Rhizobacterial community of Jatropha curcas associated with pyrene biodegradation by consortium of PAH-degrading bacteria

Abstract

A bacterial consortium consisting five efficient polyaromatic hydrocarbon (PAH) degraders (Pseudomonas aeruginosa PDB1, Pseudomonas fragi DBC, Klebsiella pneumoniae AWD5, Alcaligenes faecalis BDB4 and Acinetobacter sp. PDB4) was bioaugmented in pyrene contaminated soil through Jatropha curcas rhizosphere, to understand its effect on changes in bacterial community structure during the process of rhizosphere mediated biodegradation of pyrene. This consortium was highly effective in rhizosphere mediated remediation, as 97.2% of pyrene was degraded within 60 days. The better degradation of pyrene in soil was correlated with the changes in bacterial community structure in rhizosphere of J. curcas, for different trials. The Proteobacteria remained the most abundant group among different treatments, but its abundance was 30.7% higher in the rhizosphere of plants growing in pyrene contaminated soil augmented with consortium. Sphingomonas, Sphingobium, Achromobacter, Ralstonia, Pseudoxanthomonas, Devosia, Cupriavidus, and the members of Sphingomonadeceae, Rhizobiaceae, Xanthomonadeceae, were dominant within Proteobacteria, where pyrene degradation was maximum. There was strong correlation between abundances of group of bacteria which were being affected with pyrene contamination or consortium treatment, and this effect was spread over for a group of bacteria, whose abundances were interdependent. Consequently, the treatment of PAH degrading consortium restored and recruited group of bacteria, which were otherwise depleted in presence of pyrene. Therefore, the application of consortium not only facilitated the degradation of pyrene, but also resulted in modulation of the bacterial community in the process of rhizosphere mediated biodegradation of pyrene in soil.

Introduction

Polycyclic aromatic hydrocarbons (PAH) are highly toxic, carcinogenic and persistent organic pollutants, which disturb ecosystems function and human health, and therefore require for efficient remediation strategies (Gan et al., 2009). The success of biodegradation strategy of hydrocarbons is credited to physiological reactions available in bacterial populations (Dell'Anno et al., 2012). Despite the high microbial diversity in bulk soil, the PAH biodegradation is relatively low due to the lesser number of bacteria that participate in effective bioremediation process (Gaskin et al., 2008).

Rhizoremediation or rhizosphere mediated bioremediation has benefit over other augmentation strategies as this strategy takes the benefit of 10–1000 times higher abundance of microbes available in soil (Martin et al., 2012; Ukaegbu-Obi and Mbakwem-Aniebo, 2014; Eskandary et al., 2017). These microbes in rhizosphere derive nutrients and signals from the growing roots of host plants to induce dioxygenases and stimulate co-metabolic processes which involve the oxidation/mineralization of petroleum hydrocarbons. Further, they release secondary metabolites i.e., low molecular weight organic acids (such as citric acids and oxalic acids) which significantly promote desorption of PAH from the soil and increase the bioavailability of PAH to microorganisms (Singer et al., 2006; Bais et al., 2008). Hence, the role of plants and rhizospheric bacteria in rhizoremediation process is equally important (Gaskin et al., 2008). In fact, not much is known about the identity, activity, and short-term temporal dynamics of rhizospheric assemblages in contaminated habitats (Dell'Anno et al., 2012) in response to augmentation of contaminant-degrading organisms. However, there are few studies on active rhizospheric microbiome changes during short term exposure of phenanthrene spiked aged oil contaminated soil (Thomas and Cébron, 2016). Recently, the complete mineralization of phenanthrene was achieved by active phenanthrene degraders in a consortium through the combined activity of taxonomically diverse co-occurring bacteria (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively performing successive metabolic steps, which was studied using DNA-SIP (Single Isotope Probing) (Thomas et al., 2019). Instead, most of the studies of “meta-omics” approaches focused on unpolluted soil providing a fundamental knowledge of how plants shape the soil microbiome in the absence of perturbation (Reinhold-Hurek et al., 2015).

Shifting of native microbial community in response to inoculation with beneficial microbes is recently been recognized as an important phenomenon with respect to microbial functions (Thounaojam et al., 2018). For example, it was reported that bioaugmentation with a fungal-bacterial consortium resulted in appreciable changes in the microbial diversity of polluted soils, shifting native microbial communities in favor of degrading specific populations (Zafra et al., 2016). Similarly, a combination of the microorganisms was applied with methyl-β-cyclodextrin in PAH contaminated soil which changed the physiological functions of microbial communities and also stimulated the remediation efficiency of PAH (Tian et al., 2017). There had been few reports where the bacterial diversity associated with the rhizosphere of host plant growing in contaminated soil has been elucidated for the understanding of an essential bacterial group that participates in the process of rhizoremediation. However, it is interesting to study the consequence of bioaugmentation of bacteria inoculated through rhizosphere in contaminated soil, on microbial community structure and bioremediation process (Yergeau et al., 2014; Kotoky et al., 2018).

Therefore, in the present study, a consortium of bacteria, with superior PAH degradation ability and also having efficient plant growth promoting attributes were inoculated in pyrene contaminated soil using Jatropha curcas rhizosphere, to evaluate the efficiency of plant-rhizobacterial interaction in rhizoremediation of pyrene from contaminated soil. Sterilized and non-sterilized soils were experimented in parallel, with J. curcas rhizosphere. Further, the effect on the shape of the normal bacterial flora of the host plant in rhizosphere due to augmentation of pyrene degrading bacterial consortium has been elucidated.