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Xu Q, Zhang H, Vandenkoornhuyse P, Guo S, Kuzyakov Y, Shen Q, Ling N. Carbon starvation raises capacities in bacterial antibiotic resistance and viral auxiliary carbon metabolism in soils. Proc Natl Acad Sci U S A 2024; 121:e2318160121. [PMID: 38598339 PMCID: PMC11032446 DOI: 10.1073/pnas.2318160121] [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: 10/18/2023] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
Organic carbon availability in soil is crucial for shaping microbial communities, yet, uncertainties persist concerning microbial adaptations to carbon levels and the ensuing ecological and evolutionary consequences. We investigated organic carbon metabolism, antibiotic resistance, and virus-host interactions in soils subjected to 40 y of chemical and organic fertilization that led to contrasting carbon availability: carbon-poor and carbon-rich soils, respectively. Carbon-poor soils drove the enrichment of putative genes involved in organic matter decomposition and exhibited specialization in utilizing complex organic compounds, reflecting scramble competition. This specialization confers a competitive advantage of microbial communities in carbon-poor soils but reduces their buffering capacity in terms of organic carbon metabolisms, making them more vulnerable to environmental fluctuations. Additionally, in carbon-poor soils, viral auxiliary metabolic genes linked to organic carbon metabolism increased host competitiveness and environmental adaptability through a strategy akin to "piggyback the winner." Furthermore, putative antibiotic resistance genes, particularly in low-abundance drug categories, were enriched in carbon-poor soils as an evolutionary consequence of chemical warfare (i.e., interference competition). This raises concerns about the potential dissemination of antibiotic resistance from conventional agriculture that relies on chemical-only fertilization. Consequently, carbon starvation resulting from long-term chemical-only fertilization increases microbial adaptations to competition, underscoring the importance of implementing sustainable agricultural practices to mitigate the emergence and spread of antimicrobial resistance and to increase soil carbon storage.
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Affiliation(s)
- Qicheng Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
- CNRS, UMR 6553 EcoBio, Université de Rennes, Rennes Cedex35042, France
| | - He Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou730020, China
| | | | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen37077, Germany
- Department of Agricultural Soil Science, University of Göttingen, Göttingen37077, Germany
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
| | - Ning Ling
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou730020, China
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Hong W, Mei H, Shi X, Lin X, Wang S, Ni R, Wang Y, Song L. Viral community distribution, assembly mechanism, and associated hosts in an industrial park wastewater treatment plant. ENVIRONMENTAL RESEARCH 2024; 247:118156. [PMID: 38199475 DOI: 10.1016/j.envres.2024.118156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/02/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
Viruses manipulate bacterial community composition and impact wastewater treatment efficiency. Some viruses pose threats to the environment and human populations through infection. Improving the efficiency of wastewater treatment and ensuring the health of the effluent and receptor pools requires an understanding of how viral communities assemble and interact with hosts in wastewater treatment plants (WWTPs). We used metagenomic analysis to study the distribution, assembly mechanism, and sensitive hosts for the viral communities in raw water, anaerobic tanks, and returned activated sludge units of a large-scale industrial park WWTP. Uroviricota (53.42% ± 0.14%) and Nucleocytoviricota (26.1% ± 0.19%) were dominant in all units. Viral community composition significantly differed between units, as measured by β diversity (P = 0.005). Compared to raw water, the relative viral abundance decreased by 29.8% in the anaerobic tank but increased by 9.9% in the activated sludge. Viral community assembly in raw water and anaerobic tanks was predominantly driven by deterministic processes (MST <0.5) versus stochastic processes (MST >0.5) in the activated sludge, indicating that differences in diffusion limits may fundamentally alter the assembly mechanisms of viral communities between the solid and liquid-phase environments. Acidobacteria was identified as the sensitive host contributing to viral abundance, exhibiting strong interactions and a mutual dependence (degree = 59). These results demonstrate the occurrence and prevalence of viruses in WWTPs, their different assembly mechanism, and sensitive hosts. These observations require further study of the mechanisms of viral community succession, ecological function, and roles in the successive wastewater treatment units.
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Affiliation(s)
- Wenqing Hong
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Hong Mei
- East China Engineering Science and Technology Co., Ltd, Hefei, 230024, China
| | - Xianyang Shi
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China.
| | - Xiaoxing Lin
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Shuijing Wang
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Renjie Ni
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China
| | - Yan Wang
- East China Engineering Science and Technology Co., Ltd, Hefei, 230024, China
| | - Liyan Song
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China; Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base, Dongzhi, 247230, China.
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Zheng Y, Gao Z, Wu S, Ruan A. Community Structure, Drivers, and Potential Functions of Different Lifestyle Viruses in Chaohu Lake. Viruses 2024; 16:590. [PMID: 38675931 PMCID: PMC11053968 DOI: 10.3390/v16040590] [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: 03/22/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Viruses, as the most prolific entities on Earth, constitute significant ecological groups within freshwater lakes, exerting pivotal ecological roles. In this study, we selected Chaohu Lake, a representative eutrophic freshwater lake in China, as our research site to explore the community distribution, driving mechanisms, and potential ecological functions of diverse viral communities, the intricate virus-host interaction systems, and the overarching influence of viruses on global biogeochemical cycling.
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Affiliation(s)
- Yu Zheng
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Zihao Gao
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Shuai Wu
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, China
| | - Aidong Ruan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210024, China; (Y.Z.); (Z.G.); (S.W.)
- College of Geography and Remote Sensing, Hohai University, Nanjing 210098, China
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Shen S, Tominaga K, Tsuchiya K, Matsuda T, Yoshida T, Shimizu Y. Virus-prokaryote infection pairs associated with prokaryotic production in a freshwater lake. mSystems 2024; 9:e0090623. [PMID: 38193708 PMCID: PMC10878036 DOI: 10.1128/msystems.00906-23] [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: 08/25/2023] [Accepted: 12/06/2023] [Indexed: 01/10/2024] Open
Abstract
Viruses infect and kill prokaryotic populations in a density- or frequency-dependent manner and affect carbon cycling. However, the effects of the stratification transition, including the stratified and de-stratified periods, on the changes in prokaryotic and viral communities and their interactions remain unclear. We conducted a monthly survey of the surface and deep layers of a large and deep freshwater lake (Lake Biwa, Japan) for a year and analyzed the prokaryotic production and prokaryotic and viral community composition. Our analysis revealed that, in the surface layer, 19 prokaryotic species, accounting for approximately 40% of the total prokaryotic abundance, could potentially contribute to the majority of prokaryotic production, which is the highest during the summer and is suppressed by viruses. This suggests that a small fraction of prokaryotes and phages were the key infection pairs during the peak period of prokaryotic activity in the freshwater lake. We also found that approximately 50% of the dominant prokaryotic and viral species in the deep layer were present throughout the study period. This suggests that the "kill the winner" model could explain the viral impact on prokaryotes in the surface layer, but other dynamics may be at play in the deep layer. Furthermore, we found that annual vertical mixing could result in a similar rate of community change between the surface and deep layers. These findings may be valuable in understanding how communities and the interaction among them change when freshwater lake stratification is affected by global warming in the future.IMPORTANCEViral infection associated with prokaryotic production occurs in a density- or frequency-dependent manner and regulates the prokaryotic community. Stratification transition and annual vertical mixing in freshwater lakes are known to affect the prokaryotic community and the interaction between prokaryotes and viruses. By pairing measurements of virome analysis and prokaryotic production of a 1-year survey of the depths of surface and deep layers, we revealed (i) the prokaryotic infection pairs associated with prokaryotic production and (ii) the reset in prokaryotic and viral communities through annual vertical mixing in a freshwater lake. Our results provide a basis for future work into changes in stratification that may impact the biogeochemical cycling in freshwater lakes.
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Affiliation(s)
- Shang Shen
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, Japan
- Lake Biwa Branch Office, National Institute for Environmental Studies, Otsu, Shiga, Japan
- Department of Civil and Environmental Engineering, Ritsumeikan University, Kusatsu, Japan
| | - Kento Tominaga
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kenji Tsuchiya
- Regional Environment Conservation Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Tomonari Matsuda
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Yoshihisa Shimizu
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, Japan
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Xiong L, Li Y, Zeng K, Wei Y, Li H, Ji X. Revealing viral diversity in the Napahai plateau wetland based on metagenomics. Antonie Van Leeuwenhoek 2023; 117:3. [PMID: 38153618 DOI: 10.1007/s10482-023-01912-2] [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: 08/30/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.
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Affiliation(s)
- Lingling Xiong
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yanmei Li
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Kun Zeng
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yunlin Wei
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Xiuling Ji
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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Butina TV, Zemskaya TI, Bondaryuk AN, Petrushin IS, Khanaev IV, Nebesnykh IA, Bukin YS. Viral Diversity in Samples of Freshwater Gastropods Benedictia baicalensis (Caenogastropoda: Benedictiidae) Revealed by Total RNA-Sequencing. Int J Mol Sci 2023; 24:17022. [PMID: 38069344 PMCID: PMC10707223 DOI: 10.3390/ijms242317022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Previously, the main studies were focused on viruses that cause disease in commercial and farmed shellfish and cause damage to food enterprises (for example, Ostreavirusostreidmalaco1, Aurivirus haliotidmalaco1 and Aquabirnavirus tellinae). Advances in high-throughput sequencing technologies have extended the studies to natural populations of mollusks (and other invertebrates) as unexplored niches of viral diversity and possible sources of emerging diseases. These studies have revealed a huge diversity of mostly previously unknown viruses and filled gaps in the evolutionary history of viruses. In the present study, we estimated the viral diversity in samples of the Baikal endemic gastropod Benedictia baicalensis using metatranscriptomic analysis (total RNA-sequencing); we were able to identify a wide variety of RNA-containing viruses in four samples (pools) of mollusks collected at three stations of Lake Baikal. Most of the identified viral genomes (scaffolds) had only distant similarities to known viruses or (in most cases) to metagenome-assembled viral genomes from various natural samples (mollusks, crustaceans, insects and others) mainly from freshwater ecosystems. We were able to identify viruses similar to those previously identified in mollusks (in particular to the picornaviruses Biomphalaria virus 1 and Biomphalaria virus 3 from the freshwater gastropods); it is possible that picorna-like viruses (as well as a number of other identified viruses) are pathogenic for Baikal gastropods. Our results also suggested that Baikal mollusks, like other species, may bioaccumulate or serve as a reservoir for numerous viruses that infect a variety of organisms (including vertebrates).
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Affiliation(s)
| | - Tamara I. Zemskaya
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia; (T.V.B.); (A.N.B.); (I.S.P.); (I.V.K.); (I.A.N.); (Y.S.B.)
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Ter Horst AM, Fudyma JD, Sones JL, Emerson JB. Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography. THE ISME JOURNAL 2023; 17:2079-2089. [PMID: 37735616 PMCID: PMC10579374 DOI: 10.1038/s41396-023-01516-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023]
Abstract
Wetlands store 20-30% of the world's soil carbon, and identifying the microbial controls on these carbon reserves is essential to predicting feedbacks to climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding of wetland viral ecology. Here 63 viral size-fraction metagenomes (viromes) and paired total metagenomes were generated from three time points in 2021 at seven fresh- and saltwater wetlands in the California Bodega Marine Reserve. We recovered 12,826 viral population genomic sequences (vOTUs), only 4.4% of which were detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly among the seven wetland sites and were also structured by habitat (plant community composition and salinity). Read mapping to a new version of our reference database, PIGEONv2.0 (515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared habitat characteristics. Wetland vOTU microdiversity was significantly lower locally than globally and lower within than between time points, indicating greater divergence with increasing spatiotemporal distance. Viruses tended to have broad predicted host ranges via CRISPR spacer linkages to metagenome-assembled genomes, and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest potential viral eco-evolutionary dynamics in response to both immune targeting and changes in host cell receptors involved in viral attachment. Together, these results highlight the importance of dispersal, environmental selection, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.
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Affiliation(s)
| | - Jane D Fudyma
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - Jacqueline L Sones
- Bodega Marine Reserve, University of California, Davis, Bodega Bay, CA, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA.
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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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Coutinho FH, Silveira CB, Sebastián M, Sánchez P, Duarte CM, Vaqué D, Gasol JM, Acinas SG. Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities. MICROBIOME 2023; 11:118. [PMID: 37237317 PMCID: PMC10224230 DOI: 10.1186/s40168-023-01547-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/10/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Viruses play important roles in the ocean's biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and functioning of their communities or how they interact with their free-living or particle-attached microbial hosts. RESULTS We analysed 58 viral communities associated with size-fractionated free-living (0.2-0.8 μm) and particle-attached (0.8-20 μm) cellular metagenomes from bathypelagic (2150-4018 m deep) microbiomes obtained during the Malaspina expedition. These metagenomes yielded 6631 viral sequences, 91% of which were novel, and 67 represented high-quality genomes. Taxonomic classification assigned 53% of the viral sequences to families of tailed viruses from the order Caudovirales. Computational host prediction associated 886 viral sequences to dominant members of the deep ocean microbiome, such as Alphaproteobacteria (284), Gammaproteobacteria (241), SAR324 (23), Marinisomatota (39), and Chloroflexota (61). Free-living and particle-attached viral communities had markedly distinct taxonomic composition, host prevalence, and auxiliary metabolic gene content, which led to the discovery of novel viral-encoded metabolic genes involved in the folate and nucleotide metabolisms. Water mass age emerged as an important factor driving viral community composition. We postulated this was due to changes in quality and concentration of dissolved organic matter acting on the host communities, leading to an increase of viral auxiliary metabolic genes associated with energy metabolism among older water masses. CONCLUSIONS These results shed light on the mechanisms by which environmental gradients of deep ocean ecosystems structure the composition and functioning of free-living and particle-attached viral communities. Video Abstract.
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Affiliation(s)
- Felipe H Coutinho
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, 08003, Barcelona, Spain.
| | - Cynthia B Silveira
- Department of Biology, University of Miami, Coral Gables, FL, USA
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Sciences, University of Miami, Miami, FL, USA
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, 08003, Barcelona, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, 08003, Barcelona, Spain
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, 08003, Barcelona, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, 08003, Barcelona, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, 08003, Barcelona, Spain.
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Composition and function of viruses in sauce-flavor baijiu fermentation. Int J Food Microbiol 2023; 387:110055. [PMID: 36527793 DOI: 10.1016/j.ijfoodmicro.2022.110055] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/21/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
Viruses are highly abundant in nature, associated with quality and safety of traditional fermented foods. However, the overall viral diversity and function are still poorly understood in food microbiome. Traditional baijiu fermentation is an ideal model system to examine the diversity and function of viruses owing to easy access, stable operation, and domesticated microbial community. Equipped with cutting-edge viral metagenomics, we investigated the viral community in the fermented grain and fermentation environment, as well as their contribution to baijiu fermentation. Viral communities in the fermented grains and fermentation environment are highly similar. The dominant viruses were bacteriophages, mainly including the order Caudovirales and the family Inoviridae. Furtherly, association network analysis showed that viruses and bacteria were significantly negatively correlated (P < 0.01). Viral diversity could significantly influence bacterial and fungal succession (P < 0.05). Moreover, we proved that starter phages could significantly inhibit the growth of Bacillus licheniformis in the logarithmic growth stage (P < 0.05) under culture condition. Based on the functional annotations, viruses and bacteria both showed high distribution of genes related to amino acid and carbohydrate metabolism. In addition, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were also identified in viruses, indicating that viruses were involved in the decomposition of complex polysaccharides during fermentation. Our results revealed that viruses could crucially affect microbial community and metabolism during traditional fermentation.
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11
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Albright S, Louca S. Trait biases in microbial reference genomes. Sci Data 2023; 10:84. [PMID: 36759614 PMCID: PMC9911409 DOI: 10.1038/s41597-023-01994-7] [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] [Received: 06/23/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
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Affiliation(s)
- Sage Albright
- Department of Biology, University of Oregon, Eugene, USA
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, USA. .,Institute of Ecology and Evolution, University of Oregon, Eugene, USA.
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12
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Luo XQ, Wang P, Li JL, Ahmad M, Duan L, Yin LZ, Deng QQ, Fang BZ, Li SH, Li WJ. Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts. MICROBIOME 2022; 10:190. [PMID: 36333738 PMCID: PMC9636769 DOI: 10.1186/s40168-022-01384-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/04/2022] [Indexed: 06/02/2023]
Abstract
BACKGROUND Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts' metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments. RESULTS Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders. CONCLUSIONS Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions. Video Abstract.
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Affiliation(s)
- Xiao-Qing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- School of Ecology, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Manzoor Ahmad
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Li Duan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ling-Zi Yin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Shan-Hui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Genomes from Uncultivated Pelagiphages Reveal Multiple Phylogenetic Clades Exhibiting Extensive Auxiliary Metabolic Genes and Cross-Family Multigene Transfers. mSystems 2022; 7:e0152221. [PMID: 35972150 PMCID: PMC9599517 DOI: 10.1128/msystems.01522-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
For the abundant marine Alphaproteobacterium Pelagibacter (SAR11), and other bacteria, phages are powerful forces of mortality. However, little is known about the most abundant Pelagiphages in nature, such as the widespread HTVC023P-type, which is currently represented by two cultured phages. Using viral metagenomic data sets and fluorescence-activated cell sorting, we recovered 80 complete, undescribed Podoviridae genomes that form 10 phylogenomically distinct clades (herein, named Clades I to X) related to the HTVC023P-type. These expanded the HTVC023P-type pan-genome by 15-fold and revealed 41 previously unknown auxiliary metabolic genes (AMGs) in this viral lineage. Numerous instances of partner-AMGs (colocated and involved in related functions) were observed, including partners in nucleotide metabolism, DNA hypermodification, and Curli biogenesis. The Type VIII secretion system (T8SS) responsible for Curli biogenesis was identified in nine genomes and expanded the repertoire of T8SS proteins reported thus far in viruses. Additionally, the identified T8SS gene cluster contained an iron-dependent regulator (FecR), as well as a histidine kinase and adenylate cyclase that can be implicated in T8SS function but are not within T8SS operons in bacteria. While T8SS are lacking in known Pelagibacter, they contribute to aggregation and biofilm formation in other bacteria. Phylogenetic reconstructions of partner-AMGs indicate derivation from cellular lineages with a more recent transfer between viral families. For example, homologs of all T8SS genes are present in syntenic regions of distant Myoviridae Pelagiphages, and they appear to have alphaproteobacterial origins with a later transfer between viral families. The results point to an unprecedented multipartner-AMG transfer between marine Myoviridae and Podoviridae. Together with the expansion of known metabolic functions, our studies provide new prospects for understanding the ecology and evolution of marine phages and their hosts. IMPORTANCE One of the most abundant and diverse marine bacterial groups is Pelagibacter. Phages have roles in shaping Pelagibacter ecology; however, several Pelagiphage lineages are represented by only a few genomes. This paucity of data from even the most widespread lineages has imposed limits on the understanding of the diversity of Pelagiphages and their impacts on hosts. Here, we report 80 complete genomes, assembled directly from environmental data, which are from undescribed Pelagiphages and render new insights into the manipulation of host metabolism during infection. Notably, the viruses have functionally related partner genes that appear to be transferred between distant viruses, including a suite that encode a secretion system which both brings a new functional capability to the host and is abundant in phages across the ocean. Together, these functions have important implications for phage evolution and for how Pelagiphage infection influences host biology in manners extending beyond canonical viral lysis and mortality.
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Wang D, Wang Y, Liu L, Chen Y, Wang C, Xu X, Yang Y, Wang Y, Zhang T. Niche differentiation and symbiotic association among ammonia/nitrite oxidizers in a full-scale rotating biological contactor. WATER RESEARCH 2022; 225:119137. [PMID: 36198208 DOI: 10.1016/j.watres.2022.119137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
Although the distribution of ammonia/nitrite oxidizers had been profiled in different habitats, current understanding is still limited regarding their niche differentiation in the integrated biofilm reactors, the symbiotic associations of ammonia/nitrite oxidizers, as well as the parasitic interaction between viruses and those functional organisms involved in the nitrogen cycle. Here, the integrated metagenomics and metatranscriptomics are applied to profile the ammonia/nitrite oxidizers communities and transcriptional activities changes along the flowpath of a concatenated full-scale rotating biological contactor (RBC) (frontend Stage-A and backend Stage-B). 19 metagenome-assembled genomes (MAGs) of ammonia/nitrite oxidizers were recovered by using a hybrid assembly approach, including four ammonia-oxidizing bacteria (AOB), two ammonia-oxidizing archaea (AOA), two complete ammonia oxidation bacteria (comammox), eight nitrite-oxidizing bacteria (NOB), and three anaerobic ammonium oxidation bacteria (anammox). Diverse AOB and anammox dominated Stage-A and collectively contributed to nitrogen conversion. With the decline of ammonia concentration along the flowpath, comammox and AOA appeared and increased in relative abundance in Stage-B, accounting for 8.8% of the entire community at the end of this reactor, and their dominating role in nitrogen turnover was indicated by the high transcription activity of their corresponding function genes. Moreover, the variation in the abundance of viruses infecting ammonia and nitrite oxidizers suggests that viruses likely act as a biotic factor mediating ammonia/nitrite oxidizer populations. This study demonstrates that complex factors shaped niche differentiation and symbiotic associations of ammonia/nitrite oxidizers in the RBC and highlights the importance of RBCs as model systems for the investigation of biotic and abiotic factors affecting the composition of microbiomes.
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Affiliation(s)
- Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yiqiang Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China; School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China; Shenzhen Bay Laboratory, Shenzhen, China.
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15
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Viruses direct carbon cycling in lake sediments under global change. Proc Natl Acad Sci U S A 2022; 119:e2202261119. [PMID: 36206369 PMCID: PMC9564219 DOI: 10.1073/pnas.2202261119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Global change is altering the vast amount of carbon cycled by microbes between land and freshwater, but how viruses mediate this process is poorly understood. Here, we show that viruses direct carbon cycling in lake sediments, and these impacts intensify with future changes in water clarity and terrestrial organic matter (tOM) inputs. Using experimental tOM gradients within sediments of a clear and a dark boreal lake, we identified 156 viral operational taxonomic units (vOTUs), of which 21% strongly increased with abundances of key bacteria and archaea, identified via metagenome-assembled genomes (MAGs). MAGs included the most abundant prokaryotes, which were themselves associated with dissolved organic matter (DOM) composition and greenhouse gas (GHG) concentrations. Increased abundances of virus-like particles were separately associated with reduced bacterial metabolism and with shifts in DOM toward amino sugars, likely released by cell lysis rather than higher molecular mass compounds accumulating from reduced tOM degradation. An additional 9.6% of vOTUs harbored auxiliary metabolic genes associated with DOM and GHGs. Taken together, these different effects on host dynamics and metabolism can explain why abundances of vOTUs rather than MAGs were better overall predictors of carbon cycling. Future increases in tOM quantity, but not quality, will change viral composition and function with consequences for DOM pools. Given their importance, viruses must now be explicitly considered in efforts to understand and predict the freshwater carbon cycle and its future under global environmental change.
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16
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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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17
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Elbehery AHA, Deng L. Insights into the global freshwater virome. Front Microbiol 2022; 13:953500. [PMID: 36246212 PMCID: PMC9554406 DOI: 10.3389/fmicb.2022.953500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
Viruses are by far the most abundant life forms on this planet. Yet, the full viral diversity remains mostly unknown, especially in environments like freshwater. Therefore, we aimed to study freshwater viruses in a global context. To this end, we downloaded 380 publicly available viral metagenomes (>1 TB). More than 60% of these metagenomes were discarded based on their levels of cellular contamination assessed by ribosomal DNA content. For the remaining metagenomes, assembled contigs were decontaminated using two consecutive steps, eventually yielding 273,365 viral contigs longer than 1,000 bp. Long enough contigs (≥ 10 kb) were clustered to identify novel genomes/genome fragments. We could recover 549 complete circular and high-quality draft genomes, out of which 10 were recognized as being novel. Functional annotation of these genomes showed that most of the annotated coding sequences are DNA metabolic genes or phage structural genes. On the other hand, taxonomic analysis of viral contigs showed that most of the assigned contigs belonged to the order Caudovirales, particularly the families of Siphoviridae, Myoviridae, and Podoviridae. The recovered viral contigs contained several auxiliary metabolic genes belonging to several metabolic pathways, especially carbohydrate and amino acid metabolism in addition to photosynthesis as well as hydrocarbon degradation and antibiotic resistance. Overall, we present here a set of prudently chosen viral contigs, which should not only help better understanding of freshwater viruses but also be a valuable resource for future virome studies.
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Affiliation(s)
- Ali H. A. Elbehery
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
- *Correspondence: Ali H. A. Elbehery,
| | - Li Deng
- Helmholtz Centre Munich – German Research Centre for Environmental Health, Institute of Virology, Neuherberg, Germany
- Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, Freising, Germany
- Li Deng,
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18
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Zeng J, Tu Q, Yu X, Qian L, Wang C, Shu L, Liu F, Liu S, Huang Z, He J, Yan Q, He Z. PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes. MICROBIOME 2022; 10:101. [PMID: 35787295 PMCID: PMC9252087 DOI: 10.1186/s40168-022-01292-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/12/2022] [Indexed: 05/29/2023]
Abstract
BACKGROUND Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database. RESULTS In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments. CONCLUSIONS We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.
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Affiliation(s)
- Jiaxiong Zeng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Shengwei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Zhijian Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Jianguo He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128 China
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19
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Sun L, Zhu M, Zhang L, Peng M, Li C, Wang L, Wang W, Ma Z, Li S, Zeng W, Yin M, Wang W, Chunyu W. Differences in microbiome of healthy Sprague Dawley rats with Paragonimus proliferus infection and potential pathogenic role of microbes in paragonimiasis. Acta Trop 2022; 233:106578. [PMID: 35779592 DOI: 10.1016/j.actatropica.2022.106578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/12/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022]
Abstract
Paragonimiasis, which is caused by Paragonimus, is considered to be a neglected tropical disease by the World Health Organization. The pathogenicity of Paragonimus mainly manifests as mechanical damage and immunotoxicity caused by adult worms and larvae. However, microbiota associated with Paragonimus and potential disturbance of host microbiota after infection are unknown. Paragonimus proliferus is a rare species, and its successful infection rate in experimental rats is 100%. In the current study, we compared the microbial community in lung tissues, small intestine contents, and fecal samples from Sprague Dawley (SD) rats with and without P. proliferus infection. To determine the impact of P. proliferus on the microbial community in rats, we identified the microbiota in adult worms of P. proliferus via high-throughput sequencing. Results showed dramatic differences in the composition of microbiota in lung tissues between infected and uninfected rats. Paragonimus metacercariae introduced both environmental and gut microbes into the lung tissues of rats. Many potentially pathogenic microbes were also found in the lung of infected rats. Paragonimus infection increased the chances of potentially pathogenic microbiota invading and colonizing the lungs. However, for the purpose of long-term parasitism, there might be a complex interrelationship between Paragonimus and microorganisms. Our study might shed lights on the understanding of the pathogenicity of Paragonimus.
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Affiliation(s)
- Le Sun
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Min Zhu
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China; Department of Clinical Laboratory, Jiangyou People's Hospital, Mianyang, Sichuan 621700, China
| | - Lei Zhang
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Man Peng
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Cuiying Li
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Liming Wang
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Weiqun Wang
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Zhiqiang Ma
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China; The Third People's Hospital of Kunming, Kunming, Yunnan 650043, China
| | - Shenghao Li
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China; The Third People's Hospital of Kunming, Kunming, Yunnan 650043, China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Min Yin
- School of Medicine, Yunnan University, 2 North Cui Hu Road, Kunming, Yunnan 650091, China.
| | - Wenlin Wang
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China.
| | - Weixun Chunyu
- Department of Pathogen Biology and Immunology, School of Basic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China.
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20
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Smith SE, Huang W, Tiamani K, Unterer M, Khan Mirzaei M, Deng L. Emerging technologies in the study of the virome. Curr Opin Virol 2022; 54:101231. [DOI: 10.1016/j.coviro.2022.101231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 11/03/2022]
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21
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Wang S, Yang Y, Jing J. A Synthesis of Viral Contribution to Marine Nitrogen Cycling. Front Microbiol 2022; 13:834581. [PMID: 35547115 PMCID: PMC9083009 DOI: 10.3389/fmicb.2022.834581] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 11/22/2022] Open
Abstract
Nitrogen is an essential component of major cellular macromolecules, such as DNA and proteins. Its bioavailability has a fundamental influence on the primary production of both terrestrial and oceanic ecosystems. Diverse marine microbes consume nitrogen, while only a limited taxon could replenish it, leaving nitrogen one of the most deficient nutrients in the ocean. A variety of microbes are involved in complex biogeochemical transformations of nitrogen compounds, and their ecological functions might be regulated by viruses in different manners. First and foremost, viruses drive marine nitrogen flow via host cell lysis, releasing abundant organic nitrogen into the surrounding environment. Secondly, viruses can also participate in the marine nitrogen cycle by expressing auxiliary metabolic genes (AMGs) to modulate host nitrogen metabolic pathways, such as nitrification, denitrification, anammox, and nitrogen transmembrane transport. Additionally, viruses also serve as a considerable reservoir of nitrogen element. The efficient turnover of viruses fundamentally promotes nitrogen flow in the oceans. In this review, we summarize viral contributions in the marine nitrogen cycling in different aspects and discuss challenges and issues based on recent discoveries of novel viruses involved in different processes of nitrogen biotransformation.
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Affiliation(s)
- Shuai Wang
- Shandong Collaborative Innovation Center for Diagnosis, Treatment and Behavioral Interventions of Mental Disorders, Institute of Mental Health, Jining Medical University, Jining, China
| | - Yu Yang
- Shandong Collaborative Innovation Center for Diagnosis, Treatment and Behavioral Interventions of Mental Disorders, Institute of Mental Health, Jining Medical University, Jining, China
| | - Jiaojiao Jing
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Department of Pediatric Dentistry, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Stomatological Center, Peking University Shenzhen Hospital, Shenzhen, China
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22
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Kieft K, Adams A, Salamzade R, Kalan L, Anantharaman K. vRhyme enables binning of viral genomes from metagenomes. Nucleic Acids Res 2022; 50:e83. [PMID: 35544285 PMCID: PMC9371927 DOI: 10.1093/nar/gkac341] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/17/2022] [Accepted: 04/22/2022] [Indexed: 01/11/2023] Open
Abstract
Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs supervised machine learning to identify nucleotide feature similarities, which are compiled into iterations of weighted networks and refined bins. To refine bins, vRhyme utilizes unique features of viral genomes, namely a protein redundancy scoring mechanism based on the observation that viruses seldom encode redundant genes. Using simulated viromes, we displayed superior performance of vRhyme compared to available binning tools in constructing more complete and uncontaminated vMAGs. When applied to 10,601 viral scaffolds from human skin, vRhyme advanced our understanding of resident viruses, highlighted by identification of a Herelleviridae vMAG comprised of 22 scaffolds, and another vMAG encoding a nitrate reductase metabolic gene, representing near-complete genomes post-binning. vRhyme will enable a convention of binning uncultivated viral genomes and has the potential to transform metagenome-based viral ecology.
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Affiliation(s)
- Kristopher Kieft
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, USA,Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
| | - Alyssa Adams
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, USA,Computation and Informatics in Biology and Medicine, University of Wisconsin–Madison, Madison, WI, USA
| | - Rauf Salamzade
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA,Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, USA
| | - Lindsay Kalan
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, USA,Department of Medicine, University of Wisconsin–Madison, Madison, WI, USA
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23
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Increased Diversity of Rhizosphere Bacterial Community Confers Adaptability to Coastal Environment for Sapium sebiferum Trees. FORESTS 2022. [DOI: 10.3390/f13050667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sapium sebiferum (L.) Roxb. is an economically important tree in eastern Asia, and it exhibits many traits associated with good forestation species in coastal land. However, scarce research has been conducted to elucidate the effects of rhizosphere bacterial diversity on the adaptability and viability of S. sebiferum trees grown in the coastal environment. Field trials were conducted, and rhizosphere soil samples were collected from typical coastal and forestry nursery environments. Rhizosphere bacterial communities were evaluated using 16S rRNA pyrosequencing. A total of 43 bacterial phyla were detected in all the coastal and nursery rhizospheric soil samples. Relatively higher rhizosphere community diversity was found in coastal field-grown trees. Proteobacteria, Acidobacteriota, Bacteroidota, Chloroflex, and Gemmatimonadota were dominant bacterial phyla in rhizosphere communities of tallow trees. However, the rare groups in the coastal rhizosphere soils, with a relative abundance lower than 1%, including Latescibacterota, Methylomirabilota, NB1-j, and Nitrospirota, were largely absent in the nursery field-grown tree’s rhizosphere soils. LEfSe analysis identified a total of 43 bacterial groups that were more significantly abundant in the coastal rhizosphere environment than in that of forestry nursery grown trees. Further, our cladogram analysis identified Nitrospirota, Methylomirabilota, NB1-j, and Latescibacterota as biomarkers for the coastal environment at the phylum taxonomic level. These results suggested that the adaptability of S. sebiferum trees in coastal environment might be promoted by rhizosphere microbial interactions. Complex tree–microbe interactions might enhance the resistance of the trees to coastal environment, partially by recruiting certain bacterial microbiome species, which is of high saline-alkali resistance.
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24
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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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25
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Potapov SA, Tikhonova IV, Krasnopeev AY, Suslova MY, Zhuchenko NA, Drucker VV, Belykh OI. Communities of T4-like bacteriophages associated with bacteria in Lake Baikal: diversity and biogeography. PeerJ 2022. [DOI: 10.7717/peerj.12748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lake Baikal phage communities are important for lake ecosystem functioning. Here we describe the diversity of T4-bacteriophage associated with the bacterial fraction of filtered water samples collected from the pelagic zone, coastal zone and shallow bays. Although the study of the diversity of phages for the g23 gene has been carried out at Lake Baikal for more than ten years, shallow bays that comprise a significant part of the lake’s area have been neglected, and this gene has not previously been studied in the bacterial fraction. Phage communities were probed using amplicon sequencing methods targeting the gene of major capsid protein (g23) and compared phylogenetically across sample locations and with sequences previously retrieved from non-bacterial fractions (<0.2 um) and biofilms (non-fractionated). In this study, we examined six water samples, in which 24 to 74 viral OTUs were obtained. The sequences from shallow bays largely differed from those in the pelagic and coastal samples and formed individual subcluster in the UPGMA tree that was obtained from the comparison of phylogenetic distances of g23 sequence sets from various ecosystems, reflecting differences in viral communities depending on the productivity of various sites of Lake Baikal. According to the RefSeq database, from 58.3 to 73% of sequences of each sample had cultivated closest relatives belonging to cyanophages. In this study, for phylogenetic analysis, we chose the closest relatives not only from the RefSeq and GenBank NR databases but also from two marine and one freshwater viromes: eutrophic Osaka Bay (Japan), oligotrophic area of the Pacific Ocean (Station ALOHA) and mesotrophic and ancient Lake Biwa (Japan), which allowed us to more fully compare the diversity of marine and freshwater phages. The identity with marine sequences at the amino acid level ranged from 35 to 80%, and with the sequences from the viral fraction and bacterial one from Lake Biwa—from 35.3 to 98% and from 33.9 to 89.1%, respectively. Therefore, the sequences from marine viromes had a greater difference than those from freshwater viromes, which may indicate a close relationship between freshwater viruses and differences from marine viruses.
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Affiliation(s)
| | | | | | - Maria Yurjevna Suslova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | | | | | - Olga Ivanovna Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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26
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Gu C, Liang Y, Li J, Shao H, Jiang Y, Zhou X, Gao C, Li X, Zhang W, Guo C, He H, Wang H, Sung YY, Mok WJ, Wong LL, Suttle CA, McMinn A, Tian J, Wang M. Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption. iScience 2021; 24:103439. [PMID: 34988389 PMCID: PMC8710556 DOI: 10.1016/j.isci.2021.103439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/10/2021] [Accepted: 11/10/2021] [Indexed: 12/21/2022] Open
Abstract
The highest plateau on Earth, Qinghai-Tibet Plateau, contains thousands of lakes with broad salinity and diverse and unique microbial communities. However, little is known about their co-occurring viruses. Herein, we identify 4,560 viral Operational Taxonomic Units (vOTUs) from six viromes of three saline lakes on Qinghai-Tibet Plateau, with less than 1% that could be classified. Most of the predicted vOTUs were associated with the dominant bacterial and archaeal phyla. Virus-encoded auxiliary metabolic genes suggest that viruses influence microbial metabolisms of carbon, nitrogen, sulfur, and lipid; the antibiotic resistance mediation; and their salinity adaption. The six viromes clustered together with the ice core viromes and bathypelagic ocean viromes and might represent a new viral habitat. This study has revealed the unique characteristics and potential ecological roles of DNA viromes in the lakes of the highest plateau and established a foundation for the recognition of the viral roles in plateau lake ecosystems.
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Affiliation(s)
- Chengxiang Gu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Jiansen Li
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
- Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Xinhao Zhou
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Chen Gao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Xianrong Li
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Wenjing Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Cui Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Hui He
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
| | - Yeong Yik Sung
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), 21030 Kuala Nerus, Malaysia
| | - Curtis A. Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany and Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, Australia
| | - Jiwei Tian
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China
- UMT-OUC Joint Center for Marine Studies, Qingdao 266003, China
- The affiliated hospital of Qingdao University, Qingdao 266000, China
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27
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Abstract
Viruses are ubiquitous on Earth and are keystone components of environments, ecosystems, and human health. Yet, viruses remain poorly studied because most cannot be isolated in a laboratory. In the field of biogeochemistry, which aims to understand the interactions between biology, geology, and chemistry, there is progress to be made in understanding the different roles played by viruses in nutrient cycling, food webs, and elemental transformations. In this commentary, we outline current microbial ecology frameworks for understanding biogeochemical cycling in aquatic ecosystems. Next, we review some existing experimental and computational techniques that are enabling us to study the role of viruses in biogeochemical cycling, using examples from aquatic environments. Finally, we provide a conceptual model that balances limitations of computational tools when combined with biogeochemistry and ecological data. We envision meeting the grand challenge of understanding how viruses impact biogeochemical cycling by using a multifaceted approach to viral ecology.
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28
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Bhattarai B, Bhattacharjee AS, Coutinho FH, Goel RK. Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake. Front Microbiol 2021; 12:701414. [PMID: 34650523 PMCID: PMC8506154 DOI: 10.3389/fmicb.2021.701414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/06/2021] [Indexed: 01/15/2023] Open
Abstract
Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. However, there is much that we do not yet understand about viruses and the processes mediated by them in the extreme environments such as hypersaline habitats. The Great Salt Lake (GSL) in Utah, United States is a hypersaline ecosystem where the biogeochemical role of viruses is poorly understood. This study elucidates the diversity of viruses and describes virus–host interactions in GSL sediments along a salinity gradient. The GSL sediment virosphere consisted of Haloviruses (32.07 ± 19.33%) and members of families Siphoviridae (39.12 ± 19.8%), Myoviridae (13.7 ± 6.6%), and Podoviridae (5.43 ± 0.64%). Our results demonstrate that salinity alongside the concentration of organic carbon and inorganic nutrients (nitrogen and phosphorus) governs the viral, bacteria, and archaeal diversity in this habitat. Computational host predictions for the GSL viruses revealed a wide host range with a dominance of viruses that infect Proteobacteria, Actinobacteria, and Firmicutes. Identification of auxiliary metabolic genes for photosynthesis (psbA), carbon fixation (rbcL, cbbL), formaldehyde assimilation (SHMT), and nitric oxide reduction (NorQ) shed light on the roles played by GSL viruses in biogeochemical cycles of global relevance.
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Affiliation(s)
- Bishav Bhattarai
- Department of Civil and Environmental Engineering, The University of Utah, Salt Lake City, UT, United States
| | - Ananda S Bhattacharjee
- Carl R. Woese Institute for Genomic Biology, The University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Felipe H Coutinho
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Ramesh K Goel
- Department of Civil and Environmental Engineering, The University of Utah, Salt Lake City, UT, United States
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29
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Teulière J, Bernard C, Bapteste E. Interspecific interactions that affect ageing: Age-distorters manipulate host ageing to their own evolutionary benefits. Ageing Res Rev 2021; 70:101375. [PMID: 34082078 DOI: 10.1016/j.arr.2021.101375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023]
Abstract
Genetic causes for ageing are traditionally investigated within a species. Yet, the lifecycles of many organisms intersect. Additional evolutionary and genetic causes of ageing, external to a focal species/organism, may thus be overlooked. Here, we introduce the phrase and concept of age-distorters and its evidence. Age-distorters carry ageing interfering genes, used to manipulate the biological age of other entities upon which the reproduction of age-distorters relies, e.g. age-distorters bias the reproduction/maintenance trade-offs of cells/organisms for their own evolutionary interests. Candidate age-distorters include viruses, parasites and symbionts, operating through specific, genetically encoded interferences resulting from co-evolution and arms race between manipulative non-kins and manipulable species. This interference results in organismal ageing when age-distorters prompt manipulated organisms to favor their reproduction at the expense of their maintenance, turning these hosts into expanded disposable soma. By relying on reproduction/maintenance trade-offs affecting disposable entities, which are left ageing to the reproductive benefit of other physically connected lineages with conflicting evolutionary interests, the concept of age-distorters expands the logic of the Disposable Soma theory beyond species with fixed germen/soma distinctions. Moreover, acknowledging age-distorters as external sources of mutation accumulation and antagonistic pleiotropic genes expands the scope of the mutation accumulation and of the antagonistic pleiotropy theories.
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Affiliation(s)
- Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Charles Bernard
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France.
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30
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Kazantseva OA, Piligrimova EG, Shadrin AM. vB_BcM_Sam46 and vB_BcM_Sam112, members of a new bacteriophage genus with unusual small terminase structure. Sci Rep 2021; 11:12173. [PMID: 34108535 PMCID: PMC8190038 DOI: 10.1038/s41598-021-91289-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
One of the serious public health concerns is food contaminated with pathogens and their vital activity products such as toxins. Bacillus cereus group of bacteria includes well-known pathogenic species such as B. anthracis, B. cereus sensu stricto (ss), B. cytotoxicus and B. thuringiensis. In this report, we describe the Bacillus phages vB_BcM_Sam46 and vB_BcM_Sam112 infecting species of this group. Electron microscopic analyses indicated that phages Sam46 and Sam112 have the myovirus morphotype. The genomes of Sam46 and Sam112 comprise double-stranded DNA of 45,419 bp and 45,037 bp in length, respectively, and have the same GC-content. The genome identity of Sam46 and Sam112 is 96.0%, indicating that they belong to the same phage species. According to the phylogenetic analysis, these phages form a distinct clade and may be members of a new phage genus, for which we propose the name 'Samaravirus'. In addition, an interesting feature of the Sam46 and Sam112 phages is the unusual structure of their small terminase subunit containing N-terminal FtsK_gamma domain.
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Affiliation(s)
- Olesya A Kazantseva
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia.
| | - Emma G Piligrimova
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia
| | - Andrey M Shadrin
- Laboratory of Bacteriophage Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290, Pushchino, Russia.
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31
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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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32
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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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Moon K, Cho JC. Metaviromics coupled with phage-host identification to open the viral 'black box'. J Microbiol 2021; 59:311-323. [PMID: 33624268 DOI: 10.1007/s12275-021-1016-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 12/22/2022]
Abstract
Viruses are found in almost all biomes on Earth, with bacteriophages (phages) accounting for the majority of viral particles in most ecosystems. Phages have been isolated from natural environments using the plaque assay and liquid medium-based dilution culturing. However, phage cultivation is restricted by the current limitations in the number of culturable bacterial strains. Unlike prokaryotes, which possess universally conserved 16S rRNA genes, phages lack universal marker genes for viral taxonomy, thus restricting cultureindependent analyses of viral diversity. To circumvent these limitations, shotgun viral metagenome sequencing (i.e., metaviromics) has been developed to enable the extensive sequencing of a variety of viral particles present in the environment and is now widely used. Using metaviromics, numerous studies on viral communities have been conducted in oceans, lakes, rivers, and soils, resulting in many novel phage sequences. Furthermore, auxiliary metabolic genes such as ammonic monooxygenase C and β-lactamase have been discovered in viral contigs assembled from viral metagenomes. Current attempts to identify putative bacterial hosts of viral metagenome sequences based on sequence homology have been limited due to viral sequence variations. Therefore, culture-independent approaches have been developed to predict bacterial hosts using single-cell genomics and fluorescentlabeling. This review focuses on recent viral metagenome studies conducted in natural environments, especially in aquatic ecosystems, and their contributions to phage ecology. Here, we concluded that although metaviromics is a key tool for the study of viral ecology, this approach must be supplemented with phage-host identification, which in turn requires the cultivation of phage-bacteria systems.
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Affiliation(s)
- Kira Moon
- Biological Resources Utilization Division, Honam National Institute of Biological Resources, Mokpo, 58762, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
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The Novel Halovirus Hardycor1, and the Presence of Active (Induced) Proviruses in Four Haloarchaea. Genes (Basel) 2021; 12:genes12020149. [PMID: 33498646 PMCID: PMC7911831 DOI: 10.3390/genes12020149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/15/2022] Open
Abstract
The virus Hardycor1 was isolated in 1998 and infects the haloarchaeon Halorubrum coriense. DNA from a frozen stock (HC1) was sequenced and the viral genome found to be 45,142 bp of dsDNA, probably having redundant, circularly permuted termini. The genome showed little similarity (BLASTn) to known viruses. Only twenty-two of the 53 (41%) predicted proteins were significantly similar to sequences in the NCBI nr protein database (E-value ≤ 10-15). Six caudovirus-like proteins were encoded, including large subunit terminase (TerL), major capsid protein (Mcp) and tape measure protein (Tmp). Hardycor1 was predicted to be a siphovirus (VIRFAM). No close relationship to other viruses was found using phylogenetic tree reconstructions based on TerL and Mcp. Unexpectedly, the sequenced virus stock HC1 also revealed two induced proviruses of the host: a siphovirus (Humcor1) and a pleolipovirus (Humcor2). A re-examination of other similarly sequenced, archival virus stocks revealed induced proviruses of Haloferax volcanii, Haloferax gibbonsii and Haloarcula hispanica, three of which were pleolipoviruses. One provirus (Halfvol2) of Hfx. volcanii showed little similarity (BLASTn) to known viruses and probably represents a novel virus group. The attP sequences of many pleolipoproviruses were found to be embedded in a newly detected coding sequence, split in the provirus state, that spans between genes for integrase and a downstream CxxC-motif protein. This gene might play an important role in regulation of the temperate state.
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