ALLELOPATHIC INHIBITION OF NITRIFICATION AND NITRIFYING BACTERIA IN A PONDEROSA PINE (PINUS PONDEROSA DOUGL.) COMMUNITY

The dynamics of ponderosa pine (Pinus ponderosa Dougl.) stands in western North Dakota were studied to determine the influence of plant-produced chemicals on nitrification rates and competitive interactions within the stands. Ponderosa pine accounted for more than 98% of all tree and shrub stratum stems in this climax community. Low levels of nitrate-nitrogen relative to ammonium-nitrogen and low numbers of Nitrosomonas and Nitrobacter in the soils indicated that nitrification rates were low. Inhibition of nitrification is often attributed to low soil pH in coniferous forests, but the slightly alkaline soils in this study (pH 7.25–7.75) suggested that another factor caused the low nitrification. Evidence obtained suggested that the reduction in nitrate synthesis was due to the production and subsequent transfer to the soil of secondary plant chemicals that were toxic to Nitrosomonas. Chemical inhibitors of nitrification, including caffeic acid, chlorogenic acid, quercitin, and condensed tannins, were found in extracts from ponderosa pine needles, bark, and A horizon soils. These extracts proved to be toxic to soil suspensions of Nitrosomonas causing reductions of from 68–93% of the control. These findings indicate that climax ponderosa pine communities minimize the conversion of ammonia-nitrogen to nitrate-nitrogen by chemically inhibiting nitrification.     

COMPARATIVE INHIBITION OF NITRIFIERS AND NITRIFICATION IN A FOREST COMMUNITY AS A RESULT OF THE ALLELOPATHIC NATURE OF VARIOUS TREE SPECIES

Inhibition of nitrification and nitrifiers was significantly variable under different tree species in the same forest ecosystem. Nitrate nitrogen was always lower than ammonium nitrogen when compared under each species. On the other hand, low numbers of Nitrosomonas and Nitrobacter showed an inverse relationship with large amounts of ammonium in most samples. Aforementioned variation is due to the variable tree litter under different species, which in turn produces inhibitors of nitrification and nitrifiers. Inhibition of nitrification in natural ecosystems increases the amounts of ammonium nitrogen thus resulting in a conservation of energy, if plants utilize such nitrogen directly.     

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.     

INHIBITION OF NITRIFICATION BY CLIMAX ECOSYSTEMS. III. INHIBITORS OTHER THAN TANNINS

We obtained considerable evidence in earlier work that inhibition of nitrification begins during old-field succession and increases to a maximum in the climax (Rice and Pancholy, 1972, 1973). Moreover, we found that tannins and tannin derivatives appear to be important inhibitors of nitrification. In the present project, other potential phenolic inhibitors of nitrification were identified in acetone extracts of entire plants of most herbaceous species and leaves of tree species important in an intermediate stage of succession and the climax in three vegetation types in Oklahoma. Attempts were made also to identify potential inhibitors in acetone extracts of soil from the top 15 cm of the oak-pine climax. Seventeen potential inhibitors were identified from the eleven important species of plants surveyed. These were mostly phenolic acids and flavonoids, but one coumarin compound, scopolin, was found in high amounts in several species. The potential inhibitors were most common in green tops or green leaves, but roots, dead tops (of previous year), and dead leaves had high amounts of some compounds. Caffeic and ferulic acids were prominent in dead leaves or dead tops, and one flavonoid, myricetin, occurred in sizeable amounts in dead tops of Sorghastrum nutans. The aglycones of most of the compounds were tested against nitrification in soil suspensions, and all completely inhibited oxidation of NH⁺₄ to NO⁻₂ by Nitrosomonas at concentrations as low as 10⁻⁶ to 10⁻⁸ M. Oxidation of NO⁻₂ to NO⁻₃ by Nitrobacter, however, was affected much less severely by these inhibitors. The greater resistance of Nitrobacter is not significant biologically because inhibition of the first step carried out by Nitrosomonas effectively inhibits the entire process of nitrification. The 3-glucoside of quercetin, isoquercitrin, inhibited the activity of Nitrosomonas completely at the same concentration as quercetin. We found a compound in large quantities in the oak-pine climax soil which appeared in all tests to be a flavonoid aglycone, but we were never able to identify it to our satisfaction. This substance was extremely inhibitory to germination and seedling growth of ‘Crimson Giant’ radish seeds. These have hard seed coats and germinate very rapidly so most inhibitors do not affect their germination at all. It is likely that some, if not all, of the nitrification inhibitors identified may be important in inhibition of nitrification in the later stages of succession and in the climax along with the tannins.     

Exopolymers: An ecological characteristic of a floc-attached,ammonia-oxidizing bacterium

A lithotrophic ammonia-oxidizing bacterium of the Nitrosomonas type was isolated from the lower River Elbe. Enrichment was attained from suspended particulate matter (SPM) of a water sample. At its natural environment, this species almost exclusively occurred attached to flocs, as demonstrated with the immunofluorescence technique. On the species level, the isolate was not related to any of the described Nitrosomonas species. The strain was characterized by strong production of exopolymeric substances (EPS) and was observed to occur self-flocculating in pure cultures. Low ammonia concentrations stimulated EPS production. The EPS revealed an extensive capacity for binding particulate and dissolved materials, as well as cells of other bacterial species. This capacity was affected by changing pH values or salt concentrations of the medium. The EPS appeared to function as a buffer against toxic compounds and against changing environmental conditions. Another Nitrosomonas strain isolated from the Elbe estuary, but lacking recognizable EPS production, was used for comparison. Correspondence to: G. Stehr     

A bioluminescence assay to detect nitrification inhibitors released from plant roots: a case study with Brachiaria humidicola

A bioluminescence assay using recombinant Nitrosomonas europaea was adopted to detect and quantify natural nitrification inhibitors in plant–soil systems. The recombinant strain of N. europaea produces a distinct two-peak luminescence due to the expression of luxAB genes, introduced from Vibrio harveyi, during nitrification. The bioluminescence produced in this assay is highly correlated with NO₂⁻ production (r ² = 0.94). Using the assay, we were able to detect significant amounts of a nitrification inhibitor produced by the roots of Brachiaria humidicola (Rendle) Schweick. We propose that the inhibitory activity produced/released from plants be termed ‘biological nitrification inhibition’ (BNI) to distinguish it from industrially produced inhibitors. The amount of BNI activity produced by roots was expressed in units defined in terms of the action of a standard inhibitor allylthiourea (AT). The inhibitory effect from 0.22 μM AT in an assay containing 18.9 mM of NH₄⁺ is defined as one AT unit of activity. A substantial amount of BNI activity was released from the roots of B. humidicola (15–25 AT unit g⁻¹ root dry wt day⁻¹). The BNI activity released was a function of the growth stage and N content of the plant. Shoot N levels were positively correlated with the release of BNI activity from roots (r ² = 0.76). The inhibitor/s released from B. humidicola roots suppressed soil nitrification. Additions of 20 units of BNI per gram of soil completely inhibited NO₃⁻ formation in a 55-day study and remained functionally stable in the soil for 50 days. Both the ammonia monooxygenase and the hydroxylaminooxidoreductase enzymatic pathways in Nitrosomonas were effectively blocked by the BNI activity released from B. humidicola roots. The proposed bioluminescence assay can be used to characterize and determine the BNI activity of plant roots, thus it could become a powerful tool in genetically exploiting the BNI trait in crops and pastures.     

Effect of continuous Cd feeding on the performance of a nitrification reactor

The inhibitory effect of Cd on nitrification was investigated in a continuous-flow system with enriched nitrifying bacteria. The maximum specific ammonium utilization rate and the half-saturation constant were found as 671 mg NH₄–N/g VSS day and 0.48 mg/l, respectively. In the case of continuous Cd input at 1 and 2.5 mg/l, nitrification was inhibited by 30% and 47%, respectively. Inhibition ranged from 20% to 40% and no further increase in inhibition was exhibited in new runs except at 10 mg/l influent Cd. At 10 mg/l influent Cd, specific ammonium utilization and nitrate production rates were inhibited by 90%. On the contrary, a serious nitrite accumulation was not observed during this period. When Cd feeding was stopped, recovery from inhibition was observed after 37 day which was seen by the improvement in ammonium utilization and nitrate production rates. A shift in microbial population from the initial Nitrosomonas sp. to the Cd-tolerant Nitrosospira sp. was observed in the recovery period from severe Cd inhibition. After the domination of Nitrosospira species, redosing at 10 mg/l and then at 15 mg/l did not affect the performance as before.     

Application of Molecular Biological Techniques to a Seasonal Study of Ammonia Oxidation in a Eutrophic Freshwater Lake

The autotrophic ammonia-oxidizing bacteria in a eutrophic freshwater lake were studied over a 12-month period. Numbers of ammonia oxidisers in the lakewater were small throughout the year, and tangential-flow concentration was required to obtain meaningful estimates of most probable numbers. Sediments from littoral and profundal sites supported comparatively large populations of these bacteria, and the nitrification potential was high, particularly in summer samples from the littoral sediment surface. In enrichment cultures, lakewater samples nitrified at low (0.67 mM) ammonium concentrations only whereas sediment samples exhibited nitrification at high (12.5 mM) ammonium concentrations also. Enrichments at low ammonium concentration did not nitrify when inoculated into high-ammonium medium, but the converse was not true. This suggests that the water column contains a population of ammonia oxidizers that is sensitive to high ammonium concentrations. The observation of nitrification at high ammonium concentration by isolates from some winter lakewater samples, identified as nitrosospiras by 16S rRNA probing, is consistent with the hypothesis that sediment ammonia oxidizers enter the water column at overturn. With only one exception, nested PCR amplification enabled the detection of Nitrosospira 16S rDNA in all samples, but Nitrosomonas (N. europaea-eutropha lineage) 16S rDNA was never obtained. However, the latter were part of the sediment and water column communities, because their 16S rRNA could be detected by specific oligonucleotide probing of enrichment cultures. Furthermore, a specific PCR amplification regime for the Nitrosomonas europaea ammonia monooxygenase gene (amoA) yielded positive results when applied directly to sediment and lakewater samples. Patterns of Nitrosospira and Nitrosomonas detection by 16S rRNA oligonucleotide probing of sediment enrichment cultures were complex, but lakewater enrichments at low ammonium concentration were positive for nitrosomonads and not nitrosospiras. Analysis of enrichment cultures has therefore provided evidence for the existence of subpopulations within the lake ammonia-oxidizing community distinguishable on the basis of ammonium tolerance and possibly showing a seasonal distribution between the sediment and water column.     

Effect of methyl 3-4-hydroxyphenyl propionate, a Sorghum root exudate, on N dynamic, potential nitrification activity and abundance of ammonia-oxidizing bacteria and archaea

Aims

It has been reported that root exudates of Sorghum bicolor can inhibit nitrification in a bioassay using Nitrosomonas, and methyl 3-(4-hydroxyphenyl) propionate (MHPP) was identified as one of the nitrification inhibiting compounds. Therefore, we have investigated the effects of this compound on nitrogen dynamic, potential nitrification activity and on soil microorganisms.

Methods

We conducted soil incubation experiments using synthetic MHPP to evaluate its effect on changes in inorganic soil nitrogen pools, on nitrification activity and on abundance of ammonia-oxidizing bacteria and archaea. Addition of MHPP at two concentrations equivalent to 70 and 350 μg C g^?1 soil was compared to glucose as a carbon source and to the commercially available nitrification inhibitor dicyandiamide (DCD).

Results

Soil amended with the high dose of MHPP and with DCD showed reduced nitrate content and low nitrification activity after 3 and 7 days of incubation. This was mirrored by a 70 % reduction in potential nitrification activity compared to a nitrogen-only control. None of the incubation treatments affected non-target microbial counts as estimated by 16S rRNA gene copy numbers, however, the high dose of MHPP significantly reduced the abundance of ammonia-oxidizing bacteria and archaea.

Conclusions

These findings suggest that MHPP is capable of suppressing nitrification in soil, possibly by reducing the population size and activity of ammonia-oxidizing microorganisms.     

Nitrification in fixed-bed reactors treating saline wastewater

Halophilic nitrifiers belonging to the genus Nitrosomonas and Nitrospira were enriched from seawater and marine sediment samples of the North Sea. The maximal ammonia oxidation rate (AOR) in batch enrichments with seawater was 15.1 mg N L⁻¹ day⁻¹. An intermediate nitrite accumulation was observed. Two fixed-bed reactors for continuous nitrification with either polyethylene/clay sinter lamellas (FBR A) or porous ceramic rings (FBR B) were run at two different ammonia concentrations, three different ammonia loading rates (ALRs), ± pH adjustment, and at an increased upflow velocity. A better overall nitrification without nitrite accumulation was observed in FBR B. However, FBR A revealed a higher AOR and nitrite oxidation rate of 6 and 7 mg N L⁻¹ h⁻¹, compared to FBR B with 5 and 5.9 mg N L⁻¹ h⁻¹, respectively. AORs in the FBRs were at least ten times higher than in suspended enrichment cultures. Whereas a shift within the ammonia-oxidizing population in the genus Nitrosomonas at the subspecies level occurred in FBR B with synthetic seawater at an increasing ALR and a decreasing pH, the nitrite oxidizing Nitrospira population apparently did not change.     

Properties of a new strain of Nitrosomonas isolated from an aerobic biofilm in a domestic sewage-treatment system

A new ammonia-oxidizing strain, isolated from an aerobic biofilm in a domestic sewage-treatment system, was identified as a species of Nitrosomonas different from Nitrosomonas europaea. This strain had morphological features and growth characteristics typical of members of the genus Nitrosomonas. The G+C content of the DNA of this strain was 48.5 mol%, being lower than that of known strains of N. europaea. The extent of the homology between the DNA of this strain and that of other strains of N. europaea was less than 30%. After cells of this isolate, immobilized in a polyacrylamide gel, had been added to the aerobic reactor of a laboratory-scale sewage-treatment system, the concentration of ammonium nitrogen in the effluent decreased to 2 mg/l without the accumulation of nitrite, and removal of more than 70% of the nitrogen from the input sewage was achieved.     

INHIBITION OF NITRIFICATION BY CLIMAX ECOSYSTEMS. II. ADDITIONAL EVIDENCE AND POSSIBLE ROLE OF TANNINS

The same nine plots were used in this study as in our previous study on inhibition of nitrification (Rice and Pancholy, 1972). These consisted of three stands representing two stages of old field succession and the climax in each of three vegetation types in Oklahoma: tall grass prairie, post oak-blackjack oak forest, and oak-pine forest. Soil samples were analyzed three times during the growing season of 1972 for exchangeable ammonium nitrogen, nitrate, and numbers of Nitrosomonas and Nitrobacter. Results were similar to those obtained during the entire year of 1971. The amount of ammonium nitrogen was lowest in the first successional stage, intermediate in the intermediate successional stage, and highest in the climax. The amount of nitrate was highest in the first successional stage, intermediate in the intermediate successional stage, and lowest in the climax. The numbers of nitrifiers were highest in the first successional stage usually and decreased to a very low number in the climax. These data furnish additional evidence that the nitrifiers are inhibited in the climax so that ammonium nitrogen is not oxidized to nitrate as readily in the climax as in the successional stages. This would aid in the conservation of nitrogen and energy in the climax ecosystem. Some inhibition of nitrification occurred in the intermediate stage of succession also. Previous studies of tannins indicated that these are inhibitory to nitrification, so all important plant species in the intermediate successional stage and the climax were analyzed for total tannin content. A method for extracting and quantifying condensed tannins from soils was developed and the amounts of tannins were determined in each 15-cm level down to 60 cm in the same two plots in each vegetation type. Gallic and ellagic acids, which result from the digestion of hydrolyzable tannins in oak species, were also extracted and quantified in the climax oak-pine forest. All the important herbaceous species, including the grasses, were found to have considerable amounts of condensed tannins. The highest amounts of tannins occurred in the oaks and pine, however. Condensed tannins, hydrolyzable tannins, ellagic acid, gallic acid, digallic acid, and commercial tannic acid (hydrolyzable tannin), in very small concentrations, were all found to completely inhibit nitrification by Nitrosomonas in soil suspensions for 3 weeks, the duration of the tests. Slightly larger concentrations were required to inhibit nitrification by Nitrobacter under similar conditions. The concentrations of tannins, gallic acid, and ellagic acid found in the soil of the research plots were several times higher than the minimum concentrations necessary to completely inhibit nitrification. The inhibition of nitrification was always greater in the climax stand than in the intermediate successional stage in each vegetation type, and the concentration of tannins in the top 15 cm of soil was always higher in the climax stand than in the intermediate successional stage. Moreover, the amounts of tannins calculated to be added to each plot each year are much less than the amounts found in the soil, indicating that the tannins accumulate over a period of time. Thus, it appears that the tannins and tannin derivatives may play a continuous and rather prominent role in the inhibition of nitrification by vegetation.     

Analysis of Microbial Population Dynamics in a Partial Nitrifying SBR at Ambient Temperature

In this study, a lab-scale partial nitrifying sequencing batch reactor (SBR) was developed to investigate partial nitrification at ambient temperature (16–22 °C). Techniques of denaturing gradient gel electrophoresis (DGGE), cloning, and fluorescence in situ hybridization (FISH) were utilized simultaneously to study microbial population dynamics. Partial nitrification was effectively achieved in response to shifts of influent ammonium concentrations. DGGE results showed that higher ammonia concentration referred to lower ammonia-oxidizing bacteria (AOB) diversity in the SBR. Phylogenetic analysis revealed that all the predominant AOB was affiliated with Nitrosomonas genus. FISH analysis illustrated AOB was the predominant nitrifying bacteria of microbial compositions when SBR achieved partial nitrification (PN) at ambient temperature.     

Cold temperature decreases bacterial species richness in nitrogen‐removing bioreactors treating inorganic mine waters

Explosives used in mining, such as ammonium nitrate fuel oil (ANFO), can cause eutrophication of the surrounding environment by leakage of ammonium and nitrate from undetonated material that is not properly treated. Cold temperatures in mines affect nitrogen removal from water when such nutrients are treated with bioreactors in situ. In this study we identified bacteria in the bioreactors and studied the effect of temperature on the bacterial community. The bioreactors consisted of sequential nitrification and denitrification units running at either 5 or 10°C. One nitrification bioreactor running at 5°C was fed with salt spiked water. From the nitrification bioreactors, sequences from both ammonia‐ and nitrite‐oxidizing bacteria were identified, but the species were distinct at different temperatures. The main nitrifiers in the lower temperature were closely related to the genera Nitrosospira and Candidatus Nitrotoga. 16S rRNA gene sequences closely related to halotolerant Nitrosomonas eutropha were found only from the salt spiked nitrification bioreactor. At 10°C the genera Nitrosomonas and Nitrospira were the abundant nitrifiers. The results showed that bacterial species richness estimates were low, <150 operational taxonomic units (OTUs), in all bioreactor clone libraries, when sequences were assigned to operational taxonomic units at an evolutionary distance of 0.03. The only exception was the nitrification bioreactor running at 10°C where species richness was higher, >300 OTUs. Species richness was lower in bioreactors running at 5°C compared to those operating at 10°C. Biotechnol. Bioeng. 2011;108: 2876–2883. © 2011 Wiley Periodicals, Inc.     

Estimation of nitrifier abundances in a partial nitrification reactor treating ammonium-rich saline wastewater using DGGE, T-RFLP and mathematical modeling

The bacterial community in a partial nitrification reactor was analyzed on the basis of 16S rRNA gene by cloning–sequencing method, and the percentages of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in the activated sludge were quantified by three independent methods, namely, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP) and Double Monod modeling. The clone library results suggested that there were only a dominant AOB and a dominant NOB species in the reactor, belonging to Nitrosomonas genus and Nitrospira genus, respectively. The percentages of NOB in total bacterial community increased from almost 0% to 30% when dissolved oxygen (DO) levels were changed from 0.15 mg/L to 0.5 mg/L, coinciding with the accumulation and conversion of nitrite, while the percentages of AOB changed little in the two phases. The results confirmed the importance of low DO level for inhibiting NOB to achieve partial nitrification. Furthermore, the percentages of AOB and NOB in the total bacteria community were estimated based on the results of batch experiments using Double Monod model, and the results were comparable with those determined according to profiles of DGGE and T-RFLP.     

Rapid start-up of nitrifying MBBRs at low temperatures: nitrification,biofilm response and microbiome analysis

The moving bed biofilm reactor (MBBR), operated as a post carbon removal system, requires long start-up times in comparison to carbon removal systems due to slow growing autotrophic organisms. This study investigates the use of carriers seeded in a carbon rich treatment system prior to inoculation in a nitrifying MBBR system to promote the rapid development of nitrifying biofilm in an MBBR system at temperatures between 6 and 8 °C. Results show that nitrification was initiated by the carbon removal carriers after 22 h of operation. High throughput 16S-rDNA sequencing indicates that the sloughing period was a result of heterotrophic organism detachment and the recovery and stabilization period included a growth of Nitrosomonas and Nitrospira as the dominant ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) in the biofilm. Peripheral microorganisms such as Myxococcales, a rapid EPS producer, appear to have contributed to the recovery and stabilization of the biofilm.

     

Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea

Ammonia‐oxidizing bacteria (AOB) have long been considered key to the removal of nitrogen in activated sludge bioreactors. Culture‐independent molecular analyses have established that AOB lineages in bioreactors are dynamic, but the underlying operational or environmental factors are unclear. Furthermore, the contribution of ammonia‐oxidizing archaea (AOA) to nitrogen removal in bioreactors has not been studied. To this end, we investigated the abundance of AOA and AOB as well as correlations between dynamics in AOB lineages and operational parameters at a municipal wastewater treatment plant sampled weekly over a 1 year period. Quantitative PCR measurements of bacterial and archaeal ammonia monooxygenase subunit A (amoA) genes revealed that the bacterial homologue predominated by at least three orders of magnitude in all samples. Archaeal amoA was only detectable in ～15% of these samples. Using terminal restriction fragment length polymorphism analysis, we monitored AOB lineages based on amoA genes. The Nitrosomonas europaea lineage and a novel Nitrosomonas‐like cluster were the dominant AOB signatures, with a Nitrosospira lineage present at lower relative abundance. These lineages exhibited strong temporal oscillations, with one becoming sequentially dominant over the other. Using non‐metric multidimensional scaling and redundancy analyses, we tested correlations between terminal restriction fragment length polymorphism profiles and 20 operational and environmental parameters. The redundancy analyses indicated that the dynamics of AOB lineages correlated most strongly with temperature, dissolved oxygen and influent nitrite and chromium. The Nitrosospira lineage signal had a strong negative correlation to dissolved oxygen and temperature, while the Nitrosomonas‐like (negative correlations) and N. europaea lineages (positive correlations) were inversely linked (relative to one another) to influent nitrite and chromium. Overall, this study suggests that AOA may be minor contributors to ammonia oxidation in highly aerated activated sludge, and provides insight into parameters controlling the diversity and dominance of AOB lineages within bioreactors during periods of stable nitrification.     

Deoxyribonucleic acid homologies among 96 strains of ammonia-oxidizing bacteria

DNA of 96 strains of the genera Nitrosomonas, Nitrosococcus, Nitrosospira, Nitrosolobus, and Nitrosovibrio was isolated and analysed spectrophotometrically. Percentages of guanine plus cytosine (G+C) content, genome sizes, and DNA-DNA homologies were determined. The results indicated the presence of eight Nitrosomonas species, three or four Nitrosococcus species, five Nitrosospira species, and two species of both Nitrosolobus and Nitrosovibrio. DNA homologies between strains of a separate species ranged from 56–100%. Average homologies between strains of different species were 33% in Nitrosococcus, 36% in Nitrosomonas, 37% in Nitrosolobus, 40% in Nitrosospira, and 42% in Nitrosovibrio. Average homologies between species of different genera were 33% and thus not significantly above the background value of 30% detected between DNA of ammonia-oxidizing bacteria and Escherichia coli. Genome sizes ranged from 1.90–2.74×10⁹ dalton in Nitrosomonas, 2.09–2.37×10⁹ dalton in Nitrosococcus, 1.87–2.15×10⁹ dalton in Nitrosospira, 1.92–2.10×10⁹ dalton in Nitrosolobus, and 1.91–2.15×10⁹ dalton in Nitrosovibrio. Differences in genome sizes were in accordance with DNA homologies.     

Diversity of ammonia monooxygenase (amoA) genes across environmental gradients in Chesapeake Bay sediments

Chesapeake Bay, the largest estuary in North America, encompasses a wide range of nutrient loading and trophic levels from the rivers and upper Bay to the sea, providing an ideal natural environment in which to explore relationships between functional diversity, physical/chemical complexity and ecosystem function (e.g. nitrification). In this study, amoA gene fragments (encoding subunit A of the key nitrification enzyme, ammonia monooxygenase) were PCR‐amplified from DNA extracted from sediment cores collected at five stations spanning gradients of salinity, ammonium, nitrate, oxygen and organic carbon along the Bay and Choptank River, a subestuary of the Bay. Phylogenetic analysis of ～30 amoA clones from each station revealed extensive diversity within the β‐Proteobacteria group of ammonia‐oxidizing bacteria (AOB), with the vast majority of sequences falling into coherent phylogenetic clusters distinct from sequences of cultivated AOB. Over 70% of the clones fell into two major phylogenetic clusters that appear to represent novel groups of Nitrosomonas‐like and Nitrosospira‐like amoA sequences that may be specific to estuarine and marine environments. Rarefaction analysis, estimators of genetic variation and dissimilarity indices all revealed differences in the relative amoA‐based diversity and/or richness among most of the stations, with the highest diversity at the North Bay station and the lowest at the mesohaline stations. Although salinity appears to play a role, no single physical or chemical parameter entirely explains the pattern of diversity along the estuary, suggesting that a complex combination of environmental factors may shape the overall level of AOB diversity in this dynamic environment.