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.

Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.

The use of sulfate reducing bacteria (SRBs) in laboratory studies is a common approach for investigating microbially influenced corrosion (MIC). The characteristic formation of black iron sulfide precipitates during SRB growth, however, preclude the use of traditional spectrophotometric approaches for capturing growth data instead necessitating labour-intensive or technically specialized approaches. As such, an understanding of SRB growth responses to experimental conditions is often missing from MIC studies. Bernardez and de Andrade Lima (2015) have outlined a spectrophotometric approach for estimating SRB cell mass via the addition of HCl. This method has potential for the study SRB growth however its applicability is currently limited by the use of large aliquot volumes (45 mL), which restrict the number of timepoints that can sampled from one culture, and the extensive time devoted to cell preparation prior to OD readings. •We demonstrate an improved method for capturing SRB growth data via spectrophotometry following acidification. We incorporate lower sample volumes and adapt the method described in Bernardez and de Andrade Lima (2015) to a high throughput microtiter plate approach that increases the efficiency of this method and its applicability to growth rate studies.•Our results allay theoretical concerns that acidification may distort growth rate analysis by impacting cells differently depending on their metabolic state.•We further demonstrate that this method (acid-amended OD measurements) is more accurate and far more cost efficient than traditional methods (dilution spread-plate counting) and popular molecular methods (quantitative PCR) currently in use in SRB growth research.

Plant growth-promoting yeasts are often over looked as a mechanism to improve phytoremediation of heavy metals. In this study, Cryptococcus sp. NSE1, a Cd-tolerant yeast with plant growth capabilities, was isolated from the rhizosphere of the heavy metal hyperaccumulator Sedum plumbizincicola. The yeast exhibited strong tolerance to a range of heavy metals including Cd, Cu, and Zn on plate assays. The adsorption rate Cd, Cu, Zn by NSE1 was 26.1, 13.2, and 25.2 %, respectively. Irregular spines were formed on the surface of NSE1 when grown in MSM medium supplemented with 200 mg L⁻¹ Cd. NSE1 was capable of utilizing 1-aminocyclopropane-1-carboxylate (ACC) as a sole nitrogen source and was capable of solubilization of inorganic phosphate at rates of 195.2 mg L⁻¹. Field experiments demonstrated that NSE1 increased phytoremediation by increasing the biomass of Cd hyperaccumulator S. plumbizincicola (46 %, p < 0.05) during phytoremediation. Overall, Cd accumulation by S. plumbizincicola was increased from 19.6 to 31.1 mg m⁻² though no difference in the concentration of Cd in the shoot biomass was observed between NSE1 and control. A Cd accumulation ratio of 38.0 % for NSE1 and 17.2 % for control was observed. The HCl-extractable Cd and CaCl₂-extractable Cd concentration in the soil of the NSE1 treatment were reduced by 39.2 and 29.5 %, respectively. Community-level physiology profiling, assessed using Biolog Eco plates, indicated functional changes to the rhizosphere community inoculated with NSE1 by average well color development (AWCD) and measurement of richness (diversity). Values of Shannon-Weiner index, Simpson index, and McIntosh index showed a slight but no significant increases. These results indicate that inoculation of NSE1 could increase the shoot biomass of S. plumbizincicola, enhance the Cd accumulation in S. plumbizincicola, and decrease the available heavy metal content in soils significantly without overall significant changes to the microbial community.