Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny

Abstract

Phytoremediation is an attractive alternative to excavating and chemically treating contaminated soils. Certain plants can directly bioremediate by sequestering and/or transforming pollutants, but plants may also enhance bioremediation by promoting contaminant-degrading microorganisms in soils. In this study, we used high-throughput sequencing of bacterial 16S rRNA genes and the fungal internal transcribed spacer (ITS) region to compare the community composition of 66 soil samples from the rhizosphere of planted willows (Salix spp.) and six unplanted control samples at the site of a former petrochemical plant. The Bray-Curtis distance between bacterial communities across willow cultivars was significantly correlated with the distance between fungal communities in uncontaminated and moderately contaminated soils but not in highly contaminated (HC) soils (>2000 mg kg(-1) hydrocarbons). The mean dissimilarity between fungal, but not bacterial, communities from the rhizosphere of different cultivars increased substantially in the HC blocks. This divergence was partly related to high fungal sensitivity to hydrocarbon contaminants, as demonstrated by reduced Shannon diversity, but also to a stronger influence of willows on fungal communities. Abundance of the fungal class Pezizomycetes in HC soils was directly related to willow phylogeny, with Pezizomycetes dominating the rhizosphere of a monophyletic cluster of cultivars, while remaining in low relative abundance in other soils. This has implications for plant selection in phytoremediation, as fungal associations may affect the health of introduced plants and the success of co-inoculated microbial strains. An integrated understanding of the relationships between fungi, bacteria and plants will enable the design of treatments that specifically promote effective bioremediating communities.

High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis

“…2013; Bell et al. 2014). Multihost studies in temperate mixed forests also revealed positive correlations between host taxonomic distance and the distinctiveness of the EM communities they support (Ishida et al.…”

“…2013; Bell et al. 2014). Moreover, the few significant differences that we detected in both richness and community structure separated Picea mariana from the two Pinus species, reinforcing the idea that taxonomic relatedness is a key factor governing host effect and explaining variations in EM community composition.…”

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

“…Willow trees have several key advantages for phytoremediation when compared with other plants: they are genetically very diverse (400 species and over 200 hybrids, Newsholme, 2003), some species can be harvested frequently by coppicing, they are pioneer plants that have invasive growth strategies and very effective nutrient uptake systems, they grow fast and have high evapotranspiration rates and high productivity (Pulford and Watson, 2003). Although several studies have assessed the microbial communities associated with willows growing in contaminated soils (Leigh et al, 2006;de Carcer et al, 2007a,b;Kuffner et al, 2008;Hrynkiewicz et al, 2009;Zimmer et al, 2009;Weyens et al, 2013;Bell et al, 2014), the details of willow interactions with microbes are still not well understood.…”

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants

“…In terms of a direct response, there is little evidence suggesting similar organic contaminates are often absorbed and mobilized to above-ground tissue (Alkio et al, 2005;Watts et al, 2006;El Amrani et al, 2015;Shiri et al, 2015) or metabolized to any degree by willow directly. There is, however, a growing body of evidence pertaining to metaorganismal interactions whereby a multitude of organisms collectively exploit these unique environmental conditions (Weyens et al, 2009;Kang et al, 2012;Bell et al, 2014a;Yergeau et al, 2014;Gonzalez et al, 2015).…”

“…Recent evidence, such as the seemingly ubiquitous presence of mites in human epidermis (Thoemmes et al, 2014), opens a door toward a relatively unexplored, more inclusive strategy indicating the value of an organism-blind approach to interpretation of RNAseq data. This is particularly important for phytoremediation tree systems where rhizospheric bacteria and fungi, as hypothesized from expression profiles, seem essential to understanding organic contamination tolerance (Bell et al, 2014a;Yergeau et al, 2014). Above ground, less research has been conducted with a metaorganismal approach in trees, although endophytes have been demonstrated interacting within the system (Doty et al, 2005;Kang et al, 2012;Khan et al, 2014;Delhomme et al, 2015).…”