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PubMed1998

Application of a fine thread beam to the structure analysis of a hemihedrally twinned crystal of hydroxylamine oxidoreductase.

Accurate diffraction intensity data have been collected from a twinned P6(3) crystal of the 24-haem protein hydroxylamine oxidoreductase, from a nitrifying chemoautotrophic bacterium Nitrosomonas europaea, using synchrotron radiation at station BL6A of the Photon Factory. Estimation of the twinning fraction and deconvoluted intensity data, including native and heavy-atom derivative data, gave an improved Patterson function. Four diffraction data sets were collected from one crystal and an estimation of the twinning fraction to confirm the phenomena was undertaken. The successfully detwinned data sets were utilized in the structure analysis of the present enzyme. The mechanism of twinned-crystal formation is also discussed.

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PubMed2006

Characterization and quantification of ammonia-oxidizing bacteria in eutrophic coastal marine sediments using polyphasic molecular approaches and immunofluorescence staining.

Tokyo Bay, a eutrophic bay in Japan, receives nutrients from wastewater plants and other urban diffuse sources via river input. A transect was conducted along a line from the Arakawa River into Tokyo Bay to investigate the ecological relationship between the river outflow and the distribution, abundance and population structure of ammonia-oxidizing bacteria (AOB). Five surficial marine sediments were collected and analysed with polyphasic approaches. Heterogeneity and genetic diversity of beta-AOB populations were examined using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA and amoA genes. A shift of the microbial community was detected in samples along the transect. Both 16S rRNA and amoA genes generated polymorphisms in the restriction profiles that were distinguishable at each sampling site. Two 16S rRNA gene libraries were constructed using the reverse transcription polymerase chain reaction (RT-PCR) method to determine the major ammonia oxidizers maintaining high cellular rRNA content. Two major groups were observed in the Nitrosomonas lineage; no Nitrosospira were detected. The effort to isolate novel AOB was successful; the isolate dominated in the gene libraries. For quantitative analysis, a real-time PCR assay targeting the 16S rRNA gene was developed. The population sizes of beta-AOB ranged from 1.6 x 10(7) to 3.0 x 10(8) cells g(-1) in dry sediments, which corresponded to 0.1-1.1% of the total bacterial population. An immunofluorescence staining using anti-hydroxylamine oxidoreductase (HAO) antibody was also tested to obtain complementary data. The population sizes of ammonia oxidizers ranged between 2.4 x 10(8) and 1.2 x 10(9) cells g(-1) of dry sediments, which corresponded to 1.2-4.3% of the total bacterial fraction. Ammonia-oxidizing bacteria cell numbers deduced by the two methods were correlated (R = 0.79, P < 0.01). In both methods, the number of AOB increased with the distance from the river mouth; ammonia-oxidizing bacteria were most numerous at B30, where the ammonium concentration in the porewater was markedly lower and the nitrite concentration was slightly higher than nearby sites. These results reveal spatial distribution and shifts in the population structure of AOB corresponding to nutrients and organic inputs from the river run-off and phytoplankton bloom.

Ammonia↗

PubMed1999

Comparison of Nitrosospira strains isolated from terrestrial environments.

Most of our knowledge about the physiology of ammonia-oxidizing bacteria is based on experiments with Nitrosomonas europaea, which appears to be less ubiquitous than Nitrosospira. We have isolated Nitrosospiras from widely different environments and compared their specific growth rate, substrate affinity, urease activity, temperature response, pH tolerance and cell morphology. Two of the strains had a variable morphology: the spirals were less tightly coiled than the classical Nitrosospira type and a fraction of the culture had a vibrioid appearance. These vibrioid strains were also peculiar in having a much higher apparent activation energy for ammonia monooxygenase (AMO) (129 and 151 kJ mol(-1)) than that of the more classical Nitrosospiras (78 and 79 kJ mol(-1)). The differences in morphology and activation energy were congruent with the phylogeny of the genes for 16S rRNA (Utåker et al., System. Appl. Microbiol. 18) and AMO. The response to pH in the medium was investigated for four strains. The oxidation rate at the onset of the pH exposure experiment was found to obey classical steady state enzyme kinetics, assuming that NH(3) (not NH(4)(+)) is the rate-limiting substrate. The calculated half saturation constants (K(s)) for AMO were 6-11 µM NH(3). Growth had a narrower pH range than oxidation activity and appeared to be restricted by pH-dependent factors other than NH(3). All the isolated strains were urease positive, with a specific urease activity ranging from 60 to 158% of their specific AMO activity. The urease activity was unaffected by acetylene inhibition of the energy metabolism. The substrate affinity for one strain was found to be around 670 µM.

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PubMed2000

Molecular analysis of ammonia-oxidising bacteria in soil of successional grasslands of the Drentsche A (The Netherlands).

Changes in the community structure of chemolitho-autotrophic ammonia-oxidising bacteria of the beta-subgroup Proteobacteria were monitored during nutrient-impoverishment management of slightly acidic, peaty grassland soils, which decreased in pH with succession. Specific PCR, cloning and sequence analysis, denaturing gradient gel electrophoresis (DGGE) and probe hybridisation were used to analyse rDNA sequences directly recovered from successional soils. Four previously characterised ammonia oxidiser sequence clusters were recovered from each soil, three associated with the genus Nitrosospira and one with the genus Nitrosomonas. All samples were dominated by Nitrosospira-like sequences. Nitrosospira cluster 3 was the most commonly recovered ammonia oxidiser group in all fields, but a greater representation of Nitrosospira clusters 2 and 4 was observed in older fields. Most probable number (MPN) counts were conducted using neutral and slightly acid conditions. Neutral pH (7.5) MPNs suggested a decrease in ammonia oxidiser numbers in later successional fields, but this trend was not observed using slightly acid (pH 5.8) conditions. Analysis of terminal MPN dilutions revealed a distribution of sequence clusters similar to direct soil DNA extractions. However, an increased relative recovery of Nitrosospira cluster 2 was observed for acid pH MPNs compared to neutral pH MPNs from the most acidic soil tested, in agreement with current hypotheses on the relative acid tolerance of this group.

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PubMed2006

Long-term monitoring of the succession of a microbial community in activated sludge from a circulation flush toilet as a closed system.

The microbial diversity and community succession of a circulation flush toilet were investigated by terminal restriction fragment length polymorphism and cloning analyses. Clonal libraries of 16S rRNA gene on day 3 and day 127 were constructed. On day 3, 102 clones were sequenced; Proteobacteria and Bacteroidetes accounted for 27% and 45%, respectively. On day 127, Proteobacteria had increased to 43% and Bacteroidetes had decreased to 26% of a total of 100 clones. Terminal restriction fragment length polymorphism peaks were identified by in silico analysis of clone libraries. The relative abundances of Nitrosomonas increased from 1% to 6% with commencement of nitrification and denitrification. Similarly, the relative abundance of terminal restriction fragments generated from Xanthomonas increased from 3% to 10%. Therefore, these bacteria could play a prominent role in this process. To reveal the relationship between stability of the microbial community and performance of the system, microbial community succession was visualized by multidimensional scaling analysis. The microbial community structure changed markedly, particularly during the start-up period of the system. The plots then became stable after the start of nitrification and denitrification. This result suggests that the succession of microbial community structure had a correlation with the performance of the system.

Bacteroidetes↗

PubMed1994

Molecular analysis of enrichment cultures of marine ammonia oxidisers.

Marine ammonia oxidising bacteria were enriched by incubation of sea water, amended with ammonium sulphate, and subsequent subculture in liquid inorganic medium. PCR primers were designed to be specific for rDNA sequences from ammonia oxidisers belonging to the beta-sub-group of the proteobacteria. These primers were then used to amplify rRNA genes from ammonia oxidiser enrichment cultures containing heterotrophs. PCR products were recovered from all cultures in which complete ammonia oxidation occurred. Subsequent rDNA sequence analysis indicated the presence of three new lineages within the clade defined by sequences of cultured beta-sub-group ammonia oxidisers. Two of the new lineages showed moderate similarity to sequences from pure cultures of ammonia oxidisers previously isolated from marine and brackish environments. The third lineage (AEM-3) was deep branching and occupied an intermediate position between clades defined by Nitrosomonas or Nitrosospira, which were isolated from soil or sewage. The phylogenetic analysis suggests that, in enrichment cultures, the primers are specific for members of the target group, the beta-proteobacteria ammonia oxidisers. The results also indicate the presence of previously unknown ammonia oxidisers in marine samples. The approach enabled analysis of ammonia oxidiser enrichments at an early stage and without the requirement for isolation of pure cultures, significantly reducing the time required and facilitating quantitative assessment of relatedness of strains.

Ammonia↗

PubMed1997

A gene encoding a membrane protein exists upstream of the amoA/amoB genes in ammonia oxidizing bacteria: a third member of the amo operon?

The gene cluster encoding ammonia monooxygenase (AMO) in the chemolithotrophic soil bacterium Nitrosospira sp. NpAV was found to contain a third open reading frame, termed amoC, upstream of the genes amoA and amoB that encode the subunits of AMO. The amoC gene and its flanking regions were isolated and sequenced from a 4.4 kb EcoRI fragment that contains one of three copies of the ammonia monooxygenase gene cluster. The presence of this gene upstream of the other two amoA gene copies in Nitrosospira NpAV as well as upstream of amoA genes in the genomes of other ammonia oxidizing nitrifiers (strains in the genera Nitrosomonas, Nitrosopira, Nitrosolobus and Nitrosovibrio) was confirmed using genomic DNA, oligodeoxyribonucleotide primers and the PCR. The amoC gene in Nitrosospira sp. NpAV encodes a 270 amino acid polypeptide of approximately 36 kDa. Topological analysis of the predicted primary structure revealed 6 membrane spanning domains. The amoC gene was expressed in recombinant Escherichia coli from its indigenous promoter.

Amino Acid Sequence↗

PubMed1981

Inhibitory effect of nitrapyrin on three genera of ammonia-oxidizing nitrifiers.

Five strains of Nitrosomonas and one each of Nitrosospira and Nitrosolobus were examined for sensitivity to the nitrification inhibitor nitrapyrin. Considerable variation in sensitivity was observed, with some strains about five times more resistant than others. Sensitivity to nitrapyrin varied more with strain than with genus.

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PubMed1982

Stimulation of autotrophic ammonium oxidation in rice rhizosphere soil by the insecticide carbofuran.

The application of the insecticide carbofuran (technical or formulated) to rice rhizosphere soil suspensions at 10 and 100 ppm (mug/ml) of active ingredient distinctly stimulated the autotrophic oxidation of ammonium. Evidence suggested that Nitrosomonas sp. was enriched in the presence of carbofuran. Formulated carbofuran (Furadan 3G) exhibited a more pronounced stimulation of ammonium oxidation than that exhibited by technical-grade (99.5%) carbofuran, a result which was attributed to the CaCO(3) present in the formulation.

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PubMed1983

Inhibition of chemoautotrophic nitrification by sodium chlorate and sodium chlorite: a reexamination.

The oxidation of NH(4) by Nitrosomonas europaea was insensitive to 10 mM NaClO(3) (sodium chlorate) but was strongly inhibited by NaClO(2) (sodium chlorite; K(i), 2 muM). The oxidation of NO(2) by Nitrobacter winogradskyi was inhibited by both ClO(3) and ClO(2) (K(i) for ClO(2), 100 muM). N. winogradskyi reduced ClO(3) to ClO(2) under both aerobic and anaerobic conditions, and as much as 0.25 mM ClO(2) was detected in the culture filtrate. In mixed N. europaea-N. winogradskyi cell suspensions, the oxidation of both NH(4) and NO(2) was inhibited in the presence of 10 mM ClO(3) after a 2-h lag period, despite the fact that, under these conditions, ClO(2) was not detected in the filtrate. The data are consistent with the hypothesis that, in mixed culture, NH(4) oxidation is inhibited by ClO(2) produced by reduction of ClO(3) by the NO(2) oxidizer. The use of ClO(3) inhibition of NO(2) oxidation in assays of nitrification by mixed populations necessitates cautious interpretation unless it can be shown that the oxidation of NH(4) is not affected.

Journal Article↗

PubMed1984

Bicarbonate Uptake by Nitrifiers: Effects of Growth Rate, pH, Substrate Concentration, and Metabolic Inhibitors.

The ratios of bicarbonate uptake to substrate oxidation were measured for three genera of nitrifying bacteria. The ratios for the two ammonium oxidizers tested were essentially the same; 0.0863 +/- 0.0055 and 0.0868 +/- 0.0091 mumol of bicarbonate were taken up per umol ammonium oxidized for Nitrosomonas europaea and a Nitrosospira strain, respectively. For Nitrobacter sp., a ratio of 0.0236 +/- 0.0013 mumol of bicarbonate taken up per umol of nitrite oxidized was obtained. Cells were grown in substrate-limited continuous culture and in batch culture, with generation times ranging between 16 and 189 h for the ammonium oxidizers and 18 and 69 h for Nitrobacter sp. All ratios appeared to be independent of growth rates and pH. However, short-term changes in substrate concentration and certain metabolic inhibitors significantly changed the efficiency of bicarbonate uptake. The significance of these results to the application of the nitrapyrin-sensitive bicarbonate uptake method for measuring nitrification rates in natural samples is discussed.

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PubMed1986

Inhibition of ammonium oxidation by nitrapyrin in soil and liquid culture.

Inhibition of growth of axenic cultures of Nitrosomonas europaea by nitrapyrin was investigated in liquid culture and in soil. In liquid culture, exponentially growing cells were more sensitive than stationary-phase cells, possibly due to a requirement for uptake of nitrapyrin, metabolism of nitrapyrin, or both before inhibition. Differences in sensitivity were observed between the parent strain and two strains, sp1 and sp2, that were selected through repeated subculturing. These differences were reflected in the length of the lag period induced by nitrapyrin and in the specific growth rate and were due to different bactericidal and bacteriostatic effects. Soil provided significant protection from inhibition, with concentrations of nitrapyrin approximately one order of magnitude greater than those required for equivalent inhibition in liquid culture. The data show that strain differences alone do not explain differences in sensitivity between nitrification in soil and in liquid culture and suggest that the inhibitor may be more effective against actively nitrifying soils.

Journal Article↗

PubMed1987

Nitrifying bacteria in wastewater reservoirs.

Deep wastewater reservoirs are used throughout Israel to store domestic wastewater effluents for summer irrigation. These effluents contain high concentrations of ammonia (</=5 mM) that are frequently toxic to photosynthetic microorganisms and that lead to development of anoxic conditions. Population dynamics of nitrifying bacteria and rates of nitrification were studied in two wastewater reservoirs that differed in organic load and degree of oxygenation and in the laboratory under controlled conditions, both by serial dilutions in mineral medium and microscopically with fluorescein isothiocyanate-conjugated antibodies prepared against local isolates. The difference in counts by the two methods was within 1 order of magnitude. In the laboratory, an O(2) concentration of 0.2 mg liter was close to optimal with respect to growth of NH(3) oxidizers on domestic wastewater, while O(2) concentrations of 0.05 mg liter supported significant rates of nitrification. It was found that even hypertrophic anaerobic environments such as the anaerobic hypolimnion of the wastewater reservoir or the anaerobic settling ponds are capable of sustaining a viable, although not actively nitrifying, population of Nitrosomonas spp. and Nitrobacter spp., in contrast to their rapid decline when maintained anaerobically in mineral medium in the laboratory. Nitrification rates of NH(3) in effluents during storage in the reservoirs were slower by 1 to 2 orders of magnitude compared with corresponding rates in water samples brought to the laboratory. The factors causing this inhibition were not identified.

Journal Article↗

PubMed1988

Effects of Light and CO on the Survival of a Marine Ammonium-Oxidizing Bacterium during Energy Source Deprivation.

The chemolithotrophic ammonium-oxidizing bacterium Nitrosomonas cryotolerans responds uniquely to nutrient deprivation by lowering its endogenous respiration and anabolic processes to undetectable levels during starvation, thus appearing to enter a dormant state. To ascertain whether this state protects the cells from further stresses (as seen with endospore-forming bacteria), the starved cells were subjected to two known inhibitors, CO and light. It was found that long-term-starved cells were less resistant than freshly starved cells to light inhibition. Both long-term-starved cells and freshly starved cells were unaffected by CO.

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PubMed1990

Ammonia-oxidizing bacteria in a chloraminated distribution system: seasonal occurrence, distribution and disinfection resistance.

Nitrification in chloraminated drinking water can have a number of adverse effects on water quality, including a loss of total chlorine and ammonia-N and an increase in the concentration of heterotrophic plate count bacteria and nitrite. To understand how nitrification develops, a study was conducted to examine the factors that influence the occurrence of ammonia-oxidizing bacteria (AOB) in a chloraminated distribution system. Samples were collected over an 18-month period from a raw-water source, a conventional treatment plant effluent, and two covered, finished-water reservoirs that previously experienced nitrification episodes. Sediment and biofilm samples were collected from the interior wall surfaces of two finished-water pipelines and one of the covered reservoirs. The AOB were enumerated by a most-probable-number technique, and isolates were isolated and identified. The resistance of naturally occurring AOB to chloramines and free chlorine was also examined. The results of the monitoring program indicated that the levels of AOB, identified as members of the genus Nitrosomonas, were seasonally dependent in both source and finished waters, with the highest levels observed in the warm summer months. The concentrations of AOB in the two reservoirs, both of which have floating covers made of synthetic rubber (Hypalon; E.I. du Pont de Nemours & Co., Inc., Wilmington, Del.), had most probable numbers that ranged from less than 0.2 to greater than 300/ml and correlated significantly with temperature and levels of heterotrophic plate count bacteria. No AOB were detected in the chloraminated reservoirs when the water temperature was below 16 to 18 degrees C. The study indicated that nitrifiers occur throughout the chloraminated distribution system. Higher concentrations of AOB were found in the reservoir and pipe sediment materials than in the pipe biofilm samples. The AOB were approximately 13 times more resistant to monochloramine than to free chlorine. After 33 min of exposure to 1.0 mg of monochloramine per liter (pH 8.2, 23 degrees C), 99% of an AOB culture was inactivated. The amounts of this disinfectant that are currently used (1.5 mg/liter at a 3:1 ratio of chlorine to ammonia-N) may be inadequate to control the growth of these organisms in the distribution system.

Ammonia↗

PubMed1990

Biodegradation of Halogenated Hydrocarbon Fumigants by Nitrifying Bacteria.

Three species of nitrifying bacteria were tested for the ability to degrade the halocarbon fumigants methyl bromide, 1,2-dichloropropane, and 1,2-dibromo-3-chloropropane. The soil nitrifiers Nitrosomonas europaea and Nitrosolobus multiformis degraded all three fumigants, while the marine nitrifier Nitrosococcus oceanus degraded only methyl bromide under the conditions tested. Inhibition of biodegradation by allylthiourea and acetylene, specific inhibitors of ammonia monooxygenase, suggests that ammonia monooxygenase is the enzyme which catalyzes fumigant degradation.

Journal Article↗

PubMed1991

Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Dual Energy-Limited Chemostats.

The absence of nitrification in soils rich in organic matter has often been reported. Therefore, competition for limiting amounts of ammonium between the chemolithotrophic ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis was studied in the presence of Nitrobacter winogradskyi in continuous cultures at dilution rates of 0.004 and 0.01 h. Ammonium limitation of A. globiformis was achieved by increasing the glucose concentration in the reservoir stepwise from 0 to 5 mM while maintaining the ammonium concentration at 2 mM. The numbers of N. europaea and N. winogradskyi cells decreased as the numbers of heterotrophic bacteria rose with increasing glucose concentrations for both dilution rates. Critical carbon-to-nitrogen ratios of 11.6 and 9.6 were determined for the dilution rates of 0.004 and 0.01 h, respectively. Below these critical values, coexistence of the competing species was found in steady-state situations. Although the numbers were strongly reduced, the nitrifying bacteria were not fully outcompeted by the heterotrophic bacteria above the critical carbon-to-nitrogen ratios. Nitrifying bacteria could probably maintain themselves in the system above the critical carbon-to-nitrogen ratios because they are attached to the glass wall of the culture vessels. The numbers of N. europaea decreased more than did those of N. winogradskyi. This was assumed to be due to heterotrophic growth of the latter species on organic substrates excreted by the heterotrophic bacteria.

Journal Article↗

PubMed1992

Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Continuously Percolated Soil Columns.

Although the absence of nitrate formation in grassland soils rich in organic matter has often been reported, low numbers of nitrifying bacteria are still found in these soils. To obtain more insight into these observations, we studied the competition for limiting amounts of ammonium between the chemolithotrophic ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis in the presence of Nitrobacter winogradskyi with soil columns containing calcareous sandy soil. The soil columns were percolated continuously at a dilution rate of 0.007 h, based on liquid volumes, with medium containing 5 mM ammonium and different amounts of glucose ranging from 0 to 12 mM.A. globiformis was the most competitive organism for limiting amounts of ammonium. The numbers of N. europaea and N. winogradskyi cells were lower at higher glucose concentrations, and the potential ammonium-oxidizing activities in the uppermost 3 cm of the soil columns were nonexistent when at least 10 mM glucose was present in the reservoir, although 10 nitrifying cells per g of dry soil were still present. This result demonstrated that there was no correlation between the numbers of nitrifying bacteria and their activities. The numbers and activities of N. winogradskyi cells decreased less than those of N. europaea cells in all layers of the soil columns, probably because of heterotrophic growth of the nitrite-oxidizing bacteria on organic substrates excreted by the heterotrophic bacteria or because of nitrate reduction at reduced oxygen concentrations by the nitrite-oxidizing bacteria. Our conclusion was that the nitrifying bacteria were less competitive than the heterotrophic bacteria for ammonium in soil columns but that they survived as viable inactive cells. Inactive nitrifying bacteria may also be found in the rhizosphere of grassland plants, which is rich in organic carbon. They are possibly reactivated during periods of net mineralization.

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