Search

Biodiversity is more than just the diversity of living species. It includes genetic and phenotypic diversity of organisms, functional diversity, interactions and the diversity of populations and whole ecosystems. The recent Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) report confirmed that our planet experiences a rapid loss of biodiversity with dramatic consequences for mankind. Answers to scientifically and societal relevant questions can only be found based on the availability of data integrated from multiple sources and building on different knowledge domains in science and society. The FAIR data principles provide a framework towards such integration. To foster access to interoperable data, NFDI4BioDiversity focuses on the following six objectives: 1) Promoting research data management as an integral part of biodiversity research, 2) Enabling FAIRness of data, 3) Consolidating FAIRness with quality, 4) Embedding NFDI4BioDiversity into the (inter-)national landscape, 5) Addressing NFDI-wide cross-cutting topics and 6) Promoting collaborative governance, viability and sustainability of data infrastructure services and science. These objectives are implemented by the NFDI4BioDiversity work programme and its five task areas: Task Area 1 - Community engagement (2involve): This task area will integrate across different knowledge holders and take care of research data management requests related to biodiversity data. A large part of all species data is collected by volunteers in natural history societies, NGOs, museums and citizen science projects as well as collected by different authorities This task area includes 23 use cases with community-driven topics and cross-domain user groups. Task Area 2 - National and international networking (2connect): This task area ensures that any cross-domain activities and developments of NFDI4BioDiversity are coordinated and in-line with the overall development of the NFDI as well as inte

Biodiversity is more than just the diversity of living species. It includes genetic and phenotypic diversity of organisms, functional diversity, interactions and the diversity of populations and whole ecosystems. The recent Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) report confirmed that our planet experiences a rapid loss of biodiversity with dramatic consequences for mankind. Answers to scientifically and societal relevant questions can only be found based on the availability of data integrated from multiple sources and building on different knowledge domains in science and society. The FAIR data principles provide a framework towards such integration. To foster access to interoperable data, NFDI4BioDiversity focuses on the following six objectives: 1) Promoting research data management as an integral part of biodiversity research, 2) Enabling FAIRness of data, 3) Consolidating FAIRness with quality, 4) Embedding NFDI4BioDiversity into the (inter-)national landscape, 5) Addressing NFDI-wide cross-cutting topics and 6) Promoting collaborative governance, viability and sustainability of data infrastructure services and science. These objectives are implemented by the NFDI4BioDiversity work programme and its five task areas: Task Area 1 - Community engagement (2involve): This task area will integrate across different knowledge holders and take care of research data management requests related to biodiversity data. A large part of all species data is collected by volunteers in natural history societies, NGOs, museums and citizen science projects as well as collected by different authorities This task area includes 23 use cases with community-driven topics and cross-domain user groups. Task Area 2 - National and international networking (2connect): This task area ensures that any cross-domain activities and developments of NFDI4BioDiversity are coordinated and in-line with the overall development of the NFDI as well as inte

In the spirit of our common interest to build what could become an international beacon for sharing the benefits of high-quality research data and research data management, the signing NFDI consortia strongly support the idea that NFDI must build on a coordinated and inclusive effort fostering the FAIR data principles. Recalling the challenges that interoperability and sharing of data faces, the 21 consortia signing this declaration agreed on a common list of cross-cutting topics.

In the spirit of our common interest to build what could become an international beacon for sharing the benefits of high-quality research data and research data management, the signing NFDI consortia strongly support the idea that NFDI must build on a coordinated and inclusive effort fostering the FAIR data principles. Recalling the challenges that interoperability and sharing of data faces, the 21 consortia signing this declaration agreed on a common list of cross-cutting topics.

n

BackgroundSeveral fungi-specific primers target the 18S rRNA gene sequence, one of the prominent markers for fungal classification. The design of most primers goes back to the last decades. Since then, the number of sequences in public databases increased leading to the discovery of new fungal groups and changes in fungal taxonomy. However, no reevaluation of primers was carried out and relevant information on most primers is missing. With this study, we aimed to develop an 18S rRNA gene sequence primer toolkit allowing an easy selection of the best primer pair appropriate for different sequencing platforms, research aims (biodiversity assessment versus isolate classification) and target groups.ResultsWe performed an intensive literature research, reshuffled existing primers into new pairs, designed new Illumina-primers, and annealing blocking oligonucleotides. A final number of 439 primer pairs were subjected to in silico PCRs. Best primer pairs were selected and experimentally tested. The most promising primer pair with a small amplicon size, nu-SSU-1333-5′/nu-SSU-1647-3′ (FF390/FR-1), was successful in describing fungal communities by Illumina sequencing. Results were confirmed by a simultaneous metagenomics and eukaryote-specific primer approach. Co-amplification occurred in all sample types but was effectively reduced by blocking oligonucleotides.ConclusionsThe compiled data revealed the presence of an enormous diversity of fungal 18S rRNA gene primer pairs in terms of fungal coverage, phylum spectrum and co-amplification. Therefore, the primer pair has to be carefully selected to fulfill the requirements of the individual research projects. The presented primer toolkit offers comprehensive lists of 164 primers, 439 primer combinations, 4 blocking oligonucleotides, and top primer pairs holding all relevant information including primer’s characteristics and performance to facilitate primer pair selection.

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.

Due to its extreme salinity and high Mg concentration the Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several underwater fresh to brackish water springs in the Dead Sea harboring dense microbial communities. We provide the first characterization of these communities, discuss their possible origin, hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and community fingerprinting methods showed that the spring community originates from the Dead Sea sediments and not from the aquifer. Furthermore, it suggested that there is a dense Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifiers iron oxidizers and iron reducers were identified as well. Analysis of white and green biofilms suggested that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. Analysis of the water’s chemistry shows evidence of microbial activity along the path and suggests that the springs supply nitrogen, phosphorus and organic matter to the microbial communities in the Dead Sea. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red Sea−Dead Sea water conduit.

In flow cytometric analyses of marine prokaryotic picoplankton often two populations with distinct differences in their apparent nucleic acid content are discernable, one with a high and one with a low nucleic acid content (HNA and LNA, respectively). In this study we determined the phylogenetic composition of flow cytometrically sorted HNA and LNA populations, collected at six stations along a transect across three oceanic provinces from Iceland to the Azores. Catalysed reporter deposition fluorescence in situ hybridisation (CARD-FISH) analysis of sorted cells revealed distinct differences in phylogenetic composition between the LNA and HNA populations with only little overlap. At all stations the LNA population was dominated by the alphaproteobacterial clade SAR11 (45-74%). Also, Betaproteobacteria were always present at 2-4%. While the LNA composition was rather stable, the HNA populations were composed of distinct phylogenetic clades in the different oceanic provinces of Arctic and Tropics. For example Cyanobacteria dominated the North Atlantic Gyre HNA population (29-44%) with Prochlorococcus as the major clade (34-44%), but were low in Arctic and Polar waters (1% and 5%, respectively). In contrast, Bacteroidetes accounted for the majority of HNA cells in the Polar and Arctic province (26% and 32%, respectively), but were low in the Gyre region (3-10%). The DNA content of the HNA population was about 3.5 times higher than that of the LNA populations. This reflects differences in the genome sizes of closely related cultured representatives of HNA clades (3-6 Mbp) and LNA clades (1.3-1.5 Mbp).

Increasingly, we are aware as a community of the growing need to manage the avalanche of genomic and metagenomic data, in addition to related data types like ribosomal RNA and barcode sequences, in a way that tightly integrates contextual data with traditional literature in a machine-readable way. It is for this reason that the Genomic Standards Consortium (GSC) formed in 2005. Here we suggest that we move beyond the development of standards and tackle standards compliance and improved data capture at the level of the scientific publication. We are supported in this goal by the fact that the scientific community is in the midst of a publishing revolution. This revolution is marked by a growing shift away from a traditional dichotomy between “journal articles” and “database entries” and an increasing adoption of hybrid models of collecting and disseminating scientific information. With respect to genomes and metagenomes and related data types, we feel the scientific community would be best served by the immediate launch of a central repository of short, highly structured “Genome Notes” that must be standards compliant. This could be done in the context of an existing journal, but we also suggest the more radical solution of launching a new journal. Such a journal could be designed to cater to a wide range of standards-related content types that are not currently centralized in the published literature. It could also support the demand for centralizing aspects of the “gray literature” (documents developed by institutions or communities) such as the call by the GSC for a central repository of Standard Operating Procedures describing the genomic annotation pipelines of the major sequencing centers. We argue that such an “eJournal,” published under the Open Access paradigm by the GSC, could be an attractive publishing forum for a broader range of standardization initiatives within, and beyond, the GSC and thereby fill an unoccupied yet increasingly important niche within, Increasingly, we are aware as a community of the growing need to manage the avalanche of genomic and metagenomic data, in addition to related data types like ribosomal RNA and barcode sequences, in a way that tightly integrates contextual data with traditional literature in a machine-readable way. It is for this reason that the Genomic Standards Consortium (GSC) formed in 2005. Here we suggest that we move beyond the development of standards and tackle standards compliance and improved data capture at the level of the scientific publication. We are supported in this goal by the fact that the scientific community is in the midst of a publishing revolution. This revolution is marked by a growing shift away from a traditional dichotomy between “journal articles” and “database entries” and an increasing adoption of hybrid models of collecting and disseminating scientific information. With respect to genomes and metagenomes and related data types, we feel the scientific community would be best served by the immediate launch of a central repository of short, highly structured “Genome Notes” that must be standards compliant. This could be done in the context of an existing journal, but we also suggest the more radical solution of launching a new journal. Such a journal could be designed to cater to a wide range of standards-related content types that are not currently centralized in the published literature. It could also support the demand for centralizing aspects of the “gray literature” (documents developed by institutions or communities) such as the call by the GSC for a central repository of Standard Operating Procedures describing the genomic annotation pipelines of the major sequencing centers. We argue that such an “eJournal,” published under the Open Access paradigm by the GSC, could be an attractive publishing forum for a broader range of standardization initiatives within, and beyond, the GSC and thereby fill an unoccupied yet increasingly important niche within