1
|
Zhang L, Zhao P, Xia Y, Hu Y, Wang C, Fang R, Zhao J. A novel easy-to-desorb eluant contributes to address environmental contamination of African swine fever virus. AMB Express 2024; 14:55. [PMID: 38730054 PMCID: PMC11087445 DOI: 10.1186/s13568-024-01697-1] [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: 08/07/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
African swine fever virus (ASFV) is a highly pathogenic and rapidly disseminated virus with strong viability in the environment, suggesting the importance of environmental detection for prevention and control in all the pig industry. However, the detection results of environmental swabs cannot always reflect the accurate status of viral pollution, leading to persistent ASFV environmental contamination. In this study, we developed an ASFV eluant with higher environmental ASFV detection efficiency relative to 0.85% saline solution, which obtains the patent certificate issued by the China Intellectual Property Office (patent number:202010976050.9). qPCR analysis showed that in the environmental swab samples, the number of viral copies was 100 times higher for the ASFV eluant treatment than the traditional eluant treatment (0.85% saline solution). And besides, the high sensitivity of the ASFV eluant had be verified in a slaughterhouse environmental sampling detection. In soil samples, the ASFV eluent showed the same extraction effect as the TIANamp Soil DNA Kit, in contrast to no extraction effect for 0.85% saline solution. Simultaneously, this eluent could protect ASFV from degradation and allow the transportation of samples at ambient temperature without refrigeration. In clinical practice, we monitored the environmental contamination condition of the ASFV in a large-scale pig farm. The results shown that the ASFV load decreased after every disinfection in environment. This study provides an effective solution for surveilling the potential threat of ASFV in environment.
Collapse
Affiliation(s)
- Li Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, 430070, China
- Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Pengfei Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, 430070, China
- Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yingjun Xia
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, 430070, China
- Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yanli Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, 430070, China
- Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chaofei Wang
- Wuhan keweichuang biology science and technology co., ltd., Wuhan, Hubei, 430076, China
| | - Rui Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei, 430070, China.
- Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| |
Collapse
|
2
|
Wang X, Tang Y, Yue X, Wang S, Yang K, Xu Y, Shen Q, Friman VP, Wei Z. The role of rhizosphere phages in soil health. FEMS Microbiol Ecol 2024; 100:fiae052. [PMID: 38678007 PMCID: PMC11065364 DOI: 10.1093/femsec/fiae052] [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: 12/31/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
Collapse
Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yike Tang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiufeng Yue
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
3
|
Schwarz C, Mathieu J. Isolation of Enterococcus Bacteriophages from Municipal Wastewater Samples Using an Enrichment Step. Methods Mol Biol 2024; 2738:111-123. [PMID: 37966595 DOI: 10.1007/978-1-0716-3549-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Municipal wastewater, as an aggregate mixture of household and industrial effluents, harbors a highly diverse population of bacteria and their associated bacteriophages. Accordingly, it is a commonly used source of bacteriophages against many human-associated bacterial pathogens. Here, we describe a method for bacteriophage isolation from municipal wastewater with several optional enrichment and concentration steps.
Collapse
Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
- Sentinel Environmental, Houston, TX, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA.
- Sentinel Environmental, Houston, TX, USA.
| |
Collapse
|
4
|
Abstract
Soil viruses are highly abundant and have important roles in the regulation of host dynamics and soil ecology. Climate change is resulting in unprecedented changes to soil ecosystems and the life forms that reside there, including viruses. In this Review, we explore our current understanding of soil viral diversity and ecology, and we discuss how climate change (such as extended and extreme drought events or more flooding and altered precipitation patterns) is influencing soil viruses. Finally, we provide our perspective on future research needs to better understand how climate change will impact soil viral ecology.
Collapse
Affiliation(s)
- Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| |
Collapse
|
5
|
Characterization of a New Temperate Escherichia coli Phage vB_EcoP_ZX5 and Its Regulatory Protein. Pathogens 2022; 11:pathogens11121445. [PMID: 36558779 PMCID: PMC9782041 DOI: 10.3390/pathogens11121445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
The study of the interaction between temperate phages and bacteria is vital to understand their role in the development of human diseases. In this study, a novel temperate Escherichia coli phage, vB_EcoP_ZX5, with a genome size of 39,565 bp, was isolated from human fecal samples. It has a short tail and belongs to the genus Uetakevirus and the family Podoviridae. Phage vB_EcoP_ZX5 encodes three lysogeny-related proteins (ORF12, ORF21, and ORF4) and can be integrated into the 3'-end of guaA of its host E. coli YO1 for stable transmission to offspring bacteria. Phage vB_EcoP_ZX5 in lysogenized E. coli YO1+ was induced spontaneously, with a free phage titer of 107 PFU/mL. The integration of vB_EcoP_ZX5 had no significant effect on growth, biofilm, environmental stress response, antibiotic sensitivity, adherence to HeLa cells, and virulence of E. coli YO1. The ORF4 anti-repressor, ORF12 integrase, and ORF21 repressors that affect the lytic-lysogenic cycle of vB_EcoP_ZX5 were verified by protein overexpression. We could tell from changes of the number of total phages and the transcription level of phage genes that repressor protein is the key determinant of lytic-to-lysogenic conversion, and anti-repressor protein promotes the conversion from lysogenic cycle to lytic cycle.
Collapse
|
6
|
Wang S, Yu S, Zhao X, Zhao X, Mason-Jones K, Zhu Z, Redmile-Gordon M, Li Y, Chen J, Kuzyakov Y, Ge T. Experimental evidence for the impact of phages on mineralization of soil-derived dissolved organic matter under different temperature regimes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157517. [PMID: 35872205 DOI: 10.1016/j.scitotenv.2022.157517] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/08/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Microbial mineralization of dissolved organic matter (DOM) plays an important role in regulating C and nutrient cycling. Viruses are the most abundant biological agents on Earth, but their effect on the density and activity of soil microorganisms and, consequently, on mineralization of DOM under different temperatures remains poorly understood. To assess the impact of viruses on DOM mineralization, we added soil phage concentrate (active vs. inactive phage control) to four DOM extracts containing inoculated microbial communities and incubated them at 18 °C and 23 °C for 32 days. Infection with active phages generally decreased DOM mineralization at day one and showed accelerated DOM mineralization later (especially from day 5 to 15) compared to that with the inactivated phages. Overall, phage infection increased the microbially driven CO2 release. Notably, while higher temperature increased the total CO2 release, the cumulative CO2 release induced by phage infection (difference between active phages and inactivated control) was not affected. However, higher temperatures advanced the response time of the phages but shortening its active period. Our findings suggest that bacterial predation by phages can significantly affect soil DOM mineralization. Therefore, higher temperatures may accelerate host-phage interactions and thus, the duration of C recycling.
Collapse
Affiliation(s)
- Shuang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Senxiang Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xiaoyan Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Xiaolei Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Kyle Mason-Jones
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Zhenke Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Marc Redmile-Gordon
- Department of Environmental Horticulture, Royal Horticultural Society, Wisley GU23 6QB, UK
| | - Yong Li
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, 37077 Göttingen, Germany
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| |
Collapse
|
7
|
Florent P, Cauchie HM, Herold M, Jacquet S, Ogorzaly L. Soil pH, Calcium Content and Bacteria as Major Factors Responsible for the Distribution of the Known Fraction of the DNA Bacteriophage Populations in Soils of Luxembourg. Microorganisms 2022; 10:microorganisms10071458. [PMID: 35889177 PMCID: PMC9321959 DOI: 10.3390/microorganisms10071458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages participate in soil life by influencing bacterial community structure and function, biogeochemical cycling and horizontal gene transfer. Despite their great abundance, diversity, and importance in microbial processes, they remain little explored in environmental studies. The influence of abiotic factors on the persistence of bacteriophages is now recognized; however, it has been mainly studied under experimental conditions. This study aimed to determine whether the abiotic factors well-known to influence bacteriophage persistence also control the natural distribution of the known DNA bacteriophage populations. To this end, soil from eight study sites including forests and grasslands located in the Attert River basin (Grand Duchy of Luxembourg) were sampled, covering different soil and land cover characteristics. Shotgun metagenomics, reference-based bioinformatics and statistical analyses allowed characterising the diversity of known DNA bacteriophage and bacterial communities. After combining soil properties with the identified DNA bacteriophage populations, our in-situ study highlighted the influence of pH and calcium cations on the diversity of the known fraction of the soil DNA bacteriophages. More interestingly, significant relationships were established between bacteriophage and bacterial populations. This study provides new insights into the importance of abiotic and biotic factors in the distribution of DNA bacteriophages and the natural ecology of terrestrial bacteriophages.
Collapse
Affiliation(s)
- Perrine Florent
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), 4422 Belvaux, Luxembourg; (P.F.); (H.-M.C.); (M.H.)
- Faculté des Sciences, de la Technologie et de la Communication (FSTC), Doctoral School in Science and Engineering (DSSE), University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Henry-Michel Cauchie
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), 4422 Belvaux, Luxembourg; (P.F.); (H.-M.C.); (M.H.)
| | - Malte Herold
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), 4422 Belvaux, Luxembourg; (P.F.); (H.-M.C.); (M.H.)
| | - Stéphan Jacquet
- INRAE, UMR CARRTEL, Université Savoie Mont Blanc, 74200 Thonon-les-Bains, France;
| | - Leslie Ogorzaly
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), 4422 Belvaux, Luxembourg; (P.F.); (H.-M.C.); (M.H.)
- Correspondence: ; Tel.: +352-2758885-5069
| |
Collapse
|
8
|
Nair A, Ghugare GS, Khairnar K. An Appraisal of Bacteriophage Isolation Techniques from Environment. MICROBIAL ECOLOGY 2022; 83:519-535. [PMID: 34136953 DOI: 10.1007/s00248-021-01782-z] [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: 01/18/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
Researchers have recently renewed interest in bacteriophages. Being valuable models for the study of eukaryotic viruses, and more importantly, natural killers of bacteria, bacteriophages are being tapped for their potential role in multiple applications. Bacteriophages are also being increasingly sought for bacteriophage therapy due to rising antimicrobial resistance among pathogens. Reports show that there is an increasing trend in therapeutic application of natural bacteriophages, genetically engineered bacteriophages, and bacteriophage-encoded products as antimicrobial agents. In view of these applications, the isolation and characterization of bacteriophages from the environment has caught attention. In this review, various methods for isolation of bacteriophages from environmental sources like water, soil, and air are comprehensively described. The review also draws attention towards a handful on-field bacteriophage isolation techniques and the need for their further rapid development.
Collapse
Affiliation(s)
- Aparna Nair
- Environmental Virology Cell, Council of Scientific and Industrial Research-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gaurav S Ghugare
- Environmental Virology Cell, Council of Scientific and Industrial Research-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Krishna Khairnar
- Environmental Virology Cell, Council of Scientific and Industrial Research-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
APTC-EC-2A: A Lytic Phage Targeting Multidrug Resistant E. coli Planktonic Cells and Biofilms. Microorganisms 2022; 10:microorganisms10010102. [PMID: 35056551 PMCID: PMC8779906 DOI: 10.3390/microorganisms10010102] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 02/04/2023] Open
Abstract
Escherichia coli (E. coli) are common bacteria that colonize the human and animal gastrointestinal tract, where they help maintain a balanced microbiome. However, some E. coli strains are pathogenic and can cause serious infectious diseases and life-threatening complications. Due to the overuse of antibiotics and limited development of novel antibiotics, the emergence of antibiotic-resistant strains has threatened modern medicine, whereby common infections can become lethal. Phage therapy has once again attracted interest in recent years as an alternative treatment option to antibiotics for severe infections with antibiotic-resistant strains. The aim of this study was to isolate and characterize phage against multi-drug resistant E. coli isolated from clinical samples and hospital wastewater. For phage isolation, wastewater samples were collected from The Queen Elizabeth Hospital (Adelaide, SA, Australia) followed by phage enrichment as required. Microbiological assays, electron microscopy and genomic sequencing were carried out to characterize the phage. From the 10 isolated E. coli phages, E. coli phage APTC-EC-2A was the most promising and could lyse 6/7 E. coli clinical isolates. APTC-EC-2A was stable at a broad pH range (3–11) and could lyse the host E. coli at temperatures ranging between 30–50 °C. Furthermore, APTC-EC-2A could kill E. coli in planktonic and biofilm form. Electron microscopy and genomic sequencing indicated the phage to be from the Myoviridae family and of lytic nature. In conclusion, the newly isolated phage APTC-EC-2A has the desired properties that support its potential for development as a therapeutic agent against therapy refractory E. coli infections.
Collapse
|
11
|
ter Horst AM, Santos-Medellín C, Sorensen JW, Zinke LA, Wilson RM, Johnston ER, Trubl G, Pett-Ridge J, Blazewicz SJ, Hanson PJ, Chanton JP, Schadt CW, Kostka JE, Emerson JB. Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. MICROBIOME 2021; 9:233. [PMID: 34836550 PMCID: PMC8626947 DOI: 10.1186/s40168-021-01156-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/02/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. RESULTS Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. CONCLUSIONS Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.
Collapse
Affiliation(s)
| | | | - Jackson W. Sorensen
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
| | - Laura A. Zinke
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
| | - Rachel M. Wilson
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | - Eric R. Johnston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Paul J. Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jeffrey P. Chanton
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL USA
| | | | - Joel E. Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Joanne B. Emerson
- Department of Plant Pathology, University of California, Davis, Davis, CA USA
- Genome Center, University of California, Davis, Davis, CA USA
| |
Collapse
|
12
|
Runa V, Wenk J, Bengtsson S, Jones BV, Lanham AB. Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function. Front Microbiol 2021; 12:730071. [PMID: 34803947 PMCID: PMC8600467 DOI: 10.3389/fmicb.2021.730071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.
Collapse
Affiliation(s)
- Viviane Runa
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
| | | | - Brian V Jones
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Ana B Lanham
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
| |
Collapse
|
13
|
Turzynski V, Monsees I, Moraru C, Probst AJ. Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples. Viruses 2021; 13:2126. [PMID: 34834933 PMCID: PMC8622608 DOI: 10.3390/v13112126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses-bacteriophages and archaeal viruses-influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage-host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth's ecosystems.
Collapse
Affiliation(s)
- Victoria Turzynski
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Indra Monsees
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany;
| | - Alexander J. Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| |
Collapse
|
14
|
Pietramellara G, Pathan SI, Datta R, Vranová V, Ceccherini M, Nannipieri P. Perspective on the status and behaviour of SARS-CoV-2 in soil. Saudi J Biol Sci 2021; 29:1014-1020. [PMID: 34608369 PMCID: PMC8482646 DOI: 10.1016/j.sjbs.2021.09.073] [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: 07/21/2021] [Revised: 09/20/2021] [Accepted: 09/25/2021] [Indexed: 11/30/2022] Open
Abstract
Soil contamination by SARS-CoV-2 is highly probable because soil can collect several transporters of the virus, such as fallout aerosols, wastewaters, relatively purified sludges, and organic residues. However, the fate and status of SARS-CoV-2 in soil and the possible risks for human health through contaminated food are unknown. Therefore, this perspective paper discusses the challenges of determining the SARS-CoV-2 in soil and the mechanisms concerning its adsorption, movement, and infectivity in soil, considering what has already been reported by perspective papers published up to May 2021. These issues are discussed, drawing attention to the soil virus bibliography and considering the chemical structure of the virus. The mechanistic understanding of the status and behavior of SARS-CoV-2 in soil requires setting up an accurate determination method. In addition, future researches should provide insights into i) plant uptake and movement inside the plant, ii) virus adsorption and desorption in soil with the relative infectivity, and iii) its effects on soil functions. Models should simulate spatial localization of virus in the soil matrix.
Collapse
Affiliation(s)
- Giacomo Pietramellara
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Firenze, P.le delle Cascine 24, 50144 Firenze, Italy
- Corresponding author at: Department of Agrifood Production and Environmental Sciences, Piazzale delle Cascine 28, 50144 Florence, Italy.
| | - Shamina Imran Pathan
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Firenze, P.le delle Cascine 24, 50144 Firenze, Italy
| | - Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Czech Republic
| | - Valerie Vranová
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Czech Republic
| | - MariaTeresa Ceccherini
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Firenze, P.le delle Cascine 24, 50144 Firenze, Italy
| | - Paolo Nannipieri
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Firenze, P.le delle Cascine 24, 50144 Firenze, Italy
| |
Collapse
|
15
|
Mkwata HM, Omoregie AI, Nissom PM. Lytic bacteriophages isolated from limestone caves for biocontrol of Pseudomonas aeruginosa. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
16
|
Anand U, Bianco F, Suresh S, Tripathi V, Núñez-Delgado A, Race M. SARS-CoV-2 and other viruses in soil: An environmental outlook. ENVIRONMENTAL RESEARCH 2021; 198:111297. [PMID: 33971130 PMCID: PMC8102436 DOI: 10.1016/j.envres.2021.111297] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/30/2021] [Accepted: 05/01/2021] [Indexed: 05/15/2023]
Abstract
In the present review, the authors shed light on the SARS-CoV-2 impact, persistence, and monitoring in the soil environment. With this purpose, several aspects have been deepened: i) viruses in soil ecosystems; ii) direct and indirect impact on the soil before and after the pandemic, and iii) methods for quantification of viruses and SARS-CoV-2 monitoring in soil. Viruses are present in soil (i.e. up to 417 × 107 viruses per g TS-1 in wetlands) and can affect the behavior and ecology of other life forms (e.g. bacteria), which are remarkably important for maintaining environmental equilibrium. Also, SARS-CoV-2 can be found in soil (i.e. up to 550 copies·g-1). Considering that the SARS-CoV-2 is very recent, poor knowledge is available in the literature on persistence in the soil and reference has been made to coronaviruses and other families of viruses. For instance, the survival of enveloped viruses (e.g. SARS-CoV) can reach 90 days in soils with 10% of moisture content at ambient. In such a context, the possible spread of the SARS-CoV-2 in the soil was evaluated by analyzing the possible contamination routes.
Collapse
Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Francesco Bianco
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio 43, 03043, Cassino, Italy
| | - S Suresh
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, 462 003, Madhya Pradesh, India
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, 211007, India
| | - Avelino Núñez-Delgado
- Department Soil Science and Agricultural Chemistry, Engineering Polytechnic School, Campus Univ. Lugo, Univ. Santiago de Compostela, 27002, Spain
| | - Marco Race
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio 43, 03043, Cassino, Italy.
| |
Collapse
|
17
|
Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils. mSphere 2021; 6:e0116020. [PMID: 34077260 PMCID: PMC8265675 DOI: 10.1128/msphere.01160-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
During the last several decades, viruses have been increasingly recognized for their abundance, ubiquity, and important roles in different ecosystems. Despite known contributions to aquatic systems, few studies examine viral abundance and community structure over time in terrestrial ecosystems. The effects of land conversion and land management on soil microbes have been previously investigated, but their effects on virus population are not well studied. This study examined annual dynamics of viral abundance in soils from a native tallgrass prairie and two croplands, conventional till winter wheat and no-till canola, in Oklahoma. Virus-like particle (VLP) abundance varied across sites, and showed clear seasonal shifts. VLP abundance significantly correlated with environmental variables that were generally reflective of land use, including air temperature, soil nitrogen, and plant canopy coverage. Structural equation modeling supported the effects of land use on soil communities by emphasizing interactions between management, environmental factors, and viral and bacterial abundance. Between the viral metagenomes from the prairie and tilled wheat field, 1,231 unique viral operational taxonomic units (vOTUs) were identified, and only five were shared that were rare in the contrasting field. Only 13% of the vOTUs had similarity to previously identified viruses in the RefSeq database, with only 7% having known taxonomic classification. Together, our findings indicated land use and tillage practices influence virus abundance and community structure. Analyses of viromes over time and space are vital to viral ecology in providing insight on viral communities and key information on interactions between viruses, their microbial hosts, and the environment. IMPORTANCE Conversion of land alters the physiochemical and biological environments by not only changing the aboveground community, but also modifying the soil environment for viruses and microbes. Soil microbial communities are critical to nutrient cycling, carbon mineralization, and soil quality; and viruses are known for influencing microbial abundance, community structure, and evolution. Therefore, viruses are considered an important part of soil functions in terrestrial ecosystems. In aquatic environments, virus abundance generally exceeds bacterial counts by an order of magnitude, and they are thought to be one of the greatest genetic reservoirs on the planet. However, data are extremely limited on viruses in soils, and even less is known about their responses to the disturbances associated with land use and management. The study provides important insights into the temporal dynamics of viral abundance and the structure of viral communities in response to the common practice of turning native habitats into arable soils.
Collapse
|
18
|
Hyman P, Trubl G, Abedon ST. Virus-Like Particle: Evolving Meanings in Different Disciplines. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:11-15. [PMID: 36148434 PMCID: PMC9041479 DOI: 10.1089/phage.2020.0026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Virus-like particle (VLP) is a term that has been in use for about 80 years. Usually, VLP has meant a particle that is like a virus, generally by appearance, but without either proven or actual virus functionality. Initially VLP referred to particles seen in electron microscope images of tissues. More recently, VLP has come to mean other things to other researchers. A key divergence has been use of VLP in association with vaccine and biotechnology applications versus use of VLP in enumeration of viruses in environmental samples. To these viral ecologists, a VLP is a particle that is virus sized, has nucleic acid, and could be a functional virus. But to vaccine developers and biotechnology researchers a VLP instead is a viral structure that intentionally lacks a viral genome. In this study, we look at the history of use of VLP, following changes in meaning as the technology to study VLPs changed.
Collapse
Affiliation(s)
- Paul Hyman
- Department of Biology and Toxicology, Ashland University, Ashland, Ohio, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, USA
| |
Collapse
|
19
|
The Role of Rhizosphere Bacteriophages in Plant Health. Trends Microbiol 2020; 28:709-718. [DOI: 10.1016/j.tim.2020.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/11/2020] [Accepted: 04/02/2020] [Indexed: 12/12/2022]
|
20
|
DeFelice T. Relationship between temporal anomalies in PM 2.5 concentrations and reported influenza/influenza-like illness activity. Heliyon 2020; 6:e04726. [PMID: 32835121 PMCID: PMC7428445 DOI: 10.1016/j.heliyon.2020.e04726] [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: 04/13/2020] [Revised: 06/06/2020] [Accepted: 08/11/2020] [Indexed: 12/20/2022] Open
Abstract
A small number of studies suggest atmospheric particulate matter with diameters 2.5 micron and smaller (PM2.5) may possibly play a role in the transmission of influenza and influenza-like illness (ILI) symptoms. Those studies were predominantly conducted under moderately to highly polluted outdoor atmospheres. The purpose of this study was to extend the data set to include a less polluted atmospheric environment. A relationship between PM2.5 and ILI activity extended to include lightly to moderately polluted atmospheres could imply a more complicated mechanism than that suggested by existing studies. We obtained concurrent PM2.5 mass concentration data, meteorological data and reported Influenza and influenza-like illness (ILI) activity for the light to moderately polluted atmospheres over the Tucson, AZ region. We found no relation between PM2.5 mass concentration and ILI activity. There was an expected relation between ILI, activity, temperature, and relative humidity. There was a possible relation between PM2.5 mass concentration anomalies and ILI activity. These results might be due to the small dataset size and to the technological limitations of the PM measurements. Further study is recommended since it would improve the understanding of ILI transmission and thereby improve ILI activity/outbreak forecasts and transmission model accuracies.
Collapse
|
21
|
Roy K, Ghosh D, DeBruyn JM, Dasgupta T, Wommack KE, Liang X, Wagner RE, Radosevich M. Temporal Dynamics of Soil Virus and Bacterial Populations in Agricultural and Early Plant Successional Soils. Front Microbiol 2020; 11:1494. [PMID: 32733413 PMCID: PMC7358527 DOI: 10.3389/fmicb.2020.01494] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
As reported in many aquatic environments, recent studies in terrestrial ecosystems implicate a role for viruses in shaping the structure, function, and evolution of prokaryotic soil communities. However, given the heterogeneity of soil and the physical constraints (i.e., pore-scale hydrology and solid-phase adsorption of phage and host cells) on the mobility of viruses and bacteria, phage-host interactions likely differ from those in aquatic systems. In this study, temporal changes in the population dynamics of viruses and bacteria in soils under different land management practices were examined. The results showed that bacterial abundance was significantly and positively correlated to both virus and inducible prophage abundance. Bacterial and viral abundance were also correlated with soil organic carbon and nitrogen content as well as with C:N ratio. The seasonal variability in viral abundance increased with soil organic carbon content. The prokaryotic community structure was influenced more by land use than by seasonal variation though considerable variation was evident in the early plant successional and grassland sites. The free extracellular viral communities were also separated by land use, and the forest soil viral assemblage exhibiting the most seasonal variability was more distinct from the other sites. Viral assemblages from the agricultural soils exhibited the least seasonal variability. Similar patterns were observed for inducible prophage viral assemblages. Seasonal variability of viral assemblages was greater in mitomycin-C (mitC) induced prophages than in extracellular viruses irrespective of land use and management. Taken together, the data suggest that soil viral production and decay are likely balanced but there was clear evidence that the structure of viral assemblages is influenced by land use and by season.
Collapse
Affiliation(s)
- Krishnakali Roy
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Dhritiman Ghosh
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, United States
| | - Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Regan E Wagner
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| |
Collapse
|
22
|
Göller PC, Haro-Moreno JM, Rodriguez-Valera F, Loessner MJ, Gómez-Sanz E. Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil. MICROBIOME 2020; 8:17. [PMID: 32046783 PMCID: PMC7014677 DOI: 10.1186/s40168-020-0795-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 01/20/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Bacteriophages (phages) are the most numerous biological entities on Earth and play a crucial role in shaping microbial communities. Investigating the bacteriophage community from soil will shed light not only on the yet largely unknown phage diversity, but may also result in novel insights towards their functioning in the global biogeochemical nutrient cycle and their significance in earthbound ecosystems. Unfortunately, information about soil viromes is rather scarce compared to aquatic environments, due to the heterogeneous soil matrix, which rises major technical difficulties in the extraction process. Resolving these technical challenges and establishing a standardized extraction protocol is, therefore, a fundamental prerequisite for replicable results and comparative virome studies. RESULTS We here report the optimization of protocols for the extraction of phage DNA from agricultural soil preceding metagenomic analysis such that the protocol can equally be harnessed for phage isolation. As an optimization strategy, soil samples were spiked with Listeria phage A511 (Myovirus), Staphylococcus phage 2638AΔLCR (Siphovirus) and Escherichia phage T7 (Podovirus) (each 106 PFU/g soil). The efficacy of phage (i) elution, (ii) filtration, (iii) concentration and (iv) DNA extraction methods was tested. Successful extraction routes were selected based on spiked phage recovery and low bacterial 16S rRNA gene contaminants. Natural agricultural soil viromes were then extracted with the optimized methods and shotgun sequenced. Our approach yielded sufficient amounts of inhibitor-free viral DNA for shotgun sequencing devoid of amplification prior library preparation, and low 16S rRNA gene contamination levels (≤ 0.2‰). Compared to previously published protocols, the number of bacterial read contamination was decreased by 65%. In addition, 379 novel putative complete soil phage genomes (≤ 235 kb) were obtained from over 13,000 manually identified viral contigs, promising the discovery of a large, previously inaccessible viral diversity. CONCLUSION We have shown a considerably enhanced extraction of the soil phage community by protocol optimization that has proven robust in both culture-dependent as well as through viromic analyses. Our huge data set of manually curated soil viral contigs substantially increases the amount of currently available soil virome data, and provides insights into the yet largely undescribed soil viral sequence space.
Collapse
Affiliation(s)
- Pauline C Göller
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
| | - Jose M Haro-Moreno
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
| | - Elena Gómez-Sanz
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland.
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain.
| |
Collapse
|
23
|
Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales. Appl Environ Microbiol 2019; 85:AEM.00324-19. [PMID: 31076430 DOI: 10.1128/aem.00324-19] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and organic carbon that persist through mechanical disruptions and wetting events. Their spatial structure is important for biogeochemical cycling, and we cannot reliably predict soil biological activities and variability by studying bulk soils alone. To fully understand the biogeochemical processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as "microbial villages" that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. We describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining "model system" approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a critical next step for developing a predictive understanding of how geochemical and community interactions govern microbial community structure and nutrient cycling in soil.
Collapse
|
24
|
Molecular Diversity of Cyanopodoviruses in Two Coastal Wetlands in Northeast China. Curr Microbiol 2019; 76:863-871. [DOI: 10.1007/s00284-019-01700-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/30/2019] [Indexed: 11/27/2022]
|
25
|
Pan D, Morono Y, Inagaki F, Takai K. An Improved Method for Extracting Viruses From Sediment: Detection of Far More Viruses in the Subseafloor Than Previously Reported. Front Microbiol 2019; 10:878. [PMID: 31110497 PMCID: PMC6501758 DOI: 10.3389/fmicb.2019.00878] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/05/2019] [Indexed: 01/21/2023] Open
Abstract
Viruses are the most abundant biological entities on Earth and perform essential ecological functions in aquatic environments by mediating biogeochemical cycling and lateral gene transfer. Cellular life as well as viruses have been found in deep subseafloor sediment. However, the study of deep sediment viruses has been hampered by the complexities involved in efficiently extracting viruses from a sediment matrix. Here, we developed a new method for the extraction of viruses from sediment based on density separation using a Nycodenz density step gradient. The density separation method resulted in up to 2 orders of magnitude greater recovery of viruses from diverse subseafloor sediments compared to conventional methods. The density separation method also showed more consistent performance between samples of different sediment lithology, whereas conventional virus extraction methods were highly inconsistent. Using this new method, we show that previously published virus counts have underestimated viral abundances by up to 2 orders of magnitude. These improvements suggest that the carbon contained within viral biomass in the subseafloor environment may potentially be revised upward to 0.8-3.7 Gt from current estimates of 0.2 Gt. The vastly improved recovery of viruses indicate that viruses represent a far larger pool of organic carbon in subseafloor environments than previously estimated.
Collapse
Affiliation(s)
- Donald Pan
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Nankoku, Japan
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Nankoku, Japan
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science and Technology, Yokohama, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| |
Collapse
|
26
|
Li Y, Sun H, Yang W, Chen G, Xu H. Dynamics of Bacterial and Viral Communities in Paddy Soil with Irrigation and Urea Application. Viruses 2019; 11:E347. [PMID: 31014039 PMCID: PMC6520780 DOI: 10.3390/v11040347] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 01/21/2023] Open
Abstract
Viruses are ubiquitous in natural systems. By influencing bacterial abundance (BA) and community structure through lysis-lysogenic conversion, viruses are involved in various ecological processes. In agricultural management, nitrogen addition and irrigation should be considered as important factors that can modify soil viral dynamics but have been ignored. In our study, short-term dynamics of autochthonous soil viral and bacterial abundance and diversity after irrigation and urea application were examined in a long-term experimental paddy field. Urea addition delayed the emergence of peak viral abundance for three days, suggesting that viruses are sensitive to N addition. Under short-term eutrophic conditions through urea application, viruses undertake a lysogenic-biased strategy. Moreover, nitrogen-fixing bacteria were most likely specifically lysed in urea-treated soil, which suggests that soil viruses block N accumulation by killing nitrogen-fixing bacteria. To the best of our knowledge, this study is the first to investigate dynamic changes in autochthonous viruses in paddy fields.
Collapse
Affiliation(s)
- Yuting Li
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- National Field Observation and Research Station of Shenyang Agro-Ecosystems, Shenyang 110016, China.
| | - Hao Sun
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Weichao Yang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Guanxiong Chen
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Hui Xu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| |
Collapse
|
27
|
Chopyk J, Kulkarni P, Nasko DJ, Bradshaw R, Kniel KE, Chiu P, Sharma M, Sapkota AR. Zero-valent iron sand filtration reduces concentrations of virus-like particles and modifies virome community composition in reclaimed water used for agricultural irrigation. BMC Res Notes 2019; 12:223. [PMID: 30975220 PMCID: PMC6458639 DOI: 10.1186/s13104-019-4251-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 04/03/2019] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE Zero-valent iron sand filtration can remove multiple contaminants, including some types of pathogenic bacteria, from contaminated water. However, its efficacy at removing complex viral populations, such as those found in reclaimed water used for agricultural irrigation, has not been fully evaluated. Therefore, this study utilized metagenomic sequencing and epifluorescent microscopy to enumerate and characterize viral populations found in reclaimed water and zero-valent iron-sand filtered reclaimed water sampled three times during a larger greenhouse study. RESULTS Zero-valent iron-sand filtered reclaimed water samples had significantly less virus-like particles than reclaimed water samples at all collection dates, with the reclaimed water averaging between 108 and 109 and the zero-valent iron-sand filtered reclaimed water averaging between 106 and 107 virus-like particles per mL. In addition, for both sample types, viral metagenomes (viromes) were dominated by bacteriophages of the order Caudovirales, largely Siphoviridae, and genes related to DNA metabolism. However, the proportion of sequences homologous to bacteria, as well as the abundance of genes possibly originating from a bacterial host, was higher in the viromes of zero-valent iron-sand filtered reclaimed water samples. Overall, zero-valent iron-sand filtered reclaimed water had a lower total concentration of virus-like particles and a different virome community composition compared to unfiltered reclaimed water.
Collapse
Affiliation(s)
- Jessica Chopyk
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, School of Public Health Building (255), 4200 Valley Drive, Room 2234P, College Park, MD, 20742, USA
| | - Prachi Kulkarni
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, School of Public Health Building (255), 4200 Valley Drive, Room 2234P, College Park, MD, 20742, USA
| | - Daniel J Nasko
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Rhodel Bradshaw
- United States Department of Agriculture, Agricultural Research Service, Environmental and Microbial Food Safety Laboratory, Beltsville, MD, 20705, USA
| | - Kalmia E Kniel
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Pei Chiu
- Department of Civil and Environmental Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Manan Sharma
- United States Department of Agriculture, Agricultural Research Service, Environmental and Microbial Food Safety Laboratory, Beltsville, MD, 20705, USA
| | - Amy R Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, School of Public Health Building (255), 4200 Valley Drive, Room 2234P, College Park, MD, 20742, USA.
| |
Collapse
|
28
|
More than Rotating Flagella: Lipopolysaccharide as a Secondary Receptor for Flagellotropic Phage 7-7-1. J Bacteriol 2018; 200:JB.00363-18. [PMID: 30012730 DOI: 10.1128/jb.00363-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/10/2018] [Indexed: 12/13/2022] Open
Abstract
Bacteriophage 7-7-1, a member of the family Myoviridae, infects the soil bacterium Agrobacterium sp. strain H13-3. Infection requires attachment to actively rotating bacterial flagellar filaments, with flagellar number, length, and rotation speed being important determinants for infection efficiency. To identify the secondary receptor(s) on the cell surface, we isolated motile, phage-resistant Agrobacterium sp. H13-3 transposon mutants. Transposon insertion sites were pinpointed using arbitrary primed PCR and bioinformatics analyses. Three genes were recognized, whose corresponding proteins had the following computationally predicted functions: AGROH133_07337, a glycosyltransferase; AGROH133_13050, a UDP-glucose 4-epimerase; and AGROH133_08824, an integral cytoplasmic membrane protein. The first two gene products are part of the lipopolysaccharide (LPS) synthesis pathway, while the last is predicted to be a relatively small (13.4-kDa) cytosolic membrane protein with up to four transmembrane helices. The phenotypes of the transposon mutants were verified by complementation and site-directed mutagenesis. Additional characterization of motile, phage-resistant mutants is also described. Given these findings, we propose a model for Agrobacterium sp. H13-3 infection by bacteriophage 7-7-1 where the phage initially attaches to the flagellar filament and is propelled down toward the cell surface by clockwise flagellar rotation. The phage then attaches to and degrades the LPS to reach the outer membrane and ejects its DNA into the host using its syringe-like contractile tail. We hypothesize that the integral membrane protein plays an important role in events following viral DNA ejection or in LPS processing and/or deployment. The proposed two-step attachment mechanism may be conserved among other flagellotropic phages infecting Gram-negative bacteria.IMPORTANCE Flagellotropic bacteriophages belong to the tailed-phage order Caudovirales, the most abundant phages in the virome. While it is known that these viruses adhere to the bacterial flagellum and use flagellar rotation to reach the cell surface, their infection mechanisms are poorly understood. Characterizing flagellotropic-phage-host interactions is crucial to understanding how microbial communities are shaped. Using a transposon mutagenesis approach combined with a screen for motile, phage-resistant mutants, we identified lipopolysaccharides as the secondary cell surface receptor for phage 7-7-1. This is the first cell surface receptor identified for flagellotropic phages. One hypothetical membrane protein was also recognized as essential for infection. These new findings, together with previous results, culminated in an infection model for phage 7-7-1.
Collapse
|
29
|
Rosario K, Fierer N, Miller S, Luongo J, Breitbart M. Diversity of DNA and RNA Viruses in Indoor Air As Assessed via Metagenomic Sequencing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1014-1027. [PMID: 29298386 DOI: 10.1021/acs.est.7b04203] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Diverse bacterial and fungal communities inhabit human-occupied buildings and circulate in indoor air; however, viral diversity in these man-made environments remains largely unknown. Here we investigated DNA and RNA viruses circulating in the air of 12 university dormitory rooms by analyzing dust accumulated over a one-year period on heating, ventilation, and air conditioning (HVAC) filters. A metagenomic sequencing approach was used to determine the identity and diversity of viral particles extracted from the HVAC filters. We detected a broad diversity of viruses associated with a range of hosts, including animals, arthropods, bacteria, fungi, humans, plants, and protists, suggesting that disparate organisms can contribute to indoor airborne viral communities. Viral community composition and the distribution of human-infecting papillomaviruses and polyomaviruses were distinct in the different dormitory rooms, indicating that airborne viral communities are variable in human-occupied spaces and appear to reflect differential rates of viral shedding from room occupants. This work significantly expands the known airborne viral diversity found indoors, enabling the design of sensitive and quantitative assays to further investigate specific viruses of interest and providing new insight into the likely sources of viruses found in indoor air.
Collapse
Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida , Saint Petersburg, Florida 33701, United States
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado , Boulder, Colorado 80309, United States
- Cooperative Institute for Research in Environmental Sciences, University of Colorado , Boulder, Colorado 80309, United States
| | - Shelly Miller
- Department of Mechanical Engineering, University of Colorado , Boulder, Colorado 80309, United States
| | - Julia Luongo
- Department of Mechanical Engineering, University of Colorado , Boulder, Colorado 80309, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida , Saint Petersburg, Florida 33701, United States
| |
Collapse
|
30
|
Yu DT, Han LL, Zhang LM, He JZ. Diversity and Distribution Characteristics of Viruses in Soils of a Marine-Terrestrial Ecotone in East China. MICROBIAL ECOLOGY 2018; 75:375-386. [PMID: 28825127 DOI: 10.1007/s00248-017-1049-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
A substantial gap remains in our understanding of the abundance, diversity, and ecology of viruses in soil although some advances have been achieved in recent years. In this study, four soil samples according to the salinity gradient from shore to inland in East China have been characterized. Results showed that spherical virus particles represented the largest viral component in all of the four samples. The viromes had remarkably different taxonomic compositions, and most of the sequences were derived from single-stranded DNA viruses, especially from families Microviridae and Circoviridae. Compared with viromes from other aquatic and sediment samples, the community compositions of our four soil viromes resembled each other, meanwhile coastal sample virome closely congregated with sediment and hypersaline viromes, and high salinity paddy soil sample virome was similar with surface sediment virome. Phylogenetic analysis of functional genes showed that four viromes have high diversity of the subfamily Gokushovirinae in family Microviridae and most of Circoviridae replicase protein sequences grouped within the CRESS-DNA viruses. This work provided an initial outline of the viral communities in marine-terrestrial ecotone and will improve our understanding of the ecological functions of soil viruses.
Collapse
Affiliation(s)
- Dan-Ting Yu
- 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
| | - 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.
| | - 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
- 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.
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, 3010, Australia.
| |
Collapse
|
31
|
Corallivory and the microbial debacle in two branching scleractinians. ISME JOURNAL 2018; 12:1109-1126. [PMID: 29339825 DOI: 10.1038/s41396-017-0033-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/21/2017] [Accepted: 12/01/2017] [Indexed: 02/01/2023]
Abstract
The grazing activity by specific marine organisms represents a growing threat to the survival of many scleractinian species. For example, the recent proliferation of the corallivorous gastropod Drupella now constitutes a critical case in all South-East Asian waters. If the damaging effects caused by this marine snail on coral polyps are relatively well known, the indirect incidence of predation on coral microbial associates is still obscure and might also potentially impair coral health. In this study, we compared the main ecological traits of coral-associated bacterial and viral communities living in the mucus layer of Acropora formosa and Acropora millepora, of healthy and predated individuals (i.e., colonized by Drupella rugosa), in the Bay of Van Phong (Vietnam). Our results show a substantial impact of the gastropod on a variety of microbiological markers. Colonized corals harbored much more abundant and active epibiotic bacteria whose community composition shifted toward more pathogenic taxa (belonging to the Vibrionales, Clostridiales, Campylobacterales, and Alteromonadales orders), together with their specific phages. Viral epibionts were also greatly influenced by Drupella corallivory with spectacular modifications in their concentrations, life strategies, genotype richness, and diversity. Novel and abundant circular Rep-encoding ssDNA viruses (CRESS-DNA viruses) were detected and characterized in grazed corals and we propose that their occurrence may serve as indicator of the coral health status. Finally, our results reveal that corallivory can cause severe dysbiosis by altering virus-bacteria interactions in the mucus layer, and ultimately favoring the development of local opportunistic infections.
Collapse
|
32
|
Abstract
Prokaryotic viruses, or bacteriophages, are viruses that infect bacteria and archaea. These viruses have been known to associate with host systems for decades, yet only recently have their influence on the regulation of host-associated bacteria been appreciated. These studies have been conducted in many host systems, from the base of animal life in the Cnidarian phylum to mammals. These prokaryotic viruses are useful for regulating the number of bacteria in a host ecosystem and for regulating the strains of bacteria useful for the microbiome. These viruses are likely selected by the host to maintain bacterial populations. Viral metagenomics allows researchers to profile the communities of viruses associating with animal hosts, and importantly helps to determine the functional role these viruses play. Further, viral metagenomics show the sphere of viral involvement in gene flow and gene shuffling in an ever-changing host environment. The influence of prokaryotic viruses could, therefore, have a clear impact on host health.
Collapse
Affiliation(s)
- Juris A Grasis
- School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| |
Collapse
|
33
|
Williamson KE, Fuhrmann JJ, Wommack KE, Radosevich M. Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory. Annu Rev Virol 2017; 4:201-219. [PMID: 28961409 DOI: 10.1146/annurev-virology-101416-041639] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viral abundance in soils can range from below detection limits in hot deserts to over 1 billion per gram in wetlands. Abundance appears to be strongly influenced by water availability and temperature, but a lack of informational standards creates difficulties for cross-study analysis. Soil viral diversity is severely underestimated and undersampled, although current measures of viral richness are higher for soils than for aquatic ecosystems. Both morphometric and metagenomic analyses have raised questions about the prevalence of nontailed, ssDNA viruses in soils. Soil is complex and critically important to terrestrial biodiversity and human civilization, but impacts of viral activities on soil ecosystem services are poorly understood. While information from aquatic systems and medical microbiology suggests the potential for viral influences on nutrient cycles, food web interactions, gene transfer, and other key processes in soils, very few empirical data are available. To understand the soil virome, much work remains.
Collapse
Affiliation(s)
- Kurt E Williamson
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185;
| | - Jeffry J Fuhrmann
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716
| | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716.,Department Biological Sciences, University of Delaware, Newark, Delaware 19716.,College of Earth, Ocean, and Environment, University of Delaware, Newark, Delaware 19716
| | - Mark Radosevich
- Biosystems Engineering and Soil Science Department, University of Tennessee, Knoxville, Tennessee 37996
| |
Collapse
|
34
|
Narr A, Nawaz A, Wick LY, Harms H, Chatzinotas A. Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD). Front Microbiol 2017; 8:1975. [PMID: 29067022 PMCID: PMC5641378 DOI: 10.3389/fmicb.2017.01975] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/25/2017] [Indexed: 11/13/2022] Open
Abstract
Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors.
Collapse
Affiliation(s)
- Anja Narr
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Ali Nawaz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research—UFZ, Halle/Saale, Germany
| | - Lukas Y. Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| |
Collapse
|
35
|
Adriaenssens EM, Kramer R, Van Goethem MW, Makhalanyane TP, Hogg I, Cowan DA. Environmental drivers of viral community composition in Antarctic soils identified by viromics. MICROBIOME 2017; 5:83. [PMID: 28724405 PMCID: PMC5518109 DOI: 10.1186/s40168-017-0301-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 07/06/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of microorganisms from primary producers to grazers, yet their ecology and particularly the role of viruses is poorly understood. In this study, we examined the virus community structures of 14 soil samples from the Mackay Glacier region. METHODS Viral communities were extracted from soil and the dsDNA was extracted, amplified using single-primer amplification, and sequenced using the Ion Torrent Proton platform. Metadata on soil physico-chemistry was collected from all sites. Both read and contig datasets were analyzed with reference-independent and reference-dependent methods to assess viral community structures and the influence of environmental parameters on their distribution. RESULTS We observed a high heterogeneity in virus signatures, independent of geographical proximity. Tailed bacteriophages were dominant in all samples, but the incidences of the affiliated families Siphoviridae and Myoviridae were inversely correlated, suggesting direct competition for hosts. Viruses of the families Phycodnaviridae and Mimiviridae were present at significant levels in high-diversity soil samples and were found to co-occur, implying little competition between them. Combinations of soil factors, including pH, calcium content, and site altitude, were found to be the main drivers of viral community structure. CONCLUSIONS The pattern of viral community structure with higher levels of diversity at lower altitude and pH, and co-occurring viral families, suggests that these cold desert soil viruses interact with each other, the host, and the environment in an intricate manner, playing a potentially crucial role in maintaining host diversity and functioning of the microbial ecosystem in the extreme environments of Antarctic soil.
Collapse
Affiliation(s)
- Evelien M. Adriaenssens
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Rolf Kramer
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Marc W. Van Goethem
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Thulani P. Makhalanyane
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Ian Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Polar Knowledge Canada, 170 Laurier Avenue West, Ottawa, Ontario K1P 5V5 Canada
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| |
Collapse
|
36
|
Sharma S, Chatterjee S, Datta S, Prasad R, Dubey D, Prasad RK, Vairale MG. Bacteriophages and its applications: an overview. Folia Microbiol (Praha) 2016; 62:17-55. [PMID: 27718043 DOI: 10.1007/s12223-016-0471-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 09/12/2016] [Indexed: 01/21/2023]
Abstract
Bacteriophages (or phages), the most abundant viral entity of the planet, are omni-present in all the ecosystems. On the basis of their unique characteristics and anti-bacterial property, phages are being freshly evaluated taxonomically. Phages replicate inside the host either by lytic or lysogenic mode after infecting and using the cellular machinery of a bacterium. Since their discovery by Twort and d'Herelle in the early 1900s, phage became an important agent for combating pathogenic bacteria in clinical treatments and its related research gained momentum. However, due to recent emergence of bacterial resistance on antibiotics, applications of phage (phage therapy) become an inevitable option of research. Phage particles become popular as a biotechnological tool and treatment of pathogenic bacteria in a range of applied areas. However, there are few concerns over the application of phage-based solutions. This review deals with the updated phage taxonomy (ICTV 2015 Release and subsequent revision) and phage biology and the recent development of its application in the areas of biotechnology, biosensor, therapeutic medicine, food preservation, aquaculture diseases, pollution remediation, and wastewater treatment and issues related with limitations of phage-based remedy.
Collapse
Affiliation(s)
- Sonika Sharma
- Defence Research Laboratory, DRDO, Tezpur, Assam, 784001, India
| | | | | | - Rishika Prasad
- Defence Research Laboratory, DRDO, Tezpur, Assam, 784001, India
- School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, USA
| | | | | | - Mohan G Vairale
- Defence Research Laboratory, DRDO, Tezpur, Assam, 784001, India
| |
Collapse
|
37
|
Fister S, Robben C, Witte AK, Schoder D, Wagner M, Rossmanith P. Influence of Environmental Factors on Phage-Bacteria Interaction and on the Efficacy and Infectivity of Phage P100. Front Microbiol 2016; 7:1152. [PMID: 27516757 PMCID: PMC4964841 DOI: 10.3389/fmicb.2016.01152] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/11/2016] [Indexed: 11/13/2022] Open
Abstract
When using bacteriophages to control food-borne bacteria in food production plants and processed food, it is crucial to consider that environmental conditions influence their stability. These conditions can also affect the physiological state of bacteria and consequently host–virus interaction and the effectiveness of the phage ability to reduce bacteria numbers. In this study we investigated the stability, binding, and replication capability of phage P100 and its efficacy to control Listeria monocytogenes under conditions typically encountered in dairy plants. The influences of SDS, Lutensol AO 7, salt, smear water, and different temperatures were investigated. Results indicate that phage P100 is stable and able to bind to the host under most conditions tested. Replication was dependent upon the growth of L. monocytogenes and efficacy was higher when bacterial growth was reduced by certain environmental conditions. In long-term experiments at different temperatures phages were initially able to reduce bacteria up to seven log10 units after 2 weeks at 4°C. However, thereafter, re-growth and development of phage-resistant L. monocytogenes isolates were encountered.
Collapse
Affiliation(s)
- Susanne Fister
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Public Veterinary Health, University of Veterinary Medicine Vienna, Austria
| | - Christian Robben
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Public Veterinary Health, University of Veterinary Medicine Vienna, Austria
| | - Anna K Witte
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Public Veterinary Health, University of Veterinary Medicine Vienna, Austria
| | - Dagmar Schoder
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Public Veterinary Health, University of Veterinary MedicineVienna, Austria; Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Public Veterinary Health, University of Veterinary MedicineVienna, Austria
| | - Martin Wagner
- Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Public Veterinary Health, University of Veterinary Medicine Vienna, Austria
| | - Peter Rossmanith
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Public Veterinary Health, University of Veterinary MedicineVienna, Austria; Institute for Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Public Veterinary Health, University of Veterinary MedicineVienna, Austria
| |
Collapse
|
38
|
Trubl G, Solonenko N, Chittick L, Solonenko SA, Rich VI, Sullivan MB. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient. PeerJ 2016; 4:e1999. [PMID: 27231649 PMCID: PMC4878379 DOI: 10.7717/peerj.1999] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/11/2016] [Indexed: 01/23/2023] Open
Abstract
Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g−1 of soil than other methods tested. All method combinations yielded VLPs g−1 of soil on the 108 order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g−1 of soil among the soil types. This research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.
Collapse
Affiliation(s)
- Gareth Trubl
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Natalie Solonenko
- Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Lauren Chittick
- Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Sergei A Solonenko
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Ecology, Evolution and Organismal Biology, Ohio State University, Columbus, OH, United States
| | - Virginia I Rich
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Matthew B Sullivan
- Current affiliation: Department of Microbiology, Ohio State University, Columbus, OH, United States; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States; Current affiliation: Department of Ecology, Evolution and Organismal Biology, Ohio State University, Columbus, OH, United States; Current affiliation: Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States
| |
Collapse
|
39
|
Enumerating Virus-Like Particles and Bacterial Populations in the Sinuses of Chronic Rhinosinusitis Patients Using Flow Cytometry. PLoS One 2016; 11:e0155003. [PMID: 27171169 PMCID: PMC4865123 DOI: 10.1371/journal.pone.0155003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/25/2016] [Indexed: 01/28/2023] Open
Abstract
There is increasing evidence to suggest that the sinus microbiome plays a role in the pathogenesis of chronic rhinosinusitis (CRS). However, the concentration of these microorganisms within the sinuses is still unknown. We show that flow cytometry can be used to enumerate bacteria and virus-like particles (VLPs) in sinus flush samples of CRS patients. This was achieved through trialling 5 sample preparation techniques for flow cytometry. We found high concentrations of bacteria and VLPs in these samples. Untreated samples produced the highest average bacterial and VLP counts with 3.3 ± 0.74 x 107 bacteria ml-1 and 2.4 ± 1.23 x 109 VLP ml-1 of sinus flush (n = 9). These counts were significantly higher than most of the treated samples (p < 0.05). Results showed 103 and 104 times inter-patient variation for bacteria and VLP concentrations. This wide variation suggests that diagnosis and treatment need to be personalised and that utilising flow cytometry is useful and efficient for this. This study is the first to enumerate bacterial and VLP populations in the maxillary sinus of CRS patients. The relevance of enumeration is that with increasing antimicrobial resistance, antibiotics are becoming less effective at treating bacterial infections of the sinuses, so alternative therapies are needed. Phage therapy has been proposed as one such alternative, but for dosing, the abundance of bacteria is required. Knowledge of whether phages are normally present in the sinuses will assist in gauging the safety of applying phage therapy to sinuses. Our finding, that large numbers of VLP are frequently present in sinuses, indicates that phage therapy may represent a minimally disruptive intervention towards the nasal microbiome. We propose that flow cytometry can be used as a tool to assess microbial biomass dynamics in sinuses and other anatomical locations where infection can cause disease.
Collapse
|
40
|
Abstract
In recent years, remarkable progress has been made in the field of virus environmental ecology. In marine ecosystems, for example, viruses are now thought to play pivotal roles in the biogeochemical cycling of nutrients and to be mediators of microbial evolution through horizontal gene transfer. The diversity and ecology of viruses in soils are poorly understood, but evidence supports the view that the diversity and ecology of viruses in soils differ substantially from those in aquatic systems. Desert biomes cover ∼ 33% of global land masses, and yet the diversity and roles of viruses in these dominant ecosystems remain poorly understood. There is evidence that hot hyperarid desert soils are characterized by high levels of bacterial lysogens and low extracellular virus counts. In contrast, cold desert soils contain high extracellular virus titers. We suggest that the prevalence of microbial biofilms in hyperarid soils, combined with extreme thermal regimens, exerts strong selection pressures on both temperate and virulent viruses. Many desert soil virus sequences show low values of identity to virus genomes in public databases, suggesting the existence of distinct and as-yet-uncharacterized soil phylogenetic lineages (e.g., cyanophages). We strongly advocate for amplification-free metavirome analyses while encouraging the classical isolation of phages from dominant and culturable microbial isolates in order to populate sequence databases. This review provides an overview of recent advances in the study of viruses in hyperarid soils and of the factors that contribute to viral abundance and diversity in hot and cold deserts and offers technical recommendations for future studies.
Collapse
|
41
|
Viral and Bacterial Epibionts in Thermally-Stressed Corals. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2015. [DOI: 10.3390/jmse3041272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
42
|
Motlagh AM, Bhattacharjee AS, Goel R. Microbiological study of bacteriophage induction in the presence of chemical stress factors in enhanced biological phosphorus removal (EBPR). WATER RESEARCH 2015; 81:1-14. [PMID: 26024959 DOI: 10.1016/j.watres.2015.04.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/10/2015] [Accepted: 04/11/2015] [Indexed: 06/04/2023]
Abstract
Polyphosphate accumulating organisms (PAOs) are responsible for carrying the enhanced biological phosphorus removal (EBPR). Although the EBPR process is well studied, the failure of EBPR performance at both laboratory and full-scale plants has revealed a lack of knowledge about the ecological and microbiological aspects of EBPR processes. Bacteriophages are viruses that infect bacteria as their sole host. Bacteriophage infection of polyphosphate accumulating organisms (PAOs) has not been considered as a main contributor to biological phosphorus removal upsets. This study examined the effects of different stress factors on the dynamics of bacteriophages and the corresponding effects on the phosphorus removal performance in a lab-scale EBPR system. The results showed that copper (heavy metal), cyanide (toxic chemical), and ciprofloxacin (antibiotic), as three different anthropogenic stress factors, can induce phages integrated onto bacterial genomes (i.e. prophages) in an enriched EBPR sequencing batch reactor, resulting in a decrease in the polyphosphate kinase gene ppk1 clades copy number, phosphorus accumulation capacity, and phosphorus removal performance. This study opens opportunities for further research on the effects of bacteriophages in nutrient cycles both in controlled systems such as wastewater treatment plants and natural ecosystems.
Collapse
Affiliation(s)
- Amir Mohaghegh Motlagh
- Department of Civil and Environmental Engineering, University of Utah, 110 S Central Campus Drive, Salt Lake City, UT 84112, USA
| | - Ananda S Bhattacharjee
- Department of Civil and Environmental Engineering, University of Utah, 110 S Central Campus Drive, Salt Lake City, UT 84112, USA
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, 110 S Central Campus Drive, Salt Lake City, UT 84112, USA.
| |
Collapse
|
43
|
Mohiuddin M, Schellhorn HE. Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis. Front Microbiol 2015; 6:960. [PMID: 26441894 PMCID: PMC4569853 DOI: 10.3389/fmicb.2015.00960] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 08/31/2015] [Indexed: 12/19/2022] Open
Abstract
Viruses are the most abundant microorganisms in the aquatic environment, yet the identification of viruses and assessing their diversity still remains a challenge. Here, we present a robust, routinely usable approach to identify viruses from two freshwater lakes of the lower Great Lakes region, Lake Ontario, and Lake Erie. We collected water samples from six different beaches of these two lakes during the summer period of 2012 and 2013, and separated into three distinct fractions, namely a bacterial fraction, a virus like particle (VLP) fraction, and a fraction of eDNA (environmental DNA). DNA extracted from all three fractions was sequenced and bioinformatic analyses of sequences revealed the presence of viruses from major viral families. The analyzed viral sequences were dominated by bacteriophage sequences, but also contained many plant and animal viruses. Within the context of this study, geographic location does not appear to have a major impact on viral abundance and diversity, since virome composition of both lakes were similar. Comparative analyses between eDNA and viral fractions showed that eDNA can be used in combination with VLP fractions to identify viruses from the environment.
Collapse
|
44
|
Cai L, Yang Y, Jiao N, Zhang R. Evaluation of Tangential Flow Filtration for the Concentration and Separation of Bacteria and Viruses in Contrasting Marine Environments. PLoS One 2015; 10:e0136741. [PMID: 26305356 PMCID: PMC4549332 DOI: 10.1371/journal.pone.0136741] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 08/07/2015] [Indexed: 11/18/2022] Open
Abstract
Tangential flow filtration (TFF), which has been widely adopted to concentrate a diverse array of microbes from water, is a promising method of microbial separation or removal. However, it is essential to select an optimal membrane suitable for the specific filtration application. This study evaluated two different scales of TFF systems for concentrating and separating microbes (including bacteria and viruses) from contrasting marine waters. Among bacteria-size membranes, polyvinylidene difluoride (PVDF) membranes showed higher bacterial recovery, but lower viral permeation efficiencies than polyethersulfone (PES) membranes, regardless of environments and scales of TFF. Estuary samples showed significantly higher percentages of bacterial retention than nearshore and ocean samples. For virus-size membranes, a higher viral recovery and lower sorption was observed for regenerated cellulose membrane than PES membranes in the small-scale TFF. Similar viral recoveries were observed between PES membranes in the large-scale TFF, with higher viral concentrations being observed in estuary samples than in nearshore samples. Deep ocean samples showed the lowest recovery of viruses, which was consistent with observations of bacterial recovery. Synthetically, PVDF may be more suitable for the concentration of bacterial cells, while PES would be a better choice for the collection of viruses. When compared with the PES membrane, regenerated cellulose is better for viral concentration, while PES is recommended to obtain bacteria- and virus-free seawater.
Collapse
Affiliation(s)
- Lanlan Cai
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang’an), Xiamen, Fujian, 361102, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang’an), Xiamen, Fujian, 361102, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang’an), Xiamen, Fujian, 361102, China
- * E-mail: (RZ); (NJ)
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang’an), Xiamen, Fujian, 361102, China
- * E-mail: (RZ); (NJ)
| |
Collapse
|
45
|
Srinivasiah S, Lovett J, Ghosh D, Roy K, Fuhrmann JJ, Radosevich M, Wommack KE. Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation. FEMS Microbiol Ecol 2015; 91:fiv063. [PMID: 26149131 DOI: 10.1093/femsec/fiv063] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2015] [Indexed: 11/14/2022] Open
Abstract
Viruses are highly abundant in soils with their numbers exceeding those of cooccurring bacterial cells by 10- to over 1000-fold. Water and organic matter content influence the magnitude of the viral-to-bacterial ratio in soils; thus, ecosystem type and land use shape interactions between viral and host microbial communities in soils. Less understood are the shorter term interactions between viral and host communities that ultimately maintain the large viral standing stock within soils. This study examined short-term dynamics of viral and bacterial communities in soils to determine whether the growth of soil bacterial communities results in the production of soil viruses, and if viral community responses occur within specific populations. In microcosms amended with different carbon sources, increases in viral abundance (VA) accompanied increases in bacterial abundance (BA) and bacterial respiration rate (BRR). The timing and intensity of increases in BA, VA and BRR were different across C sources suggesting differences in the predominant mode of viral replication within growth-stimulated bacterial populations. Moreover, compositional changes occurred in soil bacterial and viral communities indicating that new viral production arose from a subset of host populations. To our knowledge, these are the first observations of soil viral populations responding to short-term changes in soil bacterial communities.
Collapse
Affiliation(s)
- Sharath Srinivasiah
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Jacqueline Lovett
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Dhritiman Ghosh
- Biosystems Engineering & Soil Science Department, University of Tennessee, Knoxville, TN 37996 USA
| | - Krishnakali Roy
- Biosystems Engineering & Soil Science Department, University of Tennessee, Knoxville, TN 37996 USA
| | - Jeffry J Fuhrmann
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Mark Radosevich
- Biosystems Engineering & Soil Science Department, University of Tennessee, Knoxville, TN 37996 USA
| | - K Eric Wommack
- Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| |
Collapse
|
46
|
Coral Mucus Is a Hot Spot for Viral Infections. Appl Environ Microbiol 2015; 81:5773-83. [PMID: 26092456 DOI: 10.1128/aem.00542-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/04/2015] [Indexed: 11/20/2022] Open
Abstract
There is increasing suspicion that viral communities play a pivotal role in maintaining coral health, yet their main ecological traits still remain poorly characterized. In this study, we examined the seasonal distribution and reproduction pathways of viruses inhabiting the mucus of the scleractinians Fungia repanda and Acropora formosa collected in Nha Trang Bay (Vietnam) during an 11-month survey. The strong coupling between epibiotic viral and bacterial abundance suggested that phages are dominant among coral-associated viral communities. Mucosal viruses also exhibited significant differences in their main features between the two coral species and were also remarkably contrasted with their planktonic counterparts. For example, their abundance (inferred from epifluorescence counts), lytic production rates (KCN incubations), and the proportion of lysogenic cells (mitomycin C inductions) were, respectively, 2.6-, 9.5-, and 2.2-fold higher in mucus than in the surrounding water. Both lytic and lysogenic indicators were tightly coupled with temperature and salinity, suggesting that the life strategy of viral epibionts is strongly dependent upon environmental circumstances. Finally, our results suggest that coral mucus may represent a highly favorable habitat for viral proliferation, promoting the development of both temperate and virulent phages. Here, we discuss how such an optimized viral arsenal could be crucial for coral viability by presumably forging complex links with both symbiotic and adjacent nonsymbiotic microorganisms.
Collapse
|
47
|
Abstract
Bacteriophages are the most abundant biological entities in the biosphere, and this dynamic and old population is, not surprisingly, highly diverse genetically. Relative to bacterial genomics, phage genomics has advanced slowly, and a higher-resolution picture of the phagosphere is only just emerging. This view reveals substantial diversity even among phages known to infect a common host strain, but the relationships are complex, with mosaic genomic architectures generated by illegitimate recombination over a long period of evolutionary history.
Collapse
|
48
|
Wommack KE, Nasko DJ, Chopyk J, Sakowski EG. Counts and sequences, observations that continue to change our understanding of viruses in nature. J Microbiol 2015; 53:181-92. [PMID: 25732739 DOI: 10.1007/s12275-015-5068-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 02/10/2015] [Indexed: 12/01/2022]
Abstract
The discovery of abundant viruses in the oceans and on land has ushered in a quarter century of groundbreaking advancements in our understanding of viruses within ecosystems. Two types of observations from environmental samples--direct counts of viral particles and viral metagenomic sequences--have been critical to these discoveries. Accurate direct counts have established ecosystem-scale trends in the impacts of viral infection on microbial host populations and have shown that viral communities within aquatic and soil environments respond to both short term and seasonal environmental change. Direct counts have been critical for estimating viral production rate, a measurement essential to quantifying the implications of viral infection for the biogeochemical cycling of nutrients within ecosystems. While direct counts have defined the magnitude of viral processes; shotgun sequences of environmental viral DNA--virome sequences--have enabled researchers to estimate the diversity and composition of natural viral communities. Virome-enabled studies have found the virioplankton to contain thousands of viral genotypes in communities where the most dominant viral population accounts for a small fraction of total abundance followed by a long tail of diverse populations. Detailed examination of long virome sequences has led to new understanding of genotype-to-phenotype connections within marine viruses and revealed that viruses carry metabolic genes that are important to maintaining cellular energy during viral replication. Increased access to long virome sequences will undoubtedly reveal more genetic secrets of viruses and enable us to build a genomics rulebook for predicting key biological and ecological features of unknown viruses.
Collapse
Affiliation(s)
- K Eri Wommack
- Delaware Biotechnology Institute, University of Delaware, Newark Delaware, USA,
| | | | | | | |
Collapse
|
49
|
Brown MR, Camézuli S, Davenport RJ, Petelenz-Kurdziel E, Øvreås L, Curtis TP. Flow cytometric quantification of viruses in activated sludge. WATER RESEARCH 2015; 68:414-22. [PMID: 25462748 DOI: 10.1016/j.watres.2014.10.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 09/22/2014] [Accepted: 10/08/2014] [Indexed: 05/21/2023]
Abstract
Viruses may play a critical role in the microbial dynamics of activated sludge systems; however the difficulty of their quantification makes long term and large scale studies costly, timely and challenging. Thus a flow cytometric protocol was optimised and employed to determine virus abundance in activated sludge samples. The best flow cytometry signature and highest virus count was obtained by separating the indigenous floc-associated viruses using Tween 80 and sodium pyrophosphate, diluting the sample with Tris-EDTA and staining with SYBR Green II. Using the optimised protocol viral concentrations from 25 activated sludge plants were determined, with average concentrations of 2.35 × 10⁹ mL⁻¹ observed. Direct counts by transmission electron microscopy were highly correlated with flow cytometric counts (p = <0.05 and r² = 0.77), with concentrations from both quantification methods comparable at the order of magnitude level. The high counting efficiency, ease of preparation and rapidity and reproducibility of analysis makes flow cytometric quantification of viruses in activated sludge ideal for routine investigation and thus invaluable in unravelling the complexity of phage host interactions in such systems.
Collapse
Affiliation(s)
- M R Brown
- School of Civil Engineering and Geosciences, Newcastle University, NE1 7RU, UK.
| | | | | | | | | | | |
Collapse
|
50
|
Efficient purification and concentration of viruses from a large body of high turbidity seawater. MethodsX 2014; 1:197-206. [PMID: 26150953 PMCID: PMC4473021 DOI: 10.1016/j.mex.2014.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 09/11/2014] [Accepted: 09/12/2014] [Indexed: 11/29/2022] Open
Abstract
Marine viruses are the most abundant entities in the ocean and play crucial roles in the marine ecological system. However, understanding of viral diversity on large scale depends on efficient and reliable viral purification and concentration techniques. Here, we report on developing an efficient method to purify and concentrate viruses from large body of high turbidity seawater. The developed method characterizes with high viral recovery efficiency, high concentration factor, high viral particle densities and high-throughput, and is reliable for viral concentration from high turbidity seawater. Recovered viral particles were used directly for subsequent analysis by epifluorescence microscopy, transmission electron microscopy and metagenomic sequencing. Three points are essential for this method:The sampled seawater (>150 L) was initially divided into two parts, water fraction and settled matter fraction, after natural sedimentation. Both viruses in the water fraction concentrated by tangential flow filtration (TFF) and viruses isolated from the settled matter fraction were considered as the whole viral community in high turbidity seawater. The viral concentrates were re-concentrated by using centrifugal filter device in order to obtain high density of viral particles.
Collapse
|