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George NA, Hug LA. CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts. Sci Rep 2023; 13:5611. [PMID: 37019939 PMCID: PMC10076291 DOI: 10.1038/s41598-023-32078-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
Viruses are the most abundant microbial guild on the planet, impacting microbial community structure and ecosystem services. Viruses are specifically understudied in engineered environments, including examinations of their host interactions. We examined host-virus interactions via host CRISPR spacer to viral protospacer mapping in a municipal landfill across two years. Viruses comprised ~ 4% of both the unassembled reads and assembled basepairs. A total of 458 unique virus-host connections captured hyper-targeted viral populations and host CRISPR array adaptation over time. Four viruses were predicted to infect across multiple phyla, suggesting that some viruses are far less host-specific than is currently understood. We detected 161 viral elements that encode CRISPR arrays, including one with 187 spacers, the longest virally-encoded CRISPR array described to date. Virally-encoded CRISPR arrays targeted other viral elements in interviral conflicts. CRISPR-encoding proviruses integrated into host chromosomes were latent examples of CRISPR-immunity-based superinfection exclusion. The bulk of the observed virus-host interactions fit the one-virus-one-host paradigm, but with limited geographic specificity. Our networks highlight rare and previously undescribed complex interactions influencing the ecology of this dynamic engineered system. Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for atypical virus-host dynamics.
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Affiliation(s)
- Nikhil A George
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
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2
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High Level of Interaction between Phages and Bacteria in an Artisanal Raw Milk Cheese Microbial Community. mSystems 2023; 8:e0056422. [PMID: 36475872 PMCID: PMC9948729 DOI: 10.1128/msystems.00564-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Microbial starter cultures are used in the production of many cheeses around the world, such as Parmigiano-Reggiano, in Italy, Époisses, in France, and Canastra, in Brazil, providing many of the unique features of these cheeses. Bacteriophages (phages) are ubiquitous and well known to modulate the structure of bacterial communities, and recent data indicate that cheeses contain a high abundance of naturally occurring phages. Here, we analyze the viral and bacterial metagenomes of Canastra cheese: a traditional artisanal Brazilian cheese produced using an endogenous starter culture and raw milk. Over 1,200 viral operational taxonomic units were recovered using both isolated viral-like particles and complete metagenomic DNA. Common viral families identified included Siphoviridae and Myoviridae, with 40% of putative phage genomes unidentified at the family level of classification. We observed very high phage diversity, which varied greatly across different cheese producers, with 28% of phage genomes detected in only one producer. Several metagenome-assembled genomes were recovered for lactic acid-producing bacteria, as well as nonstarter bacterial species, and we identified several phage-bacterium interactions, at the strain level of resolution, varying across distinct cheese producers. We postulate that at least one bacterial strain detected could be endogenous and unique to the Canastra cheese-producing region in Brazil and that its growth seems to be modulated by autochthonous phages present in this artisanal production system. This phage-host relationship is likely to influence the fermentation dynamics and ultimately the sensorial profile of these cheeses, with implications for other similar cheese production systems around the world. IMPORTANCE Our work demonstrated a dynamic yet stable microbial ecosystem during cheese production using an endogenous starter culture. This was observed across several distinct producers and was marked by genomic evidence of continued phage-bacterium interactions, such as the presence of bacterial defense mechanisms. Furthermore, we provide evidence of unique microbial signatures for each individual cheese producer studied in the region, a fact that may have profound consequences on product traceability. This was the first effort to describe and understand the bacteriophage composition and ecological dynamics within the Brazilian Canastra cheese production system. The study of this prototypical backslopping production system provides a solid background for further mechanistic studies of the production of many cheeses around the world.
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Sun M, Chen F. Distribution of rare N4-like viruses in temperate estuaries unveiled by viromics. Environ Microbiol 2022; 24:6100-6111. [PMID: 36054739 DOI: 10.1111/1462-2920.16172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/11/2022] [Indexed: 01/12/2023]
Abstract
The relative abundance of N4-like viruses in two temperate estuaries was assessed using four different methods, read mapping to known N4-like virus isolates, read mapping to native viral contigs, reciprocal blast search based on core genes, and read taxonomy classification using Kaiju. Overall, N4-like viruses were found to be of low abundance in the estuarine viromes. When mapping reads to only known N4-like virus genomes, high occurrences of N4-like viruses infecting Roseobacter were found, with their diversity consisting mostly of locally isolated Roseobacter N4-like virus species. Both contig-based methods and Kaiju classification showed similar seasonal patterns for N4-like viruses, and redundancy analysis revealed a negative correlation between N4-like viruses and temperature, suggesting that N4-like viruses may be more abundant in colder water. The discrepancy of relative abundance estimates using different methods indicates that N4-like viruses are best represented by native viral sequences. Our study indicates that N4-like viruses are rare in the marine environment and also provide insight into the importance of including local viral sequences in reference databases.
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Affiliation(s)
- Mengqi Sun
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
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Brahim Belhaouari D, Pires De Souza GA, Lamb DC, Kelly SL, Goldstone JV, Stegeman JJ, Colson P, La Scola B, Aherfi S. Metabolic arsenal of giant viruses: Host hijack or self-use? eLife 2022; 11:e78674. [PMID: 35801640 PMCID: PMC9270025 DOI: 10.7554/elife.78674] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/22/2022] [Indexed: 12/11/2022] Open
Abstract
Viruses generally are defined as lacking the fundamental properties of living organisms in that they do not harbor an energy metabolism system or protein synthesis machinery. However, the discovery of giant viruses of amoeba has fundamentally challenged this view because of their exceptional genome properties, particle sizes and encoding of the enzyme machinery for some steps of protein synthesis. Although giant viruses are not able to replicate autonomously and still require a host for their multiplication, numerous metabolic genes involved in energy production have been recently detected in giant virus genomes from many environments. These findings have further blurred the boundaries that separate viruses and living organisms. Herein, we summarize information concerning genes and proteins involved in cellular metabolic pathways and their orthologues that have, surprisingly, been discovered in giant viruses. The remarkable diversity of metabolic genes described in giant viruses include genes encoding enzymes involved in glycolysis, gluconeogenesis, tricarboxylic acid cycle, photosynthesis, and β-oxidation. These viral genes are thought to have been acquired from diverse biological sources through lateral gene transfer early in the evolution of Nucleo-Cytoplasmic Large DNA Viruses, or in some cases more recently. It was assumed that viruses are capable of hijacking host metabolic networks. But the giant virus auxiliary metabolic genes also may represent another form of host metabolism manipulation, by expanding the catalytic capabilities of the host cells especially in harsh environments, providing the infected host cells with a selective evolutionary advantage compared to non-infected cells and hence favoring the viral replication. However, the mechanism of these genes' functionality remains unclear to date.
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Affiliation(s)
- Djamal Brahim Belhaouari
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - Gabriel Augusto Pires De Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
| | - David C Lamb
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Steven L Kelly
- Faculty of Medicine, Health and Life Sciences, Institute of Life Science, Swansea UniversitySwanseaUnited Kingdom
| | - Jared V Goldstone
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic InstitutionWoods HoleUnited States
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), IHU Méditerranée Infection, Marseille, France, Aix-Marseille UniversitéMarseilleFrance
- Assistance Publique - Hôpitaux de Marseille (AP-HM)MarseilleFrance
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Pourhasanzade F, Iyer S, Tjendra J, Landor L, Våge S. Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence. PLoS Comput Biol 2022; 18:e1010228. [PMID: 35675415 PMCID: PMC9212155 DOI: 10.1371/journal.pcbi.1010228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/21/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022] Open
Abstract
Viruses play diverse and important roles in ecosystems. In recent years, trade-offs between host and virus traits have gained increasing attention in viral ecology and evolution. However, microbial organism traits, and viral population parameters in particular, are challenging to monitor. Mathematical and individual-based models are useful tools for predicting virus-host dynamics. We have developed an individual-based evolutionary model to study ecological interactions and evolution between bacteria and viruses, with emphasis on the impacts of trade-offs between competitive and defensive host traits on bacteria-phage population dynamics and trait diversification. Host dynamics are validated with lab results for different initial virus to host ratios (VHR). We show that trade-off based, as opposed to random bacteria-virus interactions, result in biologically plausible evolutionary outcomes, thus highlighting the importance of trade-offs in shaping biodiversity. The effects of nutrient concentration and other environmental and organismal parameters on the virus-host dynamics are also investigated. Despite its simplicity, our model serves as a powerful tool to study bacteria-phage interactions and mechanisms for evolutionary diversification under various environmental conditions.
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Affiliation(s)
| | - Swami Iyer
- Computer Science Department, University of Massachusetts, Boston, Massachusetts, United States of America
| | - Jesslyn Tjendra
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Lotta Landor
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Selina Våge
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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6
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Abstract
Microfluidics has enabled a new era of cellular and molecular assays due to the small length scales, parallelization, and the modularity of various analysis and actuation functions. Droplet microfluidics, in particular, has been instrumental in providing new tools for biology with its ability to quickly and reproducibly generate drops that act as individual reactors. A notable beneficiary of this technology has been single-cell RNA sequencing, which has revealed new heterogeneities and interactions for the fundamental unit of life. However, viruses far surpass the diversity of cellular life, affect the dynamics of all ecosystems, and are a chronic source of global health crises. Despite their impact on the world, high-throughput and high-resolution viral profiling has been difficult, with conventional methods being limited to population-level averaging, large sample volumes, and few cultivable hosts. Consequently, most viruses have not been identified and studied. Droplet microfluidics holds the potential to address many of these limitations and offers new levels of sensitivity and throughput for virology. This Feature highlights recent efforts that have applied droplet microfluidics to the detection and study of viruses, including for diagnostics, virus-host interactions, and cell-independent virus assays. In combination with traditional virology methods, droplet microfluidics should prove a potent tool toward achieving a better understanding of the most abundant biological species on Earth.
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Affiliation(s)
- Wenyang Jing
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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Nasrullah N, Syahrizal S, Kartini K. Analysis of the Content of Escherichia Coli in Public Bathing Pools Before and After Using Visitors. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.9093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: Escherichia coli is a bacterium that commonly causes diarrhea almost all over the world. E. coli can grow well on almost all media commonly used to isolate enteric bacteria. E. coli bacteria are organisms that generally live in the human digestive tract. E. coli bacteria are commonly found in polluted swimming pools, causing its users.
AIM: The aim of this study was to determine the difference in E. coli content in swimming pool water in public baths.
METHODS: The method in this study uses a descriptive survey method. The research location is at the Poltekkes Laboratory of the Ministry of Health, Aceh, October to December 2021. Sampling is at one of the natural attractions used for public baths in the Aceh Besar area. The subject of this research is swimming pool water in public baths for children as much as 5 points of 5 L/point, and adults 5 points of 5 L/point; all water taken is 50 L.
RESULTS: The results showed that before visitors bathed in the swimming pool, the number of E. coli colonies had a minimal average (12.1) with a deviation of 4.977. The distribution of the number of E. coli colonies after 9 h was used by visitors, which had an average E. coli colony of 190.9 with a deviation of 30.490 MPN, who received that the intervention also showed that the number of E. coli colonies after 9 h was very high, with an average of 159.4 and a deviation of 32.898 MPN.
CONCLUSION: There is a difference in the average content of E. coli before and after using public baths by visitors. The number of users of public baths affects the number of microorganisms in the water, such as E. coli and Enterococci.
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Nogueira WG, Gois BVA, Pinheiro KDC, Aragão ADO, Queiroz ALC, da Silva AL, Folador AC, Ramos RTJ. Viral Metagenomics Reveals Widely Diverse Viral Community of Freshwater Amazonian Lake. Front Public Health 2022; 10:869886. [PMID: 35548089 PMCID: PMC9081339 DOI: 10.3389/fpubh.2022.869886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/24/2022] [Indexed: 11/28/2022] Open
Abstract
Despite the importance of understanding the ecology of freshwater viruses, there are not many studies on the subject compared to marine viruses. The microbiological interactions in these environments are still poorly known, especially between bacteriophages and their host bacteria and between cyanophages and cyanobacteria. Lake Bologna, Belém, capital of the Brazilian State of Pará, is a water source that supplies the city and its metropolitan region. However, it remains unexplored regarding the contents of its virome and viral diversity composition. Therefore, this work aims to explore the taxonomic diversity of DNA viruses in this lake, especially bacteriophages and cyanophages, since they can act as transducers of resistance genes and reporters of water quality for human consumption. We used metagenomic sequencing data generated by previous studies. We analyzed it at the taxonomic level using the tools Kraken2, Bracken, and Pavian; later, the data was assembled using Genome Detective, which performs the assembly of viruses. The results observed here suggest the existence of a widely diverse viral community and established microbial phage-regulated dynamics in Lake Bolonha. This work is the first ever to describe the virome of Lake Bolonha using a metagenomic approach based on high-throughput sequencing, as it contributes to the understanding of water-related public health concerns regarding the spreading of antibiotic resistance genes and population control of native bacteria and cyanobacteria.
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Affiliation(s)
| | | | | | - Andressa de Oliveira Aragão
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Brazil
| | | | - Artur Luiz da Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Brazil
| | - Adriana Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Brazil
| | - Rommel Thiago Jucá Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
- *Correspondence: Rommel Thiago Jucá Ramos
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9
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French R, Charon J, Lay CL, Muller C, Holmes EC. Human Land-Use Impacts Viral Diversity and Abundance in a New Zealand River. Virus Evol 2022; 8:veac032. [PMID: 35494173 PMCID: PMC9049113 DOI: 10.1093/ve/veac032] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/11/2022] [Accepted: 04/01/2022] [Indexed: 11/29/2022] Open
Abstract
Although water-borne viruses have important implications for the health of humans and other animals, little is known about the impact of human land use on viral diversity and evolution in water systems such as rivers. We used metatranscriptomic sequencing to compare the diversity and abundance of viruses at sampling sites along a single river in New Zealand that differed in human land-use impacts, ranging from pristine to urban. From this, we identified 504 putative virus species, of which 97 per cent were novel. Many of the novel viruses were highly divergent and likely included a new subfamily within the Parvoviridae. We identified at least sixty-three virus species that may infect vertebrates—most likely fish and water birds—from the Astroviridae, Birnaviridae, Parvoviridae, and Picornaviridae. No putative human viruses were detected. Importantly, we observed differences in the composition of viral communities at sites impacted by human land use (farming and urban) compared to native forest sites (pristine). At the viral species level, the urban sites had higher diversity (327 virus species) than the farming (n = 150) and pristine sites (n = 119), and more viruses were shared between the urban and farming sites (n = 76) than between the pristine and farming or urban sites (n = 24). The two farming sites had a lower viral abundance across all host types, while the pristine sites had a higher abundance of viruses associated with animals, plants, and fungi. We also identified viruses linked to agriculture and human impact at the river sampling sites in farming and urban areas that were not present at the native forest sites. Although based on a small sample size, our study suggests that human land use can impact viral communities in rivers, such that further work is needed to reduce the impact of intensive farming and urbanisation on water systems.
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Affiliation(s)
- Rebecca French
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead NSW 2145, Australia
| | - Justine Charon
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead NSW 2145, Australia
| | - Callum Le Lay
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead NSW 2145, Australia
| | - Chris Muller
- Wildbase, School of Veterinary Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead NSW 2145, Australia
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10
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Urayama SI, Takaki Y, Chiba Y, Zhao Y, Kuroki M, Hagiwara D, Nunoura T. Eukaryotic Microbial RNA Viruses-Acute or Persistent? Insights into Their Function in the Aquatic Ecosystem. Microbes Environ 2022; 37:ME22034. [PMID: 35922920 PMCID: PMC9763035 DOI: 10.1264/jsme2.me22034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Isolated RNA viruses mainly parasitize eukaryotes. RNA viruses either expand horizontally by infecting hosts (acute type) or coexist with the host and are vertically inherited (persistent type). The significance of persistent-type RNA viruses in environmental viromes (the main hosts are expected to be microbes) was only recently reported because they had previously been overlooked in virology. In this review, we summarize the host-virus relationships of eukaryotic microbial RNA viruses. Picornavirales and Reoviridae are recognized as representative acute-type virus families, and most of the microbial viruses in Narnaviridae, Totiviridae, and Partitiviridae are categorized as representative persistent-type viruses. Acute-type viruses have only been found in aquatic environments, while persistent-type viruses are present in various environments, including aquatic environments. Moreover, persistent-type viruses are potentially widely spread in the RNA viral sequence space. This emerging evidence provides novel insights into RNA viral diversity, host-virus relationships, and their history of co-evolution.
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Affiliation(s)
- Syun-ichi Urayama
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan, Corresponding author. E-mail: ; Tel: +81–29–853–6636; Fax: +81–29–853–4605
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yuto Chiba
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Yanjie Zhao
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Misa Kuroki
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Daisuke Hagiwara
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC, 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
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11
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Lu J, Yang S, Zhang X, Tang X, Zhang J, Wang X, Wang H, Shen Q, Zhang W. Metagenomic Analysis of Viral Community in the Yangtze River Expands Known Eukaryotic and Prokaryotic Virus Diversity in Freshwater. Virol Sin 2022; 37:60-69. [PMID: 35234628 PMCID: PMC8922420 DOI: 10.1016/j.virs.2022.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
Viruses in aquatic ecosystems are characterized by extraordinary abundance and diversity. Thus far, there have been limited studies focused on viral communities in river water systems. Here, we investigated the virome of the Yangtze River Delta using viral metagenomic analysis. The compositions of viral communities from six sampling sites were analyzed and compared. By using library construction and next generation sequencing, contigs and singlet reads similar to viral sequences were classified into 17 viral families, including nine dsDNA viral families, four ssDNA viral families and four RNA viral families. Statistical analysis using Friedman test suggested that there was no significant difference among the six sampling sites (P > 0.05). The viromes in this study were all dominated by the order Caudovirales, and a group of Freshwater phage uvFW species were particularly prevalent among all the samples. The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae. Phylogenetic analyses based on virus hallmark genes showed that the Caudovirales order and CRESS-DNA viruses presented high genetic diversity, while viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative. Our study provides the first insight into viral community composition in large river ecosystem, revealing the diversity and stability of river water virome, contributing to the proper utilization of freshwater resource. First insight into viral community composition in large river ecosystem. Virus hallmark genes present both diverse and conservative characteristics. The composition of viral communities is similar on the whole. Slight regional variation of virome is existed in individual areas.
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Viral Characteristics of the Warm Atlantic and Cold Arctic Water Masses in the Nordic Seas. Appl Environ Microbiol 2021; 87:e0116021. [PMID: 34469192 DOI: 10.1128/aem.01160-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nordic Seas are the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean with complex water masses, experiencing an abrupt climate change. Though knowledge of the marine virosphere has expanded rapidly, the diversity of viruses and their relationships with host cells and water masses in the Nordic Seas remain to be fully revealed. Here, we establish the Nordic Sea DNA virome (NSV) data set of 55,315 viral contigs including 1,478 unique viral populations from seven stations influenced by both the warm Atlantic and cold Arctic water masses. Caudovirales dominated in the seven NSVs, especially in the warm Atlantic waters. The major giant nucleocytoplasmic large DNA viruses (NCLDVs) contributed a significant proportion of the classified viral contigs in the NSVs (32.2%), especially in the cold Arctic waters (44.9%). The distribution patterns of Caudovirales and NCLDVs were a reflection of the community structure of their hosts in the corresponding water masses and currents. Latitude, pH, and flow speed were found to be key factors influencing the microbial communities and coinfluencing the variation of viral communities. Network analysis illustrated the tight coupling between the variation of viral communities and microbial communities in the Nordic Seas. This study suggests a probable linkage between viromes, host cells, and surface water masses from both the cool Arctic and warm Atlantic Oceans. IMPORTANCE This is a systematic study of Nordic Sea viromes using metagenomic analysis. The viral diversity, community structure, and their relationships with host cells and the complex water masses from both the cool Arctic and the warm Atlantic oceans were illustrated. The NCLDVs and Caudovirales are proposed as the viral characteristics of the cold Arctic and warm Atlantic waters, respectively. This study provides an important background for the viromes in the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean and sheds light on their responses to abrupt climate change in the future.
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Padilha VA, Alkhnbashi OS, Tran VD, Shah SA, Carvalho ACPLF, Backofen R. Casboundary: automated definition of integral Cas cassettes. Bioinformatics 2021; 37:1352-1359. [PMID: 33226067 PMCID: PMC8208735 DOI: 10.1093/bioinformatics/btaa984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/28/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION CRISPR-Cas are important systems found in most archaeal and many bacterial genomes, providing adaptive immunity against mobile genetic elements in prokaryotes. The CRISPR-Cas systems are encoded by a set of consecutive cas genes, here termed cassette. The identification of cassette boundaries is key for finding cassettes in CRISPR research field. This is often carried out by using Hidden Markov Models and manual annotation. In this article, we propose the first method able to automatically define the cassette boundaries. In addition, we present a Cas-type predictive model used by the method to assign each gene located in the region defined by a cassette's boundaries a Cas label from a set of pre-defined Cas types. Furthermore, the proposed method can detect potentially new cas genes and decompose a cassette into its modules. RESULTS We evaluate the predictive performance of our proposed method on data collected from the two most recent CRISPR classification studies. In our experiments, we obtain an average similarity of 0.86 between the predicted and expected cassettes. Besides, we achieve F-scores above 0.9 for the classification of cas genes of known types and 0.73 for the unknown ones. Finally, we conduct two additional study cases, where we investigate the occurrence of potentially new cas genes and the occurrence of module exchange between different genomes. AVAILABILITY AND IMPLEMENTATION https://github.com/BackofenLab/Casboundary. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Victor A Padilha
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, SP 13566-590, Brazil
| | - Omer S Alkhnbashi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Van Dinh Tran
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Shiraz A Shah
- COPSAC, Copenhagen University Hospitals Herlev and Gentofte, DK-2820 Gentofte, Denmark
| | - André C P L F Carvalho
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, SP 13566-590, Brazil
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
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14
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Łobocka M, Dąbrowska K, Górski A. Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future. BioDrugs 2021; 35:255-280. [PMID: 33881767 PMCID: PMC8084836 DOI: 10.1007/s40259-021-00480-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/20/2022]
Abstract
The current problems with increasing bacterial resistance to antibacterial therapies, resulting in a growing frequency of incurable bacterial infections, necessitates the acceleration of studies on antibacterials of a new generation that could offer an alternative to antibiotics or support their action. Bacteriophages (phages) can kill antibiotic-sensitive as well as antibiotic-resistant bacteria, and thus are a major subject of such studies. Their efficacy in curing bacterial infections has been demonstrated in in vivo experiments and in the clinic. Unlike antibiotics, phages have a narrow range of specificity, which makes them safe for commensal microbiota. However, targeting even only the most clinically relevant strains of pathogenic bacteria requires large collections of well characterized phages, whose specificity would cover all such strains. The environment is a rich source of diverse phages, but due to their complex relationships with bacteria and safety concerns, only some naturally occurring phages can be considered for therapeutic applications. Still, their number and diversity make a detailed characterization of all potentially promising phages virtually impossible. Moreover, no single phage combines all the features required of an ideal therapeutic agent. Additionally, the rapid acquisition of phage resistance by bacteria may make phages already approved for therapy ineffective and turn the search for environmental phages of better efficacy and new specificity into an endless race. An alternative strategy for acquiring phages with desired properties in a short time with minimal cost regarding their acquisition, characterization, and approval for therapy could be based on targeted genome modifications of phage isolates with known properties. The first example demonstrating the potential of this strategy in curing bacterial diseases resistant to traditional therapy is the recent successful treatment of a progressing disseminated Mycobacterium abscessus infection in a teenage patient with the use of an engineered phage. In this review, we briefly present current methods of phage genetic engineering, highlighting their advantages and disadvantages, and provide examples of genetically engineered phages with a modified host range, improved safety or antibacterial activity, and proven therapeutic efficacy. We also summarize novel uses of engineered phages not only for killing pathogenic bacteria, but also for in situ modification of human microbiota to attenuate symptoms of certain bacterial diseases and metabolic, immune, or mental disorders.
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Affiliation(s)
- Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Krystyna Dąbrowska
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
| | - Andrzej Górski
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
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15
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Girard C, Langlois V, Vigneron A, Vincent WF, Culley AI. Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake. Viruses 2020; 12:v12111204. [PMID: 33105728 PMCID: PMC7690404 DOI: 10.3390/v12111204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022] Open
Abstract
Permafrost thaw lakes including thermokarst lakes and ponds are ubiquitous features of Subarctic and Arctic landscapes and are hotspots of microbial activity. Input of terrestrial organic matter into the planktonic microbial loop of these lakes may greatly amplify global greenhouse gas emissions. This microbial loop, dominated in the summer by aerobic microorganisms including phototrophs, is radically different in the winter, when metabolic processes shift to the anaerobic degradation of organic matter. Little is known about the viruses that infect these microbes, despite evidence that viruses can control microbial populations and influence biogeochemical cycling in other systems. Here, we present the results of a metagenomics-based study of viruses in the larger than 0.22 µm fraction across two seasons (summer and winter) in a permafrost thaw lake in Subarctic Canada. We uncovered 351 viral populations (vOTUs) in the surface waters of this lake, with diversity significantly greater during the summer. We also identified and characterized several phage genomes and prophages, which were mostly present in the summer. Finally, we compared the viral community of this waterbody to other habitats and found unexpected similarities with distant bog lakes in North America.
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Affiliation(s)
- Catherine Girard
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC G1V 0A6, Canada; (C.G.); (V.L.)
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
| | - Valérie Langlois
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC G1V 0A6, Canada; (C.G.); (V.L.)
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
| | - Adrien Vigneron
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Warwick F. Vincent
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Alexander I. Culley
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC G1V 0A6, Canada; (C.G.); (V.L.)
- Centre d’études Nordiques (CEN), Université Laval, Québec, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
- Correspondence:
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16
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Abstract
Viruses are extremely diverse and modulate important biological and ecological processes globally. However, much of viral diversity remains uncultured and yet to be discovered. Several powerful culture-independent tools, in particular metagenomics, have substantially advanced virus discovery. Among those tools is single-virus genomics, which yields sequenced reference genomes from individual sorted virus particles without the need for cultivation. This new method complements virus culturing and metagenomic approaches and its advantages include targeted investigation of specific virus groups and investigation of genomic microdiversity within viral populations. In this Review, we provide a brief history of single-virus genomics, outline how this emergent method has facilitated advances in virus ecology and discuss its current limitations and future potential. Finally, we address how this method may synergistically intersect with other single-virus and single-cell approaches.
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17
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Abstract
The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation. High-latitude, perennially stratified (meromictic) lakes are likely to be especially vulnerable to climate warming because of the importance of ice in maintaining their water column structure and associated distribution of microbial communities. This study aimed to characterize viral abundance, diversity, and distribution in a meromictic lake of marine origin on the far northern coast of Ellesmere Island, in the Canadian High Arctic. We collected triplicate samples for double-stranded DNA (dsDNA) viromics from five depths that encompassed the major features of the lake, as determined by limnological profiling of the water column. Viral abundance and virus-to-prokaryote ratios were highest at greater depths, while bacterial and cyanobacterial counts were greatest in the surface waters. The viral communities from each zone of the lake defined by salinity, temperature, and dissolved oxygen concentrations were markedly distinct, suggesting that there was little exchange of viral types among lake strata. Ten viral assembled genomes were obtained from our libraries, and these also segregated with depth. This well-defined structure of viral communities was consistent with that of potential hosts. Viruses from the monimolimnion, a deep layer of ancient Arctic Ocean seawater, were more diverse and relatively abundant, with few similarities to available viral sequences. The Lake A viral communities also differed from published records from the Arctic Ocean and meromictic Ace Lake in Antarctica. This first characterization of viral diversity from this sentinel environment underscores the microbial richness and complexity of an ecosystem type that is increasingly exposed to major perturbations in the fast-changing Arctic. IMPORTANCE The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation.
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18
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Zhao Y, Zhao Y, Zheng S, Zhao L, Li X, Zhang W, Grégori G, Xiao T. Virioplankton distribution in the tropical western Pacific Ocean in the vicinity of a seamount. Microbiologyopen 2020; 9:1207-1224. [PMID: 32180355 PMCID: PMC7294315 DOI: 10.1002/mbo3.1031] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/24/2020] [Accepted: 02/27/2020] [Indexed: 11/05/2022] Open
Abstract
The shallow Caroline Seamount is located in the tropical western Pacific Ocean. Its summit is 57 m below the surface and penetrates the euphotic zone. Therefore, it is ideal for the study of the influence of seamount on plankton distribution. Here, virioplankton abundance and distribution were investigated by flow cytometry (FCM) in the Caroline Seamount in August and September 2017. The total abundance of virus‐like particles (VLP) was in the range of 0.64 × 106–18.77 × 106 particles/ml and the average was 5.37 ± 3.75 × 106 particles/ml. Three to four distinct viral subclusters with similar side scatter but different green fluorescence intensities were identified. Above the deep chlorophyll maximum (DCM), two medium fluorescence virus (MFV) subclusters were discriminated. Between the DCM and the deeper layers, only one MFV subcluster was resolved. In general, low fluorescence viruses (LFV) comprised the most abundant subclusters. In the 75–150 m water column, however, the MFV abundance was higher than the LFV abundance. High fluorescence viruses (HFV) constituted the least abundant subcluster throughout the entire water column. Virioplankton abundance was significantly enhanced at the seamount stations. Environmental factors including water temperature and nitrate concentration were the most correlated with the variation in virioplankton abundance at the seamount stations. Interactions between shallow seamounts and local currents can support large virus standing stocks, causing a so‐called indirect “seamount effect” on the virioplankton.
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Affiliation(s)
- Yanchu Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shan Zheng
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Jiaozhou Bay Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xuegang Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Wuchang Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Gérald Grégori
- Aix-Marseille University, Toulon University, CNRS, IRD, Mediterranean Institute of Oceanography UM110, Marseille, France
| | - Tian Xiao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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19
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Turan T, Isidan H, Atasoy MO, Sozdutmaz İ, Bulut H. GENETIC DIVERSITY of OVINE HERPESVIRUS 2 STRAINS OBTAINED FROM MALIGNANT CATARRHAL FEVER CASES in EASTERN TURKEY. Virus Res 2019; 276:197801. [PMID: 31722243 DOI: 10.1016/j.virusres.2019.197801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 11/18/2022]
Abstract
Malignant Catarrhal Fever (MCF) is a generalized, definitive lethal disease affecting the epithelial and lymphoid tissues of the respiratory and digestive tract, mainly cattle and some wild ruminants such as deer, buffalo or antelope. The sheep-related form of MCF is known to be present in Turkey and is caused by ovine herpesvirus 2 (OvHV-2). The aim of this study was to reveal the genetic diversity of OvHV-2 strains obtained from MCF cases in Eastern Turkey where the livestock industry has an important impact on economic activities. For this purpose, RTA (Replication and transcription activator), FGARAT (formylglycineamide ribotide amidotransferase) and some of glycoprotein genes (Ov7, Ov8 ex2, ORF27 and Ov9.5) were investigated in blood samples from 24 cattles, clinically diagnosed with MCF. Genomic data of chosen samples were furthermore used to characterize and undergo combined phylogenetic analysis to determine possible alleles and subvariants. The results showed that high level of OvHV-2 diversity existed in selected genes and strains carrying allelic variants might circulate both in two geographically distinct regions and in a region itself. Moreover, three different OvHV-2 types and various subtypes were identified based on multi locus approach. This study provides important data to epidemiological research and thereby helps to determine the source of the virus and understand the spread of the disease.
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Affiliation(s)
- Turhan Turan
- Sivas Cumhuriyet University Faculty of Veterinary Medicine, Department of Veterinary Virology, 58140, Sivas, Turkey.
| | - Hakan Isidan
- Sivas Cumhuriyet University Faculty of Veterinary Medicine, Department of Veterinary Virology, 58140, Sivas, Turkey.
| | - Mustafa Ozan Atasoy
- Sivas Cumhuriyet University Faculty of Veterinary Medicine, Department of Veterinary Virology, 58140, Sivas, Turkey.
| | - İbrahim Sozdutmaz
- Erciyes University Faculty of Veterinary Medicine, Department of Veterinary Virology, 38280, Kayseri, Turkey.
| | - Hakan Bulut
- Namik Kemal University Faculty of Veterinary Medicine, Department of Veterinary Virology, 59030, Tekirdag, Turkey.
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20
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Abstract
Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution. RNA viruses, particularly genetically diverse members of the Picornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, and Heterosigma akashiwo RNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans. IMPORTANCE Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.
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21
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Abstract
In the past, viruses were considered nonliving infectious particles, little more than genetic material wrapped in a protein capsid. Today, virologists are beginning to think of viruses as living organisms that can be classified phylogenetically into defined species, much like any other living organism. The primary reasons for this shift in attitude can be partially attributed to the discovery of giant viruses, having large genomes and complex regulatory systems. Aside from that, it has become obvious that viruses lead complex lives; they evolve, speciate, and participate in the evolution of all classes of living organisms. In this chapter, we will discuss the early attempts to classify viruses, and review the biologic properties of the classes of virus that contain human pathogens.
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22
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Garin-Fernandez A, Pereira-Flores E, Glöckner FO, Wichels A. The North Sea goes viral: Occurrence and distribution of North Sea bacteriophages. Mar Genomics 2018; 41:31-41. [PMID: 29866485 DOI: 10.1016/j.margen.2018.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/19/2018] [Accepted: 05/19/2018] [Indexed: 01/17/2023]
Abstract
Marine viruses are dominated by phages and have an enormous influence on microbial population dynamics, due to lysis and horizontal gene transfer. The aim of this study is to analyze the occurrence and diversity of phages in the North Sea, considering the virus-host interactions and biogeographic factors. The virus community of four sampling stations were described using virus metagenomics (viromes). The results show that the virus community was not evenly distributed throughout the North Sea. The dominant phage members were identified as unclassified phage group, followed by Caudovirales order. Myoviridae was the dominant phage family in the North Sea, which occurrence decreased from the coast to the open sea. In contrast, the occurrence of Podoviridae increased and the occurrence of Siphoviridae was low throughout the North Sea. The occurrence of other groups such as Phycodnaviridae decreased from the coast to the open sea. The coastal virus community was genetically more diverse than the open sea community. The influence of riverine inflow and currents, for instance the English Channel flow affects the genetic virus diversity with the community carrying genes from a variety of metabolic pathways and other functions. The present study offers the first insights in the virus community in the North Sea using viromes and shows the variation in virus diversity and the genetic information moved from coastal to open sea areas.
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23
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Wang Y, Jiang X, Liu L, Li B, Zhang T. High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:10337-10346. [PMID: 30148618 DOI: 10.1021/acs.est.8b03446] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Wastewater treatment plants (WWTPs) are considered reservoirs of viruses, but the diversity and dynamic changes of viruses are not well understood. In this study, we recovered 8478 metagenomic viral contigs (mVCs; >5 kb) from two WWTPs (Shatin, 2806; Shek Wu Hui, 5672) in Hong Kong. Approximately 60% of the mVCs were poorly covered (<35% of genes in identified mVCs) by the current NCBI and IMG/VR viral databases. The temporal profile of the newly identified mVCs among 98 Shatin AS samples collected monthly (for approximately 9 years) revealed the presence of periodic dynamics at an interval of approximately one year (341 days). The spatial distribution pattern of the virome in the wastewater treatment systems showed that shared viral clusters (viral populations categorized based on shared gene content and network analysis) can be globally found among similar samples of wastewater treatment systems, indicating the presence of core viral communities among geographically isolated wastewater treatment systems. These results not only supplemented the current virome database of engineered systems but also, to some extent, expanded the understanding of long-term cyclical development and spatial distributions of viral communities in wastewater treatment systems.
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Affiliation(s)
- Yulin Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong
| | - Lei Liu
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong
| | - Bing Li
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong
- Division of Energy and Environment , Graduate School at Shenzhen, Tsinghua University , Shenzhen , 518055 , China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering , The University of Hong Kong , Pokfulam Road , Hong Kong
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24
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Urayama SI, Takaki Y, Nishi S, Yoshida-Takashima Y, Deguchi S, Takai K, Nunoura T. Unveiling the RNA virosphere associated with marine microorganisms. Mol Ecol Resour 2018; 18:1444-1455. [PMID: 30256532 DOI: 10.1111/1755-0998.12936] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/28/2018] [Indexed: 01/01/2023]
Abstract
The study of extracellular DNA viral particles in the ocean is currently one of the most advanced fields of research in viral metagenomic analysis. However, even though the intracellular viruses of marine microorganisms might be the major source of extracellular virus particles in the ocean, the diversity of these intracellular viruses is not well understood. Here, our newly developed method, referred to herein as fragmented and primer ligated dsRNA sequencing (flds) version 2, identified considerable genetic diversity of marine RNA viruses in cell fractions obtained from surface seawater. The RNA virus community appears to cover genome sequences related to more than half of the established positive-sense ssRNA and dsRNA virus families, in addition to a number of unidentified viral lineages, and such diversity had not been previously observed in floating viral particles. In this study, more dsRNA viral contigs were detected in host cells than in extracellular viral particles. This illustrates the magnitude of the previously unknown marine RNA virus population in cell fractions, which has only been partially assessed by cellular metatranscriptomics and not by contemporary viral metagenomic studies. These results reveal the importance of studying cell fractions to illuminate the full spectrum of viral diversity on Earth.
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Affiliation(s)
- Syun-Ichi Urayama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.,Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshihiro Takaki
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.,Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka, Kanagawa, Japan.,Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Japan
| | - Shinro Nishi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.,Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Japan
| | - Yukari Yoshida-Takashima
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Shigeru Deguchi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.,Ecosystem Observation and Evaluation Methodology Research Unit, Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Japan
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25
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Lázaro E, Arribas M, Cabanillas L, Román I, Acosta E. Evolutionary adaptation of an RNA bacteriophage to the simultaneous increase in the within-host and extracellular temperatures. Sci Rep 2018; 8:8080. [PMID: 29795535 PMCID: PMC5967308 DOI: 10.1038/s41598-018-26443-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/11/2018] [Indexed: 01/09/2023] Open
Abstract
Bacteriophages are the most numerous biological entities on Earth. They are on the basis of most ecosystems, regulating the diversity and abundance of bacterial populations and contributing to the nutrient and energy cycles. Bacteriophages have two well differentiated phases in their life cycle, one extracellular, in which they behave as inert particles, and other one inside their hosts, where they replicate to give rise to a progeny. In both phases they are exposed to environmental conditions that often act as selective pressures that limit both their survival in the environment and their ability to replicate, two fitness traits that frequently cannot be optimised simultaneously. In this study we have analysed the evolutionary ability of an RNA bacteriophage, the bacteriophage Qβ, when it is confronted with a temperature increase that affects both the extracellular and the intracellular media. Our results show that Qβ can optimise its survivability when exposed to short-term high temperature extracellular heat shocks, as well as its replicative ability at higher-than-optimal temperature. Mutations responsible for simultaneous adaptation were the same as those selected when adaptation to each condition proceeded separately, showing the absence of important trade-offs between survival and reproduction in this virus.
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Affiliation(s)
- Ester Lázaro
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain. .,Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| | - María Arribas
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Laura Cabanillas
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Ismael Román
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Esther Acosta
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Ctra de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
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26
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Abstract
Viruses represent the most abundant and diverse of the biological entities in environmental waters, including the seas and probably also freshwater systems. They are important players in ecological networks in waters and influence global biochemical cycling and community composition dynamics. Among the many diverse viruses from terrestrial environments found in environmental waters, some are plant, animal, and/or human pathogens. The majority of pathogenic viral species found in waters are very stable and can survive outside host cells for long periods. The occurrence of such viruses in environmental waters has raised concerns because of the confirmation of the infectivity of waterborne viruses even at very low concentrations. This chapter focuses mainly on the survival of human, animal, and plant pathogenic viruses in aqueous environments, the possibility of their water-mediated transmission, the ecological implications of viruses in water, the methods adapted for detecting such viruses, and how to minimize the risk of viruses spreading through water.
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27
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Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? ZOOLOGY 2018; 127:1-19. [DOI: 10.1016/j.zool.2018.02.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
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28
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Krüger A, Burgán J, Friedrich AW, Rossen JWA, Lucchesi PMA. ArgO145, a Stx2a prophage of a bovine O145:H- STEC strain, is closely related to phages of virulent human strains. INFECTION GENETICS AND EVOLUTION 2018; 60:126-132. [PMID: 29476813 DOI: 10.1016/j.meegid.2018.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 01/18/2018] [Accepted: 02/17/2018] [Indexed: 01/08/2023]
Abstract
Shiga toxins (Stx) are the main virulence factor of a pathogroup of Escherichia coli strains that cause severe human diseases. These toxins are encoded in prophages (Stx prophages), and generally their expression depends on prophage induction. Several studies have reported high diversity among both Stx prophages and Stx. In particular, the toxin subtype Stx2a is associated with high virulence and HUS. Here, we report the genome of ArgO145, an inducible Stx2a prophage identified in a bovine O145:H- strain which produced high levels of Shiga toxin and Stx phage particles. The ArgO145 genome shared lambda phage organization, with recombination, regulation, replication, lysis, and head and tail structural gene regions, although some lambda genes encoding regulatory proteins could not be identified. Remarkably, some Stx2a phages of strains isolated from patients in other countries showed high similarity to ArgO145.
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Affiliation(s)
- A Krüger
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CONICET-CIC, Laboratorio de Inmunoquímica y Biotecnología, Argentina.
| | - J Burgán
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CONICET-CIC, Laboratorio de Inmunoquímica y Biotecnología, Argentina
| | - A W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands
| | - J W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands
| | - P M A Lucchesi
- Centro de Investigación Veterinaria de Tandil (CIVETAN), UNCPBA-CONICET-CIC, Laboratorio de Inmunoquímica y Biotecnología, Argentina
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29
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Deposition rates of viruses and bacteria above the atmospheric boundary layer. ISME JOURNAL 2018; 12:1154-1162. [PMID: 29379178 DOI: 10.1038/s41396-017-0042-4] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/10/2017] [Accepted: 12/09/2017] [Indexed: 11/09/2022]
Abstract
Aerosolization of soil-dust and organic aggregates in sea spray facilitates the long-range transport of bacteria, and likely viruses across the free atmosphere. Although long-distance transport occurs, there are many uncertainties associated with their deposition rates. Here, we demonstrate that even in pristine environments, above the atmospheric boundary layer, the downward flux of viruses ranged from 0.26 × 109 to >7 × 109 m-2 per day. These deposition rates were 9-461 times greater than the rates for bacteria, which ranged from 0.3 × 107 to >8 × 107 m-2 per day. The highest relative deposition rates for viruses were associated with atmospheric transport from marine rather than terrestrial sources. Deposition rates of bacteria were significantly higher during rain events and Saharan dust intrusions, whereas, rainfall did not significantly influence virus deposition. Virus deposition rates were positively correlated with organic aerosols <0.7 μm, whereas, bacteria were primarily associated with organic aerosols >0.7 μm, implying that viruses could have longer residence times in the atmosphere and, consequently, will be dispersed further. These results provide an explanation for enigmatic observations that viruses with very high genetic identity can be found in very distant and different environments.
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30
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Danovaro R, Corinaldesi C, Dell'Anno A, Rastelli E. Potential impact of global climate change on benthic deep-sea microbes. FEMS Microbiol Lett 2018; 364:4553516. [PMID: 29045616 DOI: 10.1093/femsle/fnx214] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/12/2017] [Indexed: 11/12/2022] Open
Abstract
Benthic deep-sea environments are the largest ecosystem on Earth, covering ∼65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH) and indirectly (through changes in surface oceans' productivity and in the consequent export of organic matter to the seafloor). However, the responses of the benthic deep-sea biota to such shifts remain largely unknown. This applies particularly to deep-sea microbes, which include bacteria, archaea, microeukaryotes and their viruses. Understanding the potential impacts of global change on the benthic deep-sea microbial assemblages and the consequences on the functioning of the ocean interior is a priority to better forecast the potential consequences at global scale. Here we explore the potential changes in the benthic deep-sea microbiology expected in the coming decades using case studies on specific systems used as test models.
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Affiliation(s)
- Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Cinzia Corinaldesi
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Eugenio Rastelli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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31
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Culley A. New insight into the RNA aquatic virosphere via viromics. Virus Res 2017; 244:84-89. [PMID: 29138044 DOI: 10.1016/j.virusres.2017.11.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 01/09/2023]
Abstract
RNA viruses that infect microbes are now recognized as an active, persistent and important component of the aquatic microbial community. While some information about the diversity and dynamics of the RNA virioplankton has been derived from culture-based and single gene approaches, research based on viromic and metatransciptomic methods has generated unprecedented insight into this relatively understudied class of microbes. Here, the relevant literature is summarized and discussed, including viromic studies of extracellular aquatic RNA viral assemblages, and transcriptomic studies of active and associated RNA viruses from aquatic environments followed by commentary on the present challenges and future directions of this field of research.
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Affiliation(s)
- Alexander Culley
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Québec, G1V 0A6, Canada; Centre d'études nordiques (CEN), Université Laval, Québec, Québec, G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada; Takuvik, Unité Mixte Interntionale (UMI 3376) Université Laval (Canada) & Centre National de la Recherche Scientifique (France), Québec QC GIV 0A6, Canada.
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32
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Rastelli E, Corinaldesi C, Dell'Anno A, Tangherlini M, Martorelli E, Ingrassia M, Chiocci FL, Lo Martire M, Danovaro R. High potential for temperate viruses to drive carbon cycling in chemoautotrophy-dominated shallow-water hydrothermal vents. Environ Microbiol 2017; 19:4432-4446. [DOI: 10.1111/1462-2920.13890] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/06/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Eugenio Rastelli
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn; Villa Comunale; Naples 80121 Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Michael Tangherlini
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Eleonora Martorelli
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
| | - Michela Ingrassia
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
- Department of Earth Science; University of Rome Sapienza; Rome Italy
| | - Francesco L. Chiocci
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
- Department of Earth Science; University of Rome Sapienza; Rome Italy
| | - Marco Lo Martire
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn; Villa Comunale; Naples 80121 Italy
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33
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Affiliation(s)
- Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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