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At least 649 records · Page 36Linked to original sources
PubMed2003

Metabolism of inorganic N compounds by ammonia-oxidizing bacteria.

Ammonia oxidizing bacteria extract energy for growth from the oxidation of ammonia to nitrite. Ammonia monooxygenase, which initiates ammonia oxidation, remains enigmatic given the lack of purified preparations. Genetic and biochemical studies support a model for the enzyme consisting of three subunits and metal centers of copper and iron. Knowledge of hydroxylamine oxidoreductase, which oxidizes hydroxylamine formed by ammonia monooxygenase to nitrite, is informed by a crystal structure and detailed spectroscopic and catalytic studies. Other inorganic nitrogen compounds, including NO, N2O, NO2, and N2 can be consumed and/or produced by ammonia-oxidizing bacteria. NO and N2O can be produced as byproducts of hydroxylamine oxidation or through nitrite reduction. NO2 can serve as an alternative oxidant in place of O2 in some ammonia-oxidizing strains. Our knowledge of the diversity of inorganic N metabolism by ammonia-oxidizing bacteria continues to grow. Nonetheless, many questions remain regarding the enzymes and genes involved in these processes and the role of these pathways in ammonia oxidizers.

Ammonia↗
PubMed2001

Factors influencing spatial variability in nitrogen processing in nitrogen-saturated soils.

Nitrogen (N) saturation is an environmental concern for forests in the eastern U.S. Although several watersheds of the Fernow Experimental Forest (FEF), West Virginia exhibit symptoms of N saturation, many watersheds display a high degree of spatial variability in soil N processing. This study examined the effects of temperature on net N mineralization and nitrification in N-saturated soils from FEF, and how these effects varied between high N-processing vs. low N-processing soils collected from two watersheds, WS3 (fertilized with [NH4]2SO4) and WS4 (untreated control). Samples of forest floor material (O1 horizon) and mineral soil (to a 5-cm depth) were taken from three subplots within each of four plots that represented the extremes of highest and lowest rates of net N mineralization and nitrification (hereafter, high N and low N, respectively) of untreated WS4 and N-treated WS3: control/low N, control/high N, N-treated/low N, N-treated/high N. Forest floor material was analyzed for carbon (C), lignin, and N. Subsamples of mineral soil were extracted immediately with 1 N KCl and analyzed for NH4+ and NO3- to determine preincubation levels. Extracts were also analyzed for Mg, Ca, Al, and pH. To test the hypothesis that the lack of net nitrification observed in field incubations on the untreated/low N plot was the result of absence of nitrifier populations, we characterized the bacterial community involved in N cycling by amplification of amoA genes. Remaining soil was incubated for 28 d at three temperatures (10, 20, and 30 degrees C), followed by 1 N KCl extraction and analysis for NH4+ and NO3-. Net nitrification was essentially 100% of net N mineralization for all samples combined. Nitrification rates from lab incubations at all temperatures supported earlier observations based on field incubations. At 30 degrees C, rates from N-treated/high N were three times those of N-treated/low N. Highest rates were found for untreated/high N (two times greater than those of N-treated/high N), whereas untreated/low N exhibited no net nitrification. However, soils exhibiting no net nitrification tested positive for presence of nitrifying bacteria, causing us to reject our initial hypothesis. We hypothesize that nitrifier populations in such soil are being inhibited by a combination of low Ca to Al ratios in mineral soil and allelopathic interactions with mycorrhizae of ericaceous species in the herbaceous layer.

DNA, Bacterial↗
PubMed1966

Phospholipids of bacteria with extensive intracytoplasmic membranes.

Examination of the lipids of three species of nonphotosynthetic bacteria with extensive internal membranes revealed phosphatidyl choline (lecithin) in two species. In one of these there was an unusual accumulation of phosphatidyl N-dimethylethanolamine. (The relation between lecithin and membrane elaboration in microorganisms is discussed.)

Bacteria↗
PubMed1969

Macromolecular subunits in the walls of marine nitrifying bacteria.

The outteromost laver of the cell wall of all marine ammonia-oxidizing bacteria So far isolated is made up of protein subunits arranged in a regular manner and linked together through metal-oxygen bonds. This sculptured, outer wall layver appears to be uniique to the terrestrial ammonia-oxidizing bacteria.

Bacteria↗
PubMed1982

Effects of polychlorinated biphenyls and environmental biotransformation products on aquatic nitrification.

The effects of polychlorinated biphenyls (PCBs) on nitrification were examined for pure cultures and natural reservoir samples. PCBs at concentrations greater than 10 microgram liter-1 inhibited nitrification, principally ammonium oxidation, in one of two natural reservoir environments. However, this inhibition could not be reproduced in pure high-cell-density cultures or in previously contaminated reservoir waters. A PCB environmental biotransformation product, p-chlorophenylglyoxylic acid, and p-chloromandelic acid had no effect on nitrification.

Biotransformation↗
PubMed1995

Anaerobic oxidation of ammonium is a biologically mediated process.

A newly discovered process by which ammonium is converted to dinitrogen gas under anaerobic conditions (the Anammox process) has now been examined in detail. In order to confirm the biological nature of this process, anaerobic batch culture experiments were used. All of the ammonium provided in the medium was oxidized within 9 days. In control experiments with autoclaved or raw wastewater, without added sludge or with added sterilized (either autoclaved or gamma irradiated) sludge, no changes in the ammonium and nitrate concentrations were observed. Chemical reactions could therefore not be responsible for the ammonium conversion. The addition of chloramphenicol, ampicillin, 2,4-dinitrophenol, carbonyl cyanide m-chlorophenyl-hydrazone (CCCP), and mercuric chloride (HgIICl2) completely inhibited the activity of the ammonium-oxidizing sludge. Furthermore, the rate of ammonium oxidation was proportional to the initial amount of sludge used. It was therefore concluded that anaerobic ammonium oxidation was a microbiological process. As the experiments were carried out in an oxygen-free atmosphere, the conversion of ammonium to dinitrogen gas did not even require a trace of O2. That the end product of the reaction was nitrogen gas has been confirmed by using 15NH4+ and 14NO3-. The dominant product was 14-15N2. Only 1.7% of the total labelled nitrogen gas produced was 15-15N2. It is therefore proposed that the N2 produced by the Anammox process is formed from equimolar amounts of NH4+ and NO3-.

Anaerobiosis↗
PubMed1995

Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR.

The PCR was used as the basis for the development of a sensitive and specific assay for the detection of ammonium-oxidizing bacteria belonging to the beta-subclass of the class Proteobacteria. PCR primers were selected on the basis of nucleic acid sequence data available for seven species of nitrifiers in this subclass. The specificity of the ammonium oxidizer primers was evaluated by testing known strains of nitrifiers, several serotyped environmental nitrifier isolates, and other members of the Proteobacteria, including four very closely related, nonnitrifying species (as determined by rRNA sequence analysis). DNA extracts from 19 bacterio-plankton samples collected from Lake Bonney, Antarctica, and the Southern California Bight were assayed for the presence of ammonium oxidizers. By using a two-stage amplification procedure, ammonium oxidizers were detected in samples collected from both sites. Chemical data collected simultaneously support the occurrence of nitrification and the presence of nitrifiers. This is the first report describing PCR primers specific for ammonium-oxidizing bacteria and the successful amplification of nitrifier genes coding for rRNA from DNA extracts from natural samples. This application of PCR is of particular importance for the detection and study of microbes, such as autotrophic nitrifiers, which are difficult or impossible to isolate from indigenous microbial communities.

Animals↗
PubMed1999

Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils.

Autotrophic ammonia oxidizer (AAO) populations in soils from native, tilled, and successional treatments at the Kellogg Biological Station Long-Term Ecological Research site in southwestern Michigan were compared to assess effects of disturbance on these bacteria. N fertilization effects on AAO populations were also evaluated with soils from fertilized microplots within the successional treatments. Population structures were characterized by PCR amplification of microbial community DNA with group-specific 16S rRNA gene (rDNA) primers, cloning of PCR products and clone hybridizations with group-specific probes, phylogenetic analysis of partial 16S rDNA sequences, and denaturing gradient gel electrophoresis (DGGE) analysis. Population sizes were estimated by using most-probable-number (MPN) media containing varied concentrations of ammonium sulfate. Tilled soils contained higher numbers than did native soils of culturable AAOs that were less sensitive to different ammonium concentrations in MPN media. Compared to sequences from native soils, partial 16S rDNA sequences from tilled soils were less diverse and grouped exclusively within Nitrosospira cluster 3. Native soils yielded sequences representing three different AAO clusters. Probes for Nitrosospira cluster 3 hybridized with DGGE blots from tilled and fertilized successional soils but not with blots from native or unfertilized successional soils. Hybridization results thus suggested a positive association between the Nitrosospira cluster 3 subgroup and soils amended with inorganic N. DGGE patterns for soils sampled from replicated plots of each treatment were nearly identical for tilled and native soils in both sampling years, indicating spatial and temporal reproducibility based on treatment.

Ammonia↗
PubMed2002

Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses.

The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (T(d)) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5' terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the T(d) and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the T(d) and signal intensity, and it decreased the variability of the signal. Although T(d)s of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower T(d)s than those with mismatches in the first or second position. The trained NNs predicted the T(d) with high accuracies (R(2) = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R(2) = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in T(d)s, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5' terminus plays a greater role in determining the T(d) and signal intensity of duplexes than the type of mismatch.

Base Pair Mismatch↗
PubMed2002

Exploration of inorganic C and N assimilation by soil microbes with time-of-flight secondary ion mass spectrometry.

Stable C and N isotopes have long been used to examine properties of various C and N cycling processes in soils. Unfortunately, relatively large sample sizes are needed for accurate gas phase isotope ratio mass spectrometric analysis. This limitation has prevented researchers from addressing C and N cycling issues on microbially meaningful scales. Here we explored the use of time-of-flight secondary ion mass spectrometry (TOF-SIMS) to detect 13C and 15N assimilation by individual bacterial cells and to quantify N isotope ratios in bacterial samples and individual fungal hyphae. This was accomplished by measuring the relative abundances of mass 26 (12C14N-) and mass 27 (13C14N- and 12C15N-) ions sputtered with a Ga+ probe from cells adhered to an Si contact slide. TOF-SIMS was successfully used to locate and quantify the relative 15N contents of individual hyphae that grew onto Si contact slides in intimate contact with a model organomineral porous matrix composed of kaolin, straw fragments, and freshly deposited manure that was supplemented with 15NO3-. We observed that the 15N content of fungal hyphae grown on the slides was significantly lower in regions where the hyphae were influenced by N-rich manure than in regions influenced by N-deficient straw. This effect occurred over distances of tens to hundreds of microns. Our data illustrate that TOF-SIMS has the potential to locate N-assimilating microorganisms in soil and to quantify the 15N content of cells that have assimilated 15N-labeled mineral N and shows promise as a tool with which to explore the factors controlling microsite heterogeneities in soil.

Carbon↗
PubMed1994

Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria.

Comparative 16S rRNA sequencing was used to evaluate phylogenetic relationships among selected strains of ammonia- and nitrite-oxidizing bacteria. All characterized strains were shown to be affiliated with the proteobacteria. The study extended recent 16S rRNA-based studies of phylogenetic diversity among nitrifiers by the comparison of eight strains of the genus Nitrobacter and representatives of the genera Nitrospira and Nitrospina. The later genera were shown to be affiliated with the delta subdivision of the proteobacteria but did not share a specific relationship to each other or to other members of the delta subdivision. All characterized Nitrobacter strains constituted a closely related assemblage within the alpha subdivision of the proteobacteria. As previously observed, all ammonia-oxidizing genera except Nitrosococcus oceanus constitute a monophyletic assemblage within the beta subdivision of the proteobacteria. Errors in the 16S rRNA sequences for two strains previously deposited in the databases by other investigators (Nitrosolobus multiformis C-71 and Nitrospira briensis C-128) were corrected. Consideration of physiology and phylogenetic distribution suggested that nitrite-oxidizing bacteria of the alpha and gamma subdivisions are derived from immediate photosynthetic ancestry. Each nitrifier retains the general structural features of the specific ancestor's photosynthetic membrane complex. Thus, the nitrifiers, as a group, apparently are not derived from an ancestral nitrifying phenotype.

Ammonia↗