Number Of Ammonia-oxidizing Bacteria Research Articles

High pH-enhanced soil nitrification was associated with ammonia-oxidizing bacteria rather than archaea in acidic soils

The integrated effects of environmental factors on soil nitrification are largely unknown. Here, we performed a microcosm experiment to investigate the interactive effects of pH and NH4+ on nitrification activity in two acidic soils with different land use patterns (Anhui soil, a forest soil; Jiangxi soil, a brush land soil). Both soils were incubated under native pH and CaCO3-manipulated pH in the presence or absence of added ammonium for 60 days. The addition of CaCO3 alone did not change the nitrification activity of either soil. Ammonium addition stimulated nitrification in Anhui soil, but not in Jiangxi soil, and this stimulation was more pronounced with increased CaCO3. The ammonia monooxygenase (amoA) gene copy number of both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) was much higher in Anhui soil than in Jiangxi soil. The amoA gene copy number of AOB in Anhui soil was more highly upregulated under CaCO3+NH4+ than NH4+ during incubation. In Anhui soil, changes in the denaturing gradient gel electrophoresis (DGGE) fingerprint patterns of bacterial amoA genes were parallel to changes in the amoA gene copy number of AOB. In Jiangxi soil, DGGE could not be performed because the PCR for bacterial DGGE did not yield any products, while quantitative PCR revealed that the amoA gene copy number of AOB changed during incubation. These results suggest that AOB plays an important role in CaCO3-enhanced nitrification of Anhui soil with ammonium addition. The low nitrification rates of Jiangxi soil regardless of CaCO3 with or without NH4+ supply may be ascribed to the lower activity of both AOB and AOA, especially AOA.

Monitoring the abundance and the activity of ammonia-oxidizing bacteria in a full-scale nitrifying activated sludge reactor.

Cell-specific ammonia oxidation rate (AOR) has been suggested to be an indicator of the performance of nitrification reactors and to be used as an operational parameter previously. However, published AOR values change by orders of magnitude and studies investigating full-scale nitrification reactors are limited. Therefore, this study aimed at quantifying ammonia-oxidizing bacteria (AOB) and estimating their in situ cell-specific AOR in a full-scale activated sludge reactor treating combined domestic and industrial wastewaters. Results showed that cell-specific AOR changed between 5.30 and 9.89 fmol cell(-1) h(-1), although no significant variation in AOB cell numbers were obtained (1.54E + 08 ± 0.22 cell/ml). However, ammonia-removal efficiency varied largely (52-79 %) and was proportional to the cell-specific AOR in the reactor. This suggested that the cell-specific AOR might be the factor affecting the biological ammonia-removal efficiency of nitrification reactors independent of the AOB number. Further investigation is needed to establish an empirical relationship to use cell-specific AOR as a parameter to operate full-scale nitrification systems more effectively.

Microbial Community Response to Chlorine Conversion in a Chloraminated Drinking Water Distribution System

Temporary conversion to chlorine (i.e., "chlorine burn") is a common approach to controlling nitrification in chloraminated drinking water distribution systems, yet its effectiveness and mode(s) of action are not fully understood. This study characterized occurrence of nitrifying populations before, during and after a chlorine burn at 46 sites in a chloraminated distribution system with varying pipe materials and levels of observed nitrification. Quantitative polymerase chain reaction analysis of gene markers present in nitrifying populations indicated higher frequency of detection of ammonia oxidizing bacteria (AOB) (72% of samples) relative to ammonia oxidizing archaea (AOA) (28% of samples). Nitrospira nitrite oxidizing bacteria (NOB) were detected at 45% of samples, while presence of Nitrobacter NOB could not be confirmed at any of the samples. During the chlorine burn, the numbers of AOA, AOB, and Nitrospira greatly reduced (i.e., 0.8-2.4 log). However, rapid and continued regrowth of AOB and Nitrospira were observed along with nitrite production in the bulk water within four months after the chlorine burn, and nitrification outbreaks appeared to worsen 6-12 months later, even after adopting a twice annual burn program. Although high throughput sequencing of 16S rRNA genes revealed a distinct community shift and higher diversity index during the chlorine burn, it steadily returned towards a condition more similar to pre-burn than burn stage. Significant factors associated with nitrifier and microbial community composition included water age and sampling location type, but not pipe material. Overall, these results indicate that there is limited long-term effect of chlorine burns on nitrifying populations and the broader microbial community.

Detection of ammonia-oxidizing archaea in fish processing effluent treatment plants.

Ammonia oxidation is the rate limiting step in nitrification and thus have an important role in removal of ammonia in natural and engineered systems with participation of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, their relative distribution and activity in fish processing effluent treatment plants (FPETPs) though significant, is hitherto unreported. Presence of AOA in sludge samples obtained from FPETPs was studied by amplification and sequencing of thaumarchaeal ammonia monooxygenase subunit A (AOA-amoA) gene. Different primer sets targeting 16S rRNA and AOA-amoA gene were used for the detection of AOA in FPETPs. Phylogenetic analysis of the gene revealed that the AOA was affiliated with thaumarchaeal group 1.1a lineage (marine cluster). Quantitative real time PCR of amoA gene was used to study the copy number of AOA and AOB in FPETPs. The AOA-amoA and AOB-amoA gene copy numbers of sludge samples ranged from 2.2×10(6) to 4.2×10(8) and 1.1×10(7) to 8.5×10(8)mg(-1) sludge respectively. Primer sets Arch-amoAF/Arch-amoAR and 340F/1000R were found to be useful for the sensitive detection of AOA-amoA and Archaeal 16S rRNA genes respectively in FPETPs. Their presence suggests the widespread occurrence and possible usefulness in removing ammonia from FPETPs which is in line with reports from other waste water treatment plants.

Agreement between amoA Gene-Specific Quantitative PCR and Fluorescence In Situ Hybridization in the Measurement of Ammonia-Oxidizing Bacteria in Activated Sludge

Microbial abundance is central to most investigations in microbial ecology, and its accurate measurement is a challenging task that has been significantly facilitated by the advent of molecular techniques over the last 20 years. Fluorescence in situ hybridization (FISH) is considered the gold standard of quantification techniques; however, it is expensive and offers low sample throughput, both of which limit its wider application. Quantitative PCR (qPCR) is an alternative that offers significantly higher throughput, and it is used extensively in molecular biology. The accuracy of qPCR can be compromised by biases in the DNA extraction and amplification steps. In this study, we compared the accuracy of these two established quantification techniques to measure the abundance of a key functional group in biological wastewater treatment systems, the ammonia-oxidizing bacteria (AOB), in samples from a time-series experiment monitoring a set of laboratory-scale reactors and a full-scale plant. For the qPCR analysis, we tested two different sets of AOB-specific primers, one targeting the 16SrRNA gene and one targeting the ammonia monooxygenase (amoA) gene. We found that there was a positive linear logarithmic relationship between FISH and the amoA gene-specific qPCR, where the data obtained from both techniques was equivalent at the order of magnitude level. The 16S rRNA gene-specific qPCR assay consistently underestimated AOB numbers.

Communities of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and nitrite-oxidizing bacteria in shrimp ponds

The communities of nitrifying microorganisms were identified in samples taken from six shrimp ponds in Thailand (five outdoor-earthen ponds and one indoor pond). The sequences of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and nitrite-oxidizing bacteria (NOB) were analyzed after specific PCR amplification of the 16S rRNA or amoA genes. Among the ammonia-oxidizing microorganisms, AOB appeared to be the most dispersed throughout the ponds, while AOA sequences were only retrieved from three ponds. The AOB found in the shrimp ponds belonged to only two AOB clusters, the Nitrosomonas sp. Nm143 cluster and Nitrosomonas marina cluster, which are reported with salt requirements. The majority of AOA sequences fell closer to group I.1a Thaumarcheota rather than group I.1b Thaumarcheota. For NOB, Nitrospira, but not Nitrobacter, were detected. NOB of sublineage II and IV Nitrospira, which were previously reported as salt tolerant and salt requirement NOB, were found to be common in the shrimp ponds. Insight into ammonia-oxidizing microorganisms, numbers of AOB and AOA amoA genes in two selected ponds (one outdoor-earthen ponds and one indoor pond) were quantified using qPCR. High numbers of AOA amoA genes were found in both ponds. The information obtained from this study clearly identifies the microorganisms responsible for nitrification in shrimp ponds.

Effect of high ammonia loads emitted from poultry-manure digestion on nitrification activity and nitrifier-community structure in a compost biofilter

Ammonia emissions from poultry-manure disposal and agricultural applications pose a global environmental challenge that requires the development of proper management practices. Recently, a scheme comprised of a compost-based biofilter for the treatment of high loads of ammonia emitted from poultry-manure digestion (up to 500gNH3m−3biofilterday−1) was suggested. In this study, we hypothesized that the high ammonia-adsorption capacity of the compost matrix creates an ammonia gradient along the biofilter that is occupied by adapted nitrifying communities, thus allowing high nitrification rates and ammonia removal. Accordingly, pilot-scale compost biofilters were constructed and batch-fed with ammonia emitted from digested poultry manure for over a year. The operation cycle included a nitrate washing step from the biofilter. Compost samples withdrawn at 20, 40 and 60cm distance from the gas inlet were chemically characterized and analyzed for nitrification activity and nitrifier abundance and diversity. The number of ammonia-oxidizing bacteria (AOB) was 0.5–1 order of magnitude lower in the bottom section (0–20cm), which was dominated by Nitrosomonas species, compared to the top layers which were occupied by a mixed Nitrosomonas and Nitrosospira population. In addition, ammonia-oxidizing archaea (AOA) were homogeneously distributed along the biofilter profile and their numbers were at least one order of magnitude higher than those of the AOB. Significantly lower potential nitrification activity was detected in the bottom layer, and correlated with AOB abundance. Together, the results indicate that with proper operation of compost biofilters, suitable communities of nitrifying microorganisms that are able to cope with a wide range of ammonia concentrations, sourced from manure digestion, will develop.

Nitrogen Dynamic and Microbiological Evolution During Aerobic Treatment of Digested Sludge

Anaerobic digestion produce considerable amount of digestates which may not meet the requirements for direct land spreading. Aerobic treatment provides an appropriate post-treatment method to deal with the increasing amount of digestates. In this work, we studied the nitrogen dynamic and the evolution of groups of microorganisms during aerobic treatment of digested sludge. The oxygen consumption concentrated in first 10 days which corresponded to the intense biodegradation of easily biodegradable materials. The mineralization of organic nitrogen in the digestates followed the intense biodegradation and contributed to considerable ammonia emissions. The ammonia oxidation flow decreased to around zero during the intense biodegradation phase and reestablished during the maturation phase. It contributed to the disappearance of ammonia emissions and a sharp decrease of stored ammoniacal nitrogen in compost. The low content of available carbon in the digestates probably limited the immobilization of ammoniacal nitrogen and the development of the total biomass of microorganisms. The number of ammonia-oxidizing bacteria decreased in first 5 days treatment but exhibited a significant development during the maturation phase. The development of ammonia-oxidizing archaea was not significant. Statistic correlation analysis indicates that the ammonia-oxidizing bacteria instead of the ammonia-oxidizing archaea were responsible for nitrification during the treatment of digested sludge (Sig. 0.01). Our results suggest that the length of composting process should be controlled to meet the needs of agriculture. It should ensure the consumption of excessive ammoniacal nitrogen but not reduce the fertilizer value of compost.

Spatial and temporal diversity and abundance of ammonia oxidizers in semi-arid and arid soils: indications for a differential seasonal effect on archaeal and bacterial ammonia oxidizers

Besides water, nitrogen is the limiting factor for biomass production in arid ecosystems. Global climatic changes are exacerbating aridity levels, and the response of nitrogen-transforming microorganisms to these changes is not clear yet. Using semi-arid and arid ecosystems as surrogates for conditions of increased aridity, we investigated the activity, abundance, and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in arid and semi-arid soils. Ammonia oxidation potentials were higher during the winter in both sites than in the summer, and higher nitrate concentrations were measured in the arid soil than in the semi-arid soil. Denaturing gradient gel electrophoresis (DGGE) patterns of AOB 16S rRNA gene fragments were similar for the arid and semi-arid soils with no seasonal variations. In contrast, the DGGE patterns of the AOA amoA gene fragments differed between the sites and a soil transfer experiment suggested that these differences are possibly associated with soil type. AOB numbers were higher during the winter than in the summer, while AOA numbers were higher during the summer. The results indicate the resistance of AOB and AOA community structure to arid conditions, albeit with seasonal variations in their abundance. Together, the results suggest the resilience of nitrification activity to increased aridity level.

Direct and indirect influence of arbuscular mycorrhizal fungi on abundance and community structure of ammonia oxidizing bacteria and archaea in soil microcosms

Both arbuscular mycorrhizal (AM) fungi and ammonia oxidizers are important soil microbial groups in regulating soil N cycling. However, knowledge of their interactions, especially the direct influences of AM fungi on ammonia oxidizers is very limited to date. In the present study, a controlled microcosm experiment was established to examine the effects of AM fungi and N supply level on the abundance and community structure of ammonia oxidizing bacteria (AOB) and archaea (AOA) in the rhizosphere of alfalfa plants (Medicago sativa L.) inoculated with AM fungus Glomus intraradices. Effects were studied using combined approaches of quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The results showed that inoculation with AM fungi significantly increased the plant dry weights, total N and P uptake. Concomitantly, AM fungi significantly decreased the amoA gene copy numbers of AOA and AOB in the root compartment (RC) but not in the hyphal compartment (HC). Moreover, AM fungi induced some changes in AOA community structure in HC and RC, while only marginal variations in AOA composition were observed to respond to N supply level in HC. Neither RC nor HC showed significant differences in AOB composition irrespective of experimental treatments. The experimental results suggested that AM fungi could directly shape AOA composition, but more likely exerted indirect influences on AOA and AOB abundance via the plant pathway. In general, AM fungi may play an important role in mediating ammonia oxidizers, but the AOA community appeared to be more sensitive than the AOB community to AM fungi.

Analysis of Nitrification in Agricultural Soil and Improvement of Nitrogen Circulation with Autotrophic Ammonia-Oxidizing Bacteria

Accumulations of inorganic nitrogen (NH₄⁺, NO₂⁻, and NO₃⁻) were analyzed to evaluate the nitrogen circulation activity in 76 agricultural soils. Accumulation of NH₄⁺ was observed, and the reaction of NH₄⁺→ NO₂⁻ appeared to be slower than that of NO₂⁻ → NO₃⁻ in agricultural soil. Two autotrophic and five heterotrophic ammonia-oxidizing bacteria (AOB) were isolated and identified from the soils, and the ammonia-oxidizing activities of the autotrophic AOB were 1.0 × 10³-1.0 × 10⁶ times higher than those of heterotrophic AOB. The relationship between AOB number, soil bacterial number, and ammonia-oxidizing activity was investigated with 30 agricultural soils. The ratio of autotrophic AOB number was 0.00032-0.26% of the total soil bacterial number. The soil samples rich in autotrophic AOB (>1.0 × 10⁴ cells/g soil) had a high nitrogen circulation activity, and additionally, the nitrogen circulation in the agricultural soil was improved by controlling the autotrophic AOBs.

하수처리장에서의 암모니아 전환 미생물군의 생태학적 연구

The overall goal of this study was to characterize and quantify ammonia-oxidizing bacteria (AOB) in four different full-scale sequence batch reactor (SBR) wastewater treatment plants. Also, this study focused on assessing the occurrence of the alternative ammonia-oxidizing microbes such as anammox (anaerobic ammonia oxidation) bacteria (AMX) and ammonia-oxidizing archaea (AOA) in these systems. Based on total AOB numbers and the estimated cell density in the mixed liquor samples, AOB constituted 0.3 - 1.8% of the total bacterial population in the four WWTPs. Based on clone library, Nitrosomonas ureae-like AOB were dominant in plant A and B, while plant C and D had Nitrosomonas nitrosa-like AOB as major AOB group. The four different AMX primer sets targeting AMX 16S rRNA gene produced PCR amplicons distantly related to Chlamydia and Planctomycetales group bacteria. However, it was not clear these groups of bacteria perform anammox reaction in the SBR plants. Also, molecular evidence of AOA was found in one of the SBR plants, with a sequence located in the deep branch of the sediment creanarchaeota group.

Effects of Long Exposure to Low Temperatures on Nitrifying Biofilm and Biomass in Wastewater Treatment

Attached growth biological treatment systems are a promising solution to ammonia removal in cold-temperature climates. Environmental scanning electron microscopy (ESEM) and confocal laser scanning microscopy in combination with fluorescent in situ hybridization (FISH) was used to investigate the effects of 4 months of exposure to 4 degrees C on nitrifying biofilm and biomass. These molecular and microscopic methods were modified to minimize loss of mass and distortion of in situ perspectives. Environmental scanning electron microscopy revealed that nitrifying biofilm did not exhibit significant changes in volume with exposure to 4 degrees C. Confocal laser scanning microscopy in combination with FISH showed that the number of ammonia-oxidizing bacteria (AOB) cells present in the biofilm was statistically consistent during exposure to 4 degrees C. The RNA content of AOB cells remained sufficient for FISH enumeration. The number of nitrite-oxidizing bacteria cells remained steady during exposure to 4 degrees C; however, the RNA content of the cells appeared to decrease with exposure to 4 degrees C, thereby preventing their enumeration using FISH.

Ammonia transformations and abundance of ammonia oxidizers in a clay soil underlying a manure pond

Unlined manure ponds are constructed on clay soil worldwide to manage farm waste. Seepage of ammonia-rich liquor into underlying soil layers contributes to groundwater contamination by nitrate. To identify the possible processes that lead to the production of nitrate from ammonia in this oxygen-limited environment, we studied the diversity and abundance of ammonia-transforming microorganisms under an unlined manure pond. The numbers of ammonia-oxidizing bacteria and anammox bacteria were most abundant in the top of the soil profile and decreased significantly with depth (0.5 m), correlating with soil pore-water ammonia concentrations and soil ammonia concentrations, respectively. On the other hand, the numbers of ammonia-oxidizing archaea were relatively constant throughout the soil profile (10(7) amoA copies per g(soil)). Nitrite-oxidizing bacteria were detected mainly in the top 0.2 m. The results suggest that nitrate accumulation in the vadose zone under the manure pond could be the result of complete aerobic nitrification (ammonia oxidation to nitrate) and could exist as a byproduct of anammox activity. While the majority of the nitrogen was removed within the 0.5-m soil section, possibly by combined anammox and heterotrophic denitrification, a fraction of the produced nitrate leached into the groundwater.

Nitrifying granules cultivation in a sequencing batch reactor at a low organics-to-total nitrogen ratio in wastewater

It is possible to cultivate aerobic granular sludge at a low organic loading rate and organics-to-total nitrogen (COD/N) ratio in wastewater in the reactor with typical geometry (height/diameter = 2.1, superficial air velocity = 6 mm/s). The noted nitrification efficiency was very high (99%). At the highest applied ammonia load (0.3 ± 0.002 mg NH4+–N g total suspended solids (TSS)−1 day−1, COD/N = 1), the dominating oxidized form of nitrogen was nitrite. Despite a constant aeration in the reactor, denitrification occurred in the structure of granules. Applied molecular techniques allowed the changes in the ammonia-oxidizing bacteria (AOB) community in granular sludge to be tracked. The major factor influencing AOB number and species composition was ammonia load. At the ammonia load of 0.3 ± 0.002 mg NH4+–N g TSS−1 day−1, a highly diverse AOB community covering bacteria belonging to both the Nitrosospira and Nitrosomonas genera accounted for ca. 40% of the total bacteria in the biomass.

Diversity of nitrifying bacteria in a full-scale petroleum refinery wastewater treatment plant experiencing unstable nitrification

We have investigated bacterial populations relevant to nitrification in a full-scale activated sludge plant receiving wastewater from a petroleum refinery showing unstable nitrification. Inhibition of ammonia oxidation was related to phenol concentration according to a model of non-competitive inhibition. While the number of ammonia-oxidizing bacteria (AOB) did not correlate with nitrification performance, the total number of nitrite-oxidizing bacteria (NOB) dropped considerably during periods of nitrite accumulation or no nitrification. Diversity of nitrifiers in the sludge of the full-scale facility was examined at a time of full nitrification with the construction of clone libraries of ammonia monooxygenase ( amoA) gene and of the 16S rRNA gene of NOB. Nucleotide sequences of amoA gene belonged to one dominant population, associated with Nitrosomonas europaea, and to a minor population related to the Nitrosomonas nitrosa lineage. The majority of sequences retrieved in the NOB-like clone library also clustered within a single operational taxonomic unit. The high dominance of Nitrobacter over Nitrospira and the low diversity of nitrifying bacteria observed in this wastewater treatment plant might account for the increased risk of failure in the presence of disturbances.

Ammonia-Oxidizing Bacteria and Archaea in Groundwater Treatment and Drinking Water Distribution Systems

The ammonia-oxidizing prokaryote (AOP) community in three groundwater treatment plants and connected distribution systems was analyzed by quantitative real-time PCR and sequence analysis targeting the amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Results demonstrated that AOB and AOA numbers increased during biological filtration of ammonia-rich anoxic groundwater, and AOP were responsible for ammonium removal during treatment. In one of the treatment trains at plant C, ammonia removal correlated significantly with AOA numbers but not with AOB numbers. Thus, AOA were responsible for ammonia removal in water treatment at one of the studied plants. Furthermore, an observed negative correlation between the dissolved organic carbon (DOC) concentration in the water and AOA numbers suggests that high DOC levels might reduce growth of AOA. AOP entered the distribution system in numbers ranging from 1.5 x 10(3) to 6.5 x 10(4) AOPs ml(-1). These numbers did not change during transport in the distribution system despite the absence of a disinfectant residual. Thus, inactive AOP biomass does not seem to be degraded by heterotrophic microorganisms in the distribution system. We conclude from our results that AOA can be commonly present in distribution systems and groundwater treatment, where they can be responsible for the removal of ammonia.

Diversity and abundance of ammonia-oxidizing bacteria in eutrophic and oligotrophic basins of a shallow Chinese lake (Lake Donghu)

Classical cultivation and molecular methods based on the ammonia monooxygenase gene ( amoA) were used to study the abundance and diversity of beta-proteobacterial ammonia-oxidizing bacteria (AOB) in lake sediments. The eutrophic and oligotrophic basins of a Chinese shallow lake (Lake Donghu), in terms of ammonium (NH 4 +) concentrations, were sampled. The AOB number was significantly lower in the oligotrophic basin, but significantly higher in the eutrophic basin. In addition, using restriction fragment length polymorphism targeting the amoA, ten restriction patterns including six unique ones were found in the eutrophic basin, while five patterns were observed in the oligotrophic basin with only one unique restriction group. Phylogenetic analysis for AOB revealed that Nitrosomonas oligotropha- and Nitrosomonas ureae-related AOB and Nitrosospira-affiliated AOB were ubiquitous; the former dominated in the eutrophic basin (87.2%), while the latter dominated in the oligotrophic basin (65.5%). Furthermore, Nitrosomonas communis-related AOB was only detected in the eutrophic basin, at a small proportion (3.2%). These results indicate significant selection and adaptation of sediment AOB in lakes with differing trophic status.

Long-term performance of a representative integrated constructed wetland treating farmyard runoff

The integrated constructed wetland (ICW) system studied in this research paper was constructed as part of a series of 15 wetland systems to improve the water quality of an entire catchment area (Annestown Stream watershed, Ireland) dominated by farming activities. The studied ICW comprised four cells and was used for the treatment of farmyard dirty water from a dairy farm near Dunhill (Ireland). The performance of this system was evaluated through physical, chemical and microbiological parameters collected for 7 years. The removal efficiencies were relatively good if compared to the international literature: biochemical oxygen demand (97.6%), chemical oxygen demand (94.9%), suspended solids (93.7%), ammonia-nitrogen (99%), nitrate-nitrogen (74%) and molybdate reactive phosphorus (91.8%). A molecular microbiological analysis of sediment samples collected from the site indicated that the number of denitrifying bacteria detected in the ICW system was higher than the number of ammonia-oxidizing bacteria. The monitored nutrient concentrations in groundwater and surface waters indicated that this ICW system did not pollute the receiving waters. The results showed that ICW are likely to be efficient in removing nutrients from farmyard runoff rich in nitrogen and phosphorus.

Community composition of ammonia‐oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon

This study determined nitrification activity and nitrifier community composition in soils under stands of red alder (Alnus rubra) and Douglas fir (Pseudotsuga menziesii) at two sites in Oregon. The H.J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon, has low net N mineralization and gross nitrification rates. Cascade Head Experimental Forest, in the Coast Range, has higher net N mineralization and nitrification rates and soil pH is lower. Communities of putative bacterial [ammonia-oxidizing bacteria (AOB)] and archaeal [ammonia-oxidizing archaea (AOA)] ammonia oxidizers were examined by targeting the gene amoA, which codes for subunit A of ammonia monooxygenase. Nitrification potential was significantly higher in red alder compared with Douglas-fir soil and greater at Cascade Head than H.J. Andrews. Ammonia-oxidizing bacteria amoA genes were amplified from all soils, but AOA amoA genes could only be amplified at Cascade Head. Gene copy numbers of AOB and AOA amoA were similar at Cascade Head regardless of tree type (2.3-6.0 x 10(6)amoA gene copies g(-1) of soil). DNA sequences of amoA revealed that AOB were members of Nitrosospira clusters 1, 2 and 4. Ammonia-oxidizing bacteria community composition, determined by terminal restriction fragment length polymorphism (T-RFLP) profiles, varied among sites and between tree types. Many of the AOA amoA sequences clustered with environmental clones previously obtained from soil; however, several sequences were more similar to clones previously recovered from marine and estuarine sediments. As with AOB, the AOA community composition differed between red alder and Douglas-fir soils.