Bacterial chitinolytic communities respond to chitin and pH alteration in soil

Bacteria are among main degraders of chitin in natural ecosystems like soil, using it as a source of nutrition and energy. However, we understand very little of the putative successions that take place in the degradative process. We performed an experiment in moderately acid soil, in which the level of chitin next to the pH was altered. Examination of chitinase activities revealed fast responses to chitin addition, with peaks of enzymatic activity occurring on day 7. PCR-DGGE based analyses of 16S rRNA and family-18 chiA genes showed structural changes of the phylogenetically- and functionally-based bacterial communities following chitin addition and pH alteration. Pyrosequencing analysis indicated that different chiA gene types were selected by the presence of chitin at different prevailing soil pH. Interestingly, a major role of Gram-negative bacteria versus a minor one of Actinobacteria in immediate chitin degradation (based on 16S rRNA gene abundance and chiA gene types) was indicated. Our data provide new insights in the diversity of bacterial chiA genes in soil. This study enhances our understanding of the ecology of chitin degradation and can be used for mining for novel enzymes.