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Bulletin of Chinese Academy of Sciences (Chinese Version)

Keywords

soil virus; bacteriophage; diversity; metagenome; viral ecology

Document Type

Article

Abstract

Viruses are the most abundant biological entities on the Earth, they play important roles in altering their host community structures, driving global biogeochemical cycles, and promoting the biological evolution. Viruses are commonly regarded as'dark matter'of biota. Recently, the researches on viral ecology are progressing rapidly in marine environments, while the corresponding studies in terrestrial ecosystem especially in soil environments were largely lagged. In this paper, the recent research progress on soil virus, such as viral abundance, morphological and genetic diversity, research methodology, and ecological functions were briefly reviewed from the viewpoint of ecology. The purpose of this paper aims at calling for scientists who engaged in soil microorganism and soil ecology research to pay attention on the study of soil virus, and finally promote the development of soil viral ecology.

First page

575

Last Page

584

Language

Chinese

Publisher

Bulletin of Chinese Academy of Sciences

References

Suttle C A. Viruses in the sea. Nature, 2005, 437(7057): 356-361.

Pennisi E. Ever-bigger viruses shake tree of life. Science, 2013, 341(6143): 226-227.

Brüssow B. The not so universal tree of life or the place of viruses in the living world. Philosophical Transactions of Royal Society B, 2009, 364(1527): 2263-2274.

Rohwer F, Edwards R. The phage proteomic tree: a genome based taxonomy for phage. Journal of Bacteriology, 2002, 184(16): 4529-4535.

生物探索. 噬菌体: 开启生物宇宙暗物质研究大门. [2013-09-13]. http://www.biodiscover.com/news/research/105866.html.

Kimura M, Jia Z J, Nakayama N, et al. Ecology of viruses in soils: past, present and future perspectives. Soil Science and Plant Nutrition, 2008, 54(1): 1-32.

Ratti C, Budge G, Ward L, et al. Detection and relative quantitation of soil-borne cereal mosaic virus (SBCMV) and polymyxa graminis in winter wheat using real-time PCR (TaqMan). Journal of Virological Methods, 2005, 122(1): 95-103.

Williamson K E, Wommack K E, Radosevich M. Sampling natural viral communities from culture-independent analyses. Applied Environmental Microbiology, 2003, 69(11): 6628-6633.

Weinbauer M G. Ecology of prokaryotic viruses. FEMS Microbiology Reviews, 2004, 28(2), 127-181.

Wommack K E, Colwell R R. Virioplankton: viruses in aquatic ecosystems. Microbiology and Molecular Biology Reviews, 2000, 64(1): 69-114.

Hennes J E, Suttle C A. Direct of viruses in natural waters and laboratory cultures by epifluorescence microscopy. Limnology and Oceanography, 1995, 40: 1050-1055.

Reavy B, Swanson M M, Taliansky M. Viruses in soil. In: Dighton J, Krumins J A. (eds.). Interactions in Soil: Promoting Plant Growth. Netherlands: Springer, 2014. 163-180.

Williamson K E, Radosevich M, Wommack K E. Abundance and diversity of viruses in six Delaware soils. Applied Environmental Microbiology, 2005, 71(6): 3119-3125.

Chen L, Xun W B, Sun L, et al. Effect of different long-term fertilization regimes on the viral community in an agricultural soil of Southern China. European Journal of Soil Biology, 2014, 62(6): 121-126.

Williamson K E, Radosevich M, Smith D W, et al. Incidence of lysogeny within temperate and extreme soil environments. Environmental Microbiology, 2007, 9(10): 2563-2574.

Fuhrman J A. Marine viruses and their biogeochemical and ecological effects. Nature, 1999, 399(6736): 541-548.

Nakayama N, Okumura M, Inoue K, et al. Seasonal variations in abundances of virus-like particles and bacteria in the floodwater of a Japanese paddy field. Soil Science and Plant Nutrition, 2007, 53(4): 420-429.

Gonzalez-Martin C, Teigell-Perez N, Lyles M, et al. Epifluorescent direct counts of bacteria and viruses from topsoil of various desert storm regions. Research in Microbiology, 2013, 164(1):17-21.

Swanson M M, Fraser G, Daniell T J, et al. Viruses in soils: morphological diversity and abundance in the rhizosphere. Annals of Applied Biology, 2009, 155(1): 51-60.

Williamson K E, Helton R R, Wommack K E. Bias in bacteriophage morphological classification by transmission electron microscopy due to breakage or loss of tail structures. Microscopy Research and Technique, 2012, 75(4): 452-457.

Proctor L M. Advances in the study of marine viruses. Microscopy Research Technique, 1997, 37(2): 136-161.

Nakayama N, Okumura M, Inoue K, et al. Morphological analysis of viral communities in the floodwater of a Japanese paddy field. Soil Biology & Biochemistry, 2008(12), 39: 3187-3190.

Van Etten J L, Lane K C, Meints R H. Viruses and virus like particles of eukaryotic algae. Microbiology and Molecular Biology Reviews, 1991, 55(4): 586-620.

Philippe N, Legendre M, Doutre G, et al. Pandoraviruses: Amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic Eukaryotes. Science, 2013, 341(6143): 281-286.

Stewart F M, Levin B R. The population biology of bacterial viruses: why be temperate. Theoretical Population Biology, 1984, 26(1): 93-117.

Marsh P, Wellington E M H. Phage-host interactions in soil. FEMS Microbiology Ecology, 1994, 15(1-2): 99-107.

Pantastico-Caldas M, Duncan K E, Lstock C A, et al. Population dynamics of bacteriophage and bacillus subtilis in soil. Ecology, 1992, 73(5): 1888-1902.

Williamson S J, Houchin L A, McDaniel L, et al. Seasonal variation in lysogeny as depicted by prophage induction in Tampa Bay, Florida. Applied and Environmental Microbiology, 2002, 68: 4307-4314.

Williamson K E, Schnitker J B, Radosevich M, et al. Cultivationbased assessment of lysogeny among soil bacteria. Microbial Ecology, 2008, 56(3):437-447.

Prigent M, Leroy M, Confalonieri F, et al. A diversity of bacteriophage forms and genomes can be isolated from the surface sands of the Sahara desert. Extremophiles, 2005, 9(4):289-296.

Srividhya K V, Krishnaswamy S. Identification and analysis of prophages and phage remnants in soil bacteria. In: Witzany G. (ed.). Biocommunication in Soil Microorganisms, Soil Biology 23. Berlin Heidelberg: Springer Verlag, 2010. 137-160.

Barksdale L, Arden S B. Persisting bacteriophage infections, lysogeny, and phage conversions. Annual Review of Microbiology, 1974, 28(4): 265-299.

Barondess J J, Beckwith J. Bor gene of phage lambda, involved in serum resistance, encodes a widely conserved outer membrane. Journal of Bacteriology, 1995, 177(5): 1247-1253.

Waldor M K, Mekalanos J J. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science, 1996, 272:1910-1914.

Wommack K E, Ravel J, Hill R T, et al. Population dynamics of Chesapeake Bay virioplankton: total-community analysis by pulsed-field gel electrophoresis. Applied Environmental Microbiology, 1999, 65(1): 231-240.

Steward G F, Montiel J L, Azam F. Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments. Limnology and Oceanography, 2000, 45(8): 1697-1706.

Parada V, Baudoux A C, Sintes E, et al. Dynamics and diversity of newly produced virioplankton in the North Sea. The ISME Journal, 2008, 2(9): 924-936.

Winget D, Wommack K E. Randomly amplified polymorphic DNA PCR as a tool for assessment of marine viral richness. Applied and Environmental Microbiology, 2008, 74(9): 2077-2092.

Srinivasiah S, Lovett J, Polson S, et al. Direct assessment of viral diversity in soils by random PCR amplification of polymorphic DNA. Applied and Environmental Microbiology, 2013, 79(18):5450-5457.

Paul J H, Sullivan M B, Segall A M, et al. Marine phage genomics. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 2002, 133(4): 463-476.

Filée J, Tétart F, Suttle C A, et al. Marine T4 type bacteriophages, a ubiquitous component of the dark matter of the biosphere. Proceeding National Academy of Science the USA, 2005, 102(35): 12471-12476.

Jia Z, Ishihara R, Nakajima Y, et al. Molecular characterization of T4-type bacteriophages in a rice field. Environmental Microbiology, 2007, 9(4): 1091-1096.

Zhong Y, Chen F, Wilhelm S W, et al. Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene g20. Applied and Environmental Microbiology, 2002, 68(4): 1576-1584.

Short C M, Suttle C A. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Applied and Environmental Microbiology, 2005, 71(1): 480-486.

Sullivan M B, Lindell D, Lee J A, et al. Prevalence and evolution of core photosystem Ⅱ genes in marine cyanobacterial viruses and their hosts. PLoS Biology, 2006, 4(8): 1344-1357

Chénard C, Suttle C A. Phylogenetic diversity of sequences of cyanophage photosynthetic gene psbA in marine and freshwaters. Applied and Environmental Microbiology, 2008, 74(17): 5317-5324.

Breitbart M, Miyake J H, Rohwer F. Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiology Letters, 2004, 236(2): 249-256.

Labonté J M, Reid K E, Suttle C A. Phylogenetic analysis indicates evolutionary diversity and environmental segregation of marine podovirus DNA polymerase gene sequences. Applied and Environmental Microbiology, 2009, 75(11): 3634-3640.

Adriaenssens E M, Cowan D A. Using signature genes as tools to assess environmental viral ecology and diversity. Applied and Environmental Microbiology, 2014, 80(15): 4470-4480.

Srinivasiah S, Bhavsar J, Thapar K, et al. Phages across the biosphere: contrasts of viruses in soil and aquatic environments. Research in Microbiology, 2008, 159(5): 349-357.

Wang G, Yu Z, Liu J, et al. Molecular analysis of the major capsid genes ( g23) of T4-type bacteriophages in an upland black soil in Northeast China. Biology and Fertility of Soils, 2011, 47(3): 273-282.

Liu J, Wang G, Zheng C, et al. Specific assemblages of major capsid genes ( g23) of T4-type bacteriophages isolated from upland black soils in Northeast China, Soil Biology and Biochemistry, 2011, 43(9): 1980-1984.

Books D J, Smith D L, McDonald J E, et al. 454-pyrosequencing: a molecular battiscope for freshwater viral ecology. Genes, 2010, 1(2): 210-226.

Roossinck M J, Saha P, Wiley G B, et al. Ecogenomics: using massively parallel pyrosequencing to understand virus ecology. Molecular Ecology, 2010, 19(Supplement 1): 81-88.

Alhamlan F S, Ederer M M, Brown C J, et al. Metagenomicsbased analysis of viral communities in dairy lagoon wastewater. Journal of Microbiological Methods, 2013, 92(2): 183-188.

Hurwitz B L, Sullivan M B. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One, 2013, 8(2): 269-284.

Fancello L, Trape S, Robert C, et al. Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara. The ISME Journal, 2012, 7(2):359-369.

Angly F E, Felts B, Breitbart M, et al. The marine viromes of four oceanic regions, PLoS Biology, 2006, 4(11): e368.

Thurber R V, Haynes M, Breitbart M, et al. Laboratory procedures to generate viral metagenomes. Nature Protocols, 2009, 4(4): 470-483.

Bibby K, Viau E, Peccia J. Viral metagenome analysis to guide human pathogen monitoring in environmental samples. Letters in Applied Microbiology, 2011, 52(4): 386-392.

John S G, Mendez C B, Deng L, et al. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environmental Microbiology Reports, 2011, 3(2):195-202.

Hall R J, Wang J, Todd A K, et al. Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. Journal of Virological Methods, 2014, 195(1):194-204.

Kim K H, Bae J W. Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Applied and Environmental Microbiology, 2011, 77(21):7663-7668.

Winter C, Garcia J A L, Weinbauer M G, et al. Comparison of deep-water viromes from the Atlantic ocean and the Mediterranean sea. PLoS One, 2014, 9(6): e100600.

Martinez J M, Swan B K, Wilson W H. Marine viruses, a genetic reservoir revealed by targeted viromics. The ISME Journal, 2014, 8(5): 1079-1088.

Aw T G, Howe A, Rose J B. Metagenomic approaches for direct and cell culture evaluation of thevirological quality of wastewater. Journal of Virological Methods, 2014, 210: 15-21.

Lenoir L, Persson T, Bengtsson J, et al. Bottom-up or top-down control in forest soil microcosms? Effects of soil fauna on fungal biomass and C/N mineralization. Biology and Fertility of Soils, 2007, 43(3): 281-294.

Thomas W C, David W G S, Stephen M T, et al. Top-down control of soil fungal community composition by a globally distributed keystone consumer. Ecology, 2013, 94(11): 2518-2528.

Ashelford K E, Fry J C, Bailey M J, et al. Characterization of six bacteriophages of Serratia liquefaciens CP6 isolated from sugar beet phytosphere. Applied and Environmental Microbiology, 1999, 65(5): 1959-1965.

Allen B, Willner D, Oechel W C, et al. Top-down control of microbial activity and biomass in an Arctic soil ecosystem. Environmental Microbiology, 2009, 12(3): 642-648.

Thingstad T F, Lignell R. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquatic Microbial Ecology, 1997, 13(1): 19-27.

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