Actinobacterial community structure in soils receiving long-term organic and inorganic amendments

Abstract

The impact of long-term organic and inorganic amendments on the actinobacterial community in soils was studied. Denaturing gradient gel electrophoresis patterns based on the V3 region of 16S rRNA suggested that there was no significant difference between the communities occurring in the different amendments. However, analysis of the clone libraries of the actinobacterial communities by the use of multiple statistical approaches showed that these communities were significantly different from each other. Results showed that long-term organic and inorganic soil amendments did not significantly alter the overall phylogenetic diversity of the actinobacterial communities but did significantly change the community structure.

FIG. 1.

DGGE patterns of soil samples treated with CK, NPK, M, NPK, and SN based on the sequence of the V3 region in the 16S rRNA gene. See the text for descriptions of treatments.

FIG. 2.

LIBSHUFF comparison of the homologous and heterogenous coverages between the CK and NPK libraries (A), the CK and MNPK libraries (B), and the NPK and MNPK libraries (C). X represents the CK library in panels A and B and the NPK library in panel C. Y represents the NPK library in panel A and the MNPK library in panels B and C. The fact that the P values produced by both the XY and YX comparisons are smaller than the critical P value of 0.025 indicates that the two libraries being compared are different.

FIG. 3.

A Venn diagram comparing the OTU_0.01 (OTU assigned at a DNA distance of 0.01) memberships found in the CK (n = 68), NPK (n = 91), and MNPK (n = 89) libraries. Below each library's name are the Chao1 richness estimate and the 95% confidence interval estimated by DOTUR for the respective community. The richness of the overlapping regions was estimated based on the pairwise S_{A,B Chao} richness estimates shared by the three communities and by pooling two communities and estimating the fraction shared with a third community. The Chao1 richness estimate for the three libraries pooled together was 190 (confidence interval, 148 to 274), and the sum of the richness estimates for the individual sectors in the diagram was 182.