TY - JOUR AB - Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers. AU - Meckenstock, R.U.* AU - Boll, M.* AU - Mouttaki, H. AU - Kölschbach, J.S. AU - Tarouco, P.C. AU - Weyrauch, P. AU - Dong, X. AU - Himmelberg, A.M. C1 - 48222 C2 - 41032 CY - Basel SP - 92-118 TI - Anaerobic degradation of benzene and polycyclic aromatic hydrocarbons. JO - J. Mol. Microbiol. Biotechnol. VL - 26 IS - 1-3 PB - Karger PY - 2016 SN - 1464-1801 ER - TY - JOUR AB - 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. AU - Rabus, R.* AU - Boll, M.* AU - Heider, J.* AU - Meckenstock, R.U. AU - Buckel, W.* AU - Einsle, O.* AU - Ermler, U.* AU - Golding, B.T.* AU - Gunsalus, R.P.* AU - Kroneck, P.M.* AU - Krüger, M.* AU - Lueders, T. AU - Martins, B.M.* AU - Musat, F.* AU - Richnow, H.H.* AU - Schink, B.* AU - Seifert, J.* AU - Szaleniec, M.* AU - Treude, T.* AU - Ullmann, G.M.* AU - Vogt, C.* AU - von Bergen, M.* AU - Wilkes, H.* C1 - 48114 C2 - 39914 CY - Basel SP - 5-28 TI - Anaerobic microbial degradation of hydrocarbons: From enzymatic reactions to the environment. JO - J. Mol. Microbiol. Biotechnol. VL - 26 IS - 1-3 PB - Karger PY - 2016 SN - 1464-1801 ER - TY - JOUR AB - Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using 13C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation. AU - Vogt, C.* AU - Lueders, T. AU - Richnow, H.H.* AU - Krüger, M.* AU - von Bergen, M.* AU - Seifert, J.* C1 - 48115 C2 - 39915 CY - Basel SP - 195-210 TI - Stable isotope probing approaches to study anaerobic hydrocarbon degradation and degraders. JO - J. Mol. Microbiol. Biotechnol. VL - 26 IS - 1-3 PB - Karger PY - 2016 SN - 1464-1801 ER - TY - JOUR AB - Anaerobic degradation is a key process in many environments either naturally or anthropogenically exposed to petroleum hydrocarbons. Considerable advances into the biochemistry and physiology of selected anaerobic degraders have been achieved over the last decades, especially for the degradation of aromatic hydrocarbons. However, researchers have only recently begun to explore the ecology of complex anaerobic hydrocarbon degrader communities directly in their natural habitats, as well as in complex laboratory systems using tools of molecular biology. These approaches have mainly been facilitated by the establishment of a suite of targeted marker gene assays, allowing for rapid and directed insights into the diversity as well as the identity of intrinsic degrader populations and degradation potentials established at hydrocarbon-impacted sites. These are based on genes encoding either peripheral or central key enzymes in aromatic compound breakdown, such as fumarate-adding benzylsuccinate synthases or dearomatizing aryl-coenzyme A reductases, or on aromatic ring-cleaving hydrolases. Here, we review recent advances in this field, explain the different detection methodologies applied, and discuss how the detection of site-specific catabolic gene markers has improved the understanding of processes at contaminated sites. Functional marker gene-based strategies may be vital for the development of a more elaborate population-based assessment and prediction of aromatic degradation potentials in hydrocarbon-impacted environments. AU - von Netzer, F. AU - Kuntze, K.* AU - Vogt, C.* AU - Richnow, H.H.* AU - Boll, M.* AU - Lueders, T. C1 - 48084 C2 - 39898 CY - Basel SP - 180-194 TI - Functional gene markers for fumarate-adding and dearomatizing key enzymes in anaerobic aromatic hydrocarbon degradation in terrestrial environments. JO - J. Mol. Microbiol. Biotechnol. VL - 26 IS - 1-3 PB - Karger PY - 2016 SN - 1464-1801 ER - TY - JOUR AB - Anaerobranca gottschalkii strain LBS3 T is an extremophile living at high temperature (up to 65 degrees C) and in alkaline environments (up to pH 10.5). An assembly of 696 DNA contigs representing about 96% of the 2.26-Mbp genome of A. gottschalkii has been generated with a low-sequence-coverage shotgun-sequencing strategy. The chosen sequencing strategy provided rapid and economical access to genes encoding key enzymes of the mono- and polysaccharide metabolism, without dilution of spare resources for extensive sequencing of genes lacking potential economical value. Five of these amylolytic enzymes of considerable commercial interest for biotechnological applications have been expressed and characterized in more detail after identification of their genes in the partial genome sequence: type I pullulanase, cyclodextrin glycosyltransferase (CGTase), two alpha-amylases (AmyA and AmyB), and an alpha-1,4-glucan-branching enzyme. AU - Antranikian, G.* AU - Ruepp, A. AU - Gordon, P.M.* AU - Ballschmiter, M.* AU - Zibat, A.* AU - Stark, M.* AU - Sensen, C.W.* AU - Frishman, D.* AU - Liebl, W.* AU - Klenk, H.P.* C1 - 1654 C2 - 25949 SP - 81-90 TI - Rapid access to genes of biotechnologically useful enzymes by partial genome sequencing: The thermoalkaliphile Anaerobranca gottschalkii. JO - J. Mol. Microbiol. Biotechnol. VL - 16 IS - 1-2 PY - 2009 SN - 1464-1801 ER -