Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil

• Published in: FEMS microbiology ecology 2010-02, Vol.71 (2), p.197-207
• Main Authors: Hjort, Karin, Bergström, Maria, Adesina, Modupe F, Jansson, Janet K, Smalla, Kornelia, Sjöling, Sara
• Format: Article
• Language: English
• Subjects: 54; 58; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Chitinase; Chitinases - genetics; Deoxyribonucleic acid; DISEASES; DNA; DNA, Bacterial - genetics; Ecology; Environmental Studies; Fragments; Fungicides; Gene polymorphism; GENES; Genetics; Genetik; Genome, Bacterial; Genomic Library; Libraries; Markvetenskap; metagenomic library; Metagenomics; Microbiology; Microorganisms; Mikrobiologi; Miljövetenskapliga studier; PATHOGENS; Phylogeny; Polymorphism; Polymorphism, Restriction Fragment Length; Restriction fragment length polymorphism; RNA, Ribosomal, 16S - genetics; rRNA 16S; Sequence Analysis, DNA; Soil - analysis; Soil Microbiology; Soil Science; SOILS; STREPTOMYCES; Streptomycetes; suppressive soil; suppressive soils; TARGETS; terminal restriction fragment length polymorphism (T-RFLP)
• ISSN: 0168-6496; 1574-6941; 1574-6941
• DOI: 10.1111/j.1574-6941.2009.00801.x

Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study, we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF¹⁰³ of the isolate Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.