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Jibola-Shittu MY, Heng Z, Keyhani NO, Dang Y, Chen R, Liu S, Lin Y, Lai P, Chen J, Yang C, Zhang W, Lv H, Wu Z, Huang S, Cao P, Tian L, Qiu Z, Zhang X, Guan X, Qiu J. Understanding and exploring the diversity of soil microorganisms in tea ( Camellia sinensis) gardens: toward sustainable tea production. Front Microbiol 2024; 15:1379879. [PMID: 38680916 PMCID: PMC11046421 DOI: 10.3389/fmicb.2024.1379879] [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: 01/31/2024] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
Leaves of Camellia sinensis plants are used to produce tea, one of the most consumed beverages worldwide, containing a wide variety of bioactive compounds that help to promote human health. Tea cultivation is economically important, and its sustainable production can have significant consequences in providing agricultural opportunities and lowering extreme poverty. Soil parameters are well known to affect the quality of the resultant leaves and consequently, the understanding of the diversity and functions of soil microorganisms in tea gardens will provide insight to harnessing soil microbial communities to improve tea yield and quality. Current analyses indicate that tea garden soils possess a rich composition of diverse microorganisms (bacteria and fungi) of which the bacterial Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi and fungal Ascomycota, Basidiomycota, Glomeromycota are the prominent groups. When optimized, these microbes' function in keeping garden soil ecosystems balanced by acting on nutrient cycling processes, biofertilizers, biocontrol of pests and pathogens, and bioremediation of persistent organic chemicals. Here, we summarize research on the activities of (tea garden) soil microorganisms as biofertilizers, biological control agents and as bioremediators to improve soil health and consequently, tea yield and quality, focusing mainly on bacterial and fungal members. Recent advances in molecular techniques that characterize the diverse microorganisms in tea gardens are examined. In terms of viruses there is a paucity of information regarding any beneficial functions of soil viruses in tea gardens, although in some instances insect pathogenic viruses have been used to control tea pests. The potential of soil microorganisms is reported here, as well as recent techniques used to study microbial diversity and their genetic manipulation, aimed at improving the yield and quality of tea plants for sustainable production.
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Affiliation(s)
- Motunrayo Y. Jibola-Shittu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiang Heng
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Nemat O. Keyhani
- Department of Biological Sciences, University of Illinois, Chicago, IL, United States
| | - Yuxiao Dang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ruiya Chen
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Liu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongsheng Lin
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Pengyu Lai
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinhui Chen
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chenjie Yang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weibin Zhang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huajun Lv
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ziyi Wu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuaishuai Huang
- School of Ecology and Environment, Tibet University, Lhasa, China
| | - Pengxi Cao
- School of Ecology and Environment, Tibet University, Lhasa, China
| | - Lin Tian
- Tibet Plateau Institute of Biology, Lhasa, China
| | - Zhenxing Qiu
- Fuzhou Technology and Business University, Fuzhou, Fujian, China
| | - Xiaoyan Zhang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiayu Guan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Junzhi Qiu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Yu H, Xiong L, Li Y, Wei Y, Zhang Q, Li H, Chen W, Ji X. Genetic diversity of virus auxiliary metabolism genes associated with phosphorus metabolism in Napahai plateau wetland. Sci Rep 2023; 13:3250. [PMID: 36828854 PMCID: PMC9958192 DOI: 10.1038/s41598-023-28488-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 01/19/2023] [Indexed: 02/26/2023] Open
Abstract
Viruses play important roles in ecosystems by interfering with the central metabolic pathways of the host during infection via the expression of auxiliary metabolic genes (AMGs), altering the productivity of ecosystems and thus affecting geochemical cycling. In this study, the genetic diversity of phosphorus metabolism AMGs phoH, phoU and pstS was investigated by phylogenetic analysis, PCoA analysis, and alpha diversity analysis based on metagenomic data. It was found that the majority of the sequences were unique to Napahai plateau wetland. It was shown that the genetic diversity of phoH, phoU and pstS genes was independent of both habitats and host origins. In addition, the metabolic pathway of AMGs associated with the phosphorus cycling was identified based on metagenomic data. When phosphorus is deficient, virus utilizes AMGs to affect the metabolic pathway, contributing to higher phosphorus levels in the host and facilitating virus survival, replication, and propagation in the host cell.
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Affiliation(s)
- Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, China
| | - Wei Chen
- Medical School, Kunming University of Science and Technology, Kunming, China.
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, China.
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Luo XQ, Wang P, Li JL, Ahmad M, Duan L, Yin LZ, Deng QQ, Fang BZ, Li SH, Li WJ. Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts. MICROBIOME 2022; 10:190. [PMID: 36333738 PMCID: PMC9636769 DOI: 10.1186/s40168-022-01384-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/04/2022] [Indexed: 06/02/2023]
Abstract
BACKGROUND Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts' metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments. RESULTS Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders. CONCLUSIONS Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions. Video Abstract.
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Affiliation(s)
- Xiao-Qing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- School of Ecology, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Manzoor Ahmad
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Li Duan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ling-Zi Yin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Shan-Hui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Li X, Guo R, Zou X, Yao Y, Lu L. The First Cbk-Like Phage Infecting Erythrobacter, Representing a Novel Siphoviral Genus. Front Microbiol 2022; 13:861793. [PMID: 35620087 PMCID: PMC9127768 DOI: 10.3389/fmicb.2022.861793] [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: 01/25/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Erythrobacter is an important and widespread bacterial genus in the ocean. However, our knowledge about their phages is still rare. Here, a novel lytic phage vB_EliS-L02, infecting Erythrobacter litoralis DSM 8509, was isolated and purified from Sanggou Bay seawater, China. Morphological observation revealed that the phage belonged to Cbk-like siphovirus, with a long prolate head and a long tail. The host range test showed that phage vB_EliS-L02 could only infect a few strains of Erythrobacter, demonstrating its potential narrow-host range. The genome size of vB_EliS-L02 was 150,063 bp with a G+C content of 59.43%, encoding 231 putative open reading frames (ORFs), but only 47 were predicted to be functional domains. Fourteen auxiliary metabolic genes were identified, including phoH that may confer vB_EliS-L02 the advantage of regulating phosphate uptake and metabolism under a phosphate-limiting condition. Genomic and phylogenetic analyses indicated that vB_EliS-L02 was most closely related to the genus Lacusarxvirus with low similarity (shared genes < 30%, and average nucleotide sequence identity < 70%), distantly from other reported phages, and could be grouped into a novel viral genus cluster, in this study as Eliscbkvirus. Meanwhile, the genus Eliscbkvirus and Lacusarxvirus stand out from other siphoviral genera and could represent a novel subfamily within Siphoviridae, named Dolichocephalovirinae-II. Being a representative of an understudied viral group with manifold adaptations to the host, phage vB_EliS-L02 could improve our understanding of the virus–host interactions and provide reference information for viral metagenomic analysis in the ocean.
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Affiliation(s)
- Xuejing Li
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, China
| | - Ruizhe Guo
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao Zou
- Qingdao Central Hospital, Qingdao, China
| | - Yanyan Yao
- Weihai Changqing Ocean Science Technology Co., Ltd., Weihai, China
| | - Longfei Lu
- Weihai Changqing Ocean Science Technology Co., Ltd., Weihai, China
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Bi L, Yu DT, Han LL, Du S, Yuan CY, He JZ, Hu HW. Unravelling the ecological complexity of soil viromes: Challenges and opportunities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:152217. [PMID: 34890674 DOI: 10.1016/j.scitotenv.2021.152217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
Viruses are extremely abundant and ubiquitous in soil, and significantly contribute to various terrestrial ecosystem processes such as biogeochemical nutrient cycling, microbiome regulation and community assembly, and host evolutionary dynamics. Despite their numerous dominance and functional importance, understanding soil viral ecology is a formidable challenge, because of the technological challenges to characterize the abundance, diversity and community compositions of viruses, and their interactions with other organisms in the complex soil environment. Viruses may engage in a myriad of biological interactions within soil food webs across a broad range of spatiotemporal scales and are exposed to various biotic and abiotic disturbances. Current studies on the soil viromes, however, often describe the complexity of their tremendous diversity, but lack of exploring their potential ecological roles. In this article, we summarized the major methods to decipher the ecology of soil viruses, discussed biotic and abiotic factors and global change factors that shape the diversity and composition of soil viromes, and the ecological roles of soil viruses. We also proposed a new framework to understand the ecological complexity of viruses from micro to macro ecosystem scales and to predict and unravel their activities in terrestrial ecosystems.
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Affiliation(s)
- Li Bi
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dan-Ting Yu
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian 350007, China; School of Geographical Sciences, Fujian Normal University, Fujian 350007, China.
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuai Du
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng-Yu Yuan
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian 350007, China; School of Geographical Sciences, Fujian Normal University, Fujian 350007, China
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Han LL, Yu DT, Bi L, Du S, Silveira C, Cobián Güemes AG, Zhang LM, He JZ, Rohwer F. Distribution of soil viruses across China and their potential role in phosphorous metabolism. ENVIRONMENTAL MICROBIOME 2022; 17:6. [PMID: 35130971 PMCID: PMC8822697 DOI: 10.1186/s40793-022-00401-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China. RESULTS Soil viral community were clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic composition and were mainly driven by geographic location and climate factors. A total of 972 viral populations (vOTUs) were detected spanning 23 viral families from the 19 viromes. Phylogenetic analyses of the phoH gene showed a remarkable diversity and the distribution of viral phoH genes was more dependent on the environment. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thymidylate synthase complementing protein (Thy1), and Ribonucleoside reductase (RNR), were mainly identified in agricultural soils. CONCLUSIONS The present work revealed that soil viral communities were distributed across China according to geographical location and climate factors. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems.
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Affiliation(s)
- Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA.
| | - Dan-Ting Yu
- Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, Fujian, China.
| | - Li Bi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cynthia Silveira
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Ana Georgina Cobián Güemes
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
- Viral Information Institute at San Diego State University, San Diego, CA, 92182, USA
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Novel PhoH-encoding vibriophages with lytic activity against environmental Vibrio strains. Arch Microbiol 2021; 203:5321-5331. [PMID: 34379161 DOI: 10.1007/s00203-021-02511-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 07/23/2021] [Accepted: 08/04/2021] [Indexed: 12/29/2022]
Abstract
Cholera is a devastating diarrheal disease that accounts for more than 10% of children's lives worldwide, but its treatment is hampered by a rise in antibiotic resistance. One promising alternative to antibiotic therapy is the use of bacteriophages to treat antibiotic-resistant cholera infections, and control Vibrio cholera in clinical cases and in the environment, respectively. Here, we report four novel, closely related environmental myoviruses, VP4, VP6, VP18, and VP24, which we isolated from two environmental toxigenic Vibrio cholerae strains from river Kuja and Usenge beach in Kenya. High-throughput sequencing followed by bioinformatics analysis indicated that the genomes of the four bacteriophages have closely related sequences, with sizes of 148,180 bp, 148,181 bp, 148,179 bp, and 148,179 bp, and a G + C content of 36.4%. The four genomes carry the phoH gene, which is overrepresented in marine cyanophages. The isolated phages displayed a lytic activity against 15 environmental, as well as one clinical, Vibrio cholerae strains. Thus, these novel lytic vibriophages represent potential biocontrol candidates for water decontamination against pathogenic Vibrio cholerae and ought to be considered for future studies of phage therapy.
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Zheng L, Liang X, Shi R, Li P, Zhao J, Li G, Wang S, Han S, Radosevich M, Zhang Y. Viral Abundance and Diversity of Production Fluids in Oil Reservoirs. Microorganisms 2020; 8:microorganisms8091429. [PMID: 32957569 PMCID: PMC7563284 DOI: 10.3390/microorganisms8091429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 11/16/2022] Open
Abstract
Viruses are widely distributed in various ecosystems and have important impacts on microbial evolution, community structure and function and nutrient cycling in the environment. Viral abundance, diversity and distribution are important for a better understanding of ecosystem functioning and have often been investigated in marine, soil, and other environments. Though microbes have proven useful in oil recovery under extreme conditions, little is known about virus community dynamics in such systems. In this study, injection water and production fluids were sampled in two blocks of the Daqing oilfield limited company where water flooding and microbial flooding were continuously used to improve oil recovery. Virus-like particles (VLPs) and bacteria in these samples were extracted and enumerated with epifluorescence microscopy, and viromes of these samples were also sequenced with Illumina Hiseq PE150. The results showed that a large number of viruses existed in the oil reservoir, and VLPs abundance of production wells was 3.9 ± 0.7 × 108 mL-1 and virus to bacteria ratio (VBR) was 6.6 ± 1.1 during water flooding. Compared with water flooding, the production wells of microbial flooding had relative lower VLPs abundance (3.3 ± 0.3 × 108 mL-1) but higher VBR (7.9 ± 2.2). Assembled viral contigs were mapped to an in-house virus reference data separate from the GenBank non-redundant nucleotide (NT) database, and the sequences annotated as virus accounted for 35.34 and 55.04% of total sequences in samples of water flooding and microbial flooding, respectively. In water flooding, 7 and 6 viral families were identified in the injection and production wells, respectively. In microbial flooding, 6 viral families were identified in the injection and production wells. The total number of identified viral species in the injection well was higher than that in the production wells for both water flooding and microbial flooding. The Shannon diversity index was higher in the production well of water flooding than in the production well of microbial flooding. These results show that viruses are very abundant and diverse in the oil reservoir's ecosystem, and future efforts are needed to reveal the potential function of viral communities in this extreme environment.
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Affiliation(s)
- Liangcan Zheng
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA; (X.L.); (M.R.)
| | - Rongjiu Shi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Ping Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyi Zhao
- No. 2 Oil Production Company, Daqing Oilfield Limited Company, Daqing 163414, China; (J.Z.); (G.L.)
| | - Guoqiao Li
- No. 2 Oil Production Company, Daqing Oilfield Limited Company, Daqing 163414, China; (J.Z.); (G.L.)
| | - Shuang Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Siqin Han
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA; (X.L.); (M.R.)
| | - Ying Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- Correspondence:
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Chu H, Gao GF, Ma Y, Fan K, Delgado-Baquerizo M. Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives. mSystems 2020; 5:e00803-19. [PMID: 32317392 PMCID: PMC7174637 DOI: 10.1128/msystems.00803-19] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Soil microbial communities are fundamental to maintaining key soil processes associated with litter decomposition, nutrient cycling, and plant productivity and are thus integral to human well-being. Recent technological advances have exponentially increased our knowledge concerning the global ecological distributions of microbial communities across space and time and have provided evidence for their contribution to ecosystem functions. However, major knowledge gaps in soil biogeography remain to be addressed over the coming years as technology and research questions continue to evolve. In this minireview, we state recent advances and future directions in the study of soil microbial biogeography and discuss the need for a clearer concept of microbial species, projections of soil microbial distributions toward future global change scenarios, and the importance of embracing culture and isolation approaches to determine microbial functional profiles. This knowledge will be critical to better predict ecosystem functions in a changing world.
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Affiliation(s)
- Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
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Oduor JMO, Kadija E, Nyachieo A, Mureithi MW, Skurnik M. Bioprospecting Staphylococcus Phages with Therapeutic and Bio-Control Potential. Viruses 2020; 12:E133. [PMID: 31979276 PMCID: PMC7077315 DOI: 10.3390/v12020133] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 01/27/2023] Open
Abstract
Emergence of antibiotic-resistant bacteria is a serious threat to the public health. This is also true for Staphylococcus aureus and other staphylococci. Staphylococcus phages Stab20, Stab21, Stab22, and Stab23, were isolated in Albania. Based on genomic and phylogenetic analysis, they were classified to genus Kayvirus of the subfamily Twortvirinae. In this work, we describe the in-depth characterization of the phages that electron microscopy confirmed to be myoviruses. These phages showed tolerance to pH range of 5.4 to 9.4, to maximum UV radiation energy of 25 µJ/cm2, to temperatures up to 45 °C, and to ethanol concentrations up to 25%, and complete resistance to chloroform. The adsorption rate constants of the phages ranged between 1.0 × 10-9 mL/min and 4.7 × 10-9 mL/min, and the burst size was from 42 to 130 plaque-forming units. The phages Stab20, 21, 22, and 23, originally isolated using Staphylococcusxylosus as a host, demonstrated varied host ranges among different Staphylococcus strains suggesting that they could be included in cocktail formulations for therapeutic or bio-control purpose. Phage particle proteomes, consisting on average of ca 60-70 gene products, revealed, in addition to straight-forward structural proteins, also the presence of enzymes such DNA polymerase, helicases, recombinases, exonucleases, and RNA ligase polymer. They are likely to be injected into the bacteria along with the genomic DNA to take over the host metabolism as soon as possible after infection.
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Affiliation(s)
- Joseph M. Ochieng’ Oduor
- KAVI—Institute of Clinical Research, College of Health Sciences, University of Nairobi, P.O. Box, Nairobi 19676–00202, Kenya;
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland
| | - Ermir Kadija
- Department of Biology-Chemistry, University of Shkodra “Luigj Gurakuqi”, 4001 Shkodra, Albania;
| | - Atunga Nyachieo
- Department of Reproductive Health & Biology, Phage Biology Section, Institute of Primate Research, P.O. Box, Karen-Nairobi 24481-00502, Kenya;
| | - Marianne W. Mureithi
- KAVI—Institute of Clinical Research, College of Health Sciences, University of Nairobi, P.O. Box, Nairobi 19676–00202, Kenya;
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00029 HUS Helsinki, Finland
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11
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Bai M, Cheng YH, Sun XQ, Wang ZY, Wang YX, Cui XL, Xiao W. Nine Novel Phages from a Plateau Lake in Southwest China: Insights into Aeromonas Phage Diversity. Viruses 2019; 11:v11070615. [PMID: 31284428 PMCID: PMC6669705 DOI: 10.3390/v11070615] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/18/2019] [Accepted: 07/02/2019] [Indexed: 11/16/2022] Open
Abstract
Aeromonas species are common pathogens of fish and some of them can opportunistically cause infectious diseases in humans. The overuse of antibiotics has led to the emergence of bacterial drug-resistance. To date, only 51 complete genome sequences of Aeromonas phages are available in GenBank. Here, we report the isolation of nine Aeromonas phages from a plateau lake in China. The protein cluster, dot plot and ANI analyses were performed on all 60 currently sequenced Aeromonas phage genomes and classified into nine clusters and thirteen singletons. Among the nine isolated phages, the DNA-packaging strategy of cluster 2L372D (including 2L372D, 2L372X, 4L372D, 4L372XY) is unknown, while the other five phages use the headful (P22/Sf6) DNA-packaging strategy. Notably, the isolated phages with larger genomes conservatively encode auxiliary metabolism genes, DNA replication and metabolism genes, while in smaller phage genomes, recombination-related genes were conserved. Finally, we propose a new classification scheme for Aeromonas phages.
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Affiliation(s)
- Meng Bai
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Ya-Hui Cheng
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming 650201, China
| | - Xue-Qin Sun
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Zi-Yi Wang
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming 650201, China
| | - Yong-Xia Wang
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Xiao-Long Cui
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China.
| | - Wei Xiao
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China.
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming 650500, China.
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12
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Li X, Sun Y, Liu J, Yao Q, Wang G. Survey of the bacteriophage phoH gene in wetland sediments in northeast China. Sci Rep 2019; 9:911. [PMID: 30696895 PMCID: PMC6351560 DOI: 10.1038/s41598-018-37508-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/23/2018] [Indexed: 11/29/2022] Open
Abstract
PhoH is a host-derived auxiliary metabolic gene that can be used as a new biomarker for surveying phage diversity in marine and paddy waters. However, the applicability of this gene in other environments has not been addressed. In this paper, we surveyed the phoH gene in four wetland sediments in northeast China. DNA was extracted directly from sediments and used for PCR amplification with the degenerate primers vPhoHf and vPhoHr. In total, 44 and 58 phoH sequences were identified as belonging to bacteria and phages, respectively, suggesting that this primer set is not highly specific to the phage phoH gene. A BLASTp search showed that the 58 phage phoH sequences had the highest identity to the known viral sequences, ranging from 48% to 100%. Phylogenetic analysis showed that all phage sequences from wetlands distributed into the previously designated Groups 2, 3, 4 and 6. In addition, two new subgroups, Groups 2c and 4c, which contained sequences exclusively from wetlands, were detected in this study. Nonmetric multidimensional scaling analysis showed that the phage phoH assemblage from a coastal wetland was similar to that in marine environments, while the phage phoH assemblage from a lake wetland was similar to that in paddy waters. These findings indicated that different types of wetlands had distinct phage phoH compositions.
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Affiliation(s)
- Xiang Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Qin Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
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