Phylogenetic diversity and assemblage of major capsid genes (<i>g23</i>) of T4-type bacteriophages in paddy field soils during rice growth season in Northeast China

Liu, Junjie; Wang, Qiang; Liu, Judong; Jin, Jian; Liu, Xiaobing

doi:10.1080/00380768.2012.703610

Cited by 20 publications

(25 citation statements)

References 35 publications

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“…Even in the similar environment of paddy field, the distribution of g23 genes was also distinctly different between Japan and NE China, and several specific groups of T4-type phages were observed in the two countries [36]. Thus, we concluded that the T4-type phage communities in terrestrial environments are determined by both biogeographic and ecological processes [35].…”

Section: Discussionmentioning

confidence: 83%

Phylogenetic Distribution of the Capsid Assembly Protein Gene (g20) of Cyanophages in Paddy Floodwaters in Northeast China

Jing¹,

Liu

2014

PLoS ONE

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Numerous studies have revealed the high diversity of cyanophages in marine and freshwater environments, but little is currently known about the diversity of cyanophages in paddy fields, particularly in Northeast (NE) China. To elucidate the genetic diversity of cyanophages in paddy floodwaters in NE China, viral capsid assembly protein gene (g20) sequences from five floodwater samples were amplified with the primers CPS1 and CPS8. Denaturing gradient gel electrophoresis (DGGE) was applied to distinguish different g20 clones. In total, 54 clones differing in g20 nucleotide sequences were obtained in this study. Phylogenetic analysis showed that the distribution of g20 sequences in this study was different from that in Japanese paddy fields, and all the sequences were grouped into Clusters α, β, γ and ε. Within Clusters α and β, three new small clusters (PFW-VII∼-IX) were identified. UniFrac analysis of g20 clone assemblages demonstrated that the community compositions of cyanophage varied among marine, lake and paddy field environments. In paddy floodwater, community compositions of cyanophage were also different between NE China and Japan.

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Section: Discussionmentioning

confidence: 83%

Phylogenetic Distribution of the Capsid Assembly Protein Gene (g20) of Cyanophages in Paddy Floodwaters in Northeast China

Jing¹,

Liu

2014

PLoS ONE

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“…They revealed that g23 homologues of the T4 are ubiquitous in aquatic environments. Using this primer set, a few studies then investigated the diversity of T4‐like myoviruses in both marine and freshwater ecosystems (Filée et al ., ; López‐Bueno et al ., ; Butina et al ., , ; Huang et al ., ; Jamindar et al ., ; Parvathi, Zhong & Jacquet, ; Bellas & Anesio, ; Zheng et al ., ), but also in soil and sediments (Jia et al ., ; Fujii et al ., ; Wang et al ., ,b, ; Fujihara et al ., ; Liu et al ., , ; Li et al ., ; Bellas & Anesio, ). These studies showed that T4‐like myoviruses are prevalent viral components in nature and exhibit distinct diversity between geographical locations or environments.…”

Section: Introductionmentioning

confidence: 99%

Differing assemblage composition and dynamics in T4‐like myophages of two neighbouring sub‐alpine lakes

Zhong¹,

Jacquet²

2014

Freshwater Biology

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1. Bacteriophages play an important role in plankton population dynamics and biogeochemical cycling, but their community dynamics and diversity are still poorly known, especially in fresh waters. 2. We conducted a 1-year investigation of the T4-like bacteriophages in the surface waters of two Western European peri-alpine lakes (lakes Annecy and Bourget), using fingerprinting and cloningsequencing approaches targeting the major capsid protein g23 gene. 3. Our results suggest that T4-like bacteriophages are diverse (we found several new sequences) and differed substantially between the two lakes. Further, these phages displayed seasonal patterns with marked shifts in community composition. 4. Examining the dynamics of some individual constituents (e.g. DGGE bands), we found that (i) the majority of these myoviruses were rare (mean relative abundance <1%) and only a few were abundant (mean relative abundance >5%); (ii) the dominance of the most abundant DGGE bands changed throughout the year and their dynamics were very different between the two lakes; (iii) only a few bands (e.g. <20%) were detectable throughout the year and their proportion was higher in the oligomesotrophic Lake Bourget. 5. Our results suggest a highly dynamic T4-like myoviral assemblage. T4-like-viruses seem to conform to a standard model of community organisation and a common type of species abundance curve, with mainly rare organisms that occasionally may become abundant (termed a 'seed bank' for virus assemblages).

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“…A large body of literature addresses the microbial ecology of paddy fields, including total bacterial and fungal communities3, methanogenic archaea4, methanotrophic bacteria5, and ammonia-oxidizing bacteria and archaea6. Recently, research on viral ecology or phage ecology in paddy ecosystems has aroused much attention789101112131415. For instance, Nakayama et al 9.…”

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Novel groups and unique distribution of phage phoH genes in paddy waters in northeast China

Wang

Liu

Jin

et al. 2016

Sci Rep

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Although bacteriophages are ubiquitous in various environments, their genetic diversity is primarily investigated in pelagic marine environments. Corresponding studies in terrestrial environments are few. In this study, we conducted the first survey of phage diversity in the paddy ecosystem by targeting a new viral biomarker gene, phoH. A total of 424 phoH sequences were obtained from four paddy waters generated from a pot experiment with different soils collected from open paddy fields in northeast China. The majority of phoH sequences in paddy waters were novel, with the highest identity of ≤70% with known phoH sequences. Four unique groups (Group α, Group β, Group γ and Group δ) and seven new subgroups (Group 2b, Group 3d, Group 3e, Group 6a, Group 6b, Group 6c and Group 6d) were formed exclusively with the clones from the paddy waters, suggesting novel phage phoH groups exist in the paddy ecosystem. Additionally, the distribution proportions of phoH clones in different groups varied among paddy water samples, suggesting the phage community in paddy fields is biogeographically distributed. Furthermore, non-metric multidimensional scaling analysis indicated that phage phoH assemblages in paddy waters were distinct from those in marine waters.

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Phylogenetic diversity and assemblage of major capsid genes (g23) of T4-type bacteriophages in paddy field soils during rice growth season in Northeast China

Cited by 20 publications

References 35 publications

Phylogenetic Distribution of the Capsid Assembly Protein Gene (g20) of Cyanophages in Paddy Floodwaters in Northeast China

Phylogenetic Distribution of the Capsid Assembly Protein Gene (g20) of Cyanophages in Paddy Floodwaters in Northeast China

Differing assemblage composition and dynamics in T4‐like myophages of two neighbouring sub‐alpine lakes

Novel groups and unique distribution of phage phoH genes in paddy waters in northeast China

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