Value, but high costs in post-deposition data curation

Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach

Value, but high costs in post-deposition data Curation

© The Author(s) 2016. Published by Oxford University Press. Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach

Cyanobacteria in thermal spring environments: diversity and ecology

Cyanobacteria collected from thermal springs of Greece were isolated into non-axenical unicultures. The main target of the thesis was the polyphasic taxonomic aproach of the 34 isolated strains. We combined classical taxonomy with molecular techniques and phylogenetic trees were bult with different methods like maximum parsimony, maximum likelihood and bayesian inference. Our analysis indicated at least 13 new cyanobacterial taxa at the genus level. Moreover, 4 isolated strains were sequenced for their whole genome and the de novo assembly and genome mining approach showed many interesting secondary metabolites, while the vast majority of the recognised proteins had no match to the known protein families. Finally, water samples and cyanobacterial mats were analyzed for nutrients and heavy metal concentration.Κυανοβακτήρια από 10 θερμές πηγές της Ελλάδας απομονώθηκαν σε μονοκαλλιέργειες. Εγινε προσπάθεια ταξινόμισής τους με μια πολυφασική προσέγγιση που συμπεριλάμβανε μεθόδους κλασικής ταξινομικής με τεχνικές μικροσκοπίας (Φωτονικό μικροσκόπιο, Ηλεκτρονικό μικροσκόπιο σάρωσης και διέλευσης), μοριακές τεχνικές (όπως φυλογένεση με την περιοχή 16S rRNA και δευτεροταγείς δομές της περιοχής 16S-23S Internal Trasncribed Spacer), ανάλυση λιπαρών οξέων και οικολογικές παραμέτρους. Συνολικά αναδείχτηκαν τουλάχιστον 13 νέες ταξινομικές μονάδες σε επίπεδο γένους. Επιπλέον σε 4 απομονωμένα στελέχη έγινε ανάλυση ολόκληρου του γονιδιώματός τους η οποία ανέδειξε το σημαντικό αριθμό βιοτεχνολογικά ενδιαφέροντων μονοπατιών καθώς και την πληθώρα των άγνωστων πρωτεϊνών. Σε δείγματα νερού από τις θερμές πηγές αναλύθηκαν θρεπτικά στοιχεία και βαρέα μέταλλα ενώ σε κυανοβακτηριακούς τάπητες έγινε ανάλυση των προσροφημένων μετάλλων

A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece

Strains of Cyanobacteria isolated from mats of 9 thermal springs of Greece have been studied for their taxonomic evaluation. A polyphasic taxonomic approach was employed which included: morphological observations by light microscopy and scanning electron microscopy, maximum parsimony, maximum likelihood and Bayesian analysis of 16S rDNA sequences, secondary structural comparisons of 16S-23S rRNA Internal Transcribed Spacer sequences, and finally environmental data. The 17 cyanobacterial isolates formed a diverse group that contained filamentous, coccoid and heterocytous strains. These included representatives of the polyphyletic genera of Synechococcus and Phormidium, and the orders Oscillatoriales, Spirulinales, Chroococcales and Nostocales. After analysis, at least 6 new taxa at the genus level provide new evidence in the taxonomy of Cyanobacteria and highlight the abundant diversity of thermal spring environments with many potential endemic species or ecotypes. © 2016 Elsevier Inc

Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece

Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21 Pseudomonas strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these Pseudomonas strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant Pseudomonas strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO2-rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance. © 2021, The Author(s)

The Collaborative Potential of Research Infrastructures in Addressing Global Scientific Questions

Research Infrastructures (RIs) are facilities, resources and services used by scientists to perform research and support innovation. A number of EU research infrastructures [e.g. e-Science and Technology European Infrastructure for Biodiversity and Ecosystem Research (LifeWatch) European Research Iinfrastructures Consortium (ERIC); The European life-sciences Infrastructure for biological Information (ELIXIR); the European Marine Biological Resource Centre (EMBRC ERIC); the European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences (uroBioImaging ERIC)] have been building Virtual Research Environments (VREs), which include many virtual laboratories (vLabs) offering, one stop data access to scientists, high computational capacity and collaborative research platforms in support of the requirements of the digital science. This presentation gives examples on the use of the vLabs developed by LifeWatch ERIC which have subsequently been  taken up as web services by other RIs. The RvLab operates on a high-performance computer cluster, and has been used in order to analyse various properties of taxon equality, with a focus on marine species. This taxonomic information on marine biota is organized and made publicly available through the World Register of Marine Species (WoRMS) that delivers more than 250,000 described valid species names. Although scientists consider an equal status (in terms of contribution to overall diversity) to each taxon used in taxonomy, biogeography, ecology and biodiversity, the question “are all taxa equal?” has never been tested at a global scale. We present evidence that this question can be addressed by applying relatedness indices (Taxonomic Distinctness) over the entire WoRMS metazoan tree. The virtual micro-CT laboratory (Micro-CT vLab), which can be used by the members of the scientific community interested in the digitisation methods and biological collections, makes the micro-CT data exploration of natural history specimens freely available over the internet. Micro-CT vLab makes it possible the online exploration and dissemination of micro-CT datasets, which are only rarely made available to the public due to their very large size and a lack of dedicated online platforms supporting the interactive manipulation of 3D data. Examples of how these vLabs can be used by other RIs are provided

SOP 4.2. Polyphasic approach on cyanobacterial strains

A rapid taxonomic identification is important for estimating potential risks to animal and human health caused by cyanobacteria in waters used for recreation, drinking and irrigation. Light microscopy provides a rapid means for preliminary identification and quantitative estimation of potentially toxic cyanobacteria based on their morphology (morphotypes). However, the final species assignment should rely on a polyphasic characterization of cultured strains (or population isolates) consisting of several different molecular methods, and (whenever possible) the determination of ultrastructural, physiological, biochemical, and ecological characteristics. In this chapter, we describe the major steps essential for cyanobacterial taxa identification. These include examination by light microscopy, genetic characterization by single or multiple loci sequence analyses, and by molecular typing. The value of taxonomic and molecular databases is explained. Finally, the usefulness of a polyphasic approach is highlighted by examples. Although analyses of genes known to be involved in toxin synthesis can be helpful for the identification of potentially toxic strains (or population isolates), reliable health risk assessments require confirmation by analytical measurement of the respective cyanotoxin