The extracellular DNA pool in marine sediments is the largest reservoir of DNA of the world oceans and it potentially represents an archive of genetic information and gene sequences involved in ...natural transformation processes. However, no information is at present available for the gene sequences contained in the extracellular DNA and for the factors that influence their preservation. In the present study, we investigated the depurination and degradation rates of extracellular DNA in a variety of marine sediment samples characterized by different ages (up to 10 000 years) and environmental conditions according to the presence, abundance and diversity of prokaryotic gene sequences. We provide evidence that depurination of extracellular DNA in these sediments depends upon the different environmental factors that act synergistically and proceeds at much slower rates than those theoretically predicted or estimated for terrestrial ecosystems. These findings suggest that depurination in marine sediments is not the main process that limits extracellular DNA survival. Conversely, DNase activities were high suggesting a more relevant role of biologically driven processes. Amplifiable prokaryotic 16S rDNA sequences were present in most benthic systems analysed, independent of depurination and degradation rates and of the ages of the sediment samples. Additional molecular analyses revealed that the extracellular DNA pool is characterized by relatively low-copy numbers of prokaryotic 16S rDNA sequences that are highly diversified. Overall, our results suggest that the extracellular DNA pool in marine sediments represents a repository of genetic information, which can be used for improving our understanding of the biodiversity, functioning and evolution of ecosystems over different timescales.
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.
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.
Although the negative effects of inorganic UV filters have been documented on several marine organisms, sunscreen products containing such filters are available in the market and proposed as ...eco-friendly substitutes for harmful, and already banned, organic UV filters (e.g. octinoxate and oxybenzone). In the present study, we investigated the effects of four sunscreen products, labelled by cosmetic companies as “eco-friendly”, on the early developmental stages of the sea urchin Paracentrotus lividus, a keystone species occurring in vulnerable coastal habitats. Among sunscreens tested, those containing ZnO and TiO2 or their mix caused severe impacts on sea urchin embryos. We show that inorganic UV filters were incorporated by larvae during their development and, despite the activation of defence strategies (e.g. phagocytosis by coelomocytes), generated anomalies such as skeletal malformations and tissue necrosis. Conversely, the sunscreen product containing only new-generation organic UV filters (e.g. methylene bis-benzotriazolyl tetramethyl, ethylhexyl triazone, butylphenol diethylamino hydroxybenzoyl hexyl benzoate) did not affect sea urchins, thus resulting actually eco-compatible. Our findings expand information on the impact of inorganic UV filters on marine life, corroborate the need to improve the eco-friendliness assessment of sunscreen products and warn of the risk of bioaccumulation and potential biomagnification of inorganic UV filters along the marine food chain.
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•Eco-labelled sunscreens containing inorganic UV filters can affect marine life.•Inorganic UV filters-based sunscreens can harm P. lividus populations.•Zn and Ti contained in sunscreens may accumulate in sea urchin larvae.
Molecular approaches that target the total DNA pool recovered from permanently anoxic marine ecosystems have revealed an extraordinary diversity of prokaryotes and unicellular eukaryotes. However, ...the presence of gene sequences contained within the extracellular DNA pool is still largely neglected. We have investigated the preservation, origin and genetic imprint of extracellular DNA recovered from permanently anoxic deep‐sea sediments of the Black Sea. Despite high DNase activities, huge amounts of total extracellular DNA were found in both the surface and subsurface sediment layers, suggesting reduced availability of the extracellular DNA pool to nuclease degradation. The reduced degradation of the total extracellular DNA was confirmed by its low decay rate and the high accumulation in the deeper sediment layers. The copy numbers of 16S and 18S rDNA contained within the extracellular DNA pool in both the surface and subsurface sediment layers was very high, indicating that permanently anoxic sediments of the deep Black Sea are hot spots of preserved extracellular gene sequences. The extracellular DNA recovered from these sediment layers also contained highly diversified 18S rDNA sequences. These were not only representative of the major protistan lineages, but also of new very divergent lineages, branching as independent clades at the base of the tree. Our findings indicate that the extracellular DNA pool is a major archive of present/past eukaryotic gene sequences, and they highlight the importance of integrating molecular cell‐oriented approaches with molecular analyses of the extracellular DNA pool, for a better assessment of microbial diversity and temporal changes in marine benthic ecosystems.
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, ...most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
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•eDNA metabarcoding is revolutionizing the field of aquatic biomonitoring.•The methods and protocols for sediment eDNA metabarcoding can vary considerably.•Available information on metabarcoding applied to sediment samples were reviewed.•Challenges specific to sediment eDNA analysis were discussed.•The aim was to define best-practices and recommend potential standard procedures.
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.
•We analysed the influence of contamination on the benthic prokaryotic assemblages in the highly-polluted Bagnoli-Coroglio bay.•The prokaryotic abundance in the sediments was driven by environmental factors rather than by contamination levels.•The richness of prokaryotic taxa was high but slightly decreased (by 15% to 38%) with increasing contamination.•We found large variations in prokaryotic taxa composition among sites, driven by the sediment contamination levels and types.•Chemical contamination can affect the richness but promote the turnover (β-)diversity of the benthic prokaryotic assemblages.
The effects of contaminants on marine organisms have been documented since decades, but the long-term responses and recovery rates of benthic communities to mixtures of contaminants, several years ...after the cessation of industrial activities, need to be further investigated. Bagnoli-Coroglio Bay (Gulf of Naples, Tyrrhenian Sea) is a typical example of historically contaminated coastal area due to industrial activities stopped at the beginning of nineties. In the present study we carried out a fine spatial scale analysis of the distribution of meiofaunal (and nematodes) assemblages along five bathymetric transects located at increasing distance from the historical source of contamination in relation with the polycyclic aromatic hydrocarbon and heavy metal concentrations present in the sediment. Meiofaunal abundance and biomass changed widely along transects but independent from the distance from the source of contamination. Even when the contamination levels were expected to induce significant detrimental biological consequences, meiofaunal abundance and biomass were similar to those reported in unpolluted benthic coastal areas worldwide. Conversely, biodiversity in terms of meiofaunal taxa richness was generally low (range: 5–8 taxa in 12 of the overall 15 stations investigated). This was explained by the lack of sensitive groups such as ostracods, gastrotrichs and tardigrades commonly encountered in benthic coastal ecosystems, thus reflecting an overall poor/moderate environmental quality of the investigated area. Nematode (structural and functional) diversity was also low, particularly at stations characterized by higher contamination levels. At the same time, nematode species composition did not change significantly among stations suggesting a widespread effect of contaminants able to reduce the variability (i.e., turnover diversity) within the assemblages of the whole study area. Overall, our results indicate that even decades after the cessation of contaminant emissions, benthic biodiversity was affected in terms of both meiofaunal taxa and nematode species. These findings strongly reinforce the call for reducing sources of chronic pollution in marine ecosystems and provide new insights for a better understanding of the ecological recovery of historically contaminated marine environments.
•The effects of historical contamination is evident on benthic diversity.•Meiofaunal abundance and biomass are less affected by the contamination.•The highly contaminated sediments are mostly characterized by the tolerant nematode species.•Investigating historically contamination is crucial for the assessment of the ecological recovery.
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.
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.
GLOSSary provides an expandable bioinformatics environment, able to support the scientific community in current and forthcoming environmental metagenomics analyses.
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