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Meidaninikjeh S, Mohammadi P, Elikaei A. Bacteriophages and bacterial extracellular vesicles, threat or opportunity? Life Sci 2024; 350:122749. [PMID: 38821215 DOI: 10.1016/j.lfs.2024.122749] [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] [Received: 12/04/2023] [Revised: 03/25/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
Emergence of antimicrobial-resistant bacteria (AMR) is one of the health major problems worldwide. The scientists are looking for a novel method to treat infectious diseases. Phage therapy is considered a suitable approach for treating infectious diseases. However, there are different challenges in this way. Some biological aspects can probably influence on therapeutic results and further investigations are necessary to reach a successful phage therapy. Bacteriophage activity can influence by bacterial defense system. Bacterial extracellular vesicles (BEVs) are one of the bacterial defense mechanisms which can modify the results of bacteriophage activity. BEVs have the significant roles in the gene transferring, invasion, escape, and spreading of bacteriophages. In this review, the defense mechanisms of bacteria against bacteriophages, especially BEVs secretion, the hidden linkage of BEVs and bacteriophages, and its possible consequences on the bacteriophage activity as well phage therapy will be discussed.
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Affiliation(s)
- Sepideh Meidaninikjeh
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Parisa Mohammadi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
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2
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Bi L, Yu DT, Han LL, Du S, Yuan CY, He JZ, Hu HW. Unravelling the ecological complexity of soil viromes: Challenges and opportunities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:152217. [PMID: 34890674 DOI: 10.1016/j.scitotenv.2021.152217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
Viruses are extremely abundant and ubiquitous in soil, and significantly contribute to various terrestrial ecosystem processes such as biogeochemical nutrient cycling, microbiome regulation and community assembly, and host evolutionary dynamics. Despite their numerous dominance and functional importance, understanding soil viral ecology is a formidable challenge, because of the technological challenges to characterize the abundance, diversity and community compositions of viruses, and their interactions with other organisms in the complex soil environment. Viruses may engage in a myriad of biological interactions within soil food webs across a broad range of spatiotemporal scales and are exposed to various biotic and abiotic disturbances. Current studies on the soil viromes, however, often describe the complexity of their tremendous diversity, but lack of exploring their potential ecological roles. In this article, we summarized the major methods to decipher the ecology of soil viruses, discussed biotic and abiotic factors and global change factors that shape the diversity and composition of soil viromes, and the ecological roles of soil viruses. We also proposed a new framework to understand the ecological complexity of viruses from micro to macro ecosystem scales and to predict and unravel their activities in terrestrial ecosystems.
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Affiliation(s)
- Li Bi
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dan-Ting Yu
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian 350007, China; School of Geographical Sciences, Fujian Normal University, Fujian 350007, China.
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuai Du
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng-Yu Yuan
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian 350007, China; School of Geographical Sciences, Fujian Normal University, Fujian 350007, China
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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3
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Potapov SA, Tikhonova IV, Krasnopeev AY, Suslova MY, Zhuchenko NA, Drucker VV, Belykh OI. Communities of T4-like bacteriophages associated with bacteria in Lake Baikal: diversity and biogeography. PeerJ 2022. [DOI: 10.7717/peerj.12748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lake Baikal phage communities are important for lake ecosystem functioning. Here we describe the diversity of T4-bacteriophage associated with the bacterial fraction of filtered water samples collected from the pelagic zone, coastal zone and shallow bays. Although the study of the diversity of phages for the g23 gene has been carried out at Lake Baikal for more than ten years, shallow bays that comprise a significant part of the lake’s area have been neglected, and this gene has not previously been studied in the bacterial fraction. Phage communities were probed using amplicon sequencing methods targeting the gene of major capsid protein (g23) and compared phylogenetically across sample locations and with sequences previously retrieved from non-bacterial fractions (<0.2 um) and biofilms (non-fractionated). In this study, we examined six water samples, in which 24 to 74 viral OTUs were obtained. The sequences from shallow bays largely differed from those in the pelagic and coastal samples and formed individual subcluster in the UPGMA tree that was obtained from the comparison of phylogenetic distances of g23 sequence sets from various ecosystems, reflecting differences in viral communities depending on the productivity of various sites of Lake Baikal. According to the RefSeq database, from 58.3 to 73% of sequences of each sample had cultivated closest relatives belonging to cyanophages. In this study, for phylogenetic analysis, we chose the closest relatives not only from the RefSeq and GenBank NR databases but also from two marine and one freshwater viromes: eutrophic Osaka Bay (Japan), oligotrophic area of the Pacific Ocean (Station ALOHA) and mesotrophic and ancient Lake Biwa (Japan), which allowed us to more fully compare the diversity of marine and freshwater phages. The identity with marine sequences at the amino acid level ranged from 35 to 80%, and with the sequences from the viral fraction and bacterial one from Lake Biwa—from 35.3 to 98% and from 33.9 to 89.1%, respectively. Therefore, the sequences from marine viromes had a greater difference than those from freshwater viromes, which may indicate a close relationship between freshwater viruses and differences from marine viruses.
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Affiliation(s)
| | | | | | - Maria Yurjevna Suslova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | | | | | - Olga Ivanovna Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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4
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Alharbi NM, Ziadi MM. Wastewater as a fertility source for novel bacteriophages against multi-drug resistant bacteria. Saudi J Biol Sci 2021; 28:4358-4364. [PMID: 34354420 PMCID: PMC8324929 DOI: 10.1016/j.sjbs.2021.04.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 01/21/2023] Open
Abstract
Antibiotic resistance is a common and serious public health worldwide. As an alternative to antibiotics, bacteriophage (phage) therapy offers one of the best solutions to antibiotic resistance. Bacteriophages survive where their bacterial hosts are found; thus, they exist in almost all environments and their applications are quite varied in the medical, environmental, and industrial fields. Moreover, a single phage or a mixture of phages can be used in phage therapy; mixed phages tend to be more effective in reducing the number and/or activity of pathogenic bacteria than that of a single phage.
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Affiliation(s)
- Najwa M. Alharbi
- College of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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5
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Sui X, Zhang R, Frey B, Yang L, Liu Y, Ni H, Li M. Soil physicochemical properties drive the variation in soil microbial communities along a forest successional series in a degraded wetland in northeastern China. Ecol Evol 2021; 11:2194-2208. [PMID: 33717448 PMCID: PMC7920768 DOI: 10.1002/ece3.7184] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/19/2020] [Accepted: 12/22/2020] [Indexed: 12/29/2022] Open
Abstract
The Sanjiang Plain is the biggest freshwater wetland locating in northeastern China. Due to climate change and human activities, that wetland has degraded to a successional gradient from the original flooded wetland to dry shrub vegetation and a forest area with lower ground water level, which may result in changes in soil microbiologic structure and functions. The present study investigated the microbial diversity and community structure in relation to soil properties along that successional gradient. The soil physico-chemical properties changed significantly with degradation stage. The Shannon diversity index of both soil bacteria (5.90-6.42) and fungi (1.7-4.19) varied significantly with successional stage (both p < .05). The community structures of soil bacteria and fungi in the early successional stages (i.e., the wetland) were significantly determined by water content, total nitrogen, and available nitrogen concentrations in soils, while those in the later successional stages (i.e., forests) were significantly structured by soil organic carbon, soil pH, and available phosphorus concentrations. These results suggest that the soil microbial structure is mainly determined by soil properties rather than by plant community such as plant species composition along successional stages.
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Affiliation(s)
- Xin Sui
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold RegionSchool of Life SciencesHeilongjiang UniversityHarbinChina
- Institution of Nature and EcologyHeilongjiang Academy of SciencesHarbinChina
| | - Rongtao Zhang
- Institution of Nature and EcologyHeilongjiang Academy of SciencesHarbinChina
| | - Beat Frey
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Libin Yang
- Institution of Nature and EcologyHeilongjiang Academy of SciencesHarbinChina
| | - Yingnan Liu
- Institution of Nature and EcologyHeilongjiang Academy of SciencesHarbinChina
| | - Hongwei Ni
- Heilongjiang Academy of ForestryHarbinChina
| | - Mai‐He Li
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
- Key Laboratory of Geographical Processes and Ecological Security in Changbai MountainsMinistry of EducationSchool of Geographical SciencesNortheast Normal UniversityChangchunChina
- CAS Key Laboratory of Forest Ecology and ManagementInstitute of Applied EcologyErguna Forest‐Steppe Ecotone Research StationChinese Academy of SciencesShenyangChina
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6
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Sui X, Zhang R, Frey B, Yang L, Li MH, Ni H. Land use change effects on diversity of soil bacterial, Acidobacterial and fungal communities in wetlands of the Sanjiang Plain, northeastern China. Sci Rep 2019; 9:18535. [PMID: 31811224 PMCID: PMC6898332 DOI: 10.1038/s41598-019-55063-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/18/2019] [Indexed: 12/18/2022] Open
Abstract
The bacterial, acidobacterial, and fungal communities in wetlands can undergo perturbations by various human activities, such as disturbances caused by cultivation and during the process of system restoration. In this study, we investigated the relationships between the composition of the soil bacterial, acidobacterial, and fungal communities and the transformation of wetlands by human activities in the Sanjiang Plain. Soil microbial communities were assessed in wetland soils collected from pristine marsh, neighboring cropland (wetland turned into arable land), and land that had been reforested with Larix gmelinii. The alpha-diversities of bacteria, Acidobacteria, and fungi were affected by land-use change and were highest in the arable land and lowest in the wetland soils. The soil microbial community structures were also altered with changing land-use. Canonical correlation analyses showed that beta-diversity was significantly affected by soil pH, available phosphorus, soil nitrogen, and total organic carbon. Overall, our results showed that the agricultural cultivation of wetlands changes the available soil carbon, nitrogen, and phosphorus pools, thereby influencing the bacterial, acidobacterial, and fungal diversity and community structure. Once the soil microbial community has been altered by human activity, it might be difficult to restore it to its original state. These findings highlight the importance of effectively maintaining the diversity of soil bacterial, Acidobacterial, and fungal communities despite land use change in order to sustain a microbial community diversity and ecosystem function.
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Affiliation(s)
- Xin Sui
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China.,Institute of Nature of Ecology, Heilongjiang Academy of Science, Harbin, China
| | - Rongtao Zhang
- Institute of Nature of Ecology, Heilongjiang Academy of Science, Harbin, China
| | - Beat Frey
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Libin Yang
- Institute of Nature of Ecology, Heilongjiang Academy of Science, Harbin, China
| | - Mai-He Li
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland. .,Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, 130024, China.
| | - Hongwei Ni
- Institute of Nature of Ecology, Heilongjiang Academy of Science, Harbin, China.
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7
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Bonetti G, Trevathan-Tackett SM, Carnell PE, Macreadie PI. Implication of Viral Infections for Greenhouse Gas Dynamics in Freshwater Wetlands: Challenges and Perspectives. Front Microbiol 2019; 10:1962. [PMID: 31507569 PMCID: PMC6718870 DOI: 10.3389/fmicb.2019.01962] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/09/2019] [Indexed: 01/07/2023] Open
Abstract
Viruses are non-living, acellular entities, and the most abundant biological agents on earth. They are widely acknowledged as having the capacity to influence global biogeochemical cycles by infecting the bacterial and archaeal populations that regulate carbon and nutrient turnover. Evidence suggests that the majority of viruses in wetlands are bacteriophages, but despite their importance, studies on how viruses control the prokaryotic community and the concomitant impacts on ecosystem function (such as carbon cycling and greenhouse gas flux) in wetlands are rare. Here we investigate virus-prokaryote interactions in freshwater wetland ecosystems in the context of their potential influence on biogeochemical cycling. Specifically, we (1) synthesize existing literature to establish current understanding of virus-prokaryote interactions, focusing on the implications for wetland greenhouse gas dynamics and (2) identify future research priorities. Viral dynamics in freshwater wetlands have received much less attention compared to those in marine ecosystems. However, based on our literature review, within the last 10 years, viral ecology studies on freshwater wetlands have increased twofold. Despite this increase in literature, the potential implication of viral infections on greenhouse gas emission dynamics is still a knowledge gap. We hypothesize that the rate of greenhouse gas emissions and the pool of sequestered carbon could be strongly linked to the type and rate of viral infection. Viral replication mechanism choice will consequently influence the microbial efficiency of organic matter assimilation and thus the ultimate fate of carbon as a greenhouse gas or stored in soils.
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Affiliation(s)
- Giuditta Bonetti
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Stacey M Trevathan-Tackett
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Paul E Carnell
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Peter I Macreadie
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
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8
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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]
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9
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Li X, Sun Y, Liu J, Yao Q, Wang G. Survey of the bacteriophage phoH gene in wetland sediments in northeast China. Sci Rep 2019; 9:911. [PMID: 30696895 PMCID: PMC6351560 DOI: 10.1038/s41598-018-37508-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/23/2018] [Indexed: 11/29/2022] Open
Abstract
PhoH is a host-derived auxiliary metabolic gene that can be used as a new biomarker for surveying phage diversity in marine and paddy waters. However, the applicability of this gene in other environments has not been addressed. In this paper, we surveyed the phoH gene in four wetland sediments in northeast China. DNA was extracted directly from sediments and used for PCR amplification with the degenerate primers vPhoHf and vPhoHr. In total, 44 and 58 phoH sequences were identified as belonging to bacteria and phages, respectively, suggesting that this primer set is not highly specific to the phage phoH gene. A BLASTp search showed that the 58 phage phoH sequences had the highest identity to the known viral sequences, ranging from 48% to 100%. Phylogenetic analysis showed that all phage sequences from wetlands distributed into the previously designated Groups 2, 3, 4 and 6. In addition, two new subgroups, Groups 2c and 4c, which contained sequences exclusively from wetlands, were detected in this study. Nonmetric multidimensional scaling analysis showed that the phage phoH assemblage from a coastal wetland was similar to that in marine environments, while the phage phoH assemblage from a lake wetland was similar to that in paddy waters. These findings indicated that different types of wetlands had distinct phage phoH compositions.
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Affiliation(s)
- Xiang Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Qin Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
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10
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Potapov S, Belykh O, Krasnopeev A, Gladkikh A, Kabilov M, Tupikin A, Butina T. Assessing the diversity of the g23 gene of T4-like bacteriophages from Lake Baikal with high-throughput sequencing. FEMS Microbiol Lett 2018; 365:4693836. [PMID: 29228190 DOI: 10.1093/femsle/fnx264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/04/2017] [Indexed: 01/09/2023] Open
Abstract
Based on second generation sequencing (MiSeq platform, Illumina), we determined the genetic diversity of T4-like bacteriophages of the family Myoviridae by analysing fragments of the major capsid protein gene g23 in the plankton of Lake Baikal. The sampling depth in our study was significantly higher than in those obtained by the Sanger method before. We obtained 33 701 sequences of the g23 gene fragments, 141 operational taxonomic units (OTUs) of which were identified. 86 OTUs (60.9%) had the closest relatives from lakes Bourget and Annecy, and 28 OTUs (19.8%) had the highest identity with the Baikal g23 clones, which had been previously identified in the northern and southern basins of the lake by the Sanger method. The remaining OTUs were similar to the clones from other ecosystems. We showed a high genetic diversity of T4-type bacteriophages and a genetic difference with the phage communities from other ecosystems.
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Affiliation(s)
- Sergey Potapov
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya, Irkutsk 664033, Russia
| | - Olga Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya, Irkutsk 664033, Russia
| | - Andrey Krasnopeev
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya, Irkutsk 664033, Russia
| | - Anna Gladkikh
- Laboratory of Cholera, Irkutsk Antiplague Research Institute of Siberia and Far East, Irkutsk 664047, Russia
| | - Marsel Kabilov
- Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Aleksey Tupikin
- Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Tatyana Butina
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya, Irkutsk 664033, Russia
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11
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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: 158] [Impact Index Per Article: 22.6] [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.
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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
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12
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He M, Cai L, Zhang C, Jiao N, Zhang R. Phylogenetic Diversity of T4-Type Phages in Sediments from the Subtropical Pearl River Estuary. Front Microbiol 2017; 8:897. [PMID: 28572798 PMCID: PMC5436276 DOI: 10.3389/fmicb.2017.00897] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/03/2017] [Indexed: 11/23/2022] Open
Abstract
Viruses are an abundant and active component of marine sediments and play a significant role in microbial ecology and biogeochemical cycling at local and global scales. To obtain a better understanding of the ecological characteristics of the viriobenthos, the abundance and morphology of viruses and the diversity and community structure of T4-type phages were systematically investigated in the surface sediments of the subtropical Pearl River Estuary (PRE). Viral abundances ranged from 4.49 × 108 to 11.7 × 108 viruses/g and prokaryotic abundances ranged from 2.63 × 108 to 9.55 × 108 cells/g, and both decreased from freshwater to saltwater. Diverse viral morphotypes, including tailed, spherical, filamentous, and rod-shaped viruses, were observed using transmission electron microscopy. Analysis of the major capsid gene (g23) indicated that the sediment T4-type phages were highly diverse and, similar to the trend in viral abundances, their diversity decreased as the salinity increased. Phylogenetic analysis suggested that most of the g23 operational taxonomic units were affiliated with marine, paddy soil, and lake groups. The T4-type phage communities in freshwater and saltwater sediments showed obvious differences, which were related to changes in the Pearl River discharge. The results of this study demonstrated both allochthonous and autochthonous sources of the viral community in the PRE sediments and the movement of certain T4-type viral groups between the freshwater and saline water biomes.
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Affiliation(s)
- Maoqiu He
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Lanlan Cai
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, South University of Science and TechnologyShenzhen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
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13
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Weber-Dąbrowska B, Jończyk-Matysiak E, Żaczek M, Łobocka M, Łusiak-Szelachowska M, Górski A. Bacteriophage Procurement for Therapeutic Purposes. Front Microbiol 2016; 7:1177. [PMID: 27570518 PMCID: PMC4981656 DOI: 10.3389/fmicb.2016.01177] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/18/2016] [Indexed: 01/05/2023] Open
Abstract
Bacteriophages (phages), discovered 100 years ago, are able to infect and destroy only bacterial cells. In the current crisis of antibiotic efficacy, phage therapy is considered as a supplementary or even alternative therapeutic approach. Evolution of multidrug-resistant and pandrug-resistant bacterial strains poses a real threat, so it is extremely important to have the possibility to isolate new phages for therapeutic purposes. Our phage laboratory and therapy center has extensive experience with phage isolation, characterization, and therapeutic application. In this article we present current progress in bacteriophages isolation and use for therapeutic purposes, our experience in this field and its practical implications for phage therapy. We attempt to summarize the state of the art: properties of phages, the methods for their isolation, criteria of phage selection for therapeutic purposes and limitations of their use. Perspectives for the use of genetically engineered phages to specifically target bacterial virulence-associated genes are also briefly presented.
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Affiliation(s)
- Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Maciej Żaczek
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland; Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life SciencesWarsaw, Poland
| | - Marzanna Łusiak-Szelachowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Department of Clinical Immunology, Transplantation Institute, Medical University of WarsawWarsaw, Poland
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14
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Uyaguari-Diaz MI, Chan M, Chaban BL, Croxen MA, Finke JF, Hill JE, Peabody MA, Van Rossum T, Suttle CA, Brinkman FSL, Isaac-Renton J, Prystajecky NA, Tang P. A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples. MICROBIOME 2016; 4:20. [PMID: 27391119 PMCID: PMC5011856 DOI: 10.1186/s40168-016-0166-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/04/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary. RESULTS We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels. CONCLUSION This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.
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Affiliation(s)
- Miguel I. Uyaguari-Diaz
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Michael Chan
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Bonnie L. Chaban
- South Kensington Campus, Imperial College London, Sir Ernst Chain Building, London, SW7 2AZ UK
| | - Matthew A. Croxen
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Jan F. Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4 Canada
| | - Michael A. Peabody
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Thea Van Rossum
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8 Canada
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Judith Isaac-Renton
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Natalie A. Prystajecky
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
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15
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Wang MN, Ge XY, Wu YQ, Yang XL, Tan B, Zhang YJ, Shi ZL. Genetic diversity and temporal dynamics of phytoplankton viruses in East Lake, China. Virol Sin 2015; 30:290-300. [PMID: 26248585 DOI: 10.1007/s12250-015-3603-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022] Open
Abstract
Phytoplankton viruses are important components of aquatic ecosystems. However, their prevalence and genetic diversity in marine and freshwater systems are largely under estimated owing to the immense size of water bodies and limitations in virus discovery techniques. In this study, we conducted a 1-year survey of phytoplankton virus communities by collecting surface water monthly from an inland lake (East Lake) in China between May 2012 and April 2013. We examined four phytoplankton viruses, i.e., myoviruses, podoviruses, siphoviruses, and phycodnaviruses, and seven sets of primers were used to target conserved genes within these four species. In this year-long investigation, a total of 358 different virus-related sequences from four virus families were obtained. All virus families were detected in all months, except for cyanopodoviruses, which were only identified during eight of the 12 months surveyed. Moreover, virus abundance and diversity changed dynamically over time. Phylogenetic analysis revealed that the majority of viral sequences from East Lake, China displayed distinct clustering patterns compared with published sequences. These results supported the existence of a highly diverse and unique phytoplankton virus community in East Lake, China.
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Affiliation(s)
- Mei-Niang Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
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16
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Using signature genes as tools to assess environmental viral ecology and diversity. Appl Environ Microbiol 2015; 80:4470-80. [PMID: 24837394 DOI: 10.1128/aem.00878-14] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses (including bacteriophages) are the most abundant biological entities on the planet. As such, they are thought to have a major impact on all aspects of microbial community structure and function. Despite this critical role in ecosystem processes, the study of virus/phage diversity has lagged far behind parallel studies of the bacterial and eukaryotic kingdoms, largely due to the absence of any universal phylogenetic marker. Here we review the development and use of signature genes to investigate viral diversity, as a viable strategy for data sets of specific virus groups. Genes that have been used include those encoding structural proteins, such as portal protein, major capsid protein, and tail sheath protein, auxiliary metabolism genes, such as psbA, psbB,and phoH, and several polymerase genes. These marker genes have been used in combination with PCR-based fingerprinting and/or sequencing strategies to investigate spatial, temporal, and seasonal variations and diversity in a wide range of habitats.
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17
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Jończyk-Matysiak E, Kłak M, Weber-Dąbrowska B, Borysowski J, Górski A. Possible use of bacteriophages active against Bacillus anthracis and other B. cereus group members in the face of a bioterrorism threat. BIOMED RESEARCH INTERNATIONAL 2014; 2014:735413. [PMID: 25247187 PMCID: PMC4163355 DOI: 10.1155/2014/735413] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/25/2014] [Accepted: 07/25/2014] [Indexed: 12/14/2022]
Abstract
Anthrax is an infectious fatal disease with epidemic potential. Nowadays, bioterrorism using Bacillus anthracis is a real possibility, and thus society needs an effective weapon to neutralize this threat. The pathogen may be easily transmitted to human populations. It is easy to store, transport, and disseminate and may survive for many decades. Recent data strongly support the effectiveness of bacteriophage in treating bacterial diseases. Moreover, it is clear that bacteriophages should be considered a potential incapacitative agent against bioterrorism using bacteria belonging to B. cereus group, especially B. anthracis. Therefore, we have reviewed the possibility of using bacteriophages active against Bacillus anthracis and other species of the B. cereus group in the face of a bioterrorism threat.
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Affiliation(s)
- Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Marlena Kłak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Jan Borysowski
- Department of Clinical Immunology, Transplantation Institute, The Medical University of Warsaw, Nowogrodzka 59, 02-006 Warsaw, Poland
| | - Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
- Department of Clinical Immunology, Transplantation Institute, The Medical University of Warsaw, Nowogrodzka 59, 02-006 Warsaw, Poland
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18
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Seasonal variations in PCR-DGGE fingerprinted viruses infecting phytoplankton in large and deep peri-alpine lakes. Ecol Res 2014. [DOI: 10.1007/s11284-013-1121-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Liu J, Zheng C, Song C, Guo S, Liu X, Wang G. Conversion from natural wetlands to paddy field alters the composition of soil bacterial communities in Sanjiang Plain, Northeast China. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0784-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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