Chitin-mediated changes in bacterial communities of the soil, rhizosphere and within roots of cotton in relation to nematode control

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Changes in microbial communities associated with nematode control were studied by comparing population numbers of fungi and bacteria in the soil and in internal root tissues (endorhiza) in non-amended and chitin-amended soils. Addition of chitin to soil at 1% (w/w) eliminated plant-parasitic nematodes in a first planting of cotton cv. `Rowden' and significantly reduced Meloidogyne incognita infestation in a second planting, confirming long-term nematode suppressiveness induced by this organic amendment. The chitin amendment was associated with an increase in fungal and bacterial populations, especially those with chitinolytic activity. The bacterial communities of soil, rhizosphere and endorhiza were assessed by examining the taxonomic diversity of recoverable bacteria based on identification with fatty acid analysis of sample sizes of 35 soil and rhizosphere bacteria and 25 endophytic bacteria. All major bacterial species which formed at least 2% of the total population in non-amended soils and rhizospheres also occurred with chitin amendment. In contrast, chitin-amended soils and rhizospheres yielded several species which were not found without chitin amendment, including Aureobacterium testaceum, Corynebacterium aquaticum and Rathayibacter tritici. Burkholderia cepacia was recovered from both amended and non-amended soils and rhizospheres, but it was most abundant with chitin amendment at the end of the first cotton planting. Soil was probably the major source for bacterial endophytes of cotton roots, since nearly all endophytic bacteria were also found in the soil or rhizosphere. However, two dominant genera in the soil and rhizosphere, Bacillus and Arthrobacter, were not detected as endophytes. Chitin amendment exhibited a further specific influence on the endophytic bacterial community; Phyllobacterium rubiacearum was not a common endophyte following chitin amendment, even though chitin amendment stimulated its populations in non-planted soil. Burkholderia cepacia, found in similar numbers in the soil of both treatments, was the dominant endophyte in plants grown in chitin-amended soil but rarely colonized cotton roots grown in non-amended soil. These results indicate that application of an organic amendment can lead to modifications of the bacterial communities of the soil, rhizosphere and endorhiza.