Resuscitation of the rare biosphere contributes to pulses of ecosystem activity

Abstract

Dormancy is a life history trait that may have important implications for linking microbial communities to the functioning of natural and managed ecosystems. Rapid changes in environmental cues may resuscitate dormant bacteria and create pulses of ecosystem activity. In this study, we used heavy-water (H(18) 2O) stable isotope probing (SIP) to identify fast-growing bacteria that were associated with pulses of trace gasses (CO2, CH4, and N2O) from different ecosystems [agricultural site, grassland, deciduous forest, and coniferous forest (CF)] following a soil-rewetting event. Irrespective of ecosystem type, a large fraction (69-74%) of the bacteria that responded to rewetting were below detection limits in the dry soils. Based on the recovery of sequences, in just a few days, hundreds of rare taxa increased in abundance and in some cases became dominant members of the rewetted communities, especially bacteria belonging to the Sphingomonadaceae, Comamonadaceae, and Oxalobacteraceae. Resuscitation led to dynamic shifts in the rank abundance of taxa that caused previously rare bacteria to comprise nearly 60% of the sequences that were recovered in rewetted communities. This rapid turnover of the bacterial community corresponded with a 5-20-fold increase in the net production of CO2 and up to a 150% reduction in the net production of CH4 from rewetted soils. Results from our study demonstrate that the rare biosphere may account for a large and dynamic fraction of a community that is important for the maintenance of bacterial biodiversity. Moreover, our findings suggest that the resuscitation of rare taxa from seed banks contribute to ecosystem functioning.

Keywords: CO2 pulses; desiccation; dominance; dormancy; rarity; seed bank; soil rewetting; stable isotope probing (SIP).

Figure 1

Pulses of ecosystem activity in an agricultural ecosystem stimulated by experimental rain events (upward pointing arrows). The inset panel is a plot of the observed (Obs) and predicted (Pred) CO₂ generated from a multiple regression model. We estimated soil CO₂ concentrations (2 cm depth) and soil moisture (0–5 cm) using real-time sensor data averaged on a 12 h time-step from 15 June 2007 (day 166) through 3 July 2007 (day 184).

Figure 2

CO₂ production from laboratory microcosms with dry and rewetted soils obtained from four ecosystem types. Values are means ± SEM (n = 3) with letters indicating differences (P < 0.05) based on a Two-Way ANOVA and Tukey's HSD test.

Figure 3

Stable isotope probing (SIP) revealed rapid shifts in bacterial community composition in soils that were rewetted with heavy water (H¹⁸₂O). The multivariate ordination was generated using Partial Least Squares Discriminant Analysis (PLS-DA) on a sample × OTU matrix that took into account ecosystem type and pairs of dry-rewetted samples (indicated by dashed lines).

Figure 4

Resuscitation of rare bacteria contributed to shifts in bacterial composition following the rewetting of soils with heavy water (H¹⁸₂O). High rates of turnover (estimated using Bray-Curtis dissimilarity) were due in large part to the recovery of rare OTUs that were below detection limits in the sampling of dry soils. The numbers of rare OTUs (means ± SEM) are presented in dashed solid circles, while the shared OTUs occurring in both dry and rewetted soils are present in the intersection of the dashed and solid circles. OTU numbers are based on the observed number of OTUs present after rarefaction by sequence number. Different letters indicate significant differences (P < 0.05) based on a One-Way ANOVA and Tukey's HSD test.

Figure 5

Resuscitation resulted in dynamic shifts in the rank abundance of rare bacteria in rewetted soils. OTUs are color-coded based on their ranked recovery in the dry soils (inset panel): red taxa had the highest recovery, yellow the lowest, and black were below detection in the initial (dry) sample. OTUs with ranks falling below the dashed horizontal line were below detection limits.

Figure 6

Rare bacteria demonstrated ecosystem-specific responses to rewetting. Heat map showing the distribution of rare OTUs for four phyla and three Proteobacteria subclasses that contributed ≥ 1% to the total recovery of rewetted communities. Values are based on means with hierarchal clustering of ecosystem (bottom) and phylum (left).