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Butina TV, Bukin YS, Krasnopeev AS, Belykh OI, Tupikin AE, Kabilov MR, Sakirko МV, Belikov SI. Estimate of the diversity of viral and bacterial assemblage in the coastal water of Lake Baikal. FEMS Microbiol Lett 2020; 366:5484837. [PMID: 31049590 DOI: 10.1093/femsle/fnz094] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/30/2019] [Indexed: 12/27/2022] Open
Abstract
In this study, we analysed the diversity and composition of double-stranded DNA viral and bacterial communities within the sample of surface coastal water of Southern Baikal through metagenomics and deep sequencing of the 16S ribosomal RNA gene, respectively. The 16S rRNA gene analysis has revealed 14 phyla and dominance of the 'Actinobacteria' (43.6%), 'Proteobacteria' (25.2%) and 'Bacteroidetes' (11.5%). The bacterial composition was similar to that obtained previously in Lake Baikal littoral zone. Out of 1 030 169 processed virome reads, 37.4% of sequences (385 421) were identified as viral; 15.1% were identified as nonviral and related to the domains Eukarya, Bacteria and Archaea; and 47.5% had no matches in the databases. The identified virotypes belonged to different families and were predicted to infect a wide range of organisms, from bacteria to mammals. Six families (Myoviridae, Poxviridae, Mimiviridae, Siphoviridae, Phycodnaviridae and Podoviridae) were dominant accounting for more than 90% of the identified sequences (48.3%, 17.4%, 8.3%, 6.8%, 5.8% and 4.1%, respectively). In contrast to other freshwater systems, high percentage of the Poxviridae and Mimiviridae was recorded in the water sample of Lake Baikal.
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Affiliation(s)
- Tatyana V Butina
- Laboratory of Analytical and Bioorganic Chemistry, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia
| | - Yurij S Bukin
- Laboratory of Genosystematics, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia.,Department of Biotechnology and Bioinformatics, National Research Irkutsk State Technical University, 83, Lermontov street, Irkutsk, 664074, Russia
| | - Andrey S Krasnopeev
- Laboratory of Aquatic Microbiology, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia
| | - Olga I Belykh
- Laboratory of Aquatic Microbiology, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia
| | - Aleksey E Tupikin
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Avenue, Novosibirsk, 630090, Russia
| | - Marsel R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Avenue, Novosibirsk, 630090, Russia
| | - Мaria V Sakirko
- Laboratory of Hydrochemistry and Atmosphere Chemistry, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia
| | - Sergey I Belikov
- Laboratory of Analytical and Bioorganic Chemistry, Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya street, Irkutsk, 664033, Russia
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Bonetti G, Trevathan-Tackett SM, Carnell PE, Macreadie PI. Implication of Viral Infections for Greenhouse Gas Dynamics in Freshwater Wetlands: Challenges and Perspectives. Front Microbiol 2019; 10:1962. [PMID: 31507569 PMCID: PMC6718870 DOI: 10.3389/fmicb.2019.01962] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/09/2019] [Indexed: 01/07/2023] Open
Abstract
Viruses are non-living, acellular entities, and the most abundant biological agents on earth. They are widely acknowledged as having the capacity to influence global biogeochemical cycles by infecting the bacterial and archaeal populations that regulate carbon and nutrient turnover. Evidence suggests that the majority of viruses in wetlands are bacteriophages, but despite their importance, studies on how viruses control the prokaryotic community and the concomitant impacts on ecosystem function (such as carbon cycling and greenhouse gas flux) in wetlands are rare. Here we investigate virus-prokaryote interactions in freshwater wetland ecosystems in the context of their potential influence on biogeochemical cycling. Specifically, we (1) synthesize existing literature to establish current understanding of virus-prokaryote interactions, focusing on the implications for wetland greenhouse gas dynamics and (2) identify future research priorities. Viral dynamics in freshwater wetlands have received much less attention compared to those in marine ecosystems. However, based on our literature review, within the last 10 years, viral ecology studies on freshwater wetlands have increased twofold. Despite this increase in literature, the potential implication of viral infections on greenhouse gas emission dynamics is still a knowledge gap. We hypothesize that the rate of greenhouse gas emissions and the pool of sequestered carbon could be strongly linked to the type and rate of viral infection. Viral replication mechanism choice will consequently influence the microbial efficiency of organic matter assimilation and thus the ultimate fate of carbon as a greenhouse gas or stored in soils.
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Affiliation(s)
- Giuditta Bonetti
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Stacey M Trevathan-Tackett
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Paul E Carnell
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Peter I Macreadie
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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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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Cadwell K, Niranji SS, Armstrong VL, Mowbray CA, Bailey R, Watson KA, Hall J. AvBD1 nucleotide polymorphisms, peptide antimicrobial activities and microbial colonisation of the broiler chicken gut. BMC Genomics 2017; 18:637. [PMID: 28821240 PMCID: PMC5563022 DOI: 10.1186/s12864-017-4034-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 08/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The importance of poultry as a global source of protein underpins the chicken genome and associated SNP data as key tools in selecting and breeding healthy robust birds with improved disease resistance. SNPs affecting host peptides involved in the innate defences tend to be rare, but three non-synonymous SNPs in the avian β-defensin (AvBD1) gene encoding the variant peptides NYH, SSY and NYY were identified that segregated specifically to three lines of commercial broiler chickens Line X (LX), Line Y(LY) and Line Z. The impacts of such amino acid changes on peptide antimicrobial properties were analysed in vitro and described in relation to the caecal microbiota and gut health of LX and LY birds. RESULTS Time-kill and radial immune diffusion assays indicated all three peptides to have antimicrobial properties against gram negative and positive bacteria with a hierarchy of NYH > SSY > NYY. Calcein leakage assays supported AvBD1 NYH as the most potent membrane permeabilising agent although no significant differences in secondary structure were identified to explain this. However, distinct claw regions, identified by 3D modelling and proposed to play a key role in microbial membrane attachment, and permeation, were more distinct in the NYH model. In vivo AvBD1 synthesis was detected in the bird gut epithelia. Analyses of the caecal gut microbiota of young day 4 birds suggested trends in Lactobacilli sp. colonisation at days 4 (9% LX vs × 30% LY) and 28 (20% LX vs 12% LY) respectively, but these were not statistically significant (P > 0.05). CONCLUSION Amino acid changes altering the killing capacity of the AvBD1 peptide were associated with two different bird lines, but such changes did not impact significantly on caecal gut microbiota.
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Affiliation(s)
- Kevin Cadwell
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Sherko S Niranji
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Present address: College of Veterinary Medicine, University of Sulaimani, Sulaymaniyah, Iraq
| | - Vanessa L Armstrong
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Present address: School of Biomedical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Catherine A Mowbray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | | | | | - Judith Hall
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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Kim Y, Aw TG, Teal TK, Rose JB. Metagenomic Investigation of Viral Communities in Ballast Water. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:8396-407. [PMID: 26107908 DOI: 10.1021/acs.est.5b01633] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Ballast water is one of the most important vectors for the transport of non-native species to new aquatic environments. Due to the development of new ballast water quality standards for viruses, this study aimed to determine the taxonomic diversity and composition of viral communities (viromes) in ballast and harbor waters using metagenomics approaches. Ballast waters from different sources within the North America Great Lakes and paired harbor waters were collected around the Port of Duluth-Superior. Bioinformatics analysis of over 550 million sequences showed that a majority of the viral sequences could not be assigned to any taxa associated with reference sequences, indicating the lack of knowledge on viruses in ballast and harbor waters. However, the assigned viruses were dominated by double-stranded DNA phages, and sequences associated with potentially emerging viral pathogens of fish and shrimp were detected with low amino acid similarity in both ballast and harbor waters. Annotation-independent comparisons showed that viromes were distinct among the Great Lakes, and the Great Lakes viromes were closely related to viromes of other cold natural freshwater systems but distant from viromes of marine and human designed/managed freshwater systems. These results represent the most detailed characterization to date of viruses in ballast water, demonstrating their diversity and the potential significance of the ship-mediated spread of viruses.
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Affiliation(s)
- Yiseul Kim
- †Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tiong Gim Aw
- ‡Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tracy K Teal
- †Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Joan B Rose
- †Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- ‡Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan 48824, United States
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Alhamlan F, Ederer M, Brown C, Coats E, Crawford R. Metagenomics-based analysis of viral communities in dairy lagoon wastewater. J Microbiol Methods 2013; 92:183-8. [DOI: 10.1016/j.mimet.2012.11.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 11/24/2012] [Indexed: 10/27/2022]
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Leese F, Brand P, Rozenberg A, Mayer C, Agrawal S, Dambach J, Dietz L, Doemel JS, Goodall-Copstake WP, Held C, Jackson JA, Lampert KP, Linse K, Macher JN, Nolzen J, Raupach MJ, Rivera NT, Schubart CD, Striewski S, Tollrian R, Sands CJ. Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology. PLoS One 2012. [PMID: 23185309 PMCID: PMC3504011 DOI: 10.1371/journal.pone.0049202] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
High throughput sequencing technologies are revolutionizing genetic research. With this “rise of the machines”, genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02–25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests bioinformatic analysis workflows. The results also advise a more sophisticated filtering for problematic sequences and non-target genome sequences prior to developing markers.
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Affiliation(s)
- Florian Leese
- Ruhr University Bochum, Department of Animal Ecology, Evolution and Biodiversity, Bochum, Germany.
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Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara. ISME JOURNAL 2012; 7:359-69. [PMID: 23038177 PMCID: PMC3554411 DOI: 10.1038/ismej.2012.101] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Here, we present the first metagenomic study of viral communities from four perennial ponds (gueltas) located in the central Sahara (Mauritania). Three of the four gueltas (Ilij, Molomhar and Hamdoun) are located at the source of three different wadis belonging to the same hydrologic basin, whereas the fourth (El Berbera) belongs to a different basin. Overall, sequences belonging to tailed bacteriophages were the most abundant in all four metagenomes although electron microscopy and sequencing confirmed the presence of other viral groups, such as large DNA viruses. We observed a decrease in the local viral biodiversity in El Berbera, a guelta with sustained human activities, compared with the pristine Ilij and Molomhar, and sequences related to viruses infecting crop pests were also detected as a probable consequence of the agricultural use of the soil. However, the structure of the El Berbera viral community shared the common global characteristics of the pristine gueltas, that is, it was dominated by Myoviridae and, more particularly, by virulent phages infecting photosynthetic cyanobacteria, such as Prochlorococcus and Synechococcus spp. In contrast, the Hamdoun viral community was characterized by a larger proportion of phages with the potential for a temperate lifestyle and by dominant species related to phages infecting heterotrophic bacteria commonly found in terrestrial environments. We hypothesized that the differences observed in the structural and functional composition of the Hamdoun viral community resulted from the critically low water level experienced by the guelta.
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Smith DL, Rooks DJ, Fogg PCM, Darby AC, Thomson NR, McCarthy AJ, Allison HE. Comparative genomics of Shiga toxin encoding bacteriophages. BMC Genomics 2012; 13:311. [PMID: 22799768 PMCID: PMC3430580 DOI: 10.1186/1471-2164-13-311] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 07/01/2012] [Indexed: 01/21/2023] Open
Abstract
Background Stx bacteriophages are responsible for driving the dissemination of Stx toxin genes (stx) across their bacterial host range. Lysogens carrying Stx phages can cause severe, life-threatening disease and Stx toxin is an integral virulence factor. The Stx-bacteriophage vB_EcoP-24B, commonly referred to as Ф24B, is capable of multiply infecting a single bacterial host cell at a high frequency, with secondary infection increasing the rate at which subsequent bacteriophage infections can occur. This is biologically unusual, therefore determining the genomic content and context of Ф24B compared to other lambdoid Stx phages is important to understanding the factors controlling this phenomenon and determining whether they occur in other Stx phages. Results The genome of the Stx2 encoding phage, Ф24B was sequenced and annotated. The genomic organisation and general features are similar to other sequenced Stx bacteriophages induced from Enterohaemorrhagic Escherichia coli (EHEC), however Ф24B possesses significant regions of heterogeneity, with implications for phage biology and behaviour. The Ф24B genome was compared to other sequenced Stx phages and the archetypal lambdoid phage, lambda, using the Circos genome comparison tool and a PCR-based multi-loci comparison system. Conclusions The data support the hypothesis that Stx phages are mosaic, and recombination events between the host, phages and their remnants within the same infected bacterial cell will continue to drive the evolution of Stx phage variants and the subsequent dissemination of shigatoxigenic potential.
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Affiliation(s)
- Darren L Smith
- Microbiology Research Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
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Abstract
Most of the microorganisms responsible for nutrient cycling in the environment have yet to be cultivated, and this could include those species responsible for the degradation of cellulose. Known cellulases are well defined at the protein sequence level, but gene variants are difficult to amplify from environmental DNA. The identification of novel cellulase genes independent of DNA amplification is made possible by adopting a direct metagenome sequencing approach to provide genes that can be cloned, expressed, and characterized prior to potential exploitation, all in the absence of any information on the species from which they originated. In this chapter, emerging strategies and methods that will enable the identification of novel cellulase genes and provide an unbiased perspective on gene expression in situ are presented.
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Affiliation(s)
- David J Rooks
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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