Bacterial Communities Responsible for the Decomposition of Rice Straw Compost in a Japanese Rice Paddy Field Estimated by DGGE Analysis of Amplified 16S rDNA and 16S rRNA Fragments

Myxobacteria harbor an enormous potential for new bioactive secondary metabolites and therefore the isolation of in particular new groups is of great interest. The diversity of myxobacteria present in two ecological habitats, namely sand from Kiritimati Island and German compost, was evaluated by both cultivation‐based and cultivation‐independent methods. Phylogenetic analyses of the strains in comparison with 16S rRNA gene sequences from cultured and uncultured material in GenBank revealed a great potential of undescribed myxobacteria in both sampling sites. Several OTUs (operational taxonomic units) represent unknown taxa and were detected by clone bank analyses, but not by cultivation. Clone bank analyses indicated that the myxobacterial community is predominantly indigenous. The 16S rDNA libraries from the two samples were generated from total community DNA with myxobacterial specific forward and universal reverse primer sets. The clones were partially sequenced. Cultivation was successful for exclusively bacteriolytic, but not for cellulolytic myxobacteria and revealed 42 strains from the genera Corallococcus, Myxococcus, and Polyangium. The genera of Myxococcaceae family were represented by both approaches. But, even in this well studied family, as well as in the suborders Sorangiineae and Nannocystineae, a considerable number of clones were assigned to, if any, uncultivated organisms. Our study shows an overrepresentation of the genera Myxococcus spp. and Corallococcus spp. with standard cultivation methods. However, high deficits are demonstrated in the cultivation success of the myxobacterial diversity detected by exclusively cultivation‐independent approaches. Especially, clades which are exclusively represented by clones are of high interest with regard to the cultivation of new bioactive secondary metabolite producers.

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“…Moreover, numerous studies proved that myxobacteria are naturally present in compost (Singh ; Tanahashi et al. ; Sanford et al. ).…”

Section: Introductionmentioning

confidence: 99%

Comparison of myxobacterial diversity and evaluation of isolation success in two niches: Kiritimati Island and German compost

et al. 2015

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“…Furthermore members of α-, γ-and δ-proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Verrucomicrobia and Spirochaetes were found to be close relatives of the predominant bacteria present in rice straw (Sugano et al, 2005) and/or in rice straw compost (Tanahashi et al, 2005). In the present study sequencing of some of the isolates showed predominance of gramnegative bacteria belonging to α-and γ-proteobacteria and matched with the previous report (Tanahashi et al, 2005). Altogether DGGE profile of rice rhizosphere of Indo-Nepal border showed high diversity, however detailed study is required to resolve the total bacterial population structure and range of diversity prevailing therein.…”

Section: Discussionmentioning

confidence: 98%

“…Predominance of gram-negative bacteria has been reported in the rice straw (Sugano et al, 2005) and rice straw compost (Tanahashi et al, 2005) added into the flooded paddy field soil. Furthermore members of α-, γ-and δ-proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Verrucomicrobia and Spirochaetes were found to be close relatives of the predominant bacteria present in rice straw (Sugano et al, 2005) and/or in rice straw compost (Tanahashi et al, 2005). In the present study sequencing of some of the isolates showed predominance of gramnegative bacteria belonging to α-and γ-proteobacteria and matched with the previous report (Tanahashi et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

Molecular Diversity Assessment of Plant Growth Promoting Rhizobacteria Using Denaturing Gradient Gel Electrophoresis (DGGE) of 16s rRNA Gene

Shrivastava

2017

Int J Appl Sci Biotechnol

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The rhizobacteria were isolated from rhizosphere of rice plant of different fields of 4 districts of Nepal and 5 districts of Bihar and Uttar Pradesh, adjoining states of India with Nepal. The DGGE analysis was performed for diversity analysis. For the construction of dendrogram, 16S rRNA gene was amplified by two different sets of primers. The DGGE ladder consisting of PCR amplified products of nine pure bacterial cultures were obtained. The first DGGE ladder was prepared by 400 bp fragment of 16S rDNA with GC clamp and the second DGGE ladder was prepared with 200 bp fragment of 16S rDNA with GC clamp. The perpendicular DGGE of these amplicons based on their melting behavior clearly demonstrated separation of different isolates. The 16S rDNA fragment amplified with primer set of V2-V3 regions with GC clamp showed separation between 40-60% of denaturant. The DGGE profile based on primer set F352T and 519r for various bacteria present in soil samples of 5 districts of India and 4 districts of Nepal revealed that the number of bands which might be specific for diazotrophic isolates varied from 2 to 11. The dendrogram constructed based on DGGE profile of various samples of 5 districts of India and 4 districts of Nepal showed that all the samples could be clustered in nine groups with 58-96% similarity to each other. Among all these 37 samples, only Var-4 and Var-5 showed 100% similarity, no other samples from any site showed 100% similarity.

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“…DGGE is a useful tool to reveal microbial succession during composting. Many researchers showed the efficiency of this molecular method to detect the shift of microbial changes in composting process [5][6][7]. Therefore, the aim of this study was mainly focused on the observation and identification of enteric microorganisms, biochemical changes and cellulase profiles during the cocomposting of EFB with partially treated POME in pilot scale.…”

Section: Introductionmentioning

confidence: 99%

Characteristics and Microbial Succession in Co-Composting of Oil Palm Empty Fruit Bunch and Partially Treated Palm Oil Mill Effluent

Baharuddin¹,

Nakamura²,

Abd‐Aziz³

et al. 2009

TOBIOTJ

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Microbial communities and cellulolytic enzymes activities were analyzed during the co-composting of empty fruit bunch (EFB) and partially treated palm oil mill effluent (POME) in pilot scale. The physicochemical parameters were also measured during the composting. The diversity of the bacterial community was investigated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The results indicated that the composting process of EFB with partially treated POME was dominated by uncultured bacteria species. The dominant bacterial group changed from the phylum proteobacteria in the thermophilic stage to the phylum chloroflexi in the maturing stage. Scanning electron microscope (SEM) analysis exhibited the significant degradation of EFB structure during the composting process. The maximum cellulase activity for carboxymethylcellulase (CMCase), filter paperase (FPase) and -glucosidase were 13.6, 4.1 and 20.3 U/g of dry substrate, respectively at day 30 of composting. The results of this study significantly contributed to a better understanding of mechanisms involved in co-composting process in pilot scale.

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Bacterial Communities Responsible for the Decomposition of Rice Straw Compost in a Japanese Rice Paddy Field Estimated by DGGE Analysis of Amplified 16S rDNA and 16S rRNA Fragments

Cited by 33 publications

References 18 publications

Comparison of myxobacterial diversity and evaluation of isolation success in two niches: Kiritimati Island and German compost

Comparison of myxobacterial diversity and evaluation of isolation success in two niches: Kiritimati Island and German compost

Molecular Diversity Assessment of Plant Growth Promoting Rhizobacteria Using Denaturing Gradient Gel Electrophoresis (DGGE) of 16s rRNA Gene

Characteristics and Microbial Succession in Co-Composting of Oil Palm Empty Fruit Bunch and Partially Treated Palm Oil Mill Effluent

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