An open-source GIS-enabled lookup service for Nagoya Protocol party information

Abstract The Nagoya Protocol on Access and Benefit Sharing is a transparent legal framework, which governs the access to genetic resources and the fair and equitable sharing of benefits arising from their utilization. Complying with the Nagoya regulations ensures legal use and re-use of data from genetic resources. Providing detailed provenance information and clear re-usage conditions plays a key role in ensuring the re-usability of research data according to the FAIR (findable, accessible, interoperable and re-usable) Guiding Principles for scientific data management and stewardship. Even with the framework provided by the ABS (access and benefit sharing) Clearing House and the support of the National Focal Points, establishing a direct link between the research data from genetic resources and the relevant Nagoya information remains a challenge. This is particularly true for re-using publicly available data. The Nagoya Lookup Service was developed for stakeholders in biological sciences with the aim at facilitating the legal and FAIR data management, specifically for data publication and re-use. The service provides up-to-date information on the Nagoya party status for a geolocation provided by GPS coordinates, directing the user to the relevant local authorities for further information. It integrates open data from the ABS Clearing House, Marine Regions, GeoNames and Wikidata. The service is accessible through a REST API and a user-friendly web form. Stakeholders include data librarians, data brokers, scientists and data archivists who may use this service before, during and after data acquisition or publication to check whether legal documents need to be prepared, considered or verified. The service allows researchers to estimate whether genetic data they plan to produce or re-use might fall under Nagoya regulations or not, within the limits of the technology and without constituting legal advice. It is implemented using portable Docker containers and can easily be deployed locally or on a cloud infrastructure. The source code for building the service is available under an open-source license on GitHub, with a functional image on Docker Hub and can be used by anyone free of charge.</jats:p

Marine Microbial Diversity and its role in Ecosystem Functioning and Environmental Change

Seas and oceans cover more than 70% of the Earth’s surface, host the majority of its biomass, and contribute significantly to all global cycles of matter and energy. All life on Earth most likely originated from microbes in the sea. In today’s marine ecosystems, following billions of years of evolution, microbes such as Bacteria, Archaea, viruses, fungi and protists (including microalgae), dominate the living biomass. Recent rapid developments in molecular ecology, metagenomics and ecological modelling illustrate that microbes represent the most important biological group on Earth in terms of phylogenetic and functional diversity. In addition, interdisciplinary research has uncovered new and unexpected roles of microbes in the biogeochemical cycling of carbon, nitrogen, silica and iron and many other (trace) elements in our seas and oceans. Marine microorganisms produce the organic matter and oxygen required to sustain life and facilitate the storage, transport, and turnover of key biological elements. Thus, microorganisms are the foundation of life and are of critical importance to the habitability and sustainability of our planet. (...)Peer reviewe

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

BACKGROUND: In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge of basic biological processes. The central problem of this so called metagenome-approach is that the cloned fragments often lack suitable phylogenetic marker genes, rendering the identification of clones that are likely to originate from the same genome difficult or impossible. In such cases, the analysis of intrinsic DNA-signatures like tetranucleotide frequencies can provide valuable hints on fragment affiliation. With this application in mind, the TETRA web-service and the TETRA stand-alone program have been developed, both of which automate the task of comparative tetranucleotide frequency analysis. Availability: RESULTS: TETRA provides a statistical analysis of tetranucleotide usage patterns in genomic fragments, either via a web-service or a stand-alone program. With respect to discriminatory power, such an analysis outperforms the assignment of genomic fragments based on the (G+C)-content, which is a widely-used sequence-based measure for assessing fragment relatedness. While the web-service is restricted to the calculation of correlation coefficients between tetranucleotide usage patterns of submitted DNA sequences, the stand-alone program generates a much more detailed output, comprising all raw data and graphical plots. The stand-alone program is controlled via a graphical user interface and can batch-process a multitude of sequences. Furthermore, it comes with pre-computed tetranucleotide usage patterns for 166 prokaryote chromosomes, providing a useful reference dataset and source for data-mining. CONCLUSIONS: Up to now, the analysis of skewed oligonucleotide distributions within DNA sequences is not a commonly used tool within metagenomics. With the TETRA web-service and stand-alone program, the method is now accessible in an easy to use manner for a broad audience. This will hopefully facilitate the interrelation of genomic fragments from metagenome libraries, ultimately leading to new insights into the genetic potentials of yet uncultured microorganisms

Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes

Background: DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content of microbial communities. Recently a study on marine Synechococcus strains detected differences in their genomic TF content related to environmental adaptation, but so far the effect of environmental parameters on the content of TFs in bacterial communities has not been systematically investigated. Results: We quantified the effect of environment stability on the transcription factor repertoire of marine pelagic microbes from the Global Ocean Sampling (GOS) metagenome using interpolated physico-chemical parameters and multivariate statistics. Thirty-five percent of the difference in relative TF abundances between samples could be explained by environment stability. Six percent was attributable to spatial distance but none to a combination of both spatial distance and stability. Some individual TFs showed a stronger relationship to environment stability and space than the total TF pool. Conclusions: Environmental stability appears to have a clearly detectable effect on TF gene content in bacterioplanktonic communities described by the GOS metagenome. Interpolated environmental parameters were shown to compare well to in situ measurements and were essential for quantifying the effect of the environment on the TF content. It is demonstrated that comprehensive and well-structured contextual data will strongly enhance our ability to interpret the functional potential of microbes from metagenomic data

Transcriptional response of the model planctomycete Rhodopirellula baltica SH1T to changing environmental conditions

<p>Abstract</p> <p>Background</p> <p>The marine model organism <it>Rhodopirellula baltica </it>SH1^Twas the first <it>Planctomycete </it>to have its genome completely sequenced. The genome analysis predicted a complex lifestyle and a variety of genetic opportunities to adapt to the marine environment. Its adaptation to environmental stressors was studied by transcriptional profiling using a whole genome microarray.</p> <p>Results</p> <p>Stress responses to salinity and temperature shifts were monitored in time series experiments. Chemostat cultures grown in mineral medium at 28°C were compared to cultures that were shifted to either elevated (37°C) or reduced (6°C) temperatures as well as high salinity (59.5‰) and observed over 300 min. Heat shock showed the induction of several known chaperone genes. Cold shock altered the expression of genes in lipid metabolism and stress proteins. High salinity resulted in the modulation of genes coding for compatible solutes, ion transporters and morphology. In summary, over 3000 of the 7325 genes were affected by temperature and/or salinity changes.</p> <p>Conclusion</p> <p>Transcriptional profiling confirmed that <it>R. baltica </it>is highly responsive to its environment. The distinct responses identified here have provided new insights into the complex adaptation machinery of this environmentally relevant marine bacterium. Our transcriptome study and previous proteome data suggest a set of genes of unknown functions that are most probably involved in the global stress response. This work lays the foundation for further bioinformatic and genetic studies which will lead to a comprehensive understanding of the biology of a marine <it>Planctomycete</it>.</p

Megx.net—database resources for marine ecological genomics

Marine microbial genomics and metagenomics is an emerging field in environmental research. Since the completion of the first marine bacterial genome in 2003, the number of fully sequenced marine bacteria has grown rapidly. Concurrently, marine metagenomics studies are performed on a regular basis, and the resulting number of sequences is growing exponentially. To address environmentally relevant questions like organismal adaptations to oceanic provinces and regional differences in the microbial cycling of nutrients, it is necessary to couple sequence data with geographical information and supplement them with contextual information like physical, chemical and biological data. Therefore, new specialized databases are needed to organize and standardize data storage as well as centralize data access and interpretation. We introduce Megx.net, a set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts. Megx.net includes (i) a geographic information system to systematically store and analyse marine genomic and metagenomic data in conjunction with contextual information; (ii) an environmental genome browser with fast search functionalities; (iii) a database with precomputed analyses for selected complete genomes; and (iv) a database and tool to classify metagenomic fragments based on oligonucleotide signatures. These integrative databases and webserver will help researchers to generate a better understanding of the functioning of marine ecosystems. All resources are freely accessible at

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs

Graphical representation of ribosomal RNA probe accessibility data using ARB software package

BACKGROUND: Taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. A frequently applied technology, fluorescence in situ hybridization (FISH), besides single cell identification, allows the localization and functional studies of the microbial community composition. Careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridization experiments. RESULTS: The PROBE Design tools of the ARB software package take into consideration several criteria such as number, position and quality of diagnostic sequence differences while designing oligonucleotide probes. Additionally, new visualization tools were developed to enable the user to easily examine further sequence associated criteria such as higher order structure, conservation, G+C content, transition-transversion profiles and in situ target accessibility patterns. The different types of sequence associated information (SAI) can be visualized by user defined background colors within the ARB primary and secondary structure editors as well as in the PROBE Match tool. CONCLUSION: Using this tool, in silico probe design and evaluation can be performed with respect to in situ probe accessibility data. The evaluation of proposed probe targets with respect to higher-order rRNA structure is of importance for successful design and performance of in situ hybridization experiments. The entire ARB software package along with the probe accessibility data is available from the ARB home page

NFDI4BioDiversity - NFDI-Konsortium für Biodiversitäts-, Ökologische und Umweltdaten

NFDI4BioDiversity ist ein Konsortium innerhalb der Nationalen Forschungsdateninfrastruktur (NFDI) mit einem Schwerpunkt auf Services für die Biodiversitätsforschung und Ökologie. Unzählige Studien belegen den Rückgang der Biodiversität auf unserem Planeten. Drängende Fragen in diesem Zusammenhang sind unter anderem welche Auswirkungen der Rückgang der Biodiversität auf die betroffenen Ökosysteme hat und welche (anthropogenen) Einflüsse die Biodiversität reduzieren oder fördern. Um die komplexen Zusammenhänge zu verstehen und daraus Handlungsempfehlungen abzuleiten, werden vielfältige, qualitätsgesicherte und FAIRe[1] Daten benötigt. Diese umfassen das Vorkommen von Pflanzen, Tieren und Mikroorganismen, einschließlich ihrer genotypischen, phänotypischen und funktionalen Vielfalt, sowie deren Zusammenspiel in Populationen und Ökosystemen. In NFDI4BioDiversity haben sich 49 Partner aus Wissenschaft, Behörden und Bürgerwissenschaften zusammengeschlossen, um die Mobilisierung und Publikation vorhandener Daten voranzutreiben, effiziente Workflows zu entwickeln und Tools und Services zur Unterstützung von Analysen bereitzustellen. [1] FAIR: Findable, Accessible, Interoperable, Reusable, aus: Wilkinson, Mark D., et al. „The FAIR Guiding Principles for scientific data management and stewardship”, Scientific Data 3:160018 (March 2016), doi: 10.1038/sdata.2016.1

Potential für ein starkes Netzwerk zwischen GFBio und FDM-Beratenden an Universitäten und Forschungsinstituten

GFBio (German Federation for Biological Data) hat sich in den letzten sechs Jahren als die zentrale Anlaufstelle für WissenschaftlerInnen und Datenverantwortliche rund um alle Fragen des Forschungsdatenmanagements in der Biodiversitätsforschung etabliert. Zentrales Ziel von GFBio ist die Sensibilisierung der Fachcommunity für die Themen Forschungsdatenmanagement, Langzeitarchivierung und Publikation von Forschungsdaten. Eine bisher nur unzureichend gelöste Herausforderung ist jedoch die Adressierung der Forschenden vor Ort. Die direkte Interaktion mit den Forschenden am jeweiligen Campus wird dabei durch die FDM-Beratenden geleistet. Die Erfahrung hat gezeigt, dass hier bereits hervorragende Arbeit geleistet wird, jedoch für eine in die Tiefe gehende fachspezifische Beratung oft die Ressourcen fehlen. Das von GFBio propagierte “front-office/back-office” Modell mit einer engen Verknüpfung der Aktivitäten von GFBio und der lokalen FDM-Beratenden ist durch seine Arbeitsteiligkeit zu beiderseitigem Vorteil. Im Folgenden wird GFBio mit seinen Kernservices vorgestellt sowie Anknüpfungspunkte für die Zusammenarbeit mit lokalen FDM-Beratenden aufgezeigt