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Chen PWY, Olivia M, Gong GC, Jan S, Tsai AY. Viral Dynamics in the Tropical Pacific Ocean: A Comparison between Within and Outside a Warm Eddy. Viruses 2024; 16:937. [PMID: 38932229 PMCID: PMC11209615 DOI: 10.3390/v16060937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/02/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
In mesoscale eddies, the chemical properties and biological composition are different from those in the surrounding water due to their unique physical processes. The mechanism of physical-biological coupling in warm-core eddies is unclear, especially because no studies have examined the effects of environmental factors on bacteria and viruses. The purpose of the present study was to examine the influence of an anticyclonic warm eddy on the relationship between bacterial and viral abundances, as well as viral activity (viral production), at different depths. At the core of the warm eddy, the bacterial abundance (0.48 to 2.82 × 105 cells mL-1) fluctuated less than that outside the eddy (1.12 to 7.03 × 105 cells mL-1). In particular, there was a four-fold higher viral-bacterial abundance ratio (VBR) estimated within the eddy, below the layer of the deep chlorophyll maximum, than outside the eddy. An anticyclonic warm eddy with downwelling at its center may contribute to viruses being transmitted directly into the deep ocean through adsorption on particulate organic matter while sinking. Overall, our findings provide valuable insights into the interaction between bacterial and viral abundances and their ecological mechanisms within a warm eddy.
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Affiliation(s)
- Patrichka Wei-Yi Chen
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
| | - Madeline Olivia
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
| | - Gwo-Ching Gong
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202-24, Taiwan
| | - Sen Jan
- Institute of Oceanography, National Taiwan University, Taipei 106319, Taiwan;
| | - An-Yi Tsai
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; (P.W.-Y.C.); (M.O.); (G.-C.G.)
- Doctoral Degree Program in Ocean Resource and Environmental Changes, National Taiwan Ocean University, Keelung 202-24, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202-24, Taiwan
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Zhou K, Zhou H. Distribution patterns and functional diversity of DNA viruses determined by ecological niches in huge river ecosystems. Virology 2024; 593:110015. [PMID: 38359578 DOI: 10.1016/j.virol.2024.110015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/13/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
While the vast number of DNA and RNA viruses participate in biogeochemical cycles in natural systems, little is known about virome in river ecosystems. Here, we analyzed the DNA viral composition and its metabolic potential in the Yangtze River, including freshwater (FW) and freshwater sediments (FWS). A total of 1237 river-derived virus contigs (RVCs) were obtained following de novo assembly from 62 metagenomics. We found that the viral diversity is significantly positively correlated longitudinally. Moreover, FW exhibited a greater viral variety and significantly different composition than FWS. The viral co-occurrence network suggested that positive correlations predominate between RVCs. Lastly, 1657 viral functions were predicted by gene ontology. Notably, 96 of 150 RVCs with higher weights identified by random-forest classier were more abundant in FW, which most engage organic cyclic compound metabolic processes and hydrolase activity. Together, this study highlights the previously unrecognized viruses and the importance of their distributions and functions in major river systems.
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Affiliation(s)
- Kang Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Hui Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
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3
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Potapov S, Gorshkova A, Krasnopeev A, Podlesnaya G, Tikhonova I, Suslova M, Kwon D, Patrushev M, Drucker V, Belykh O. RNA-Seq Virus Fraction in Lake Baikal and Treated Wastewaters. Int J Mol Sci 2023; 24:12049. [PMID: 37569424 PMCID: PMC10418309 DOI: 10.3390/ijms241512049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
In this study, we analyzed the transcriptomes of RNA and DNA viruses from the oligotrophic water of Lake Baikal and the effluent from wastewater treatment plants (WWTPs) discharged into the lake from the towns of Severobaikalsk and Slyudyanka located on the lake shores. Given the uniqueness and importance of Lake Baikal, the issues of biodiversity conservation and the monitoring of potential virological hazards to hydrobionts and humans are important. Wastewater treatment plants discharge treated effluent directly into the lake. In this context, the identification and monitoring of allochthonous microorganisms entering the lake play an important role. Using high-throughput sequencing methods, we found that dsDNA-containing viruses of the class Caudoviricetes were the most abundant in all samples, while Leviviricetes (ssRNA(+) viruses) dominated the treated water samples. RNA viruses of the families Nodaviridae, Tombusviridae, Dicitroviridae, Picobirnaviridae, Botourmiaviridae, Marnaviridae, Solemoviridae, and Endornavirida were found in the pelagic zone of three lake basins. Complete or nearly complete genomes of RNA viruses belonging to such families as Dicistroviridae, Marnaviridae, Blumeviridae, Virgaviridae, Solspiviridae, Nodaviridae, and Fiersviridae and the unassigned genus Chimpavirus, as well as unclassified picorna-like viruses, were identified. In general, the data of sanitary/microbiological and genetic analyses showed that WWTPs inadequately purify the discharged water, but, at the same time, we did not observe viruses pathogenic to humans in the pelagic zone of the lake.
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Affiliation(s)
- Sergey Potapov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Anna Gorshkova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Andrey Krasnopeev
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Galina Podlesnaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Irina Tikhonova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Maria Suslova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Dmitry Kwon
- National Research Center Kurchatov Institute, Academician Kurchatov Square 1, 123098 Moscow, Russia
| | - Maxim Patrushev
- National Research Center Kurchatov Institute, Academician Kurchatov Square 1, 123098 Moscow, Russia
| | - Valentin Drucker
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Olga Belykh
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
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Potapov S, Krasnopeev A, Tikhonova I, Podlesnaya G, Gorshkova A, Belykh O. The Viral Fraction Metatranscriptomes of Lake Baikal. Microorganisms 2022; 10:1937. [PMID: 36296212 PMCID: PMC9611531 DOI: 10.3390/microorganisms10101937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022] Open
Abstract
This article characterises viral fraction metatranscriptomes (smaller than 0.2 µm) from the pelagic zone of oligotrophic Lake Baikal (Russia). The study revealed the dominance of transcripts of DNA viruses: bacteriophages and algal viruses. We identified transcripts similar to Pithovirus sibericum, a nucleocytoplasmic large DNA virus (NCLDV) isolated from the permafrost region of Eastern Siberia. Among the families detected were RNA viruses assigned to Retroviridae, Metaviridae, Potyviridae, Astroviridae, and Closteroviridae. Using the PHROG, SEED subsystems databases, and the VOGDB, we indicated that the bulk of transcripts belong to the functional replication of viruses. In a comparative unweighted pair group method with arithmetic mean (UPGMA) analysis, the transcripts from Lake Baikal formed a separate cluster included in the clade with transcripts from other freshwater lakes, as well as marine and oceanic waters, while there was no separation based on the trophic state of the water bodies, the size of the plankton fraction, or salinity.
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Affiliation(s)
- Sergey Potapov
- Limnological Institute SB RAS, 3, Ulan-Batorskaya, 664033 Irkutsk, Russia
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Butina TV, Petrushin IS, Khanaev IV, Bukin YS. Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera. Microorganisms 2022; 10:microorganisms10020480. [PMID: 35208935 PMCID: PMC8876492 DOI: 10.3390/microorganisms10020480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/10/2022] Open
Abstract
Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges.
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Analysis of Different Size Fractions Provides a More Complete Perspective of Viral Diversity in a Freshwater Embayment. Appl Environ Microbiol 2021; 87:AEM.00197-21. [PMID: 33741611 DOI: 10.1128/aem.00197-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/11/2021] [Indexed: 11/20/2022] Open
Abstract
Inspired by recent discoveries of the prevalence of large viruses in the environment, we reassessed the longstanding approach of filtering water through small-pore-size filters to separate viruses from cells before metagenomic analysis. We collected samples from three sites in Hamilton Harbour, an embayment of Lake Ontario, and studied 6 data sets derived from <0.45-μm- and >0.45-μm-size fractions to compare the diversity of viruses in these fractions. At the level of virus order/family, we observed highly diverse and distinct virus communities in the >0.45-μm-size fractions, whereas the <0.45-μm-size fractions were composed primarily of Caudovirales The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions, with higher relative abundances of cyanophages in the >0.45-μm-size fractions, potentially indicating replication within cells during ongoing infections. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, were detected exclusively in the often-disregarded >0.45-μm-size fractions. In addition to observing unique virus communities associated with each size fraction from every site we examined, we detected viruses common to both fractions, suggesting that these are candidates for further exploration because they could be the product of ongoing or recent lytic events. Most importantly, our observations indicate that analysis of either fraction alone provides only a partial perspective of double-stranded DNA (dsDNA) viruses in the environment, highlighting the need for more comprehensive approaches for analyzing virus communities inferred from metagenomic sequencing.IMPORTANCE Most studies of aquatic virus communities analyze DNA sequences derived from the smaller-size "free-virus" fraction. Our study demonstrates that analysis of virus communities using only the smaller-size fraction can lead to erroneously low diversity estimates for many of the larger viruses such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, whereas analyzing only the larger->0.45-μm-size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data show that examining only the smaller-size fraction can lead to underestimations of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.
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Butina TV, Bukin YS, Petrushin IS, Tupikin AE, Kabilov MR, Belikov SI. Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics. Microorganisms 2021; 9:760. [PMID: 33916464 PMCID: PMC8066274 DOI: 10.3390/microorganisms9040760] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/22/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake's viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still unknown. The new metaviromic data will be useful for future studies of viral composition, distribution, and the dynamics associated with global climatic and anthropogenic impacts on this ecosystem.
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Affiliation(s)
- Tatyana V. Butina
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Yurij S. Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Ivan S. Petrushin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Sergey I. Belikov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; (I.S.P.); (S.I.B.)
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David GM, Moreira D, Reboul G, Annenkova NV, Galindo LJ, Bertolino P, López-Archilla AI, Jardillier L, López-García P. Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake. Environ Microbiol 2020; 23:1436-1451. [PMID: 33270368 DOI: 10.1111/1462-2920.15346] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/04/2023]
Abstract
Identifying which abiotic and biotic factors determine microbial community assembly is crucial to understand ecological processes and predict how communities will respond to environmental change. While global surveys aim at addressing this question in the world's oceans, equivalent studies in large freshwater systems are virtually lacking. Being the oldest, deepest and most voluminous freshwater lake on Earth, Lake Baikal offers a unique opportunity to test the effect of horizontal versus vertical gradients in community structure. Here, we characterized the structure of planktonic microbial eukaryotic communities (0.2-30 μm cell size) along a North-South latitudinal gradient (~600 km) from samples collected in coastal and pelagic waters and from surface to the deepest zones (5-1400 m) using an 18S rRNA gene metabarcoding approach. Our results show complex and diverse protist communities dominated by alveolates (ciliates and dinoflagellates), ochrophytes and holomycotan lineages, with cryptophytes, haptophytes, katablepharids and telonemids in moderate abundance and many low-frequency lineages, including several typical marine members, such as diplonemids, syndinians and radiolarians. Depth had a strong significant effect on protist community stratification. By contrast, the effect of the latitudinal gradient was marginal and no significant difference was observed between coastal and surface open water communities. Co-occurrence network analyses showed that epipelagic communities were significantly more interconnected than communities from the dark water column and suggest specific biotic interactions between autotrophic, heterotrophic and parasitic lineages that influence protist community structure. Since climate change is rapidly affecting Siberia and Lake Baikal, our comprehensive protist survey constitutes a useful reference to monitor ongoing community shifts.
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Affiliation(s)
- Gwendoline M David
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - David Moreira
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Guillaume Reboul
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Nataliia V Annenkova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Luis J Galindo
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Paola Bertolino
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | | | - Ludwig Jardillier
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-García
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique - CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
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Abstract
In recent years, Lake Baikal has undergone significant changes in the composition of coastal communities associated with the increasing anthropogenic influence and global climate changes. In this context, we carried out metagenomic sequencing of the DNA viral community of an integral near-bottom water sample from the littoral zone of the lake. In recent years, Lake Baikal has undergone significant changes in the composition of coastal communities associated with the increasing anthropogenic influence and global climate changes. In this context, we carried out metagenomic sequencing of the DNA viral community of an integral near-bottom water sample from the littoral zone of the lake.
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