The rational exploration of microbial diversity

Abstract

The exploration of the microbial world has been an exciting series of unanticipated discoveries despite being largely uninformed by rational estimates of the magnitude of task confronting us. However, in the long term, more structured surveys can be achieved by estimating the diversity of microbial communities and the effort required to describe them. The rates of recovery of new microbial taxa in very large samples suggest that many more taxa remain to be discovered in soils and the oceans. We apply a robust statistical method to large gene sequence libraries from these environments to estimate both diversity and the sequencing effort required to obtain a given fraction of that diversity. In the upper ocean, we predict some 1400 phylotypes, and a mere fivefold increase in shotgun reads could yield 90% of the metagenome, that is, all genes from all taxa. However, at deep ocean, hydrothermal vents and diversities in soils can be up to two orders of magnitude larger, and hundreds of times the current number of samples will be required just to obtain 90% of the taxonomic diversity based on 3% difference in 16S rDNA. Obtaining 90% of the metagenome will require tens of thousands of times the current sequencing effort. Although the definitive sequencing of hyperdiverse environments is not yet possible, we can, using taxa-abundance distributions, begin to plan and develop the required methods and strategies. This would initiate a new phase in the exploration of the microbial world.

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

“…At the 3% clustering level, each of the sediment samples contained twice as many observed OTUs (B4100) as did the water column sample (B1850 OTUs). Chao and ACE estimators tend to underestimate actual richness owing to their extrapolation from small sample sizes (Hong et al, 2006;Quince et al, 2008). However, as a minimum estimate, these estimators indicated that there are between 7000-10 000 bacterial OTUs in the sediments when clustered at 3% sequence divergence (Table 1).…”

Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells

“…An estimate of the total diversity for each sample was calculated using a Bayesian modelling approach as described by Quince et al [33], where the 'posterior distribution' of the taxa area curve is estimated from the known distribution of the data gathered in the sequencing. Three distributions are modelled: Log-normal; Inverse Gaussian; and Sichel, and the Deviance Information Criterion (DIC), as described by Spiegelhalter et al [41] is used to compare the fit from each model.…”

“…However, these techniques still only offer a partial view of diversity in a microbial system, and the diversity observed is still typically a function of the number of sequences analysed [32]. These difficulties can be overcome using Bayesian techniques that infer the underlying species abundance curves which in turn can be used to estimate the total diversity of the sample [33,34]. These techniques have the advantage of using a minimum information criteria that allows for the selection of the best fitting model representing the estimated species abundance curves, whilst also providing confidence intervals for these estimates.…”

Plants as extreme environments? Ni-resistant bacteria and Ni-hyperaccumulators of serpentine flora

“…Moreover, serpentine soils could be good models for metagenomics due to the expected low number of species, in comparison with agricultural or forest soils, and may provide many gene functions for industrial biotechnology applications. It has recently been shown (Quince et al 2008) that an estimate for a soil metagenome would require a tremendous effort, compared with ocean metagenomics. For instance, the international consortium "Terragenome" (http://www.terragenome.org), which is aimed at deciphering at large scale the metagenome of a reference soil, is in fact an ongoing effort which groups scientist from 23 countries and will constitute one of the largest genomic investigations of the next years.…”