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Tangherlini M, Corinaldesi C, Rastelli E, Musco L, Armiento G, Danovaro R, Dell'Anno A. Chemical contamination can promote turnover diversity of benthic prokaryotic assemblages: The case study of the Bagnoli-Coroglio bay (southern Tyrrhenian Sea). Mar Environ Res 2020; 160:105040. [PMID: 32907739 DOI: 10.1016/j.marenvres.2020.105040] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
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.
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Affiliation(s)
- M Tangherlini
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - C Corinaldesi
- Dipartimento di Scienze e Ingegneria Della Materia, Dell'Ambiente Ed Urbanistica, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - E Rastelli
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - L Musco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - G Armiento
- ENEA - Agenzia per le Nuove Tecnologie, L'Energia e Lo Sviluppo Economico Sostenibile, Via Anguillarese 301, 00123, Roma, Italy
| | - R Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy; Dipartimento di Scienze Della Vita e Dell'Ambiente, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - A Dell'Anno
- Dipartimento di Scienze Della Vita e Dell'Ambiente, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
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Aguzzi J, Flexas MM, Flögel S, Lo Iacono C, Tangherlini M, Costa C, Marini S, Bahamon N, Martini S, Fanelli E, Danovaro R, Stefanni S, Thomsen L, Riccobene G, Hildebrandt M, Masmitja I, Del Rio J, Clark EB, Branch A, Weiss P, Klesh AT, Schodlok MP. Exo-Ocean Exploration with Deep-Sea Sensor and Platform Technologies. Astrobiology 2020; 20:897-915. [PMID: 32267735 DOI: 10.1089/ast.2019.2129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
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.
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Affiliation(s)
- J Aguzzi
- Instituto de Ciencias del Mar (ICM-CSIC), Barcelona, Spain
- Stazione Zoologica Anton Dohrn, Naples, Italy
| | - M M Flexas
- California Institute of Technology, Pasadena, California, USA
| | - S Flögel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - C Lo Iacono
- Instituto de Ciencias del Mar (ICM-CSIC), Barcelona, Spain
- National Oceanographic Center (NOC), University of Southampton, Southampton, United Kingdom
| | | | - C Costa
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Centro di ricerca Ingegneria e Trasformazioni agroalimentari - Monterotondo, Rome, Italy
| | - S Marini
- Stazione Zoologica Anton Dohrn, Naples, Italy
- National Research Council of Italy (CNR), Institute of Marine Sciences, La Spezia, Italy
| | - N Bahamon
- Instituto de Ciencias del Mar (ICM-CSIC), Barcelona, Spain
- Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Blanes, Spain
| | - S Martini
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-mer, France
| | - E Fanelli
- Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - R Danovaro
- Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - S Stefanni
- Stazione Zoologica Anton Dohrn, Naples, Italy
| | | | - G Riccobene
- Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali del Sud, Catania, Italy
| | - M Hildebrandt
- German Research Center for Artificial Intelligence (DFKI), Bremen, Germany
| | - I Masmitja
- SARTI, Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - J Del Rio
- SARTI, Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - E B Clark
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - A Branch
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - A T Klesh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - M P Schodlok
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Tangherlini M, Miralto M, Colantuono C, Sangiovanni M, Dell’ Anno A, Corinaldesi C, Danovaro R, Chiusano ML. GLOSSary: the GLobal Ocean 16S subunit web accessible resource. BMC Bioinformatics 2018; 19:443. [PMID: 30497362 PMCID: PMC6266928 DOI: 10.1186/s12859-018-2423-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- M. Tangherlini
- Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy
| | - M. Miralto
- Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy
| | - C. Colantuono
- Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy
| | - M. Sangiovanni
- Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy
| | - A. Dell’ Anno
- Dipartimento di Scienze della Vita e dell’Ambiente, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - C. Corinaldesi
- Dipartimento di Scienze e Ingegneria della Materia, dell’Ambiente ed Urbanistica, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - R. Danovaro
- Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy
- Dipartimento di Scienze della Vita e dell’Ambiente, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - M. L. Chiusano
- Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy
- Dipartimento di Agraria, University of Naples “Federico II”, via Università 100, 80055 Portici, Italy
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Tangherlini M, Dell'Anno A, Zeigler Allen L, Riccioni G, Corinaldesi C. Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses. Sci Rep 2016; 6:28428. [PMID: 27329207 PMCID: PMC4916513 DOI: 10.1038/srep28428] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/02/2016] [Indexed: 11/09/2022] Open
Abstract
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.
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Affiliation(s)
- M Tangherlini
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - A Dell'Anno
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - L Zeigler Allen
- Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, CA, USA
| | - G Riccioni
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - C Corinaldesi
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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Corinaldesi C, Tangherlini M, Luna GM, Dell'anno A. Extracellular DNA can preserve the genetic signatures of present and past viral infection events in deep hypersaline anoxic basins. Proc Biol Sci 2014; 281:20133299. [PMID: 24523277 DOI: 10.1098/rspb.2013.3299] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Affiliation(s)
- C Corinaldesi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, , 60131 Ancona, Italy, Institute of Marine Sciences-National Research Council (ISMAR-CNR), , Castello 2737/f, 30122 Venezia, Italy
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