Anaerobic Microbial Degradation of Hydrocarbons: From Enzymatic Reactions to the Environment

Abstract

Hydrocarbons are abundant in anoxic environments and pose biochemical challenges to their anaerobic degradation by microorganisms. Within the framework of the Priority Program 1319, investigations funded by the Deutsche Forschungsgemeinschaft on the anaerobic microbial degradation of hydrocarbons ranged from isolation and enrichment of hitherto unknown hydrocarbon-degrading anaerobic microorganisms, discovery of novel reactions, detailed studies of enzyme mechanisms and structures to process-oriented in situ studies. Selected highlights from this program are collected in this synopsis, with more detailed information provided by theme-focused reviews of the special topic issue on ‘Anaerobic biodegradation of hydrocarbons' [this issue, pp. 1-244]. The interdisciplinary character of the program, involving microbiologists, biochemists, organic chemists and environmental scientists, is best exemplified by the studies on alkyl-/arylalkylsuccinate synthases. Here, research topics ranged from in-depth mechanistic studies of archetypical toluene-activating benzylsuccinate synthase, substrate-specific phylogenetic clustering of alkyl-/arylalkylsuccinate synthases (toluene plus xylenes, p-cymene, p-cresol, 2-methylnaphthalene, n-alkanes), stereochemical and co-metabolic insights into n-alkane-activating (methylalkyl)succinate synthases to the discovery of bacterial groups previously unknown to possess alkyl-/arylalkylsuccinate synthases by means of functional gene markers and in situ field studies enabled by state-of-the-art stable isotope probing and fractionation approaches. Other topics are Mo-cofactor-dependent dehydrogenases performing O₂-independent hydroxylation of hydrocarbons and alkyl side chains (ethylbenzene, p-cymene, cholesterol, n-hexadecane), degradation of p-alkylated benzoates and toluenes, glycyl radical-bearing 4-hydroxyphenylacetate decarboxylase, novel types of carboxylation reactions (for acetophenone, acetone, and potentially also benzene and naphthalene), W-cofactor-containing enzymes for reductive dearomatization of benzoyl-CoA (class II benzoyl-CoA reductase) in obligate anaerobes and addition of water to acetylene, fermentative formation of cyclohexanecarboxylate from benzoate, and methanogenic degradation of hydrocarbons.

Unexpected Diversity and High Abundance of Putative Nitric Oxide Dismutase (Nod) Genes in Contaminated Aquifers and Wastewater Treatment Systems

“…Thus, they are suggested to rely on O 2 formed via NO dismutation to activate and oxidize hydrocarbons when growing under nitrate-and nitritereducing conditions. Methane and alkanes are among the most stable compounds that require high energy for activating the first C-H bond (33). Therefore, it can be speculated that O 2 formed via NO dismutation could provide a competitive advantage for oxygenic denitrifiers thriving on recalcitrant compounds in anoxic environments.…”

Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment

“…2016; Rabus et al. 2016). The enzymes involved in the anaerobic pathways have been described in detail (for a review, see Meckenstock et al.…”

“…For the carboxylation route, a carboxylase belonging to the UbiD-like proteins family is proposed for the carboxylation of the aromatic ring (Rabus et al. 2016). For the methylation route, it is proposed to proceed via a methyl-transferase that methylates the aromatic ring (Safinowski and Meckenstock 2006) and then a naphthyl-2-methyl-succinate synthase, a glycyl-radical-containing enzyme, catalyses the addition to fumarate (Meckenstock and Mouttaki 2011).…”

COST Action CM1201 “Biomimetic Radical Chemistry”: free radical chemistry successfully meets many disciplines

“…Experimentally it has been shown that 1 (2). A higher energy barrier has been calculated for reaction with adenine, giving for the first time an explanation of the lack of reactivity of 1 O 2 toward adenine.…”

“…biosynthetic pathways to antibiotics and cofactors. In addition to this medical context, radical enzymes are essential for the degradation of alkanes and aromatic hydrocarbons derived not only from natural processes, but also as a result of environmental damage from oil spills and other industrially caused pollution [1]. The primary objectives of WG1 were:…”