Bacterial PAH degradation in marine and terrestrial habitats

Dedicated to the memory of Professor Peter J. Chapman.
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Highlights

  • PAH degradation knowledge requires a progressive cell  ecosystem omics approach.

  • Community structure/function studies need curated and culture-fed databases.

  • Bacterial PAH degradation networks are organized in funnel shaped modules.

  • Cometabolism channels individual PAHs through cooperative catabolic networks.

  • Molecular methods start to unravel the diversity of PAH degraders and catabolic genes.

Cycling of pollutants is essential to preserve functional marine and terrestrial ecosystems. Progress in optimizing these natural biological processes relies on the identification of the underlying microbial actors and deciphering their interactions at molecular, cellular, community, and ecosystem level. Novel advances on PAH biodegradation are built on a progressive approach that span from pure cultures to environmental communities, illustrating the complex metabolic networks within a single cell, and their further implications in higher complexity systems. Recent analytical chemistry and molecular tools allow a deeper insight into the active microbial processes actually occurring in situ, identifying active functions, metabolic pathways and key players. Understanding these processes will provide new tools to assess biodegradation occurrence and, as a final outcome, predict the success of bioremediation thus reducing its uncertainties, the main drawback of this environmental biotechnology.

Introduction

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants reaching particularly high concentrations in industrial soils and oil-spill impacted marine environments. Concern about PAHs is due to their high recalcitrance and (geno) toxicity, posing a serious risk for both humans and ecosystems. Bioremediation, which exploits the natural microbially mediated degradation of organic compounds, is the most cost-effective and sustainable cleaning technology [1], causing relatively minor impact on key natural soil and marine functions. However, its application is still constrained by factors related to the unpredictable endpoint PAH concentrations, the lack of adequate monitoring tools to guarantee the occurrence of active biodegradation processes, and the not entirely accurate risk assessment policies. To overcome these limitations, it is essential to unravel the complex metabolic networks determining the fate of PAHs in situ, thus allowing to move forward from the traditional ‘black box’ perspective to an actual environmental biotechnology.

Novel advances in analytical chemistry and molecular biology have gathered increasing knowledge on the different facets of microbial metabolism of hydrocarbons and their biotechnological application. This is a broad field of research involving a number of different environments, organisms, chemical compounds and, consequently, scientific disciplines. Here, we will focus on the recent developments (2010–2014) on aerobic biodegradation of PAHs by bacteria, in both marine and terrestrial environments, stressing on work performed during the last two years. Aspects that have also experienced great advance but escape the aim of this work have been reviewed elsewhere, including anaerobic biodegradation [2, 3], PAH bioavailability [4], bacterial-fungal interactions [5], or biodegradation of aromatic hydrocarbons in general [6].

Section snippets

Unraveling in situ PAH metabolic networks: from pure cultures to omics

Environmental PAH biodegradation processes involve a great variety of co-occurring contaminants and are mediated by a diversity of microbes harboring different and often interconnected metabolic pathways. As depicted in Figure 1, to decipher these complex interactions, a progressive polyphasic approach is required. As a result, a flow of metabolic, genomic, transcriptomic and proteomic information is generated including:

  • 1.

    Characterization of single cell PAH metabolic pathways in pure cultures.

  • 2.

PAH catabolic networks in pure cultures

The classical approach to study PAH metabolism has been the reconstruction of pathways after identification of metabolites produced by bacteria able to use them as sole carbon source [7, 8]. Most recent metabolic studies focus on sphingomonads and actinobacteria, especially in their ability to attack high molecular weight (HMW) compounds.

Despite their preference for low molecular weight (LMW) PAHs (i.e. phenanthrene) [9], sphingomonads show great versatility, being able to oxidize a wide range

Microbial communities reveal unknown PAH-degrading bacteria

Culture-based studies underestimate the actual diversity of natural communities and neglect potential interactions between their components. Thus, culture-independent methods have been increasingly applied to identify key microbial groups associated to PAH degradation in polluted soils and marine environments. Most widely used approaches include community structure analysis based on 16S rRNA gene-PCR amplification followed by fingerprinting (i.e. DGGE), clone libraries or tag-encoded

New tools for functional screens

The next step in the progressive unraveling of environmental PAH biodegradation networks is the identification and quantification of key functional genes. On the basis of genomic information from isolates, a large set of primers and probes targeting ring-hydroxylating and ring-cleavage dioxygenases have been designed [55, 56]. The most common approaches include gene amplification using degenerate or non-degenerate primers, and nucleic acid hybridization on functional microarrays.

RHD are

(Eco)systems biology for understanding the in situ PAH metabolic networks

Current molecular and analytical chemistry developments permit a systems biology approach to understand the microbial metabolic networks for PAH biodegradation in situ, and provide valuable tools to verify and assess biodegradation in natural attenuation and bioremediation scenarios. Studies applying such holistic analysis to unravel marine and terrestrial PAH degradation processes are still outnumbered by those focused on aliphatics and monoaromatics [6, 56, 70], but they include some

Conclusions

The understanding of the environmental networks for biodegradation of PAHs requires the integration of scientific data obtained from classical approaches, such as the characterization of pure cultures and low diversity consortia, with up-to-date high throughput screens of polluted environments. Future progress in reaching this objective requires continuity and strengthening of several lines of research initiated in recent years:

  • 1.

    Application of molecular methods to decipher the microbiomes of

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

During the writing of this manuscript, our funding included two grants (CGL2010-22068-C02-02 and CGL2013-44554-R) and a fellowship (to M.T., BES-2011-045106) from the Spanish Ministry of Economy and Competitiveness. The authors are members of the Xarxa de Referencia d’R+D+I en Biotecnologia (XRB) of the Generalitat de Catalunya.

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