Environmental distribution of prokaryotic taxa

Abstract

Background: The increasing availability of gene sequences of prokaryotic species in samples extracted from all kind of locations allows addressing the study of the influence of environmental patterns in prokaryotic biodiversity. We present a comprehensive study to address the potential existence of environmental preferences of prokaryotic taxa and the commonness of the specialist and generalist strategies. We also assessed the most significant environmental factors shaping the environmental distribution of taxa.

Results: We used 16S rDNA sequences from 3,502 sampling experiments in natural and artificial sources. These sequences were taxonomically assigned, and the corresponding samples were also classified into a hierarchical classification of environments. We used several statistical methods to analyze the environmental distribution of taxa. Our results indicate that environmental specificity is not very common at the higher taxonomic levels (phylum to family), but emerges at lower taxonomic levels (genus and species). The most selective environmental characteristics are those of animal tissues and thermal locations. Salinity is another very important factor for constraining prokaryotic diversity. On the other hand, soil and freshwater habitats are the less restrictive environments, harboring the largest number of prokaryotic taxa. All information on taxa, samples and environments is provided at the envDB online database, http://metagenomics.uv.es/envDB.

Conclusions: This is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments. Our data indicate that we are still far from characterizing prokaryotic diversity in any environment, except, perhaps, for human tissues such as the oral cavity and the vagina.

Figure 1

Quantification of specific and cosmopolitan taxa. Left side: percentage of specific taxa for the three levels of environmental classification. A particular taxa is defined as specific when a given percentage of its observations belong to a single environment. That percentage is shown in the abscissa axis. Right side: percentage of cosmopolitan taxa for the three levels of environmental classification, in relation to the number of environments in which the taxa is present.

Figure 2

Distribution of individual taxonomic families in the different environment types. The phylogenetic tree shown in the inner circle was created by taking one representative sequence from each family, and was arbitrarily rooted in the branch separating bacteria from archaea. Families are coloured by its corresponding phyla, and only families with 10 or more observations have been considered. The bars in the outer circle indicate the number of times that each family has been observed in a sample from a particular environment. The bars marked with stars have been reduced to one third of their original size, for clarity purposes. This figure was done using iTOL server[42].

Figure 3

Relations between environments, and between environments and taxonomic families. Heat-map of the posterior medians of the affinities and the resulting dendrogram from the cluster analysis of the environment types, using log-affinities and euclidean distance. Purple and orange cells represent low and high affinity values, respectively.

Figure 4

Bi-plot of environment types and taxonomic families. The axes correspond to the first two components of a detrended correspondence analysis (DCA). Percentages in brackets refer to the proportion of inertia explained by the axes.

Figure 5

Collector's curves. Collector's curves for the abundance of sequences and OTUs in all the environments.