Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil.

François Thomas,Aurélie Cébron

doi:10.3389/fmicb.2016.00092

Abstract

Over the last decades, understanding of the effects of plants on soil microbiomes has greatly advanced. However, knowledge on the assembly of rhizospheric communities in aged-contaminated industrial soils is still limited, especially with regard to transcriptionally active microbiomes and their link to the quality or quantity of carbon sources. We compared the short-term (2–10 days) dynamics of bacterial communities and potential PAH-degrading bacteria in bare or ryegrass-planted aged-contaminated soil spiked with phenanthrene, put in relation with dissolved organic carbon (DOC) sources and polycyclic aromatic hydrocarbon (PAH) pollution. Both resident and active bacterial communities (analyzed from DNA and RNA, respectively) showed higher species richness and smaller dispersion between replicates in planted soils. Root development strongly favored the activity of Pseudomonadales within the first 2 days, and of members of Actinobacteria, Caulobacterales, Rhizobiales, and Xanthomonadales within 6–10 days. Plants slowed down the dissipation of phenanthrene, while root exudation provided a cocktail of labile substrates that might preferentially fuel microbial growth. Although the abundance of PAH-degrading genes increased in planted soil, their transcription level stayed similar to bare soil. In addition, network analysis revealed that plants induced an early shift in the identity of potential phenanthrene degraders, which might influence PAH dissipation on the long-term.

Highlights

During the last decade, progress in “meta-omics” approaches has greatly improved the understanding of bacterial communities in the rhizosphere of various plant species, revealing the complexity of plant-microbes interactions and their importance for soil ecosystems (ReinholdHurek et al, 2015)
Plants can significantly promote polycyclic aromatic hydrocarbon (PAH) degradation compared to bare soils (Binet et al, 2000; Liu et al, 2013; Storey et al, 2014) and this effect can partially be mimicked by amending soil with root exudates (Miya and Firestone, 2001; Joner et al, 2002)
The presence of plants was associated with higher concentrations of total dissolved organic carbon (DOC), as well as fumarate, mannitol, trehalose, sucrose, glucose, xylose, mannose, and fructose

Summary

Introduction

Progress in “meta-omics” approaches has greatly improved the understanding of bacterial communities in the rhizosphere of various plant species, revealing the complexity of plant-microbes interactions and their importance for soil ecosystems (ReinholdHurek et al, 2015). Rhizoremediation of organic pollutants is based on the beneficial effects of plants on the degradation by soil microorganisms (Kuiper et al, 2004) This positive rhizosphere effect has been linked to increases in microbial abundance and activity due to root exudates providing carbon input, as well as the secretion of surfactant molecules or aromatic compounds homologous to PAHs (reviewed in Martin et al, 2014). Grasses offer some advantages for evaluating the rhizosphere effect on organic pollutant degradation and bacterial communities They possess a fibrous root system allowing intensive penetration of the soil together with large surface area (Aprill and Sims, 1990; Dzantor et al, 2000) and exude high quantities of soluble organic substrates (Lynch and Whipps, 1990). Ryegrass (Lolium perenne) was found as the most effective for PAH rhizoremediation in aged-polluted soil among 18 plant species representing eight families (Olson et al, 2007)

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Conclusion