Statistical Approaches for Estimating Actinobacterial Diversity in Marine Sediments

• DOI: 10.1128/aem.69.10.6189-6200.2003
• Publication Date: 2003-10-07T00:30:32Z
• Authors: James E. M. Stach; Luis A. Maldonado; Douglas G. Masson; Alan C. Ward; Michael Goodfellow; Alan T. Bull
• Keywords: Operational taxonomic unit; Dominance (genetics); Phylogenetic diversity; Diversity index

ABSTRACT Bacterial diversity in a deep-sea sediment was investigated by constructing actinobacterium-specific 16S ribosomal DNA (rDNA) clone libraries from sections taken 5 to 12, 15 18, and 43 46 cm below the sea floor at depth of 3,814 m. Clones were placed into operational taxonomic unit (OTU) groups with ≥99% rDNA sequence similarity; cutoff value for an OTU derived comparing rRNA homology DNA-DNA reassociation values members class Actinobacteria. Diversity statistics used determine how level dominance, species richness, genetic varied depth. The reciprocal Simpson's index (1/ D ) indicated that pattern shifted toward dominance uniformity increasing Nonparametric estimation richness 5- 12-, 15- 18-, 43- 46-cm revealed trend decreasing number depth, 1,406, 308, 212 OTUs, respectively. Application LIBSHUFF program 12-cm library composed OTUs significantly ( P = 0.001) different those 18- libraries. F ST phylogenetic grouping taxa (P tests) both significant < 0.00001 0.001, respectively), indicating decreased each community harbored unique lineages. It also shown even nonconservative definitions result severe underestimation richness; clades detected one group suggest do not correspond real ecological sensu Palys (T. Palys, L. K. Nakamura, F. M. Cohan, Int. J. Syst. Bacteriol. 47:1145-1156, 1997). Mechanisms responsible their implications are discussed.