Bacterial PAH degradation in marine and terrestrial habitats Joaquim Vila, Margalida Tauler and Magdalena Grifoll 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. Addresses Department of Microbiology, Faculty of Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain Corresponding author: Grifoll, Magdalena (mgrifoll@ub.edu) Dedicated to the memory of Professor Peter J. Chapman. Current Opinion in Biotechnology 2015, 33:95–102 This review comes from a themed issue on Environmental biotech- nology Edited by Spiros N Agathos and Nico Boon http://dx.doi.org/10.1016/j.copbio.2015.01.006 0958-1669/# 2015 Elsevier Ltd. All rights reserved. Introduction Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants reaching particularly high con- centrations 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 sustain- able 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 allow- ing 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 differ- ent 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, scien- tific disciplines. Here, we will focus on the recent devel- opments (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 bioavail- ability [4], bacterial-fungal interactions [5], or biodegrada- tion of aromatic hydrocarbons in general [6]. 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 interac- tions, 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. Implications of cometabolic reactions in cooperative metabolic networks. 3. Discovering the guild of microorganisms responsible for PAH biodegradation. 4. Identification of functions relevant for PAH metabo- lism in environmental samples. 5. Integration of this information to obtain a holistic view of the in situ metabolic networks. 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 Available online at www.sciencedirect.com ScienceDirect www.sciencedirect.com Current Opinion in Biotechnology 2015, 33:95–102