Linking microbial community structure to β-glucosidic function in soil aggregates

Abstract

To link microbial community 16S structure to a measured function in a natural soil, we have scaled both DNA and β-glucosidase assays down to a volume of soil that may approach a unique microbial community. β-Glucosidase activity was assayed in 450 individual aggregates, which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differences in the richness or diversity of the microbial communities associated with high β-glucosidase activities compared with the communities associated with low β-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be observed that functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to the presence or absence of particular taxonomic groups.

Figure 1

β-Glucosidase activities and ATP content in 450 macroaggregates.

Figure 2

The rank abundance of the 706 OTUs identified, plotted as a histogram (a) and the traditional Whittaker plot (b).

Figure 3

(a) Alpha diversity as a function of diversity order (given by the parameter q). Higher diversity orders increasingly emphasize abundant OTUs. Dashed lines show mean alpha diversity within each activity-level group. Solid lines encapsulate ±2 s.e., which show overlap between the two groups across all diversity orders; alpha diversity is therefore not significantly different between the two activity-level groups, irrespective of diversity order. (b) Beta diversity as a function of diversity order. The difference in beta diversity between groups is nonsignificant even at diversity order 2.

Figure 4

Heatmap of the relative abundance of the 15 most abundant OTUs. Significantly differentially represented OTUs are indicated with an arrow.

Figure 5

Non-metric multidimensional scaling (NMDS) ordination of the community structures calculated with Bray–Curtis distances. Symbols representing the high-activity (green) and low-activity (red) samples are scaled to reflect the abundance of the significantly differentially represented OTU1 (q<1e—06), identified as a member of the family Chitinophagaceae. The differential abundance of OTU3 (q=0.014) is not shown; this OTU was somewhat more abundant in the low activity samples.