Eukaryotic communities associated with the decomposition of rice straw compost in a Japanese rice paddy field estimated by DGGE analysis

Hatamoto, Masashi; Tanahashi, Takanori; Murase, Jun; Matsuya, Kazuo; Hayashi, Motoki; Kimura, Makoto; Asakawa, Susumu

doi:10.1007/s00374-007-0239-1

Cited by 17 publications

(10 citation statements)

References 8 publications

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“…previous study demonstrated that Chytridiomycota is active in the water-saturated (but oxic) rice field soil with rice straw applied (Murase et al 2014). Chytridiomycota-related sequences were also retrieved from the rice straw compost under decomposition in a rice field (Hatamoto et al 2008). These findings confirm the function of Chytridiomycota in the decomposition of dead organic materials in soil.…”

Section: Phylogeny Of Microeukaryotes In the Rice Rhizospheresupporting

confidence: 77%

Active community structure of microeukaryotes in a rice (Oryza sativaL.) rhizosphere revealed by RNA-based PCR-DGGE

Asiloglu

Murase

2016

Soil Science and Plant Nutrition

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The rhizosphere is one of the hot spots in soil ecosystems for a variety of microorganisms. In this study, we explored the seasonal change of the microeukaryotic community of a rice rhizosphere focusing on the active members through an RNA-based molecular approach. Rice plants (Oryza sativa L.) were grown in a pot where the rhizosphere was compartmented from bulk soil with a nylon gauze. The Eh in the rhizosphere compartment indicated that the rhizosphere was under oxic conditions in the initial stage of plant growth and then suddenly became anoxic or suboxic. Denaturing gradient gel electrophoresis targeting 18S rRNA-transcribed cDNA demonstrated that the active community of microeukaryotes in the rice rhizosphere was different from that in the bulk soil. The rhizosphere community showed a temporal shift in accordance with the shift of the redox conditions having three stages: the oxic before maximum tillering stage, anoxic/suboxic stage before maximum tillering stage, and anoxic/ suboxic stage in the panicle initiation stage and thereafter. Active members specific to the rhizosphere at either the oxic or anoxic/suboxic stage were found: Heterolobosea amoeba, ciliates, and Chytridiomycota fungi for the oxic stage and oomycetes, ciliates and Ascomycota fungi in the anoxic/ suboxic stage. The present results demonstrate that a specific group of microeukaryotes inhabit the rice rhizosphere even under anoxic/suboxic conditions and play various ecological roles as plant parasites, microbial grazers and organic decomposers.

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Section: Phylogeny Of Microeukaryotes In the Rice Rhizospheresupporting

confidence: 77%

Active community structure of microeukaryotes in a rice (Oryza sativaL.) rhizosphere revealed by RNA-based PCR-DGGE

Asiloglu

Murase

2016

Soil Science and Plant Nutrition

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“…Our results are consistent with previous reports that have found that Aspergillus, Trichoderma, Penicillium, Mucor, and Fusarium fungi are commonly present in compost (4,6,36). In addition, Purnomo et al (40) isolated M. circinelloides and G. geotrichum from cattle manure compost, while Hatamoto et al (23) reported that Coniochaeta is a key eukaryote associated with the decomposition of rice straw compost in Japanese rice paddy fields. Sánchez (42) also reported the isolation of filamentous fungi species of Penicillium, Trichoderma, Aspergillus, and Fusarium from lignocellulosic residues.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Cellulolytic and Hemicellulolytic Abilities of Fungi Isolated from Coffee Residue and Sawdust Composts

et al. 2011

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This study focused on the evaluation of cellulolytic and hemicellulolytic fungi isolated from sawdust compost (SDC) and coffee residue compost (CRC). To identify fungal isolates, the ITS region of fungal rRNA was amplified and sequenced. To evaluate enzyme production, isolates were inoculated onto wheat bran agar plates, and enzymes were extracted and tested for cellulase, xylanase, β-glucanase, mannanase, and protease activities using different azurine cross-linked (AZCL) substrates. In total, 18 isolates from SDC and 29 isolates from CRC were identified and evaluated. Four genera (Aspergillus, Galactomyces, Mucor, and Penicillium) and five genera (Aspergillus, Coniochaeta, Fusarium, Penicillium, and Trichoderma/Hypocrea) were dominant in SDC and CRC, respectively. Penicillium sp., Trichoderma sp., and Aspergillus sp. displayed high cellulolytic and hemicellulolytic activities, while Mucor isolates exhibited the highest β-glucanase and mannanase activities. The enzyme analyses revealed that Penicillium, Aspergillus, and Mucor isolates significantly contributed to the degradation of SDC, whereas Penicillium, Aspergillus, and Trichoderma isolates had a dominant role in the degradation of CRC. Notably, isolates SDCF5 (P. crustosum), CRCF6 (P. verruculosum), and CRCF2 and CRCF16 (T. harzianum/H. lixii) displayed high activity regarding cellulose and hemicellulose degradation, which indicates that these species could be beneficial for the improvement of biodegradation processes involving lignocellulosic materials.

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“…It could be converted into a valuable end product in a short period of time through microbial composting process. Rice straw compost is most commonly applied to paddy fields in Japan to improve soil fertility and increase yield (Hatamoto et al 2008). To make the rice straw composting process economically viable, lignocellulolytic microbes based biodegradation may be an effective alternative to in situ burning (Kumar et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Isolation and screening of potential actinobacteria for rapid composting of rice straw

et al. 2010

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Rice straw is produced as a by-product from rice cultivation, which is composed largely of lignocellulosic materials amenable to general biodegradation. Lignocellulolytic actinobacteria can be used as a potential agent for rapid composting of bulky rice straw. Twenty-five actinobacteria isolates were isolated from various in situ and in vitro rice straw compost sources. Isolates A2, A4, A7, A9 and A24 were selected through enzymatic degradation of starch, cellulose and lignin followed by the screening for their adaptability on rice straw powder amended media. The best adapted isolate (A7) was identified as Micromonospora carbonacea. It was able to degrade cellulose, hemicelluloses and carbon significantly (P ≤ 0.05) over the control. C/N ratio was reduced to 18.1 from an initial value of 29.3 in 6 weeks of composting thus having the potential to be used in large scale composting of rice straw.

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Eukaryotic communities associated with the decomposition of rice straw compost in a Japanese rice paddy field estimated by DGGE analysis

Cited by 17 publications

References 8 publications

Active community structure of microeukaryotes in a rice (Oryza sativaL.) rhizosphere revealed by RNA-based PCR-DGGE

Active community structure of microeukaryotes in a rice (Oryza sativaL.) rhizosphere revealed by RNA-based PCR-DGGE

Evaluation of Cellulolytic and Hemicellulolytic Abilities of Fungi Isolated from Coffee Residue and Sawdust Composts

Isolation and screening of potential actinobacteria for rapid composting of rice straw

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