Analysis of Molecular Diversity of Bacterial Chitinase Genes in the Maize Rhizosphere Using Culture-Independent Methods

Ikeda, Seishi; Ytow, Nozomi; Ezura, Hiroshi; Minamisawa, Kiwamu; Miyashita, Kiyotaka; Fujimura, Tatsuhito

doi:10.1264/jsme2.22.71

Cited by 19 publications

(9 citation statements)

References 30 publications

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“…Therefore, the phylogenetic and functional diversity of bacterial communities in different environments has been examined without using cultivation methods (16). Further, by using culture-independent methods, it has been shown that bacteria with chitinase genes are widely distributed in rhizospheres and arable soils (15,39). In those studies, the chitinase gene-containing bacteria in rhizospheres differed from the culturable chitinolytic bacteria in the present study; however, some chitinolytic bacteria were detected by both culture-dependent and culture-independent methods.…”

Section: Discussionmentioning

confidence: 99%

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Diversity of Culturable Chitinolytic Bacteria from Rhizospheres of Agronomic Plants in Japan

et al. 2011

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A total of 100 isolates of chitinolytic bacteria were obtained from the rhizospheres of various agronomic plants, and the 16S rRNA gene sequences of these isolates were determined. Phylogenetic analyses revealed that 81 isolates belonged to the classes Betaproteobacteria (39 isolates) and Gammaproteobacteria (42 isolates). Of the remaining 19 isolates, 16 belonged to the phylum Firmicutes. Clustering analysis identified 6 and 3 operational taxonomic units (OTUs) in Gammaproteobacteria and Betaproteobacteria, respectively, at the genus level. The majority of chitinolytic bacteria in Gammaproteobacteria belonged to the genera Serratia, Stenotrophomonas, and Lysobacter (14, 15, and 7 isolates, respectively) while those in Betaproteobacteria belonged to the genus Mitsuaria (37 isolates). The 16 isolates placed in Firmicutes belonged to 2 genera, Paenibacillus and Bacillus (8 isolates each). The isolates in the remaining OTUs belonged to the genera Erwinia, Aeromonas, Pseudomonas, Achromobacter, Flavobacterium, and Microbacterium, in less abundance. These results showed a wide distribution of culturable chitinolytic bacteria in the rhizospheres of various agronomic plants. Considering the potential antagonistic activity of chitinolytic enzymes against phytopathogenic fungi, which is exhibited by fungal cell wall degradation, the above-mentioned native chitinolytic bacteria in rhizospheres could potentially be utilized for the biological control of soil-borne phytopathogenic fungi.

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Section: Discussionmentioning

confidence: 99%

“…Most bacteria in nature are known to be unculturable (4). It has been shown that both culturable and unculturable bacteria harboring chitinase genes are also widely distributed in environments (7,15,39). However, it is difficult to utilize unculturable bacteria as biocontrol agents with current microbial technologies.…”

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Diversity of Culturable Chitinolytic Bacteria from Rhizospheres of Agronomic Plants in Japan

et al. 2011

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“…Such DNA preparations have also been used in microbial community analyses in several reports 7,10,14,15,26,42,46) . We have also utilized skim milk in the extraction of soil DNA in previous studies from our laboratory 18,20,21,23) . Recently, however, we have found that the levels of DNA contamination from skim milk are not negligible.…”

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Evaluation of the Effects of Different Additives in Improving the DNA Extraction Yield and Quality from Andosol

et al. 2008

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A series of additives were evaluated for their effects on improving the yield and quality of DNA extracted from recalcitrant soils. Levels of possible DNA contaminants in these supplements were also assessed. Three of the additives (skim milk, casein, and RNA) were shown to be effective in improving the stable extraction of DNA from recalcitrant samples of Andosol. However, whereas skim milk appeared to be the most effective additive for this purpose, our data indicated that this commercially sourced product contained considerable amounts of contaminant DNA (30 to 40 µg/g skim milk). A ribosomal intergenic spacer analysis (RISA) revealed the consistent contamination of different batches of this product with DNA of several species of both eukaryotes (cattle and protists) and prokaryotes. In particular, thermophilic bacteria such as Geobacillus and Anoxybacillus were identified in the sequenced PCR amplicons from skim milk. The results of the RISA clearly also indicated that the impact of contaminated DNA on the analysis of a microbial community could be significant when skim milk is used for extracting DNA from a recalcitrant soil. In contrast, only a trace amount of contaminating DNA was evident in casein and none was detected in the RNA examined in the present study.

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“…Use of culture independent methods led to identifi cation of novel group of bacterial chitinases in alkaline soils (Tsujibo et al 2003 ) , sandy soils (Williamson et al 2000 ) , upland pastures (Metcalfe et al 2002 ) , intertidal hot springs (Hobel et al 2005 ) , maize rhizosphere soils (Ikeda et al 2007 ) , garden and park waste compost (Poulsen et al 2008 ) and vermicompost (Yasir et al 2009 ) . Bacterial chitinases in arable soils are highly diverse and unique groups, based on the comparative analysis of sequences available in public databases.…”

Section: Soil Is a Rich Source Of Chitin And Chitinolytic Diversitymentioning

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Microbial Chitinases for Chitin Waste Management

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Neeraja

Sarma

et al. 2011

Microorganisms in Environmental Management

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Chitin is a major structural component of fungi and exoskeleton of insects, crustaceans and other arthropods. It is an insoluble, unbranched, linear chain of b -1, 4-linked N-acetyl D-glucosamine residues and is the second most abundant renewable carbohydrate polymer in nature after cellulose and fi rst in marine environment. The annual production of chitin in aquatic biosphere is around 10 11 ton. Chitinases produced by chitinolytic bacteria have the potential to convert this waste to pharmaceutically valuable end products such as N-acetyl glucosamine and chitooligosaccharides, and are viable alternatives of chemical processes currently used for the purpose. Chitinases from different bacteria, fungi, plants and animals are glycosyl hydrolases which degrade the insoluble chitin in to soluble chitooligosaccharides and glucosamine. Chitooligosaccharides possess antitumor, antifungal, antibacterial and immuno-enhancing effects . Antagonistic bacteria and chitinases have been exploited as potential biocontrol agents against fungal pathogens in plants. The growing number of application areas for chitin and chitin-derived products demand an equally diverse array of chitin-modifying enzymes for specifi c needs. The chapter will focus on the applications of chitinolytic enzymes from microbial sources and their possible applications, with special focus on conversion of large quantities of the chitinous substrates into useful biological products.

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Analysis of Molecular Diversity of Bacterial Chitinase Genes in the Maize Rhizosphere Using Culture-Independent Methods

Cited by 19 publications

References 30 publications

Diversity of Culturable Chitinolytic Bacteria from Rhizospheres of Agronomic Plants in Japan

Diversity of Culturable Chitinolytic Bacteria from Rhizospheres of Agronomic Plants in Japan

Evaluation of the Effects of Different Additives in Improving the DNA Extraction Yield and Quality from Andosol

Microbial Chitinases for Chitin Waste Management

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