Agricultural and industrial practices more than doubled the intrinsic rate of terrestrial N fixation over the past century with drastic consequences, including increased atmospheric nitrous oxide (N 2 O) concentrations. N 2 O is a potent greenhouse gas and contributor to ozone layer destruction, and its release from fixed N is almost entirely controlled by microbial activities. Mitigation of N 2 O emissions to the atmosphere has been attributed exclusively to denitrifiers possessing NosZ, the enzyme system catalyzing N 2 O to N 2 reduction. We demonstrate that diverse microbial taxa possess divergent nos clusters with genes that are related yet evolutionarily distinct from the typical nos genes of denitirifers. nos clusters with atypical nosZ occur in Bacteria and Archaea that denitrify (44% of genomes), do not possess other denitrification genes (56%), or perform dissimilatory nitrate reduction to ammonium (DNRA; (31%). Experiments with the DNRA soil bacterium Anaeromyxobacter dehalogenans demonstrated that the atypical NosZ is an effective N 2 O reductase, and PCRbased surveys suggested that atypical nosZ are abundant in terrestrial environments. Bioinformatic analyses revealed that atypical nos clusters possess distinctive regulatory and functional components (e.g., Sec vs. Tat secretion pathway in typical nos), and that previous nosZ-targeted PCR primers do not capture the atypical nosZ diversity. Collectively, our results suggest that nondenitrifying populations with a broad range of metabolisms and habitats are potentially significant contributors to N 2 O consumption. Apparently, a large, previously unrecognized group of environmental nosZ has not been accounted for, and characterizing their contributions to N 2 O consumption will advance understanding of the ecological controls on N 2 O emissions and lead to refined greenhouse gas flux models.nitrogen cycle | climate change

The 16S rRNA gene provides insufficient information to infer the range of chloroorganic electron acceptors used by different Dehalococcoides organisms. To overcome this limitation and provide enhanced diagnostic tools for growth measurements, site assessment, and bioremediation monitoring, a quantitative real-time PCR (qPCR) approach targeting 16S rRNA genes and three Dehalococcoides reductive dehalogenase (RDase) genes with assigned function (i.e., tceA, bvcA, and vcrA) was designed and evaluated. qPCR standard curves generated for the RDase genes by use of genomic DNA from Dehalococcoides pure cultures correlated with standard curves obtained for both Bacteria-and Dehalococcoides-targeted 16S rRNA genes, suggesting that the RDase genes are useful targets for quantitative assessment of Dehalococcoides organisms. RDase gene probe/primer pairs were specific for the Dehalococcoides strains known to carry the diagnostic RDase gene sequences, and the qPCR method allowed the detection of as few as 1 to 20 and quantification of as few as 50 to 100 tceA, bvcA, or vcrA gene targets per PCR volume. The qPCR approach was applied to dechlorinating enrichment cultures, microcosms, and samples from a contaminated site. In characterized enrichment cultures where known Dehalococcoides strains were enumerated, the sum of the three RDase genes equaled the total Dehalococcoides cell numbers. In site samples and chloroethane-dechlorinating microcosms, the sum of the three RDase genes was much less than that predicted by Dehalococcoides-targeted qPCR, totaling 10 to 30% of the total Dehalococcoides cell numbers. Hence, a large number of Dehalococcoides spp. contain as-yet-unidentified RDase genes, indicating that our current understanding of the dechlorinating Dehalococcoides community is incomplete.Chlorinated solvents are a well-recognized class of groundwater (GW) contaminants (1,7,41,53). Substantial knowledge regarding diverse groups of bacteria that partially dechlorinate tetrachloroethene (PCE) or trichloroethene (TCE) to cis-1,2-dichloroethene (cis-DCE) (5,12,19,30,50) or trans-DCE (13) has been accrued over the past decade. Partial reductive dechlorination contributes to the formation of DCEs and, in some cases, vinyl chloride (VC) (1,26,45). Environmental accumulation of VC is particularly troublesome because this compound is a proven human carcinogen; therefore, incomplete dechlorination of PCE and TCE does not result in detoxification.Recently, Dehalococcoides organisms were discovered as a deeply branching group within the green nonsulfur bacteria (Chloroflexi) (44). This physiologically and phylogenetically distinct bacterial group requires hydrogen as an electron donor and specific chloroorganic compounds as electron acceptors to support their energy metabolism. Dehalococcoides ethenogenes strain 195 was the first isolate described to dechlorinate PCE to VC and ethene (35); however, the last transformation step from VC to ethene occurred slowly in a cometabolic process (34). Similarly, metabolic dechlorination of TCE...

The bioreduction of U(VI) to U(IV) affects uranium mobility and fate in contaminated subsurface environments and is best understood in Gram-negative model organisms such as Geobacter and Shewanella spp. This study demonstrates that U(VI) reduction is a common trait of Gram-positive Desulfitobacterium spp. Five different Desulfitobacterium isolates reduced 100 microM U(VI) to U(IV) in <10 days, whereas U(VI) remained soluble in abiotic and heat-killed controls. U(VI) reduction in live cultures was confirmed using X-ray absorption near-edge structure (XANES) analysis. Interestingly, although bioreduction of U(VI) is almost always reported to yield the uraninite mineral (UO(2)), extended X-ray absorption fine structure (EXAFS) analysis demonstrated that the U(IV) produced in the Desulfitobacterium cultures was not UO(2). The EXAFS data indicated that the U(IV) product was a phase or mineral composed of mononuclear U(IV) atoms closely surrounded by light element shells. This atomic arrangement likely results from inner-sphere bonds between U(IV) and C/N/O- or P/S-containing ligands, such as carbonate or phosphate. The formation of a distinct U(IV) phase warrants further study because the characteristics of the reduced material affect uranium stability and fate in the contaminated subsurface.

Under anaerobic conditions, microbial reductive dechlorination of polychlorinated biphenyls (PCBs) occurs in soils and aquatic sediments. In contrast to dechlorination of supplemented single congeners for which frequently ortho dechlorination has been observed, reductive dechlorination mainly attacks meta and/or para chlorines of PCB mixtures in contaminated sediments, although in a few instances ortho dechlorination of PCBs has been observed. Different microorganisms appear to be responsible for different dechlorination activities and the occurrence of various dehalogenation routes. No axenic cultures of an anaerobic microorganism have been obtained so far. Most probable number determinations indicate that the addition of PCB congeners, as potential electron acceptors, stimulates the growth of PCB-dechlorinating microorganisms. A few PCB-dechlorinating enrichment cultures have been obtained and partially characterized. Temperature, pH, availability of naturally occurring or of supplemented carbon sources, and the presence or absence of H(2) or other electron donors and competing electron acceptors influence the dechlorination rate, extent and route of PCB dechlorination. We conclude from the sum of the experimental data that these factors influence apparently the composition of the active microbial community and thus the routes, the rates and the extent of the dehalogenation. The observed effects are due to the specificity of the dehalogenating bacteria which become active as well as changing interactions between the dehalogenating and non-dehalogenating bacteria. Important interactions include the induced changes in the formation and utilization of H(2) by non-dechlorinating and dechlorinating bacteria, competition for substrates and other electron donors and acceptors, and changes in the formation of acidic fermentation products by heterotrophic and autotrophic acidogenic bacteria leading to changes in the pH of the sediments.