Identification of active bacteria involved in decomposition of complex maize and soybean residues in a tropical Vertisol using 15N-DNA stable isotope probing

As limited information is available about the relationship between microbial processes and community structure in tropical soils, we used 15N-DNA stable isotope probing (15N-DNA-SIP) to identify bacteria actively involved in decomposition of plant residues of different biochemical quality. 15N-labeled (90 atom%) and unlabeled (control) maize (C-to-N ratio: 32; cellulose content: 24.9%) and soybean (15; 15.5%) leaf residues were incubated in a tropical Vertisol for 15 days. Soil DNA was isolated, subjected to 15N-DNA-SIP and buoyant density-resolved DNA fractions were analyzed by 16S rRNA gene-based denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of selected DGGE bands. Residue addition induced new bands and changed relative intensity of already existing bands in 15N-enriched SIP fractions. Phylogenetic analysis of selected, cloned DGGE bands from 'heaviest' 15N-enriched fractions (57.8 atom% (maize), 87.1 atom% (soybean)) revealed that soils treated with maize residues were dominated by Pseudonocardia sp., while Arthrobacter sp. and Streptomyces sp. were found in the soybean residue treated soils. Sequences related to Bacillus sp. and Saccharopolyspora sp. were found in both organic residue treatments. Our study gave clear evidence that 15N-DNA-SIP combined with 16S rRNA gene-based community fingerprinting of density-resolved fractions and an unlabeled control was suited for detecting active bacteria involved in decomposition of complex maize and soybean residues. In conclusion, we could show that residue quality, inducing contrasting N assimilation by decomposing bacteria, was a substantial determinant of certain decomposing community members assayed in this study.