Abstract
Understanding how biotic and abiotic factors govern the assembly of rhizosphere-microbial communities is a long-standing goal in microbial ecology. In phytoremediation research, where plants are used to remediate heavy metal-contaminated soils, a deeper understanding of rhizosphere-microbial ecology is needed to fully exploit the potential of microbial-assisted phytoremediation. This study investigated whether Grime's competitor/stress-tolerator/ruderal (CSR) theory could be used to describe the impact of cadmium (Cd) and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the assembly of soil-bacterial communities using Illumina 16S rRNA profiling and the predictive metagenomic-profiling program, PICRUSt. Using predictions based on CSR theory, we hypothesized that Cd and the presence of a rhizosphere would affect community assembly. We predicted that the additional resource availability in the rhizosphere would enrich for competitive life strategists, while the presence of Cd would select for stress-tolerators. Traits identified as competitive followed CSR predictions, discriminating between rhizosphere and bulk-soil communities whilst stress-tolerance traits increased with Cd dose, but only in bulk-soil communities. These findings suggest that a bacterium's competitive attributes are critical to its ability to occupy and proliferate in a Cd-contaminated rhizosphere. Ruderal traits, which relate to community re-colonization potential, were synergistically decreased by the presence of the rhizosphere and Cd dose. Taken together this microcosm study suggests that the CSR theory is broadly applicable to microbial communities. Further work toward developing a simplified and robust strategy for microbial CSR classification will provide an ecologically meaningful framework to interpret community-level changes across a range of biomes.
Highlights
Understanding how rhizosphere-microbial communities assemble and are maintained temporally is a major goal in microbial ecology that is relevant to a wide range of disciplines including: plant-pathogen interactions (Pieterse et al, 2014), agriculture (Welbaum et al, 2004), community ecology (Fitzsimons and Miller, 2010), microbiome research (Costello et al, 2012), and phytoremediation (Thijs et al, 2016)
Controlled microcosm studies were used to disentangle the impact of Cd and the presence of a Cd-accumulating plant rhizosphere on bacterial community assembly via the examination of operational taxonomic units (OTUs)
The observed and Chao1-estimated Operational taxonomic units (OTUs) richness and Shannon-Wiener diversity indices of bacterial communities associated with the Carpobrotus rossii were significantly lower when compared to bulk-soil communities (Figure 1)
Summary
Understanding how rhizosphere-microbial communities assemble and are maintained temporally is a major goal in microbial ecology that is relevant to a wide range of disciplines including: plant-pathogen interactions (Pieterse et al, 2014), agriculture (Welbaum et al, 2004), community ecology (Fitzsimons and Miller, 2010), microbiome research (Costello et al, 2012), and phytoremediation (Thijs et al, 2016). In the field of phytoremediation, where plants are utilized to remove contaminants from soils, manipulation of the rhizosphere community via the addition of beneficial microorganisms has been used to improve remediation rates (De Souza et al, 1999; Ma et al, 2009; Liu et al, 2015; Wood et al, 2016a). To fully exploit this potential, a greater understanding of factors driving community assembly in the rhizosphere during phytoremediation are needed. The assembly of rhizosphere communities is generally accepted to be under the influence of biotic factors predominant amongst which is the plant itself (Grayston et al, 1998; Smalla et al, 2001; Aira et al, 2010). Rhizosphere communities associated with phytoremediation technologies are shaped by contaminants present in the soil. In the presence of soil contaminants such as hydrocarbons or heavy metals, plant rhizospheres have been shown to contain an enrichment of hydrocarbon-degrading (Siciliano et al, 2001; Yergeau et al, 2014) or heavy-metal-resistant (Mengoni et al, 2001) microorganisms, respectively
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