (https://www.bolgermany.de/). The work- and dataflow was set up by applying the newly published MOD-CO schema, Version 1.0 which has been implemented as an instance of the database application DiversityDescriptions for data management, and for making data compliant to GFBio infrastructure for data archiving and publication. The comprehensive conceptual schema MOD-CO for 'Meta-Omics Data of Collection Objects' Version 1.0 was published as Linked Open Data representation in spring 2018 [2]. The process-oriented schema describes operations and object properties along the work- and dataflow from gathering environmental samples, to the various transformation, transaction, and measurement steps in the laboratory up to sample and data publication and archiving. By supporting various kinds of relationships, the MOD-CO schema allows for the concatenation of individual records of the operational steps along a workflow. The MOD-CO descriptor structure in version 1.0 comprises 653 descriptors (concepts) and 1,810 predefined descriptor states, organised in 37 concept collections. The published version 1.0 is available as various schema representations of identical content (https://www.mod-co.net/wiki/Schema_Representations). This schema has been implemented as data structure in the relational database DiversityDescriptions (DWB-DD) (https://diversityworkbench.net/Portal/DiversityDescriptions), a generic component of the Diversity Workbench environment (https://diversityworkbench.net). DWB-DD is considered being appropriate to be applied as a LIMS (Laboratory Information Management System) and ELN (Electronic Laboratory Notebook) for organising Fungal community barcoding data' and similar data collections in molecular laboratories. Its data export interface provides guidance to generate data and metadata in the formats CSV and XML, the latter following the SDD metadata schema with involvement of extensions by metadata elements from EML and ABCD standards; for community standards see: https://gfbio.biowikifarm.net/wiki/Data_exchange_standards,_protocols_and_formats_relevant_for_the_collection_data_domain_within_the_GFBio_network. The research data themselves are organised according to the MOD-CO data schema. The data package of the work- and dataflow 'Fungal community barcoding data' is going to be submitted to GFBio after having been checked for GFBio compliance and to be published under a creative common license. Suggestions for standardized citation will be provided, a DOI assigned, and long-term data archiving ensured. KEYWORDS: DiversityDescriptions, German Barcode of Life (GBOL), German Federation for Biological Data (GFBio), MOD-CO conceptual schema, use case for community barcoding data REFERENCES: 1. Wilkinson, M.D. et al. 2016. The FAIR Guiding Principles for scientific data management and stewardship. – Sci. Data 3: 160018. DOI: 10.1038/sdata.2016.18. 2. Rambold, G., Yilmaz, P., Harjes, J., Link, A., Glöckner, F.O., Triebel, D. 2018. MOD-CO schema – a conceptual schema for processing sample data in meta’omics research (version 1.0). http://mod-co.net/wiki/MOD-CO_Schema_Reference

Microplastic polymer properties as deterministic factors driving terrestrial plastisphere microbiome assembly and succession in the field

Environmental microplastic (MP) is ubiquitous in aquatic and terrestrial ecosystems providing artificial habitats for microbes. Mechanisms of MP colonization, MP polymer impacts, and effects on soil microbiomes are largely unknown in terrestrial systems. Therefore, we experimentally tested the hypothesis that MP polymer type is an important deterministic factor affecting MP community assembly by incubating common MP polymer types in situ in landfill soil for 14 months. 16S rRNA gene amplicon sequencing indicated that MP polymers have specific impacts on plastisphere microbiomes, which are subsets of the soil microbiome. Chloroflexota, Gammaproteobacteria, certain Nitrososphaerota, and Nanoarchaeota explained differences among MP polymers and time points. Plastisphere microbial community composition derived from different MP diverged over time and was enriched in potential pathogens. PICRUSt predictions of pathway abundances and quantitative PCR of functional marker genes indicated that MP polymers exerted an ambivalent effect on genetic potentials of biogeochemical cycles. Overall, the data indicate that (i) polymer type as deterministic factor rather than stochastic factors drives plastisphere community assembly, (ii) MP impacts greenhouse gas metabolism, xenobiotic degradation and pathogen distribution, and (iii) MP serves as an ideal model system for studying fundamental questions in microbial ecology such as community assembly mechanisms in terrestrial environments