Chemical contamination can promote turnover diversity of benthic prokaryotic assemblages: The case study of the Bagnoli-Coroglio bay (southern Tyrrhenian Sea).

Chemical contamination of marine ecosystems represents a major concern for the detrimental consequences at different levels of biological organization. However, the impact of chronic contamination on the diversity and assemblage composition of benthic prokaryotes is still largely unknown, and this limits our understanding of the potential implications on ecosystem functioning. The Bagnoli-Coroglio bay (Gulf of Naples, Tyrrhenian Sea) is a typical example of coastal area heavily contaminated by metals and hydrocarbons, released for decades by industrial activities, which ceased at the beginning of nineties. In the present study we analyzed the abundance, diversity and assemblage composition of benthic prokaryotic assemblages at increasing distance from the historical source of contamination in relation to the heavy hydrocarbons (C > 12), polycyclic aromatic hydrocarbons (PAHs) and heavy metal concentrations in the sediments. Prokaryotic abundance in the sediments differed among sites, and was mostly driven by environmental factors rather than by contamination levels. Conversely, the richness of prokaryotic taxa was relatively high in all samples, was driven by contamination levels and decreased significantly with increasing contamination (15-38%). Moreover, our results indicate large variations in the composition of the benthic prokaryotic assemblages among sites, mostly explained by the different levels and types of chemical contaminants found in the sediments. Overall, our findings suggest that chemical contaminants, even after decades from the end of their release, can profoundly influence the richness and turnover diversity of the benthic prokaryotic assemblages, in turn promoting a high diversification of the benthic bacterial and archaeal assemblages by selecting those lineages more adapted to specific mixtures of different contaminants. Our results open new perspectives for understanding of the long-term effects of chemical contamination on the benthic prokaryotic assemblages and the ecological processes they mediate.

Exo-Ocean Exploration with Deep-Sea Sensor and Platform Technologies.

One of Saturn's largest moons, Enceladus, possesses a vast extraterrestrial ocean (i.e., exo-ocean) that is increasingly becoming the hotspot of future research initiatives dedicated to the exploration of putative life. Here, a new bio-exploration concept design for Enceladus' exo-ocean is proposed, focusing on the potential presence of organisms across a wide range of sizes (i.e., from uni- to multicellular and animal-like), according to state-of-the-art sensor and robotic platform technologies used in terrestrial deep-sea research. In particular, we focus on combined direct and indirect life-detection capabilities, based on optoacoustic imaging and passive acoustics, as well as molecular approaches. Such biologically oriented sampling can be accompanied by concomitant geochemical and oceanographic measurements to provide data relevant to exo-ocean exploration and understanding. Finally, we describe how this multidisciplinary monitoring approach is currently enabled in terrestrial oceans through cabled (fixed) observatories and their related mobile multiparametric platforms (i.e., Autonomous Underwater and Remotely Operated Vehicles, as well as crawlers, rovers, and biomimetic robots) and how their modified design can be used for exo-ocean exploration.

GLOSSary: the GLobal Ocean 16S subunit web accessible resource.

BACKGROUND: Environmental metagenomics is a challenging approach that is exponentially spreading in the scientific community to investigate taxonomic diversity and possible functions of the biological components. The massive amount of sequence data produced, often endowed with rich environmental metadata, needs suitable computational tools to fully explore the embedded information. Bioinformatics plays a key role in providing methodologies to manage, process and mine molecular data, integrated with environmental metagenomics collections. One such relevant example is represented by the Tara Ocean Project. RESULTS: We considered the Tara 16S miTAGs released by the consortium, representing raw sequences from a shotgun metagenomics approach with similarities to 16S rRNA genes. We generated assembled 16S rDNA sequences, which were classified according to their lengths, the possible presence of chimeric reads, the putative taxonomic affiliation. The dataset was included in GLOSSary (the GLobal Ocean 16S Subunit web accessible resource), a bioinformatics platform to organize environmental metagenomics data. The aims of this work were: i) to present alternative computational approaches to manage challenging metagenomics data; ii) to set up user friendly web-based platforms to allow the integration of environmental metagenomics sequences and of the associated metadata; iii) to implement an appropriate bioinformatics platform supporting the analysis of 16S rDNA sequences exploiting reference datasets, such as the SILVA database. We organized the data in a next-generation NoSQL "schema-less" database, allowing flexible organization of large amounts of data and supporting native geospatial queries. A web interface was developed to permit an interactive exploration and a visual geographical localization of the data, either raw miTAG reads or 16S contigs, from our processing pipeline. Information on unassembled sequences is also available. The taxonomic affiliations of contigs and miTAGs, and the spatial distribution of the sampling sites and their associated sequence libraries, as they are contained in the Tara metadata, can be explored by a query interface, which allows both textual and visual investigations. In addition, all the sequence data were made available for a dedicated BLAST-based web application alongside the SILVA collection. CONCLUSIONS: GLOSSary provides an expandable bioinformatics environment, able to support the scientific community in current and forthcoming environmental metagenomics analyses.

Extracellular DNA as a genetic recorder of microbial diversity in benthic deep-sea ecosystems.

Extracellular DNA in deep-sea sediments represents a major repository of genes, which previously belonged to living organisms. However, the extent to which these extracellular genes influence current estimates of prokaryotic biodiversity is unknown. We investigated the abundance and diversity of 16S rDNA sequences contained within extracellular DNA from continental margins of different biogeographic regions. We also compared the taxonomic composition of microbial assemblages through the analysis of extracellular DNA and DNA associated with living cells. 16S rDNA contained in the extracellular DNA pool contributed up to 50% of the total 16S rDNA copy number determined in the sediments. Ca. 4% of extracellular Operational Taxonomic Units (OTUs) were shared among the different biogeographic regions revealing the presence of a core of preserved OTUs. A higher fraction of OTUs was exclusive of each region potentially due to its geographic and thermohaline characteristics. Ca. one third of the OTUs identified in the extracellular DNA were absent from living prokaryotic assemblages, possibly representing the signatures of past assemblages. Our findings expand the knowledge of the contribution of extracellular microbial sequences to current estimates of prokaryotic diversity obtained through the analyses of "environmental DNA", and open new perspectives for understanding microbial successions in benthic ecosystems.

Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses.

In benthic deep-sea ecosystems, which represent the largest biome on Earth, viruses have a recognised key ecological role, but their diversity is still largely unknown. Identifying the taxonomic composition of viruses is crucial for understanding virus-host interactions, their role in food web functioning and evolutionary processes. Here, we compared the performance of various bioinformatic tools (BLAST, MG-RAST, NBC, VMGAP, MetaVir, VIROME) for analysing the viral taxonomic composition in simulated viromes and viral metagenomes from different benthic deep-sea ecosystems. The analyses of simulated viromes indicate that all the BLAST tools, followed by MetaVir and VMGAP, are more reliable in the affiliation of viral sequences and strains. When analysing the environmental viromes, tBLASTx, MetaVir, VMGAP and VIROME showed a similar efficiency of sequence annotation; however, MetaVir and tBLASTx identified a higher number of viral strains. These latter tools also identified a wider range of viral families than the others, providing a wider view of viral taxonomic diversity in benthic deep-sea ecosystems. Our findings highlight strengths and weaknesses of available bioinformatic tools for investigating the taxonomic diversity of viruses in benthic ecosystems in order to improve our comprehension of viral diversity in the oceans and its relationships with host diversity and ecosystem functioning.

Extracellular DNA can preserve the genetic signatures of present and past viral infection events in deep hypersaline anoxic basins.

Deep hypersaline anoxic basins (DHABs) of the Mediterranean Sea are among the most extreme ecosystems on Earth and host abundant, active and diversified prokaryotic assemblages. However, factors influencing biodiversity and ecosystem functioning are still largely unknown. We investigated, for the first time, the impact of viruses on the prokaryotic assemblages and dynamics of extracellular DNA pool in the sediments of La Medee, the largest DHAB found on Earth. We also compared, in La Medee and L'Atalante sediments, the diversity of prokaryotic 16S rDNA sequences contained in the extracellular DNA released by virus-induced prokaryotic mortality. We found that DHAB sediments are hot-spots of viral infections, which largely contribute to the release of high amounts of extracellular DNA. DNase activities in DHAB sediments were much higher than other extracellular enzymatic activities, suggesting that extracellular DNA released from killed prokaryotes can be the most suitable trophic resource for benthic prokaryotes. Preserved extracellular DNA pools, which contained novel and diversified gene sequences, were very similar between the DHABs but dissimilar from the respective microbial DNA pools. We conclude that the strong viral impact in DHAB sediments influences the genetic composition of extracellular DNA, which can preserve the signatures of present and past infections.