Linking initial soil bacterial diversity and polycyclic aromatic hydrocarbons (PAHs) degradation potential

Abstract

The aim of this study was to understand the role of indigenous soil microbial communities on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) and to determine whether PAHs degradation potential in soils may be evaluated by analysis of bacterial diversity and potential metabolisms using a metagenomics approach. Five different soils were artificially contaminated with seven selected PAHs and the most abundant bacterial taxa were assessed by sequencing the 16S rRNA gene, and linking them to PAH biodegradation efficiencies. A PICRUSt approach was then led to estimate the degradation potentials by metagenomics inference. Although the role of bacteria in PAHs degradation is not directly established here, the presence of a large number of bacteria belonging to the Betaproteobacteria class correlated to a higher degradation of LMW PAHs. A link with specific bacterial taxa was more difficult to establish concerning HMW PAHs, which seemed to require more complex mechanisms as shown by PICRUSt.

Systems biology approach to elucidation of contaminant biodegradation in complex samples – integration of high-resolution analytical and molecular tools

“…OTUs in the COV samples were available in the reference SilvaMod 123 database (for which reference pathways are available in the Tax4Fun package) than in CH samples, which suggested that the OTUs that inhabited the more contaminated sites are more ubiquitous in nature and thus well characterised with their pathways available. The gene content for each OTU in each sample was inferred from the closest sequenced genome using the Tax4Fun package and we investigated particular pathways from the KEGG database linked to contaminant degradation 4 and related metabolic pathways. Out of the 12 tested pathways, seven presented signicantly different average relative abundance between COV and CH.…”

“…Specically, metataxogenomic and metagenomic approaches have demonstrated that contamination induces a reduction in species richness and enriches the population with species that are adapted to hydrocarbon degradation. 3 Consequently, initial microbial ecology could also be linked to the potential for PAH degradation, 4 demonstrating that microbial ecology carries meaningful information on the potential for bioremediation in soil. However, without high resolution information on the contamination prole, notably the presence of other contaminants, this information might not be sufficient for the design of an efficient site-specic bioremediation.…”

“…Here, through the comparison of soils from two different FMGs, we present an example of statistical integration of chemical and molecular data in contaminated soils. Chemical and DNA extracts were analysed and processed through robust methods and pipelines [1][2][3][4] previously developed in our laboratories and statistical analysis was rst carried out independently. Multivariate analysis enabled forensic characterisation of the site by exploring intra-and inter-site variations in distributions of PAHs and other compounds.…”

Impact of biochar on the metabolic networks of a PHE-degrading microbial community and its influencing mechanism on soil biogeochemical cycles

“…Biochar is the product of limited oxygen pyrolysis of biomass and is used in agriculture as a soil improver, compost additive and livestock feed supplement [1][2][3][4].Some studies have investigated whether biochar not only provides space for soil microorganisms with pore structures but also provides nutrients to soil microorganisms to enhance their growth, and these nutrients are adsorbed on the biochar [5,6]. In this way, biochar will positively affect soil microbes, thereby accelerating the biodegradation of organic contaminants in soil.…”

“…As a kind of soil amendment, the use of biochar with functional microorganisms to treat contaminated soil will not only affect organic contaminant degradation and catabolic pathways but also affect the global biogeochemical cycles of nutrient elements [1,16]. Studies have found that biochar produced via pyrolysis of biomass wastes can enhance and supply long-term soil organic carbon storage [17,18].…”