Analysis of a change in bacterial community in different environments with addition of chitin or chitosan

Sato, Kazuaki; Azama, Yasuhito; Nogawa, Masahiro; Taguchi, Goro; Shimosaka, Makoto

doi:10.1016/j.jbiosc.2009.10.021

Cited by 29 publications

(17 citation statements)

References 36 publications

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“…These might even be developed into biological control agents against such fungi, e.g., V. dahliae, or nematodes (11,(40)(41)(42)(43)62). However, in spite of several previous reports on bacterial chitinases in soils (11,14,44,45), the responses of the plethora of soil microorganisms to chitin addition are still largely not understood. This is particularly true for agricultural fields (26,46), in which we do not quite understand how the effect of chitin may be related to crop rotation, chemical characteristics of the soil, and time.…”

Section: Discussionmentioning

confidence: 99%

Chitin Amendment Increases Soil Suppressiveness toward Plant Pathogens and Modulates the Actinobacterial and Oxalobacteraceal Communities in an Experimental Agricultural Field

Cretoiu

Korthals

Visser

et al. 2013

Appl Environ Microbiol

148

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A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the suppressiveness of soil toward Verticillium dahliae, as well as plant-pathogenic nematodes, was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular toward Verticillium dahliae, 9 months after the (second) treatment, extending to 2 years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities, both of total soil bacteria and fungi, were found. In addition, the abundances and structures of soil actinobacteria and the Oxalobacteraceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteria also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteraceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment.

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Section: Discussionmentioning

confidence: 99%

Chitin Amendment Increases Soil Suppressiveness toward Plant Pathogens and Modulates the Actinobacterial and Oxalobacteraceal Communities in an Experimental Agricultural Field

Cretoiu

Korthals

Visser

et al. 2013

Appl Environ Microbiol

148

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“…7) Previously, we isolated a strong chitinolytic bacterium from moat water of Ueda Castle. 8,9) It was identified as a novel species belonging to a novel genus, and was registered as the type strain under the name Chitiniphilus shinanonensis SAY3…”

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confidence: 99%

Heterologous Expression and Functional Characterization of a Novel Chitinase from the Chitinolytic BacteriumChitiniphilus shinanonensis

Huang¹,

Shizume²,

Nogawa³

et al. 2012

Bioscience, Biotechnology, and Biochemistry

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Chitiniphilus shinanonensis strain SAY3T is a chitinolytic bacterium isolated from moat water of Ueda Castle in Nagano Prefecture, Japan. Fifteen genes encoding putative chitinolytic enzymes (chiA-chiO) have been isolated from this bacterium. Five of these constitute a single operon (chiCDEFG). The open reading frames of chiC, chiD, chiE, and chiG show sequence similarity to family 18 chitinases, while chiF encodes a polypeptide with two chitin-binding domains but no catalytic domain. Each of the five genes was successfully expressed in Escherichia coli, and the resulting recombinant proteins were characterized. Four of the recombinant proteins (ChiC, ChiD, ChiE, and ChiG) exhibited endo-type chitinase activity toward chitinous substrates, while ChiF showed no chitinolytic activity. In contrast to most endo-type chitinases, which mainly produce a dimer of N-acetyl-D-glucosamine (GlcNAc) as final product, ChiG completely split the GlcNAc dimer into GlcNAc monomers, indicating that it is a novel chitinase.

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“…In comparison with artificial enrichment of normal farm soil (Sato et al 2010), chances for identifying the new enzymes and microbes producing them increases in naturallyenriched soils. Soils collected from these dump yards become reservoir for many bacteria that utilize chitin over a period of time.…”

Section: Resultsmentioning

confidence: 99%

Isolation and purification of microbial community DNA from soil naturally enriched for chitin

et al. 2012

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AbstractWe made an attempt to isolate and purify metagenomic DNA from chitin enriched soil. In this communication we report a modified direct lysis method for soil DNA extraction including initial pre-lysis washing of sample, followed by a rapid polyvinylpyrrolidone-agarose-based purification and electroelution of DNA using Gene-capsule™ assembly. Rapidity was achieved using low molarity conducting media (sodium-borate buffer) for electrophoresis by reducing run time for both the gel electrophoresis and electroelution. Extracted DNA was sufficiently pure and of high quality, evidenced by amplification of 16S rDNA and chitinase genes by PCR. Metagenomic nature of the DNA was confirmed by running V3 (16S rDNA) region amplicons using denaturing gradient gel electrophoresis. This method requires 30 min for purification, and less than 2 h for complete execution of protocol and becomes the first report on the isolation of metagenomic DNA from soil naturally enriched for chitin.

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Analysis of a change in bacterial community in different environments with addition of chitin or chitosan

Abstract: 1The temporal changes of a bacterial community in soil with chitin or chitosan

Cited by 29 publications

References 36 publications

Chitin Amendment Increases Soil Suppressiveness toward Plant Pathogens and Modulates the Actinobacterial and Oxalobacteraceal Communities in an Experimental Agricultural Field

Chitin Amendment Increases Soil Suppressiveness toward Plant Pathogens and Modulates the Actinobacterial and Oxalobacteraceal Communities in an Experimental Agricultural Field

Heterologous Expression and Functional Characterization of a Novel Chitinase from the Chitinolytic BacteriumChitiniphilus shinanonensis

Isolation and purification of microbial community DNA from soil naturally enriched for chitin

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