Transplanting Soil Microbiomes Leads to Lasting Effects on Willow Growth, but not on the Rhizosphere Microbiome

Abstract

Plants interact closely with microbes, which are partly responsible for plant growth, health, and adaptation to stressful environments. Engineering the plant-associated microbiome could improve plant survival and performance in stressful environments such as contaminated soils. Here, willow cuttings were planted into highly petroleum-contaminated soils that had been gamma-irradiated and subjected to one of four treatments: inoculation with rhizosphere soil from a willow that grew well (LA) or sub-optimally (SM) in highly contaminated soils or with bulk soil in which the planted willow had died (DE) or no inoculation (CO). Samples were taken from the starting inoculum, at the beginning of the experiment (T0) and after 100 days of growth (TF). Short hypervariable regions of archaeal/bacterial 16S rRNA genes and the fungal ITS region were amplified from soil DNA extracts and sequenced on the Illumina MiSeq. Willow growth was monitored throughout the experiment, and plant biomass was measured at TF. CO willows were significantly smaller throughout the experiment, while DE willows were the largest at TF. Microbiomes of different treatments were divergent at T0, but for most samples, had converged on highly similar communities by TF. Willow biomass was more strongly linked to overall microbial community structure at T0 than to microbial community structure at TF, and the relative abundance of many genera at T0 was significantly correlated to final willow root and shoot biomass. Although microbial communities had mostly converged at TF, lasting differences in willow growth were observed, probably linked to differences in T0 microbial communities.

Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?

“…Uniporter: a transporter binding one substrate molecule at a time, facilitating diffusion across a membrane. [114,115] and higher heavy metal uptake [116]. Consequently, efforts have aimed at increasing the phytoremediation potential of heavy metal accumulators by combining them with specific microbial communities.…”

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

“…Ascertaining the specific interaction between plants and observed microbial phylotypes could generate critical information for the selection of optimized microbiomes with desirable host performance traits such as survival, growth, and fitness (Mueller and Sachs, 2015; Yergeau et al, 2015). Analysis of the microbiomes of two willow cultivars ( Salix purpurea cv.…”

Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys

“…This information has led to significantly increased understanding of the effect of natural or human-induced disturbance on soil and plant-associated microbial communities (Hart et al, 2015; Yergeau et al, 2015; Beckers et al, 2016). While there is no doubt that short-read sequencing technologies have opened up a new dimension of microbial biodiversity research, the technologies also add complexity to the experimental study design.…”

“…Soil bacterial communities have therefore been the subject of bioremediation studies aiming to optimize bacterial community function for accelerating biodegradation and soil remediation (Yang et al, 2012; Yergeau et al, 2012a, 2015). Primer pair 341f/785r used by Klindworth et al (2013) has been used on a variety of sample types, from marine samples to human samples (Hiergeist et al, 2016), but until now it has not been thoroughly tested on soil.…”

“…Primer pair 341f/785r used by Klindworth et al (2013) has been used on a variety of sample types, from marine samples to human samples (Hiergeist et al, 2016), but until now it has not been thoroughly tested on soil. Other primer pairs targeting the V3–V4 region, namely 341f/533r (Yergeau et al, 2014) and 343f/806r (Yergeau et al, 2015) have shown to amplify diverse bacterial communities in the rhizosphere of Salix purpurea , suggesting the utility of V3–V4 primer pairs for plant microbiome research.…”