Changes in agricultural management drive the diversity of Burkholderia species isolated from soil on PCAT medium

In order to assess the diversity of culturable Burkholderia populations in rhizosphere and bulk soil and to evaluate how different agricultural management regimes and land use history affect this diversity, four treatments were evaluated: permanent grassland; grassland converted into maize monoculture; arable land and arable land converted into grassland. Burkholderia isolates obtained on PCAT medium were grouped in 47 clusters using 16S ribosomal RNA gene based PCR-DGGE combined with BOX genomic fingerprinting (DGGE-BOX). The distribution of the isolates in the DGGE-BOX clusters was used to calculate the Shannon diversity index per treatment. Interestingly, we observed that the Burkholderia diversity was affected by changes in the agricultural management, since the highest diversity was observed in permanent grassland and in continuous arable land. In addition, the diversity tended to be higher in the rhizosphere than in the corresponding bulk soil. The use of species abundance models indicated that rhizosphere communities had more even distributions than communities collected from the bulk soil. Identification of isolates revealed that only 2% of these belonged to the B. cepacia complex and that the majority was assigned to either (1) new Burkholderia species or (2) Burkholderia species that had originally been isolated from soil. Isolates classified as B. hospita, B. caledonica and Burkholderia sp. ‘LMG 22934’ and ‘LMG 22936’ were found mainly in the arable land, while isolates belonging to Burkholderia sp. ‘LMG 22929’ and B. phytofirmans were associated with the grassland area. Another potentially new Burkholderia species, ‘LMG 22932’, was found in both areas, in close association with the maize rhizosphere.