Species diversity of uncultured and cultured populations of soil and marine ammonia oxidizing bacteria

Although molecular techniques are considered to provide a more comprehensiv e view of species diversity of natural microbial populations, few studies h ave compared diversity assessed by molecular and cultivation-based approach es using the same samples. To achieve this, the diversity of natural popula tions of ammonia oxidising bacteria in arable soil and marine sediments was determined by analysis of 16S rDNA sequences from enrichment cultures, pre pared using standard methods for this group, and from 16S rDNA cloned from DNA extracted directly from the same environmental samples. Soil and marine samples yielded 31 and 18 enrichment cultures, respectively, which were co mpared with 50 and 40 environmental clones. There was no evidence for selec tion for particular ammonia oxidizer clusters by different procedures emplo yed for enrichment from soil samples, although no culture was obtained in m edium at acid PH. In soil enrichment cultures, Nitrosospira cluster 3 seque nces were most abundant, whereas clones were distributed more evenly betwee n Nitrosospira clusters 2, 3, and 4. In marine samples, the majority of enr ichment cultures contained Nitrosomonas, whereas Nitrosospira sequences wer e most abundant among environmental clones. Soil enrichments contained a hi gher proportion of identical sequences than clones, suggesting laboratory s election for particular strains, but the converse was found in marine sampl es. In addition, 16% of soil enrichment culture sequences were identical to those in environmental clones, but only 1 of 40 marine enrichments was fou nd among clones, indicating poorer culturability of marine strains represen ted in the clone library, under the conditions employed. The study demonstr ates significant differences in species composition assessed by molecular a nd culture-based approaches but indicates also that, employing only a limit ed range of cultivation conditions, 7% of the observed sequence diversity i n clones of ammonia oxidizers from these environments could be obtained in laboratory enrichment culture. Further studies and experimental approaches are required to determine which approach provides better representation of the natural community.