Estimating Species Diversity

The true extent of microbial diversity is unknown; however, culture-independent microbial community analysis suggests that it could be immense. The number of micro-bial species present in an environment can be estimated using statistical analysis of census data which for micro-bial communities are derived from nucleic acid sequence-based surveys. The estimates are based upon assumptions about underlying species abundance distributions and extrapolate from data on the most abundant species. Alternatively, estimates of species abundance are derived from rarefaction analysis or nonparametric estimators (such as Chaol) that estimate total species richness based on the number of singletons and doubletons in a sample. The estimates produced by these methods for microbial communities are less accurate than for communities of macroorganisms because of the low sampling that is typical of microbial community surveys. Even large samples of microbial communities only comprise data from c. 102 to 103 individuals in a population of 106-109. Estimates of species richness based on small subunit rRNA sequences are generally conservative, since in bacteria, for example, there are many organisms which have almost identical 16S rRNA sequences but which are very distinct at the genomic level. Typically bacteria that share less than 97% 16S rRNA sequence identity are considered as different species (sometimes referred to as operational taxonomic units or OTUs to avoid interminable discussion about species definitions). However, it has been shown that for bacteria that share less than 98.6% 16S rRNA sequence identity, there is a 99% probability that they are different species and even when they share 99.8% 16S rRNA sequence identity there is still a 50% chance that they represent different species. Despite these sampling and taxonomic issues, the statistical estimates provide a framework for comparative analysis of samples analyzed and sampled in similar ways and provide some initial estimates of local and global species diversity within the prokaryotes. For instance, the number of pro-karyote species present in soil defined from 16S rRNA sequence inventories and other methods has been estimated to be as high as 103-105 per gram or 106 in a ton.

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