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The highly enriched deltaproteobacterial culture N47 anaerobically oxidizes the polycyelic aromatic hydrocarbons naphthalene and 2-methylnaphthalene, with sulfate as the electron acceptor. Combined genome sequencing and liquid chromatography-tandem mass spectrometry-based shotgun proteome analyses were performed to identify genes and proteins involved in anaerobic aromatic catabolism. Proteome analysis of 2-methylnaphthalene-grown N47 cells resulted in the identification of putative enzymes catalyzing the anaerobic conversion of 2-metbyluapbthalene to 2-naphthoyl eoenzyme A (2-naphthoyl-CoA), as well as the reductive ring cleavage of 2-naphthoyl-CoA, leading to the formation of acetyl-CoA and C[O.sub.2]. The glycyl radical-catalyzed fumarate addition to the methyl group of 2-methylnaphthalene is catalyzed by naphthyl-2-methyl-succinate synthase (Nms), composed of [alpha]-, [beta]-, and [gamma]-subunits that are encoded by the genes nmsABC. Located upstream of nmsABC is nmsD, encoding the Nms-activating enzyme, which harbors the characteristic [[Fe.sub.4][S.sub.4]] cluster sequence motifs of S-adenosylmethionine radical enzymes. The bns gene cluster, coding for enzymes involved in beta-oxidation reactions converting naphthyl-2-methyl-succinate to 2-naphthoyl-CoA, was found four intervening open reading frames further downstream. This cluster consists of eight genes (bnsABCDEFGH) corresponding to 8.1 kb, which are closely related to genes for enzymes involved in anaerobic toluene degradation within the denitrifiers 'Aromatoleum aromaticum' EbN1, Azoarcus sp. strain T, and Thauera aromatica. Another contiguous DNA sequence harbors the gene for 2-naphthoyl-CoA reductase (ncr) and 16 additional genes that were found to be expressed in 2-methylnaphthalene-grown cells. These genes code for enzymes that were supposed to catalyze the dearomatization and ring cleavage reactions converting 2-naphthoyl-CoA to acetylCoA and C[O.sub.2]. Comparative sequence analysis of the four encoding subunits (ncrABCD) showed the gene product to have the closest similarity to the Azoarcus type of benzoyl-CoA reductase. The present work provides the first insight into the genetic basis of anaerobic 2-methylnaphthalene metabolism and delivers implications for understanding contaminant degradation. doi: 10.1128/JB.00874-09

Research addresses potential bias in the polymerase chain reaction and their influence on terminal restriction fragment length polymorphism fingerprinting of methanogenic bacterial population structure in different habitats using small-subunit rRNA and the methyl-coenzyme M reductase genes as probes. Data reveal that small-subunit rRNA analysis is reproducible, whereas M reductase-based analysis is biased.

Different methanogenic bacteria are stimulated or inhibited when rice paddy soils are supplemented with ferrihydrite or gypsum. These electron acceptors are added to stimulate bacteria that would compete with methanogens. This is done to reduce methane emissions, which contribute to the greenhouse effect.

The first comprehensive analysis of the microbial community inside the gut of the termite Cubitermes orthognathus is described based on clonal analysis and terminal restriction fragment length polymorphism fingerprinting. This is also the first report of Crenarchaeota occurring in an arthropod intestinal tract.

Research has been conducted on the Archaea population dynamics after rice field soil flooding. The results of the molecular sequence retrieval and small-subunit rRNA gene fingerprinting are discussed.

The characterization of microbial community distribution across a high-resolution depth profile of a tar oil-impacted aquifer where benzene, toluene, ethylbenzene and xylene (BTEX) degradation has depended mainly on sulfate reduction is described. The results have shown that the distribution of specific aquifer microbiota and degradation processes in contaminated aquifers are tightly coupled, which are used for the assessment of natural attenuation based on intrinsic aquifer microbiota.

The first identification of active anaerobic microorganisms by stable-isotope probing (SIP), which are involved in the thermodyanimically unfavorable syntrophic oxidation of propionate under methanogenic conditions is presented. Three distinct lineages of syntrophic propionate oxidizers (Syntrophobacter, Smithella, and Pelotomaculum spp.) were identified to operate simultaneously in anoxic rice field soil slurries and their hydrogenotrophic and acetotrophic methanogenic partner organisms were also detected by assimilation of labeled intermediates.

It has recently been suggested that oxygenic dismutation of NO into N2 and O2 may occur in the anaerobic methanotrophic "Candidatus Methylomirabilis oxyfera" and the alkane-oxidizing gammaproteobacterium HdN1. It may represent a new pathway in microbial nitrogen cycling catalyzed by a putative NO dismutase (Nod). The formed O2 enables microbes to employ aerobic catabolic pathways in anoxic habitats, suggesting an ecophysiological niche space of substantial appeal for bioremediation and water treatment. However, it is still unknown whether this physiology is limited to "Ca. Methylomirabilis oxyfera" and HdN1 and whether it can be coupled to the oxidation of electron donors other than alkanes. Here, we report insights into an unexpected diversity and remarkable abundance of nod genes in natural and engineered water systems. Phylogenetically diverse nod genes were recovered from a range of contaminated aquifers and N-removing wastewater treatment systems. Together with nod genes from "Ca. Methylomirabilis oxyfera" and HdN1, the novel environmental nod sequences formed no fewer than 6 well-supported phylogenetic clusters, clearly distinct from canonical NO reductase (quinoldependent NO reductase [qNor] and cytochrome c-dependent NO reductase [cNor]) genes. The abundance of nod genes in the investigated samples ranged from 1.6 × 107 to 5.2 × 1010 copies · g-1 (wet weight) of sediment or sludge biomass, accounting for up to 10% of total bacterial 16S rRNA gene counts. In essence, NO dismutation could be a much more widespread physiology than currently perceived. Understanding the controls of this emergent microbial capacity could offer new routes for nitrogen elimination or pollutant remediation in natural and engineered water systems. [ABSTRACT FROM AUTHOR]