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Lin L, Xiong J, Liu L, Wang F, Cao W, Xu W. Microbial interactions strengthen deterministic processes during community assembly in a subtropical estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167499. [PMID: 37778550 DOI: 10.1016/j.scitotenv.2023.167499] [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: 06/11/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Systematic studies on the assembly process and driving mechanisms of microbial communities in estuaries with diverse seasonal and spatial scales are still limited. In this study, high-throughput sequencing, and microbial network analysis were combined to decipher the impact of environmental changes and biological interactions on the maintenance of microbial diversity patterns in the Jiulong River Estuary (JRE). The results showed that overall, stochastic processes dominated the bacterioplankton community assembly in the estuary, accounting for 49.66-74.78 % of the total. Additionally, bacterioplankton community diversity varied significantly across seasons and subzones. Specifically, the concentration of soluble reactive phosphorus (SRP) in the estuary steadily reduced from winter to summer, and the corresponding bacterioplankton community interactions gradually shifted from the weakest interaction in winter to the strongest in summer. The deterministic processes contributed more than half (50.34 %) to microbial assembly in the summer, but only 25.22 % in winter. Deterministic processes prevailed in the seaward with low SRP concentrations and strong bacterioplankton community interactions, while stochastic processes contributed 70.14 % to the assembly of microbial communities riverward. Biotic and abiotic factors, such as nutrients and microbial interactions, jointly drove the seasonal and spatial patterns of bacterioplankton community assembly, but overall, nutrients played a dominant role. Nevertheless, the contributions of nutrients and microbial interactions were equivalent in spatial assembly processes, albeit nutrients were the primary seasonal driver of the bacterioplankton community assembly process. This study emphasizes the significance of microbial interactions in the bacterioplankton community assemblage. These findings provide new and comprehensive insights into the microbial communities' organization in estuaries.
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Affiliation(s)
- Ling Lin
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Jiangzhiqian Xiong
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Lihua Liu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China
| | - Feifei Wang
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China
| | - Wenzhi Cao
- State Key Laboratory of Marine Environmental Science, Key Laboratory of the Ministry of Education for Coastal Wetland Ecosystems, College of the Environment and Ecology, Xiang'an South Road, Xiamen 361102, China.
| | - Wenfeng Xu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen 361022, China.
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2
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Fakhraldeen SA, Al-Haddad S, Habibi N, Alagarsamy S, F. K. Habeebullah S, Ali AK, Al-Zakri WM. Diversity and spatiotemporal variations in bacterial and archaeal communities within Kuwaiti territorial waters of the Northwest Arabian Gulf. PLoS One 2023; 18:e0291167. [PMID: 37972047 PMCID: PMC10653540 DOI: 10.1371/journal.pone.0291167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/23/2023] [Indexed: 11/19/2023] Open
Abstract
Kuwaiti territorial waters of the northwest Arabian Gulf represent a unique aquatic ecosystem prone to various environmental and anthropogenic stressors that pose significant constraints on the resident biota which must withstand extreme temperatures, salinity levels, and reducing conditions, among other factors to survive. Such conditions create the ideal environment for investigations into novel functional genetic adaptations of resident organisms. Firstly, however, it is essential to identify said organisms and understand the dynamic nature of their existence. Thus, this study provides the first comprehensive analysis of bacterial and archaeal community structures in the unique waters of Kuwait located in the Northwest Arabian Gulf and analyzes their variations with respect to depth, season, and location, as well as their susceptibility to changes in abundance with respect to various physicochemical parameters. Importantly, this study is the first of its kind to utilize a shotgun metagenomics approach with sequencing performed at an average depth of 15 million paired end reads per sample, which allows for species-level community profiling and sets the framework for future functional genomic investigations. Results showed an approximately even abundance of both archaeal (42.9%) and bacterial (57.1%) communities, but significantly greater diversity among the bacterial population, which predominantly consisted of members of the Proteobacteria, Cyanobacteria, and Bacteroidetes phyla in decreasing order of abundance. Little to no significant variations as assessed by various metrics including alpha and beta diversity analyses were observed in the abundance of archaeal and bacterial populations with respect to depth down the water column. Furthermore, although variations in differential abundance of key genera were detected at each of the three sampling locations, measurements of species richness and evenness revealed negligible variation (ANOVA p<0.05) and only a moderately defined community structure (ANOSIM r2 = 0.243; p>0.001) between the various locations. Interestingly, abundance of archaeal community members showed a significant increase (log2 median ratio of RA = 2.6) while the bacterial population showed a significant decrease (log2 median ratio = -1.29) in the winter season. These findings were supported by alpha and beta diversity analyses as well (ANOSIM r2 = 0.253; p>0.01). Overall, this study provides the first in-depth analysis of both bacterial and archaeal community structures developed using a shotgun metagenomic approach in the waters of the Northwest Arabian Gulf thus providing a framework for future investigations of functional genetic adaptations developed by resident biota attempting to survive in the uniquely extreme conditions to which they are exposed.
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Affiliation(s)
- Saja A. Fakhraldeen
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Sakinah Al-Haddad
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Nazima Habibi
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Shuwaikh, Kuwait
| | - Surendraraj Alagarsamy
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Sabeena F. K. Habeebullah
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Abdulmuhsen K. Ali
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Shuwaikh, Kuwait
| | - Walid M. Al-Zakri
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
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Mendoza-Cano F, Encinas-García T, Muhlia-Almazán A, Porchas-Cornejo M, de la Re-Vega E, Sánchez-Paz A. Development and validation of a real-time PCR assay protocol for the specific detection and quantification of pelagiphages in seawater samples. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106168. [PMID: 37708616 DOI: 10.1016/j.marenvres.2023.106168] [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: 05/18/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/16/2023]
Abstract
Earth is inhabited by numerous adaptations of cellular forms shaped by the persistent scrutiny of natural selection. Thus, as natural selection has fixed beneficial adaptations of functional traits, cellular life has conquered almost all environmental niches on our planet. However, cellular life succumbs in number and genetic diversity to viruses. Among all viruses, phages are highly prevalent in diverse environments, and due to their vast genetic diversity and abundance, their relevant role as significant players in several ecological processes is now fully recognized. Pelagiphages, bacteriophages infecting bacteria of the SAR11 clade, are the most abundant viruses in the oceans. However, the ecological contribution of pelagiphages on populations of Pelagibacterales remains largely underestimated. An essential aspect of estimating the impact of bacteriophages is their absolute and precise quantification, which provides relevant information about the host-virus interactions and the structure of viral assemblages. Consequently, due to its abundance and claimed influence in the biogeochemical cycling of elements, the accurate quantification of pelagiphages results in an essential task. This study describes the development and validation of a sensitive, specific, accurate and reproducible qPCR platform targeting pelagiphages. Moreover, this method allowed the detection and quantification of pelagiphages in the Gulf of California for the first time.
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Affiliation(s)
- F Mendoza-Cano
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México
| | - T Encinas-García
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México; Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Hermosillo, Sonora, 83000, México
| | - A Muhlia-Almazán
- Bioenergetics and Molecular Genetics Lab, Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, Hermosillo, Sonora, 83304, México
| | - M Porchas-Cornejo
- Centro de Investigaciones Biológicas del Noroeste, S.C. Km 2.35 Carretera a Las Tinajas, S/N Colonia Tinajas, Guaymas, Sonora, C.P. 85460, México
| | - E de la Re-Vega
- Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Hermosillo, Sonora, 83000, México
| | - A Sánchez-Paz
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México.
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Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis. mSystems 2023; 8:e0093122. [PMID: 36722950 PMCID: PMC9948707 DOI: 10.1128/msystems.00931-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Viruses infecting marine prokaryotes have a large impact on the diversity and dynamics of their hosts. Model systems suggest that viral infection is frequency dependent and constrained by the virus-host encounter rate. However, it is unclear whether frequency-dependent infection is pervasive among the abundant prokaryotic populations with different temporal dynamics. To address this question, we performed a comparison of prokaryotic and viral communities using 16S rRNA amplicon and virome sequencing based on samples collected monthly for 2 years at a Japanese coastal site, Osaka Bay. Concurrent seasonal shifts observed in prokaryotic and viral community dynamics indicated that the abundance of viruses correlated with that of their predicted host phyla (or classes). Cooccurrence network analysis between abundant prokaryotes and viruses revealed 6,423 cooccurring pairs, suggesting a tight coupling of host and viral abundances and their "one-to-many" correspondence. Although stable dominant species, such as SAR11, showed few cooccurring viruses, a fast succession of their viruses suggests that viruses infecting these populations changed continuously. Our results suggest that frequency-dependent viral infection prevails in coastal marine prokaryotes regardless of host taxa and temporal dynamics. IMPORTANCE There is little room for doubt that viral infection is prevalent among abundant marine prokaryotes regardless of their taxa or growth strategy. However, comprehensive evaluations of viral infections in natural prokaryotic communities are still technically difficult. In this study, we examined viral infection in abundant prokaryotes by monitoring the monthly dynamics of prokaryotic and viral communities at a eutrophic coastal site, Osaka Bay. We compared the community dynamics of viruses with those of their putative hosts based on genome-based in silico host prediction. We observed frequent cooccurrence among the predicted virus-host pairs, suggesting that viral infection is prevalent in abundant prokaryotes regardless of their taxa or temporal dynamics. This likely indicates that frequent lysis of the abundant prokaryotes via viral infection has a considerable contribution to the biogeochemical cycling and maintenance of prokaryotic community diversity.
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Voigt E, Rall BC, Chatzinotas A, Brose U, Rosenbaum B. Phage strategies facilitate bacterial coexistence under environmental variability. PeerJ 2021; 9:e12194. [PMID: 34760346 PMCID: PMC8572521 DOI: 10.7717/peerj.12194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/31/2021] [Indexed: 12/14/2022] Open
Abstract
Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as "Killing the Winner", "Piggyback the loser" (PtL) or "Piggyback the Winner" (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed 'in silico' experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.
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Affiliation(s)
- Esther Voigt
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Björn C Rall
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Antonis Chatzinotas
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.,Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany
| | - Ulrich Brose
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Benjamin Rosenbaum
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
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Forcone K, Coutinho FH, Cavalcanti GS, Silveira CB. Prophage Genomics and Ecology in the Family Rhodobacteraceae. Microorganisms 2021; 9:microorganisms9061115. [PMID: 34064105 PMCID: PMC8224337 DOI: 10.3390/microorganisms9061115] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homology with reference and metagenome-assembled viral genomes from aquatic and terrestrial ecosystems. Among the newly identified putative prophages, 35% encoded auxiliary metabolic genes (AMGs), mostly involved in secondary metabolism, amino acid metabolism, and cofactor and vitamin production. The analysis of integration sites and gene homology showed that 22 of the putative prophages were actually gene transfer agents (GTAs) similar to a GTA of Rhodobacter capsulatus. Twenty-three percent of the predicted prophages were observed in the TARA Oceans viromes generated from free viral particles, suggesting that they represent active prophages capable of induction. The distribution of these prophages was significantly associated with latitude and temperature. The prophages most abundant at high latitudes encoded acpP, an auxiliary metabolic gene involved in lipid synthesis and membrane fluidity at low temperatures. Our results show that prophages and gene transfer agents are significant sources of genomic diversity in roseobacter, with potential roles in the ecology of this globally distributed bacterial group.
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Affiliation(s)
- Kathryn Forcone
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Felipe H. Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, Aptdo. 18, Ctra. Alicante-Valencia, s/n, 03550 San Juan de Alicante, Spain;
| | - Giselle S. Cavalcanti
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Cynthia B. Silveira
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
- Correspondence:
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7
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Zhang C, Du XP, Zeng YH, Zhu JM, Zhang SJ, Cai ZH, Zhou J. The communities and functional profiles of virioplankton along a salinity gradient in a subtropical estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143499. [PMID: 33203567 DOI: 10.1016/j.scitotenv.2020.143499] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/08/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
Viruses are the major drivers shaping microorganismal communities, and impact marine biogeochemical cycling. They are affected by various environmental parameters, such as salinity. Although the spatiotemporal distribution and dynamics of virioplankton have been extensively studied in saline environments, few detailed studies of community structure and function of viruses along salinity gradients have been conducted. Here, we used the 16S and 18S rRNA gene amplicon and metagenomic sequencing from a subtropical estuary (Pearl River Estuary, PRE; located in Shenzhen, Guangdong Province, China) to explore how viral community composition and function vary along a salinity gradient. Results showed that the detected viruses were mainly bacteriophages. The double-stranded DNA viruses were the most abundant (especially Siphoviridae, Myoviridae, Mimiviridae, Phycodnaviridae, and Podoviridae), followed by a small number of single-stranded DNA (Circoviridae) and RNA (Retroviridae) viruses. Viral biodiversity significantly declined and community structure varied greatly along the salinity gradient. The salinity, ammonium and dissolved oxygen were dominated factors influencing the community composition of viruses. Association network analysis showed that viruses had a negative effect on multiple host taxa (prokaryotic and eukaryotic species). Metagenomic data revealed that the main viral functional potential was involved in organic matter metabolism by carbohydrate-active enzymes (CAZymes). Deeper comparative functional analyses showed that viruses in the low-salinity environment had more carbohydrate-binding module and glycosidase hydrolases activities than those under high-salinity conditions. However, an opposite pattern was observed for carbohydrate esterases. These results suggest that virus-encoded CAZyme genes may alter the bacterial metabolism in estuaries. Overall, our results demonstrate that there is a spatial heterogeneity in the composition and function of virioplankton along a salinity gradient. This study enhances our understanding of viral distribution and their contribution to regulating carbon degradation throughout environments with varying salinities in subtropical estuaries.
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Affiliation(s)
- Chen Zhang
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; The School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu Province, PR China
| | - Xiao-Peng Du
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Yan-Hua Zeng
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Jian-Ming Zhu
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; School of Environment, Harbin Institute of Technology, Harbin 150001, PR China
| | - Sheng-Jie Zhang
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Zhong-Hua Cai
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China
| | - Jin Zhou
- Shenzhen Public Platform for Screening & Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Institute for Ocean Engineering, Tsinghua University, Beijing 100084, PR China.
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Filipa-Silva A, Parreira R, Martínez-Puchol S, Bofill-Mas S, Barreto Crespo MT, Nunes M. The Unexplored Virome of Two Atlantic Coast Fish: Contribution of Next-Generation Sequencing to Fish Virology. Foods 2020; 9:E1634. [PMID: 33182306 PMCID: PMC7695296 DOI: 10.3390/foods9111634] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 12/24/2022] Open
Abstract
Much of the knowledge on viruses is focused on those that can be propagated using cell-cultures or that can cause disease in humans or in economically important animals and plants. However, this only reflects a small portion of the virosphere. Therefore, in this study, we explore by targeted next-generation sequencing, how the virome varies between Atlantic horse mackerels and gilthead seabreams from fisheries and aquaculture from the center and south regions of Portugal. Viral genomes potentially pathogenic to fish and crustaceans, as well as to humans, were identified namelyese included Astroviridae, Nodaviridae, Hepadnaviridae, Birnaviridae, Caliciviridae, and Picornaviridae families. Also bacteriophages sequences were identified corresponding to the majority of sequencese detected, with Myoviridae, Podoviridae, and Siphoviridae, the most widespread families in both fish species. However, these findings can also be due to the presence of bacteria in fish tissues, or even to contamination. Overall, seabreams harbored viruses from a smaller number of families in comparison with mackerels. Therefore, the obtained data show that fish sold for consumption can harbor a high diversity of viruses, many of which are unknown, reflecting the overall uncharacterized virome of fish. While cross-species transmission of bonafide fish viruses to humans is unlikely, the finding of human pathogenic viruses in fish suggest that fish virome can be a potential threat regarding food safety.
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Affiliation(s)
- Andreia Filipa-Silva
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (A.F.-S.); (M.T.B.C.)
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Ricardo Parreira
- Global Health and Tropical Medicine (GHTM) Research Center, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical (IHTM), Universidade Nova de Lisboa (NOVA), 1349-008 Lisboa, Portugal;
| | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain; (S.M.-P.); (S.B.-M.)
- The Water Research Institute (idRA), Universitat de Barcelona, 08001 Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain; (S.M.-P.); (S.B.-M.)
- The Water Research Institute (idRA), Universitat de Barcelona, 08001 Barcelona, Catalonia, Spain
| | - Maria Teresa Barreto Crespo
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (A.F.-S.); (M.T.B.C.)
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Mónica Nunes
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (A.F.-S.); (M.T.B.C.)
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
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Du XP, Cai ZH, Zuo P, Meng FX, Zhu JM, Zhou J. Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom. Microorganisms 2020; 8:microorganisms8010107. [PMID: 31940944 PMCID: PMC7023004 DOI: 10.3390/microorganisms8010107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/18/2019] [Accepted: 01/10/2020] [Indexed: 01/02/2023] Open
Abstract
Viruses are key biogeochemical engines in the regulation of the dynamics of phytoplankton. However, there has been little research on viral communities in relation to algal blooms. Using the virMine tool, we analyzed viral information from metagenomic data of field dinoflagellate (Gymnodinium catenatum) blooms at different stages. Species identification indicated that phages were the main species. Unifrac analysis showed clear temporal patterns in virioplankton dynamics. The viral community was dominated by Siphoviridae, Podoviridae, and Myoviridae throughout the whole bloom cycle. However, some changes were observed at different phases of the bloom; the relatively abundant Siphoviridae and Myoviridae dominated at pre-bloom and peak bloom stages, while at the post-bloom stage, the members of Phycodnaviridae and Microviridae were more abundant. Temperature and nutrients were the main contributors to the dynamic structure of the viral community. Some obvious correlations were found between dominant viral species and host biomass. Functional analysis indicated some functional genes had dramatic response in algal-associated viral assemblages, especially the CAZyme encoding genes. This work expands the existing knowledge of algal-associated viruses by characterizing viral composition and function across a complete algal bloom cycle. Our data provide supporting evidence that viruses participate in dinoflagellate bloom dynamics under natural conditions.
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Affiliation(s)
- Xiao-Peng Du
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Zhong-Hua Cai
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Ping Zuo
- The School of Geography and Ocean Science, Nanjing University, Nanjing 210000, China;
| | - Fan-Xu Meng
- Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310000, China
| | - Jian-Ming Zhu
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jin Zhou
- The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Correspondence:
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Kaszab E, Doszpoly A, Lanave G, Verma A, Bányai K, Malik YS, Marton S. Metagenomics revealing new virus species in farm and pet animals and aquaculture. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7149329 DOI: 10.1016/b978-0-12-816352-8.00002-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Viral metagenomics is slowly taking over the traditional and widely used molecular techniques for the investigation of pathogenic viruses responsible for illness and inflicting great economic burden on the farm animal industry. Owing to the continued improvements in sequencing technologies and the dramatic reduction of per base costs of sequencing the use of next generation sequencing have been key factors in this progress. Discoveries linked to viral metagenomics are expected to be beneficial to the field of veterinary medicine starting from the development of better diagnostic assays to the design of new subunit vaccines with minimal investments. With these achievements the research has taken a giant leap even toward the better healthcare of animals and, as a result, the animal sector could be growing at an unprecedented pace.
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Metagenomics Approaches in Discovery and Development of New Bioactive Compounds from Marine Actinomycetes. Curr Microbiol 2019; 77:645-656. [PMID: 31069462 DOI: 10.1007/s00284-019-01698-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/26/2019] [Indexed: 02/06/2023]
Abstract
Marine actinomycetes are prolific sources of marine drug discovery system contributing for several bioactive compounds of biomedical prominence. Metagenomics, a culture-independent technique through its sequence- and function-based screening has led to the discovery and synthesis of numerous biologically significant compounds like polyketide synthase, Non-ribosomal peptide synthetase, antibiotics, and biocatalyst. While metagenomics offers different advantages over conventional sequencing techniques, they also have certain limitations including bias classification, non-availability of quality DNA samples, heterologous expression, and host selection. The assimilation of advanced amplification and screening methods such as φ29 DNA polymerase, Next-Generation Sequencing, Cosmids, and recent bioinformatics tools like automated genome mining, anti-SMASH have shown promising results to overcome these constrains. Consequently, functional genomics and bioinformatics along with synthetic biology will be crucial for the success of the metagenomic approach and indeed for exploring new possibilities among the microbial consortia for the future drug discovery process.
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Wang Y, Liu Y, Wang J, Luo T, Zhang R, Sun J, Zheng Q, Jiao N. Seasonal dynamics of bacterial communities in the surface seawater around subtropical Xiamen Island, China, as determined by 16S rRNA gene profiling. MARINE POLLUTION BULLETIN 2019; 142:135-144. [PMID: 31232286 DOI: 10.1016/j.marpolbul.2019.03.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 02/03/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
This study investigated the microbial structure in the surface seawater from five coastal sites around Xiamen Island, China, over four seasons to evaluate seasonal environmental fluctuations impact on them. This subtropical island is characterized by long, hot, humid summers, and short, mild, dry winters. All sites were dominated by Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes; microbial community composition was similar across four seasons. However, larger proportions of Gammaproteobacteria and Bacillus were observed during the summer than during any other season. The high ratio of Bacillus, Bacteroidetes, and Clostridia richness to Alphaproteobacteria richness in the summer, suggested that the sites we tested were heavily affected by waste water to other seasons. Correlation-based network analyses among the bacterial species and environmental variables indicated important connections between physiochemical variables and specific taxonomic groups. Collectively, our results suggested that seasonal shifts and wastewater pollution together shape the structures of the microbial communities around Xiamen Island.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Yanting Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Tingwei Luo
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China.
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Calero-Cáceres W, Balcázar JL. Antibiotic resistance genes in bacteriophages from diverse marine habitats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:452-455. [PMID: 30447583 DOI: 10.1016/j.scitotenv.2018.11.166] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/18/2018] [Accepted: 11/11/2018] [Indexed: 06/09/2023]
Abstract
Although antibiotic resistance represents a significant and growing threat to human and environmental health worldwide, the contribution of bacteriophages (phages) to the acquisition and spread of antibiotic resistance genes (ARGs) in the environment has not been extensively explored. In this study, a comprehensive analysis of several viromes from diverse marine habitats was performed to investigate whether or not phages carry ARGs. The analysis provides strong evidence that phages from marine habitats are potential reservoirs of ARGs. In fact, genes conferring resistance to aminocoumarin, bacitracin and multidrug resistance (particularly the mexB gene) were found in all analyzed marine viromes. Given this, the role of phages as reservoirs of ARGs should not be underestimated considering their global distribution.
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Affiliation(s)
- William Calero-Cáceres
- UTA-RAM-OneHealth Group, Centro de Investigaciones Agropecuarias, Facultad de Ciencias Agropecuarias, Universidad Técnica de Ambato, Tungurahua, Ecuador
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), University of Girona, Girona, Spain.
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Cobaviruses - a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME JOURNAL 2019; 13:1404-1421. [PMID: 30718806 PMCID: PMC6775973 DOI: 10.1038/s41396-019-0362-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 11/13/2022]
Abstract
Bacteriophages are widely considered to influence bacterial communities, however most phages are still unknown or not studied well enough to understand their ecological roles. We have isolated two phages infecting Lentibacter sp. SH36, affiliated with the marine Roseobacter group, and retrieved similar phage genomes from publicly available metagenomics databases. Phylogenetic analysis placed the new phages within the Cobavirus group, in the here newly proposed genus Siovirus and subfamily Riovirinae of the Podoviridae. Gene composition and presence of direct terminal repeats in cultivated cobaviruses point toward a genome replication and packaging strategy similar to the T7 phage. Investigation of the genomes suggests that viral lysis of the cell proceeds via the canonical holin-endolysin pathway. Cobaviral hosts include members of the genera Lentibacter, Sulfitobacter and Celeribacter of the Roseobacter group within the family Rhodobacteraceae (Alphaproteobacteria). Screening more than 5,000 marine metagenomes, we found cobaviruses worldwide from temperate to tropical waters, in the euphotic zone, mainly in bays and estuaries, but also in the open ocean. The presence of cobaviruses in protist metagenomes as well as the phylogenetic neighborhood of cobaviruses in glutaredoxin and ribonucleotide reductase trees suggest that cobaviruses could infect bacteria associated with phototrophic or grazing protists. With this study, we expand the understanding of the phylogeny, classification, genomic organization, biogeography and ecology of this phage group infecting marine Rhodobacteraceae.
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Han M, Yang P, Zhong C, Ning K. The Human Gut Virome in Hypertension. Front Microbiol 2018; 9:3150. [PMID: 30619215 PMCID: PMC6305721 DOI: 10.3389/fmicb.2018.03150] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 12/05/2018] [Indexed: 12/15/2022] Open
Abstract
Objectives: Previous studies have reported that the gut microbiome has an important link with the development of hypertension. Though previous researches have focused on the links of gut bacteria with hypertension, little has been known about the linkage of gut viruses to hypertension and the development of hypertension, largely due to the lack of data mining tools for such investigation. In this work, we have analyzed 196 fecal metagenomic data related to hypertension aiming to profile the gut virome and link the gut virome to pre-hypertension and hypertension. Design: Here, we have applied a statistically sound method for mining of gut virome data and linking gut virome to hypertension. We characterized the viral composition and bacterial composition of 196 samples, identified the viral-type of each sample and linked gut virome to hypertension. Results: We stratified these 196 fecal samples into two viral-types and selected 32 viruses as the biomarkers for these groups. We found that viruses could have a superior resolution and discrimination power than bacteria for differentiation of healthy samples and pre-hypertension samples, as well as hypertension samples. Moreover, as to the co-occurrence networks linking viruses and bacteria, we found increasingly pervasive virus-bacteria linkages from healthy people to pre-hypertension people to hypertension patients. Conclusion: Overall, our results have shown ample indications of the link between human gut virome and hypertension, and could help provide microbial solutions toward early diagnoses of hypertension.
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Affiliation(s)
- Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Chaofang Zhong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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16
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Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India. Sci Rep 2018; 8:16036. [PMID: 30375431 PMCID: PMC6207776 DOI: 10.1038/s41598-018-34332-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/04/2018] [Indexed: 11/08/2022] Open
Abstract
The present study illustrates the genetic diversity of four uncultured viral communities from the surface waters of Cochin Estuary (CE), India. Viral diversity inferred using Illumina HiSeq paired-end sequencing using a linker-amplified shotgun library (LASL) revealed different double-stranded DNA (dsDNA) viral communities. The water samples were collected from four stations PR1, PR2, PR3, and PR4, during the pre-monsoon (PRM) season. Analysis of virus families indicated that the Myoviridae was the most common viral community in the CE followed by Siphoviridae and Podoviridae. There were significant (p < 0.05) spatial variations in the relative abundance of dominant families in response to the salinity regimes. The relative abundance of Myoviridae and Podoviridae were high in the euryhaline region and Siphoviridae in the mesohaline region of the estuary. The predominant phage type in CE was phages that infected Synechococcus. The viral proteins were found to be involved in major functional activities such as ATP binding, DNA binding, and DNA replication. The study highlights the genetic diversity of dsDNA viral communities and their functional protein predictions from a highly productive estuarine system. Further, the metavirome data generated in this study will enhance the repertoire of publicly available dataset and advance our understanding of estuarine viral ecology.
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Gu X, Tay QXM, Te SH, Saeidi N, Goh SG, Kushmaro A, Thompson JR, Gin KYH. Geospatial distribution of viromes in tropical freshwater ecosystems. WATER RESEARCH 2018; 137:220-232. [PMID: 29550725 PMCID: PMC7112100 DOI: 10.1016/j.watres.2018.03.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/02/2018] [Accepted: 03/07/2018] [Indexed: 05/05/2023]
Abstract
This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems.
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Affiliation(s)
- Xiaoqiong Gu
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | | | - Shu Harn Te
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Nazanin Saeidi
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Shin Giek Goh
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore
| | - Ariel Kushmaro
- School of Material Science and Engineering, Nanyang Technological University, 637819, Singapore
| | | | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore, Engineering Drive 1, T-lab Building, TL08-03, 117576, Singapore.
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18
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Avarre JC. Editorial: Molecular Tracing of Aquatic Viruses: Where Epidemiology Needs to Meet Genomics. Front Microbiol 2017; 8:1498. [PMID: 28848516 PMCID: PMC5550712 DOI: 10.3389/fmicb.2017.01498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/26/2017] [Indexed: 12/23/2022] Open
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