Chemical properties of key metabolites determine the global distribution of lichens.

In lichen symbioses, fungal secondary metabolites provide UV protection on which lichen algae such as trebouxiophycean green algae-the most prominent group of photobionts in lichen symbioses-sensitively depend. These metabolites differ in their UV absorbance capability and solvability, and thus vary in their propensity of being leached from the lichen body in humid and warm environments, with still unknown implications for the global distribution of lichens. In this study covering more than 10,000 lichenised fungal species, we show that the occurrence of fungal-derived metabolites in combination with their UV absorbance capability and their probability of being leached in warm and humid environments are important eco-evolutionary drivers of global lichen distribution. Fungal-derived UV protection seems to represent an indirect environmental adaptation in which the lichen fungus invests to protect the trebouxiophycean photobiont from high UV radiation in warm and humid climates and, by doing this, secures its carbon source.

Software infrastructure and data pipelines established for technical interoperability within a cross-border cooperation for the flora of the Bohemian Forest.

Background: The timely and geographical resolutions, as well as the quantity and taxon concepts of records on the occurrence of plants near national borders is often ambiguous. This is due to the regional focus and different approaches of the contributing national and regional databases and networks of the neighbouring countries. Careful data transformation between national data providers is essential for understanding distribution patterns and its dynamics for organisms in areas along the national borders. Sharing occurrence data through the international data aggregator Global Biodiversity Information Facility (GBIF) is also complicated and has to consider that the underlying taxonomic concept and geographic information system of each single GBIF dataset might be different. In addition, some regional data providers have a restrictive (non-cc) licensing policy which does not allow data publication via the GBIF network. Therefore, it is necessary to investigate new ways to make data fit for use for a better and comprehensive understanding of the Flora of the Bohemian Forest. New information: In this paper, we present a bilateral technical interoperability solution for vascular plant occurrence data for the area between the Czech Republic and Bavaria. We describe the initial state of data providers in both countries and the factual and technical challenges in finding a sustainable concept to establish mutual data sharing. The resulting solution for a functional infrastructure and an agreed data pipeline is described in a step-by-step approach. The new distributed infrastructure allows botanists and other stakeholders from both countries to work within the cross-border context of historical and current plants' distribution.

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.

A Rare Glimpse into the Past of the Anthrax Pathogen Bacillus anthracis.

The bacterium Bacillus anthracis is the causative agent of the zoonotic disease anthrax. While genomics of extant B. anthracis isolates established in-depth phylogenomic relationships, there is scarce information on the historic genomics of the pathogen. Here, we characterized the oldest documented B. anthracis specimen. The inactive 142-year-old material originated from a bovine diseased in Chemnitz (Germany) in 1878 and is contemporary with the seminal studies of Robert Koch on B. anthracis. A specifically developed isolation method yielded high-quality DNA from this specimen for genomic sequencing. The bacterial chromosome featuring 242 unique base-characters placed it into a major phylogenetic clade of B. anthracis (B.Branch CNEVA), which is typical for central Europe today. Our results support the notion that the CNEVA-clade represents part of the indigenous genetic lineage of B. anthracis in this part of Europe. This work emphasizes the value of historic specimens as precious resources for reconstructing the past phylogeny of the anthrax pathogen.

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.

A generic workflow for effective sampling of environmental vouchers with UUID assignment and image processing.

Database URL: http://diversityworkbench.net/Portal/DiversityImageInspector.

Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects.

With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals. Database URL: : http://cetaf.org/cetaf-stable-identifiers.

A new species of Stigmatomyces from Baltic amber, the first fossil record of Laboulbeniomycetes.

A fossil ascomycete was found attached to the thorax of a stalk eyed fly (Diopsidae: Prosphyracephala succini) in a fragment of Baltic amber. The fungus is assigned to the extant genus Stigmatomyces and described as S. succini sp. nov. This find is the first fossil record of the order Laboulbeniales. At the same time it constitutes the oldest record of a parasitic fungus on an insect. The palaeohabitat is discussed with regard to the find.

Tuberculina: rust relatives attack rusts.

Molecular sequence data together with ultrastructural features were used to infer the phylogenetic position of Tuberculina species. Additional ultrastructural characteristics were used to determine their mode of nutrition. We investigated ultrastructural morphology of the type species Tuberculina persicina and determined base sequences from the D1/ D2 region of the nuclear large-subunit ribosomal DNA of the three commonly distinguished Tuberculina species, T. maxima, T. persicina and T. sbrozzii. Analyses of sequence data by means of a Bayesian method of phylogenetic inference using a Markov Chain Monte Carlo technique reveal the basidiomycetous nature of Tuberculina. Within the Urediniomycetes, Tuberculina clusters as a sister group of Helicobasidium, closely related to the rusts (Uredinales). This phylogenetic position is supported by the uredinalean architecture of septal pores in Tuberculina. In addition, we present aspects of the ultrastructural morphology of the cellular interaction of Tuberculina and rusts showing a unique interaction with large fusion pores, revealing the mycoparasitic nature of Tuberculina on its close relatives, the rusts.