Abstract
Polycyclic aromatic hydrocarbons are distributed ubiquitously in the environment and form metabolites toxic to most organisms. Organic amendment of PAH contaminated soil with compost and farmyard manure has proven to be efficient for PAH bioremediation mediated by native microorganisms, even though information on the identity of PAH degraders in organic-amended soil is still scarce. Here we provide molecular insight into the bacterial communities in soil amended with compost or farmyard manure for which the degradation mass balances of 13C-labeled pyrene have been recently published and assess the relevant bacterial genera capable of degrading pyrene as a model PAH. We performed statistical analyses of bacterial genera abundance data based on total DNA and RNA (for comparison) extracted from the soil samples. The results revealed complex pyrene degrading communities with low abundance of individual degraders instead of a limited number of abundant key players. The bacterial degrader communities of the soil-compost mixture and soil fertilized with farmyard manure differed considerably in composition albeit showing similar degradation kinetics. Additional analyses were carried out on enrichment cultures and enabled the reconstruction of several nearly complete genomes, thus allowing to link microcosm and enrichment experiments. However, pyrene mineralizing bacteria enriched from the compost or unfertilized soil-compost samples did not dominate pyrene degradation in the soils. Based on the present findings, evaluations of PAH degrading microorganisms in complex soil mixtures with high organic matter content should not target abundant key degrading species, since the specific degraders may be highly diverse, of low abundance, and masked by high bacterial background.
Highlights
Polycyclic aromatic hydrocarbons (PAHs) are natural and man-made contaminants that are distributed ubiquitously in the environment (Srogi 2007) and potentially toxic to most organisms (ATSDR 1995)
In the present study we evaluated which communities were responsible for the PAH degradation in compost amended unfertilized soil and soil fertilized with farmyard manure (FYM)
Microbial diversity in soil‐compost mixture and soil fertilized with FYM In the amplicon-based study, 624 to 781 operational taxonomic unit (OTU) were obtained from ribonucleic acid (RNA) samples and 566 to 828 OTUs from desoxyribonucleic acid (DNA) samples of the soil-compost mixture
Summary
Polycyclic aromatic hydrocarbons (PAHs) are natural and man-made contaminants that are distributed ubiquitously in the environment (Srogi 2007) and potentially toxic to most organisms (ATSDR 1995). A number of bacteria, cyanobacteria, algae and fungi are capable of metabolizing PAHs (Bamforth and Singleton 2005; Cerniglia 1993; Kästner 2000; Loick et al 2009; Vila et al 2015) Such natural potential is promising for effective. Long-term organic fertilization of soil with farmyard manure (FYM) (Adam et al 2015) was proven to facilitate PAH degradation This kind of biostimulation was reviewed recently (Kästner and Miltner 2016) and is comprehensively affecting the soil, since compost. Adam et al AMB Expr (2017) 7:7 amendment provides living microorganisms, organic matter and nutrients, and improves aeration as well as water and pH buffer capacities of the soil matrix (Kästner and Mahro 1996) Besides biostimulation, another way of bioremediation is the introduction of PAH degraders into contaminated soil (bioaugmentation) (Bamforth and Singleton 2005; Romantschuk et al 2000). Many attempts to identify the key degrading organisms of PAHs and their catabolism were published, a recent opinion paper underlined that degrading microbial communities in complex environmental habitats (like composts or FYM) have not yet been elucidated (Vila et al 2015)
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