The ecological controls on the prevalence of candidate division TM7 in polar regions

Abstract

The candidate division TM7 is ubiquitous and yet uncultured phylum of the Bacteria that encompasses a commonly environmental associated clade, TM7-1, and a "host-associated" clade, TM7-3. However, as members of the TM7 phylum have not been cultured, little is known about what differs between these two clades. We hypothesized that these clades would have different environmental niches. To test this, we used a large-scale global soil dataset, encompassing 223 soil samples, their environmental parameters and associated bacterial 16S rRNA gene sequence data. We correlated chemical, physical and biological parameters of each soil with the relative abundance of the two major classes of the phylum to deduce factors that influence the groups' seemingly ubiquitous nature. The two classes of the phylum (TM7-1 and TM7-3) were indeed distinct from each other in their habitat requirements. A key determinant of each class' prevalence appears to be the pH of the soil. The class TM7-1 displays a facultative anaerobic nature with correlations to more acidic soils with total iron, silicon, titanium and copper indicating a potential for siderophore production. However, the TM7-3 class shows a more classical oligotrophic, heterotroph nature with a preference for more alkaline soils, and a probable pathogenic role with correlations to extractable iron, sodium and phosphate. In addition, the TM7-3 was abundant in diesel contaminated soils highlighting a resilient nature along with a possible carbon source. In addition to this both classes had unique co-occurrence relationships with other bacterial phyla. In particular, both groups had opposing correlations to the Gemmatimonadetes phylum, with the TM7-3 class seemingly being outcompeted by this phylum to result in a negative correlation. These ecological controls allow the characteristics of a TM7 phylum preferred niche to be defined and give insight into possible avenues for cultivation of this previously uncultured group.

Keywords: Antarctic; Arctic; bacterial culturing; candidate pylum TM7; siderophores; soil bacteria.

Figure 1

A phylogenetic reconstruction of the candidate division TM7. The reference sequences are obtained from GreenGenes. The tree is a maximum-likelihood phylogeny generated in FastTree 2 with a general time reversible model and 1000 bootstrap replications. TM7-1 and TM7-3 are shown with green and blue branches respectively.

Figure 2

Distance based redundancy analysis of UniFrac dissimilarity scores for samples where bacteria from the candidate division TM7 are present. Overlayed are vectors representing the correlation of edaphic predictor variables and bubbles representing the relative abundance of the different TM7 classes (TM7-1 green, TM7-3 blue). Open diamonds represent Arctic samples and shaded represent Antarctic samples.

Figure 3

A “Holosphere” representation of correlations of the abundance of the two classes of TM7 with various soil properties. The scale on the axis incorporates both positive (+0.6) and negative (−0.6) correlations.

Figure 4

Network co-occurrence analysis of the TM7 classes, TM7-1 and TM7-3 with respect to bacterial phyla present in the polar soil dataset. Only significant relationships are shown. Edges are blue if the relationship between nodes is positive and red if negative.