Community structure of bacteria and fungi responsible for rice straw decomposition in a paddy field estimated by PCR-RFLP analysis

Tun, Cho Cho; Ikenaga, Makoto; Asakawa, Susumu; Kimura, Makoto

doi:10.1080/00380768.2002.10408706

Cited by 20 publications

(32 citation statements)

References 42 publications

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“…Thus, the paddy field ecosystem is considered to be a hotspot for studying microbial ecology and biochemical cycles12. 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.…”

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confidence: 99%

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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confidence: 99%

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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“…Gene based methods involving extraction, isolating and identifying DNA or rRNA genetic material from soil aftcr amplification by the polymerase chain reaction (PCR) and subsequent DNA sequencing offer great promise for determining the structure of natural communities (Bornemann et al 1996). A combination of PCR-RFLP (Restriction Fragment Length Polymorphism) analysis has been used to study organisms responsible for straw decomposition (Tun et al 2002) and bacterial communities associated with aquatic organisms (Niswati et al 2002) in paddy fields. Denaturing gradient gel electrophoresis (DGGE), which involves electrophoresis of 16S rDNA fragments, has also been used to study soil microbial communities (Muyzer et al 1993;Kozdroj and van Elsas 200 I;Niemi et al 2001).…”

Section: Methods To Study Community Composition Of Soil Microbial Biomentioning

confidence: 99%

Role of microbial biomass in biogeochemical processes in paddy soil environments

Inubushi

Acquaye

2004

Soil Science and Plant Nutrition

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“…A 0.5 g frozen rice straw sample was lyophilized overnight (lyophylisator FDU‐540, Tokyo Rikakikai, Tokyo, Japan) and cut into 1–2 mm pieces for DNA extraction. Sodium dodecyl sulfate (SDS)‐based DNA extraction, as previously described (Tun et al . 2002), was used with further cell lysis by freezing–thawing using liquid nitrogen.…”

Section: Methodsmentioning

confidence: 99%

“…Based on phenotypic analyses of phospholipid fatty acids (Nakamura et al . 2003) and restriction fragment length polymorphism (RFLP) (Tun et al . 2002), agricultural practice (rice cultivation/winter fallow) and different sites of straw placement in rice fields (soil surface/plow layer) are assumed to be the key factors determining bacterial communities.…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of methane-oxidizing bacteria associated with rice straw decomposition in a rice field

Jia

Sugano

Asari

et al. 2007

Soil Science and Plant Nutrition

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Methane-oxidizing bacteria (MOB) are crucial to the reduction of CH 4 emitted to the atmosphere. However, it is unclear how MOB in rice straw are affected by straw decomposition processes. In a Japanese rice field, a year-round experiment was set up to study the effects of agricultural practice (rice cultivation/winter fallow), straw parts (leaf sheath/blade) and the site of straw placement (plow layer/soil surface) on MOB communities in rice straw using denaturing gradient gel electrophoresis (DGGE) and DNA sequencing analyses of key MOB functional genes (pmoA and amoA). Thirty-eight different DGGE bands were observed over the entire investigation period. Principal component analysis of DGGE pattern suggested that agricultural practice is the key factor regulating the MOB communities. Sequencing of dominant DGGE bands showed that: (1) during the rice cultivation period, methanotrophs (particularly type I methanotrophs) dominated the MOB community, (2) during the winter fallow season both type I and type II methanotrophs were dominant in sheath segments placed both on the soil surface and in the plow layer, whereas ammonia oxidizers seemed to dominate blade segments placed in the plow layer. Alignment of diagnostic amino acid sequences of MOB suggested the presence of novel ammonia oxidizers in rice straw in rice fields.

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Community structure of bacteria and fungi responsible for rice straw decomposition in a paddy field estimated by PCR-RFLP analysis

Cited by 20 publications

References 42 publications

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

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

Role of microbial biomass in biogeochemical processes in paddy soil environments

Molecular characterization of methane-oxidizing bacteria associated with rice straw decomposition in a rice field

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