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Li H, Cai L, Wang L, Wang Y, Xu J, Zhang R. The structure and assembly mechanisms of T4-like cyanophages community in the South China Sea. Microbiol Spectr 2024; 12:e0200223. [PMID: 38193726 PMCID: PMC10846272 DOI: 10.1128/spectrum.02002-23] [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: 05/13/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024] Open
Abstract
Marine ecosystems contain an immense diversity of phages, many of which infect cyanobacteria (cyanophage) that are largely responsible for primary productivity. To characterize the genetic diversity and biogeographic distribution of the marine T4-like cyanophage community in the northern South China Sea, the T4-like cyanophage portal protein gene (g20) was amplified. Phylogenetic analysis revealed that marine T4-like cyanophages were highly diverse, with g20 operational taxonomic units being affiliated with five defined clades (Clusters I-V). Cluster II had a wide geographic distribution, Cluster IV was the most abundant in the open sea, and Cluster I was dominant in coastal shelf environments. Our results showed T4-like cyanophages (based on g20) community was generally shaped via heterogeneous selection. Highly variable environmental factors (such as salinity and temperature) can heterogeneously select different cyanophage communities. Nevertheless, the dominant drivers of the T4-like cyanophage community based on the g20 and g23 (T4-like phage major capsid protein gene) were different, probably due to different coverages by the primer sets. Furthermore, the community assembly processes of T4-like cyanophages were affected by host traits (abundance and distribution), viral traits (latent period, burst size, and host range), and environmental properties (temperature and salinity).IMPORTANCECyanophages are abundant and ubiquitous in the oceans, altering population structures and evolution of cyanobacteria, which account for a large portion of global carbon fixation, through host mortality, horizontal gene transfer, and the modulation of host metabolism. However, little is known about the biogeography and ecological drivers that shape the cyanophage community. Here, we use g20 and g23 genes to examine the biogeographic patterns and the assembly mechanisms of T4-like cyanophage community in the northern part of the South China Sea. The different coverages of primer sets might lead to the different dominant drivers of T4-like cyanophage community based on g20 and g23 genes. Our results showed that characteristics of viral traits (latent period, burst size, and host range) and host traits (abundance and distribution) were found to either limit or enhance the biogeographic distribution of T4-like cyanophages. Overall, both virus and host properties are critical to consider when determining rules of community assembly for viruses.
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Affiliation(s)
- Huifang Li
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Long Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Juntian Xu
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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2
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Wu LY, Piedade GJ, Moore RM, Harrison AO, Martins AM, Bidle KD, Polson SW, Sakowski EG, Nissimov JI, Dums JT, Ferrell BD, Wommack KE. Ubiquitous, B 12-dependent virioplankton utilizing ribonucleotide-triphosphate reductase demonstrate interseasonal dynamics and associate with a diverse range of bacterial hosts in the pelagic ocean. ISME COMMUNICATIONS 2023; 3:108. [PMID: 37789093 PMCID: PMC10547690 DOI: 10.1038/s43705-023-00306-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 10/05/2023]
Abstract
Through infection and lysis of their coexisting bacterial hosts, viruses impact the biogeochemical cycles sustaining globally significant pelagic oceanic ecosystems. Currently, little is known of the ecological interactions between lytic viruses and their bacterial hosts underlying these biogeochemical impacts at ecosystem scales. This study focused on populations of lytic viruses carrying the B12-dependent Class II monomeric ribonucleotide reductase (RNR) gene, ribonucleotide-triphosphate reductase (Class II RTPR), documenting seasonal changes in pelagic virioplankton and bacterioplankton using amplicon sequences of Class II RTPR and the 16S rRNA gene, respectively. Amplicon sequence libraries were analyzed using compositional data analysis tools that account for the compositional nature of these data. Both virio- and bacterioplankton communities responded to environmental changes typically seen across seasonal cycles as well as shorter term upwelling-downwelling events. Defining Class II RTPR-carrying viral populations according to major phylogenetic clades proved a more robust means of exploring virioplankton ecology than operational taxonomic units defined by percent sequence homology. Virioplankton Class II RTPR populations showed positive associations with a broad phylogenetic diversity of bacterioplankton including dominant taxa within pelagic oceanic ecosystems such as Prochlorococcus and SAR11. Temporal changes in Class II RTPR virioplankton, occurring as both free viruses and within infected cells, indicated possible viral-host pairs undergoing sustained infection and lysis cycles throughout the seasonal study. Phylogenetic relationships inferred from Class II RTPR sequences mirrored ecological patterns in virio- and bacterioplankton populations demonstrating possible genome to phenome associations for an essential viral replication gene.
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Affiliation(s)
- Ling-Yi Wu
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Gonçalo J Piedade
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797 SZ, t'Horntje, The Netherlands
- Department of Oceanography and Fisheries and Ocean Sciences Institute-OKEANOS, University of the Azores, 9901-862 Horta, Faial, Azores, Portugal
| | - Ryan M Moore
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Amelia O Harrison
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Ana M Martins
- Department of Oceanography and Fisheries and Ocean Sciences Institute-OKEANOS, University of the Azores, 9901-862 Horta, Faial, Azores, Portugal
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd., New Brunswick, NJ, 08901, USA
| | - Shawn W Polson
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Eric G Sakowski
- Department of Earth Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Jozef I Nissimov
- Department of Biology, University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada
| | - Jacob T Dums
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
- Biotechnology Program, North Carolina State University, 2800 Faucette Dr, Raleigh, NC, 27695, USA
| | - Barbra D Ferrell
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - K Eric Wommack
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
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3
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Cai L, Xu B, Li H, Xu Y, Wei W, Zhang R. Spatiotemporal Shift of T4-Like Phage Community Structure in the Three Largest Estuaries of China. Microbiol Spectr 2023; 11:e0520322. [PMID: 36877016 PMCID: PMC10101079 DOI: 10.1128/spectrum.05203-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 02/08/2023] [Indexed: 03/07/2023] Open
Abstract
Estuaries are one of the most highly productive and economically important ecosystems at the continent-ocean interface. Estuary productivity is largely determined by the microbial community structure and activity. Viruses are major agents of microbial mortality and are key drivers of global geochemical cycles. However, the taxonomic diversity of viral communities and their spatial-temporal distribution in estuarine ecosystems have been poorly studied. In this study, we investigated the T4-like viral community composition at three major Chinese estuaries in winter and in summer. Diverse T4-like viruses, which were divided into three main clusters (Clusters I to III), were revealed. The Marine Group of Cluster III, with seven identified subgroups, was the most dominant (averaging 76.5% of the total sequences) in the Chinese estuarine ecosystems. Significant variations of T4-like viral community composition were observed among estuaries and seasons, with higher diversity occurring in winter. Among various environmental variables, temperature was a main driver of the viral communities. This study demonstrates viral assemblage diversification and seasonality in Chinese estuarine ecosystems. IMPORTANCE Viruses are ubiquitous but largely uncharacterized members of aquatic environments that cause significant mortality in microbial communities. Recent large-scale oceanic projects have greatly advanced our understanding of viral ecology in marine environments, but those studies mostly focused on oceanic regions. There have yet to be spatiotemporal studies of viral communities in estuarine ecosystems, which are unique habitats that play a significant role in global ecology and biogeochemistry. This work is the first comprehensive study that provides a detailed picture of the spatial and seasonal variation of viral communities (specifically, T4-like viral communities) in three major estuarine ecosystems in China. These findings provide much-needed knowledge regarding estuarine viral ecosystems, which currently lags in oceanic ecosystem research.
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Affiliation(s)
- Lanlan Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Bu Xu
- School of Environment, Harbin Institute of Technology, Harbin, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Huifang Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Key Laboratory of Coastal Salt Marsh Ecosystems and Resources, Ministry of Natural Resources, Jiangsu Ocean University, Lianyungang, China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Shandong, China
| | - Wei Wei
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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Habibi N, Uddin S, Al-Sarawi H, Aldhameer A, Shajan A, Zakir F, Abdul Razzack N, Alam F. Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome. Microorganisms 2023; 11:microorganisms11020531. [PMID: 36838497 PMCID: PMC9960530 DOI: 10.3390/microorganisms11020531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/03/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.
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Affiliation(s)
- Nazima Habibi
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
- Correspondence:
| | - Saif Uddin
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Hanan Al-Sarawi
- Environment Public Authority, Fourth Ring Road, Shuwaikh Industrial 70050, Kuwait
| | - Ahmed Aldhameer
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Anisha Shajan
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Farhana Zakir
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Nasreem Abdul Razzack
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Faiz Alam
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
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5
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The Beauty of Bacteriophage T4 Research: Lindsay W. Black and the T4 Head Assembly. Viruses 2022; 14:v14040700. [PMID: 35458430 PMCID: PMC9026906 DOI: 10.3390/v14040700] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023] Open
Abstract
Viruses are biochemically complex structures and mainly consist of folded proteins that contain nucleic acids. Bacteriophage T4 is one of most prominent examples, having a tail structure that contracts during the infection process. Intracellular phage multiplication leads to separate self-directed assembly reactions of proheads, tails and tail fibers. The proheads are packaged with concatemeric DNA produced by tandem replication reactions of the parental DNA molecule. Once DNA packaging is completed, the head is joined with the tail and six long fibers are attached. The mature particles are then released from the cell via lysis, another tightly regulated process. These processes have been studied in molecular detail leading to a fascinating view of the protein-folding dynamics that direct the structural interplay of assembled complexes. Lindsay W. Black dedicated his career to identifying and defining the molecular events required to form the T4 virion. He leaves us with rich insights into the astonishingly precise molecular clockwork that co-ordinates all of the players in T4 assembly, both viral and cellular. Here, we summarize Lindsay’s key research contributions that are certain to stimulate our future science for many years to come.
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A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary. Sci Data 2022; 9:49. [PMID: 35165305 PMCID: PMC8844013 DOI: 10.1038/s41597-022-01153-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/12/2022] [Indexed: 12/21/2022] Open
Abstract
Estuaries are one of the most important coastal ecosystems. While microbiomes and viromes have been separately investigated in some estuaries, few studies holistically deciphered the genomes and connections of viruses and their microbial hosts along an estuarine salinity gradient. Here we applied deep metagenomic sequencing on microbial and viral communities in surface waters of the Pearl River estuary, one of China’s largest estuaries with strong anthropogenic impacts. Overall, 1,205 non-redundant prokaryotic genomes with ≥50% completeness and ≤10% contamination, and 78,502 non-redundant viral-like genomes were generated from samples of three size fractions and five salinity levels. Phylogenomic analysis and taxonomy classification show that majority of these estuarine prokaryotic and viral genomes are novel at species level according to public databases. Potential connections between the microbial and viral populations were further investigated by host-virus matching. These combined microbial and viral genomes provide an important complement of global marine genome datasets and should greatly facilitate our understanding of microbe-virus interactions, evolution and their implications in estuarine ecosystems. Measurement(s) | bacteria • Archaea • viruses | Technology Type(s) | Shotgun Sequencing | Sample Characteristic - Organism | estuary metagenome | Sample Characteristic - Environment | subtropical estuarine | Sample Characteristic - Location | Pearl river estuary |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.17139998
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7
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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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8
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Zang L, Liu Y, Song X, Cai L, Liu K, Luo T, Zhang R. Unique T4-like phages in high-altitude lakes above 4500 m on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149649. [PMID: 34428653 DOI: 10.1016/j.scitotenv.2021.149649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/24/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Viruses are the most abundant biological entities in the biosphere; however, little is known about viral ecology in high altitude lakes. Here, we characterized viruses from 13 lakes, nine of which located ≥4500 m above sea level, on the Tibetan Plateau, the highest plateau on Earth. The abundance of virus-like particle (VLP) in Tibetan lakes ranged from 4.8 ± 0.2 × 105 VLPs mL-1 to 6.0 ± 0.2 × 107 VLPs mL-1 and the virus-to-bacterium ratio was in the lower range of values reported for other lakes. The viral population size was positively correlated with turbidity and negatively correlated with particulate organic carbon concentration. Highly diverse VLP morphologies, including large (~300 nm) morphotypes, were observed. Phylogenetic analysis of T4-like bacteriophages based on major capsid gene (g23) identified a novel viral group, which were detected in abundance in hyposaline and mesosaline Tibetan lakes. Adaptation to lake evolution, water source (glacier-fed or non-glacier-fed) and environmental conditions (e.g., salinity, phosphorus concentration and productivity) are likely responsible for the variation in T4-like myovirus community composition in contrasting Tibetan lakes. This first investigation of viruses in high-altitude alpine lakes above 4500 m could contribute to our understanding of viral ecology in global alpine lakes.
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Affiliation(s)
- Lin Zang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Science, Beijing 100101, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China; University of Chinese Academy of Science, Beijing 100101, China.
| | - Xuanying Song
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Tingwei Luo
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China.
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9
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Yang Y, Zhang F, Chen X, Li H, Jiao N, Zhang R. Insignificant Response of Bacterioplankton Community to Elevated pCO 2 During a Short-Term Microcosm Experiment in a Subtropical Eutrophic Coastal Ecosystem. Front Microbiol 2021; 12:730377. [PMID: 34867847 PMCID: PMC8633418 DOI: 10.3389/fmicb.2021.730377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Ocean acidification, as one of the major consequences of global climate change, markedly affects multiple ecosystem functions in disparate marine environments from coastal habitats to the deep ocean. Evaluation of the responses of marine microbial community to the increasing partial pressure of CO2 (pCO2) is crucial to explore the microbe-driven biogeochemical processes in the future ocean. In this study, a microcosm incubation of eutrophic coastal water from Xiamen Bay under elevated pCO2 (about 1,000 μatm) and control (ambient air, about 380-410 μatm) conditions was conducted to investigate the effect of ocean acidification on the natural bacterioplankton community. During the 5-day incubation period, the chlorophyll a concentration and bacterioplankton abundance were not significantly affected by increased pCO2. Hierarchical clustering and non-metric multidimensional scaling analysis based on Bray-Curtis similarity among the bacterioplankton community derived from the 16S rRNA genes revealed an inconspicuous impact of elevated pCO2 on the bacterial community. During the incubation period, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, and Epsilonbacteraeota were predominant in all microcosms. Despite the distinct temporal variation in the composition of the bacterioplankton community during the experimental period, statistical analyses showed that no significant difference was found on bacterioplankton taxa between elevated pCO2 and control, indicating that the bacterioplankton at the population-level were also insensitive to elevated pCO2. Our results therefore suggest that the bacterioplankton communities in the fluctuating and eutrophic coastal ecosystems appear to be adaptable to the short-term elevated pCO2.
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Affiliation(s)
- Yunlan Yang
- College of the Environment and Ecology, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Fei Zhang
- College of the Environment and Ecology, Xiamen University, Xiamen, China.,Laboratory of Marine Biology and Ecology, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Huifang Li
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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10
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Li H, Liu L, Wang Y, Cai L, He M, Wang L, Hu C, Jiao N, Zhang R. T4-like myovirus community shaped by dispersal and deterministic processes in the South China Sea. Environ Microbiol 2020; 23:1038-1052. [PMID: 33089595 PMCID: PMC7984403 DOI: 10.1111/1462-2920.15290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 11/28/2022]
Abstract
As the most abundant and genetically diverse biological entities, viruses significantly influence ecological, biogeographical and evolutionary processes in the ocean. However, the biogeography of marine viruses and the drivers shaping viral community are unclear. Here, the biogeographic patterns of T4-like viruses and the relative impacts of deterministic (environmental selection) and dispersal (spatial distance) processes were investigated in the northern South China Sea. The dominant viral operational taxonomic units were affiliated with previously defined Marine, Estuary, Lake and Paddy Groups. A clear viral biogeographic pattern was observed along the environmental gradient from the estuary to open sea. Marine Groups I and IV had a wide geographical distribution, whereas Marine Groups II, III and V were abundant in lower-salinity continental or eutrophic environments. A significant distance-decay pattern was noted for the T4-like viral community, especially for those infecting cyanobacteria. Both deterministic and dispersal processes influenced viral community assembly, although environmental selection (e.g. temperature, salinity, bacterial abundance and community, etc.) had a greater impact than spatial distance. Network analysis confirmed the strong association between viral and bacterial community composition, and suggested a diverse ecological relationship (e.g. lysis, co-infection or mutualistic) between and within viruses and their potential bacterial hosts.
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Affiliation(s)
- Huifang Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Lu Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Yu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Maoqiu He
- State Key Laboratory of Trophic Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Long Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University (Xiang'an), Xiamen, Fujian, China
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Wei W, Wang N, Cai L, Zhang C, Jiao N, Zhang R. Impacts of Freshwater and Seawater Mixing on the Production and Decay of Virioplankton in a Subtropical Estuary. MICROBIAL ECOLOGY 2019; 78:843-854. [PMID: 30972435 PMCID: PMC6842343 DOI: 10.1007/s00248-019-01362-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
Virioplankton is an important component of the aquatic ecosystem and plays multiple ecological and biogeochemical roles. Although the spatial and temporal distributions and dynamics of virioplankton have been well investigated in riverine and marine environments, little is known about the dynamics and environmental controlling mechanisms of virioplankton in estuaries. In this study, viral abundance, production and decay were examined in the Pearl River Estuary (PRE), one of the largest estuaries in China. The influences of freshwater and seawater mixing on viral ecological dynamics were evaluated with several cross-transplant experiments. In PRE, viral abundance, production and decay rates varied from 2.72 ± 0.09 to 27.5 ± 1.07 × 106 viruses ml-1, 7.98 ± 2.33 to 16.27 ± 2.85% h-1 and 0.80 ± 0.23 to 3.74 ± 0.98% h-1, respectively. When the riverine and marine microbial community were transferred into simulated brackish water, viral production rates were markedly inhibited by 83.8% and 47.3%, respectively. The decay of riverine and marine virioplankton was inhibited by 21.1% and 34.2%, respectively, in simulated brackish water. These results indicate change of estuarine environmental factors significantly alters the dynamics of riverine and marine virioplankton. In addition, the effects of mixing on viral production and decay differed between high- and low-fluorescence viruses. High-fluorescence viruses seemed more resistant to decay than low-fluorescence viruses, whereas the production of marine low-fluorescence viruses seemed more resistant to inhibition than that of marine high-fluorescence viruses. Together, these results provide new insights into the ecological dynamics of virioplankton in estuarine environments.
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Affiliation(s)
- Wei Wei
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Nannan Wang
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Lanlan Cai
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China.
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, People's Republic of China.
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
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12
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Chen X, Ma R, Yang Y, Jiao N, Zhang R. Viral Regulation on Bacterial Community Impacted by Lysis-Lysogeny Switch: A Microcosm Experiment in Eutrophic Coastal Waters. Front Microbiol 2019; 10:1763. [PMID: 31417537 PMCID: PMC6685395 DOI: 10.3389/fmicb.2019.01763] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/16/2019] [Indexed: 11/13/2022] Open
Abstract
Marine viruses are major drivers of global biogeochemical cycles and energy fluxes, yet the importance of viral impacts on the succession and diversity of the bacterial community remains largely unexplored. Here, we explored viral life strategy and its potential effect on the bacterial community by experimental incubations of eutrophic coastal waters under lysogen-induced and non-induced treatments. The lysogen-induced treatment showed relatively constant viral and bacterial abundances, lytic and lysogenic viral production throughout the experimental period, together with the progressive declines in not only the relative abundances for SAR11, Rhodobacteraceae, Alteromonadaceae, and SAR86 but the bacterial community diversity. Conversely, the non-induced treatment observed the marked variation in the abundances of viruses, bacteria and cells with high nucleic acid content over the time course of incubation, which was congruent with the drastic shift in lytic and lysogenic viral production as well as the succession of bacterial community. Our results supported the hypotheses that a high level of lysogeny would occur with the increasing density of bacteria with rapid growth rate, which may contribute to a relatively lower host community diversity, whereas the lysogeny to lysis switching would fuel growth opportunities for less-active or initially rare bacterial taxa and generate a more diverse bacterial community. Altogether, the present study underscored the crucial regulatory role of the viral lysis-lysogeny pattern in bacterial community dynamics, composition and diversity, highlighting the viral impact on the microbial food web and biogeochemical processes.
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Affiliation(s)
- Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
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13
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Sandaa RA, E Storesund J, Olesin E, Lund Paulsen M, Larsen A, Bratbak G, Ray JL. Seasonality Drives Microbial Community Structure, Shaping both Eukaryotic and Prokaryotic Host⁻Viral Relationships in an Arctic Marine Ecosystem. Viruses 2018; 10:v10120715. [PMID: 30558156 PMCID: PMC6315344 DOI: 10.3390/v10120715] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/30/2018] [Accepted: 12/08/2018] [Indexed: 12/21/2022] Open
Abstract
The Arctic marine environment experiences dramatic seasonal changes in light and nutrient availability. To investigate the influence of seasonality on Arctic marine virus communities, five research cruises to the west and north of Svalbard were conducted across one calendar year, collecting water from the surface to 1000 m in depth. We employed metabarcoding analysis of major capsid protein g23 and mcp genes in order to investigate T4-like myoviruses and large dsDNA viruses infecting prokaryotic and eukaryotic picophytoplankton, respectively. Microbial abundances were assessed using flow cytometry. Metabarcoding results demonstrated that seasonality was the key mediator shaping virus communities, whereas depth exerted a diversifying effect within seasonal virus assemblages. Viral diversity and virus-to-prokaryote ratios (VPRs) dropped sharply at the commencement of the spring bloom but increased across the season, ultimately achieving the highest levels during the winter season. These findings suggest that viral lysis may be an important process during the polar winter, when productivity is low. Furthermore, winter viral communities consisted of Operational Taxonomic Units (OTUs) distinct from those present during the spring-summer season. Our data provided a first insight into the diversity of viruses in a hitherto undescribed marine habitat characterized by extremes in light and productivity.
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Affiliation(s)
- Ruth-Anne Sandaa
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
| | - Julia E Storesund
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
| | - Emily Olesin
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
| | | | - Aud Larsen
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
- NORCE Norwegian Research Centre AS, Uni Research Environment, N-5020 Bergen, Norway.
| | - Gunnar Bratbak
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
| | - Jessica Louise Ray
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
- NORCE Norwegian Research Centre AS, Uni Research Environment, N-5020 Bergen, Norway.
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