Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures

Bacterial community structure and diversity in rhizospheres in two types of grassland, distinguished by both plant species and fertilization regimen, were assessed by performing a 16S ribosomal DNA (rDNA) sequence analysis of DNAs extracted from triplicate soil plots. PCR products were cloned, and 4 5 to 48 clones from each of the six libraries were partially sequenced, Phy logenetic analysis of the resultant 275 clone sequences indicated that ther e was considerable variation in abundance in replicate unfertilized, unimpr oved soil samples and fertilized, improved soil samples but that there were no significant differences in the abundance of any phylogenetic group. Sev eral clone sequences were identical in the 16S rDNA region analyzed, and th e clones comprised eight pairs of duplicate clones and two sets of triplica te clones. Many clones were found to be most closely related to environment al clones obtained in other studies, although three clones were found to be identical to culturable species in databases. The clones were clustered in to operational taxonomic units at a level of sequence similarity of >97% in order to quantify diversity. In all, 34 clusters containing two or more se quences were identified, and the largest group contained nine clones. A num ber of diversity, dominance, and evenness indices were calculated, and they all indicated that diversity was high, reflecting the low coverage of rDNA libraries achieved. Differences in diversity between sample types were not observed. Collector's curves, however, indicated that there were differenc es in the underlying community structures; in particular, there was reduced diversity of organisms of the or subdivision of the class Proteobacteria ( or-proteobacteria) in improved soils.