Abundance Of Ammonia-oxidizing Archaea Abundance Research Articles

Soil acidification and ammonia-oxidizing archaeal abundance dominate the contrasting responses of soil N2O emissions to NH4+ and NO3− enrichment in a subtropical plantation

Atmospheric nitrogen (N) deposition markedly increases nitrous oxide (N2O) emissions from subtropical plantation soils. However, the contrasting effects of deposited NH4+ and NO3− on soil N2O emissions and the underlying mechanisms are not well understood. Based on the long-term N fertilization manipulative experiment with two types (NH4Cl and NaNO3) and three levels (0, 40, and 120 kg N ha−1 yr−1), we investigated the response of soil N2O emissions to N addition, as well as the environmental and microbial control on soil N2O emissions using flux observations and molecular biology assays. Nitrogen addition significantly decreased soil pH by 0.30–0.67 units and increased soil N2O emissions by 6- to 21-fold relative to the control; furthermore, the effect of NH4Cl addition was significantly stronger than that of NaNO3 addition. Nitrogen addition significantly increased the abundance of ammonia-oxidizing archaea (AOA), whereas high levels of NH4Cl addition (120 kg N ha−1 yr−1) significantly decreased the abundances of nirS, nirK, and nosZ. In addition, NH4Cl addition decreased the Shannon diversity indices of AOA, nirK, and nosZ communities. Changes in soil N2O flux were positively correlated with changes in soil NO3−-N concentration and AOA abundance, whereas negatively correlated with changes in soil pH. Soil acidification and enhanced AOA-dominated nitrification led to higher soil N2O emissions under NH4Cl addition relative to NaNO3 addition. Overall, the contrasting effects of reduced NH4+ and oxidized NO3− should be incorporated into ecosystem process models to accurately assess the response of N2O emissions from subtropical plantation soils to exogenous N input.

Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions.

BackgroundNitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification.Materials and MethodsA simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively.Results and discussionsSoil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH3 concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH4+ content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA.ConclusionsPNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH4+, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.

Global meta-analysis of terrestrial nitrous oxide emissions and associated functional genes under nitrogen addition

Functional genes involved in nitrogen (N) cycling regulate soil nitrification, denitrification and N2O emissions. However, the general patterns and variability of N functional genes in response to N addition, and their association with N2O emission have not been synthesized for terrestrial ecosystems. We synthesized 2068 observations from 144 papers to explore the impact of N addition on the abundance and diversity of N functional genes, and their relationship to N2O emissions in croplands, grasslands and forests on a global scale. In croplands, N addition increased N2O emissions (109%), the abundance of ammonia-oxidizing archaea (AOA) (19%), ammonia-oxidizing bacteria (AOB) (95%), nirK (52%), nirS (40%) and nosZ (41%), and the diversity of AOB (15%), nirS (12%) and nosZ (11%). In grassland, N addition increased AOB abundance (130%) and decreased the abundance of nirS (−99%) and nosZ (−58%) genes, but in forests, significant effects were only found for the abundance of AOA (35%) and AOB (121%). N2O emission was negatively correlated with the abundance of nosZ, but positively correlated with the abundance of AOA and AOB. Apart from the abundance of functional AOA, AOB and nosZ genes, climate variables (precipitation and temperature), and available N concentrations were the main factors explaining the variation in N2O emission with N addition, as shown by random forest analysis. These findings indicate that impacts on N functional genes that encode enzymes involved in nitrification (AOA, AOB) and in the transformation of N2O to N2 (nosZ) are the main mechanisms behind the effect on N fertilizer-induced N2O emissions.

Response of nitrification and nitrifying microorganisms to different nitrogen sources in the acid Ultisols of Jinyun Mountain

ABSTRACT Nitrogen-based fertilizer applications have an effect on nitrification and nitrifying microorganisms in acidic soils of agricultural and forest lands. However, the effect of different nitrogen (N) fertilizers on nitrification and nitrifying microorganisms in acidic Ultisols of the subtropical regions are not well studied. Here, we investigated the effect of ammonium sulfate and urea applications on nitrification and nitrifying microorganisms in acidic Ultisols of Jinyun Mountain. The abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) amoA genes were quantitatively analyzed by real-time PCR. Our results indicated that there was a significant difference in soil pH among treatments and the maximum pH value (pH = 4.93) was recorded in urea addition due to the hydrolysis of urea. Similarly, significant differences in the content of NH4 +-N and NO3 −-N were observed among treatments. The result also revealed that urea addition had higher ammonium and nitrate than that of ammonium sulfate, and stimulated nitrification in acidic Ultisols, whereas nitrification was not stimulated by the application of ammonium sulfate. The net nitrification rate at the end of the experiment for control, ammonium sulfate, and urea treatment were −0.005, −0.003 and 0.004 mg N kg−1 soil day−1 respectively. Besides, the addition of urea significantly increased the AOA and AOB abundance. The abundance of AOA amoA gene was greater than AOB in all treatments. However, the ratio of AOA to AOB was lower in soils with ammonium sulfate and urea addition compared to control. This implies that N addition greatly stimulates AOB rather than AOA abundance. Therefore, AOB may be responsible for the higher nitrification potential in the urea added soil. In conclusion, urea addition significantly increased the content of ammonium, soil pH, AOA and AOB abundance, and stimulates nitrification. AOB may play a significant role in nitrification process in urea added acidic Ultisols.

Long-term organic fertilization regulates the abundance of major nitrogen-cycling-related genes in aggregates from an acidic Ultisol

The soil nitrogen (N) cycle is crucial to biogeochemical cycling, plant nutrient absorption, and greenhouse gas emissions and is primarily mediated by microorganisms. Although organic fertilization regulating aggregation has been well studied in various soils, how organic fertilization mediates microbial groups involved in soil N cycle in aggregates remained largely unclear. Therefore, the objective was to investigate the effect of 27 years of application of mineral and organic fertilizers (peanut straw, rice straw, radish, and pig manure) on the abundance of major microbial groups involved in the soil N cycle in four soil aggregate size classes. The results showed that organic fertilizers exerted significant impacts on the communities of microbes possessing N-cycling-related genes, with pig manure having a more important effect than plant residues. However, aggregate size classes contributed more to the variation (20%) than organic fertilizers (12%). Organic fertilizer types did not impact the abundance of ammonia-oxidizing archaea (AOA) or ammonia-oxidizing bacteria (AOB). However, aggregate size strongly altered the abundance of AOA, but not AOB, with AOA being particularly abundant in <53 μm aggregates. Organic fertilizers and aggregate size significantly influenced the abundance of the nirS gene rather than the nirK gene. There were greater amounts of nirS in the soils treated with rice straw and pig manure, primarily due to the higher soil organic matter content. As for fungal denitrification, there was a greater abundance of FnirK in microaggregates than in macroaggregates. Organic fertilizers and aggregate size significantly influenced the abundance of nosZ I and nosZ II genes, with aggregate size playing a more pronounced role. The abundance of nosZ I increased with increasing aggregate size while the abundance of nosZ II gene showed the opposite trends. This result revealed the clear niche differentiation of nosZ I and nosZ II genes in Ultisols, with nosZ I and nosZ II preferred to inhabit in macroaggregates and microaggregates, respectively. Overall, our results provide critical insights into the ecophysiology of major N-cycling-related genes in aggregates from an acidic Ultisol.

Effect of Manure Application on Net Nitrification Rates, Heavy Metal Concentrations and Nitrifying Archaea/Bacteria in Soils.

In this study, we determined the effect of manure application on net nitrification rates (NNRs), heavy metal concentrations (HMCs), and abundance of ammonia-oxidizing archaea (AOA)/bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in soil. HMCs were measured by atomic absorption spectroscopy. Abundance of AOA, AOB, and NOB was enumerated by q-PCR. NNRs ranged from 2.8 to 14.7mgkg-1h-1 and were significantly (p < 0.05) increased in manure soils as compared to control soils. NNRs were affected by pH 7 and temperature 30°C. Cd, Fe and Pb concentrations were classified as excessively polluted, moderate contamination and slight pollution, respectively, in the manure soils. NNRs and concentrations of Fe and Pb were significantly (p < 0.00) positive correlated, but Cu and Cd were significantly (p < 0.00) negative correlated with NNRs. Application of manure significantly (p < 0.05) increased HMCs (Fe, Cu, and Pb), which have indirect and direct effects on NNRs and nitrifying bacteria.

Community diversity and abundance of ammonia-oxidizing archaea and bacteria in shrimp pond sediment at different culture stages.

Ammonia oxidation is a significant process of nitrogen cycles in a lot of ecosystems sediments while there are few studies in shrimp culture pond (SCP) sediments. This paper attempted to explore the community diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in SCP sediments at different culture stages. We collected SCP sediments and analysed the community diversity and abundance of AOA and bacteria in shrimp pond sediment at different culture stages using the ammonia monooxygenase (amoA) gene with quantitative PCR (qPCR) and 16S rRNA gene sequencing. The AOB-amoA gene abundance was showed higher than AOA-amoA gene abundance in SCP sediments on Day 50 and Day 60 after shrimp larvae introducing into the pond, and the diversity of AOA in SCP sediments was higher than that of AOB. The phylogenetic tree revealed that the most of AOA were the member of Nitrosopumilus and Nitrososphaera, and the majority of AOB sequences were clustered into Nitrosospira, Nitrosomonas clusters 6a and 7. The AOA community has close relationship with total organic carbon (TOC), pH, total phosphorus (TP), nitrate reductase, urease, acid phosphatase and β-glucosidase. The AOB community was related to TOC, C/N and nitrate reductase. AOA and AOB play the different ecological roles in SCP sediments at different culture stages. Our results suggested that the different community diversity and abundance of AOA and AOB in SCP sediments, which may improve our ecological cognition of shrimp culture stages in SCP ecosystems.

Plants and microbes' responses to the net nitrification rates of chemical fertilizers in vegetable soils

Various types of chemical fertilizers are used in agricultural production in Bangladesh. However, plants and microbes' responses to the nitrification activity of chemical fertilizers are unknown. The goal of this study was to determine the responses of plants and nitrifying archaea/bacteria and comammox amoA Nitrospira inopinata bacteria to the net nitrification rates (NNRs) of chemical fertilizers in four vegetable soils. The abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), and comammox amoA N. inopinata was determined by q-PCR. The NNRs ranged from 2.96 ± 0.39 to 10 ± 1.19 mg kg−1 h−1 and were significantly higher (p < 0.05) in the vegetable soils than in the control soils (uncultivated soils). Temperature and pH influenced the NNRs. The abundance of comammox amoA N. inopinata ranged from 9.34E+05 to 4.55E+06 per gram dry soil in the vegetable soils and represented 28 to 72% of the nitrifying amoA genes. Among the vegetable soils, the highest NNRs and abundance of comammox amoA N. inopinata were found in Phaseolus vulgaris soils. The abundance of AOA, AOB, NOB, and comammox amoA N. inopinata was significantly (p < 0.05) higher in the vegetable soils compared to control soils and was correlated positively and significantly with the NNRs. Principal component analysis (PCA) results confirmed the distinct variation present among the vegetable soils according to their components. Finally, it may be concluded that the plants and nitrifying archaea/bacteria, as well as comammox amoA N. inopinata, can also have indirect/direct effects on the nitrification activity of chemical fertilizer among vegetable soils.

The more important role of archaea than bacteria in nitrification of wastewater treatment plants in cold season despite their numerical relationships

Nitrification failure of wastewater treatment plants (WWTPs) in cold season calls into investigations of the functional ammonia-oxidizing microorganisms (AOMs). In this study, we report the abundance of ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia-oxidizing (comammox) Nitrospira in 23 municipal WWTPs in cold season, and explore the correlations between AOMs abundance and their relative contribution to nitrification. The copy numbers of AOA and AOB amoA gene ranged from 2.42 × 107 to 2.47 × 109 and 5.54 × 106 to 3.31 × 109 copies/g sludge, respectively. The abundance of amoA gene of Candidatus Nitrospira inopinata, an important strain of comammox Nitrospira, was stable with averaged abundance of 8.47 × 106 copies/g sludge. DNA-based stable isotope probing (DNA-SIP) assays were conducted with three typical WWTPs in which the abundance of AOA was lower than, similar to and higher than that of AOB, respectively. The results showed that considerable 13C-assimilation by AOA was detected during active nitrification in all WWTPs, whereas just a much lesser extent of 13C-incorporation by AOB and comammox Nitrospira was found in one WWTP. High-throughput sequencing with 13C-labeled DNA also showed the higher reads abundance of AOA than AOB and comammox Nitrospira. Nitrososphaera viennensis was the dominant active AOA, while Nitrosomonas oligotropha and Nitrosomonas europaea were identified as active AOB. The results obtained suggest that AOA, rather than AOB and comammox Nitrospira, dominate ammonia oxidation in WWTPs in cold season despite the numerical relationships of AOMs.

Mowing and topography effects on microorganisms and nitrogen transformation processes responsible for nitrous oxide emissions in semi-arid grassland of Inner Mongolia

Few studies have been done to investigate the impact of mowing on N2O emissions and the abundance of functional microbial genes, especially in sloping landscapes. This study aims to explore the impact of mowing on key N2O-producing processes under different topographical conditions in a semi-arid grassland. Soil samples were collected from a semiarid grassland ecosystem in Xilingol region, Inner Mongolia, where long-term management practices including non-mowing and mowing in flat and sloping blocks were conducted. We then determined (1) soil moisture, total carbon (TC) and nitrogen (TN), and mineral N (NH4 +-N and NO3 −-N) content; (2) the potential N2O emission from nitrification (NN2O) and from denitrification (DN2O) and potential N2 emission (DN2); and (3) the gene abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), the narG (nitrate reductase) gene, and nosZ (nitrous oxide reductase) gene. Soil moisture and potential N2O emission from nitrification and denitrification were significantly lower in sloping than in flat conditions, whereas the TC, TN, NH4 +-N, NO3 −-N content, gene abundance of AOA, AOB, narG, and nosZ showed no difference between flat and sloping conditions. Mowing significantly decreased the gene abundance of AOA, AOB, narG in both flat and sloping areas, and significantly decreased potential N2O emissions, especially in sloping areas. The potential N2O emission was significantly lower on sloping than flat grassland. Mowing significantly decreased the potential N2O emissions, especially on sloping grassland. Our results suggest that topographical conditions should be incorporated into methods for estimating N2O emission and land management practices in semiarid grassland.

Toxicity of TiO2 nanoparticles on soil nitrification at environmentally relevant concentrations: Lack of classical dose–response relationships

Titanium-dioxide nanoparticles (TiO2-NPs) are increasingly released in agricultural soils through, e.g. biosolids, irrigation or nanoagrochemicals. Soils are submitted to a wide range of concentrations of TiO2-NPs depending on the type of exposure. However, most studies have assessed the effects of unrealistically high concentrations, and the dose–response relationships are not well characterized for soil microbial communities. Here, using soil microcosms, we assessed the impact of TiO2-NPs at concentrations ranging from 0.05 to 500 mg kg−1 dry-soil, on the activity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (Nitrobacter and Nitrospira). In addition, aggregation and oxidative potential of TiO2-NPs were measured in the spiking suspensions, as they can be important drivers of TiO2-NPs toxicity. After 90 days of exposure, non-classical dose–response relationships were observed for nitrifier abundance or activity, making threshold concentrations impossible to compute. Indeed, AOA abundance was reduced by 40% by TiO2-NPs whatever the concentration, while Nitrospira was never affected. Moreover, AOB and Nitrobacter abundances were decreased mainly at intermediate concentrations nitrification was reduced by 25% at the lowest (0.05 mg kg−1) and the highest (100 and 500 mg kg−1) TiO2-NPs concentrations. Path analyses indicated that TiO2-NPs affected nitrification through an effect on the specific activity of nitrifiers, in addition to indirect effects on nitrifier abundances. Altogether these results point out the need to include very low concentrations of NPs in soil toxicological studies, and the lack of relevance of classical dose–response tests and ecotoxicological dose metrics (EC50, IC50…) for TiO2-NPs impact on soil microorganisms.

Distribution characteristics and controlling factors of nitrifying microorganisms in freshwater and sediment of eutrophic zones in Lake Taihu in autumn

微生物参与下的氮循环是富营养化湖泊十分重要的生物地球化学循环过程.采用基于amoA功能基因和16S rRNA基因的荧光定量PCR、PCR-DGGE与高通量测序等分子生物学技术，调查秋季太湖不同水体和表层沉积物中氨氧化古菌（AOA）、氨氧化细菌（AOB）和亚硝酸盐氧化菌（NOB）群落丰度和组成，探讨影响硝化微生物分布的关键环境因子.结果表明，中度富营养化的梅梁湾湖区水体表层、中层和底层水样和表层底泥中AOA amoA基因的丰度分别低于轻度富营养化的湖心区，而不同层水样中AOB amoA基因的丰度分别高于湖心区.梅梁湾湖区和湖心区水样中AOA群落组成基本相似，2个湖区表层沉积物样品中AOA群落组成亦基本相似，水体中AOA群落组成与表层沉积物中AOA群落组成有差异，AOA群落丰度显著受硝态氮、pH和DO影响；表层沉积物中AOB群落丰度有明显差异且显著受总氮含量影响，表层沉积物中NOB群落丰度也有明显差异且显著受亚硝态氮含量影响.太湖梅梁湾湖区和湖心区水体与表层沉积物AOA群落包括Nitrosopumilium和Nitrosotalea两大属；表层沉积物AOB群落主要包括亚硝化单胞菌（Nitrosomonas）和亚硝化螺菌（Nitrosospira）两大属，NOB群落主要包括硝化刺菌（Nitrospina）和硝化螺菌（Nitrospira）两大属，其中硝化螺菌属是淡水湖泊中比较少见的亚硝酸盐氧化菌.影响太湖水体和沉积物中AOA和AOB丰度的最主要环境因子为总氮、总磷与铵态氮.研究表明典型富营养指标（总氮、总磷、铵态氮、硝态氮和硝态氮等）是影响太湖梅梁湾和湖心区水体和沉积物中AOA或AOB丰度以及硝化微生物群落丰度的重要因素.;Nitrogen cycling associated with microorganisms is the most important biogeochemical process in eutrophic lakes. In this study, molecular biological techniques including quantitative PCR, PCR-DGGE, and high-throughput sequencing based on amoA and 16S rRNA genes were used to assess the composition and community abundance of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in freshwater and sediment samples of Lake Taihu collected during autumn. The key environmental factors affecting the distribution of nitrifying microorganisms were further analyzed. Results showed that the amoA gene abundance of AOA from the upper, middle, and bottom freshwater and surface sediment samples from the mesotrophic Meiliang Bay was lower than those from the less eutrophic central lake and that the amoA gene abundance of AOB from the mesotrophic Meiliang Bay was greater than those from the central lake. The AOA community composition in freshwater was similar in both Meiliang Bay and the central lake, it was the same for AOA in the surface sediment, and the key factors affecting AOA community abundance were nitrate, pH and dissolved oxygen contents, while the community abundance of AOB mainly affected by total nitrogen content in sediments were proven to differ considerably between the two sites. The case was the same for NOB with the key factor nitrite content. AOA of freshwater and surface sediments in Meiliang Bay and central lake included two genera, Nitrosopumilis and Nitrosotalea. AOB of the surface sediment included Nitrosomonas and Nitrosospira. NOB of the surface sediment included Nitrospina and Nitrospira, and Nitrospina was scarce in freshwater. The main environmental factors affecting the abundance of AOA and AOB in Lake Taihu were TN, total phosphorus (TP), and ammonium content. This study proved that the eutrophication indexes (such as total nitrogen, total phosphorus, ammonium, nitrate and nitrite) have significant influences on the abundance of AOA or AOB and community abundance of nitrifying microorganisms in both freshwater and sediments in Lake Taihu, which may help the understanding of the nitrogen cycling in the Lake Taihu ecosystem.

Multi-year and short-term responses of soil ammonia-oxidizing prokaryotes to zinc bacitracin, monensin, and ivermectin, singly or in combination.

A field experiment was initiated whereby a series of replicated plots received annual applications of ivermectin, monensin, and zinc bacitracin, either singly or in a mixture. Pharmaceuticals were added at concentrations of 0.1 mg/kg soil or 10 mg/kg soil. The authors collected soil samples in 2013, before and after the fourth annual application of pharmaceuticals. In addition, a 30-d laboratory experiment was undertaken with the same soil and same pharmaceuticals, but at concentrations of 100 mg/kg soil. The impact of the pharmaceuticals on nitrification rates, on the abundance of ammonia-oxidizing bacteria (AOB), and on the abundance of ammonia-oxidizing archaea (AOA) was assessed. None of the pharmaceuticals at 0.1 mg/kg had any effect on nitrification. Referenced to control soil, nitrification was accelerated in soil exposed to 100 mg/kg zinc bacitracin or 10 mg/kg of the pharmaceutical mixture, but none of the treatments inhibited nitrification. Neither AOB abundance nor AOA abundance was affected by the pharmaceuticals at 0.1 mg/kg. At 10 mg/kg, monensin, zinc bacitracin, and a mixture of all 3 pharmaceuticals suppressed the abundance of AOB, and zinc bacitracin and the mixture increased AOA abundance. The decrease in AOB abundance and increase in AOA abundance when exposed to 10 mg/kg soil suggests that AOB are more sensitive to these chemicals and that AOA populations can expand to occupy the partially vacated niche.

Community structure of ammonia-oxidizing microorganisms in the Grand Canal, Zhenjiang, of Jiangsu Province, China.

In this study, we simultaneously investigated the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the Grand Canal (the Zhenjiang section). Both clone library and qPCR (quantitative polymerase chain reaction) indicated that the abundance and diversity of AOB were higher than AOA in the Grand Canal for all four seasons. Among the 109 archaeal amoA sequences retrieved, 62.39 and 37.61% fell within the Nitrosopumilus and Nitrososphaera clusters, respectively. The 128 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 81.25 and 18.75% of the AOB group, respectively. The AOA abundance was significantly and positively correlated with the NH4-N. The AOB abundance did not show significant correlations with the measured parameters. Obvious differences were observed for the AOA community compositions obtained from different seasons. The community structure of AOB changed slightly. It indicated that AOB seemed to play a more important role for the nitrification process than AOA in this environment, and was more adapted to this environment.

Diversity and abundance of ammonia-oxidizing Archaea and Bacteria in tropical and cold-water coral reef sponges

We analysed the diversity and abundance of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in the shallow warm-water sponge Halisarca caerulea and the deep cold-water sponges Higginsia thielei and Nodastrella nodastrella. The abundance of AOA and AOB was analysed using catalyzed reporter deposition-fluorescence in situ hybridization and (real-time) quantitative PCR (Q-PCR) targeting archaeal and bacterial amoA genes. Archaeal abundance was similar between sponge species, while bacterial abundance was higher in H. caerulea than in N. nodastrella and H. thielei. Q-PCR showed that AOA outnumbered AOB by a factor of 2 to 35, suggesting a larger role of AOA than of AOB in ammonia oxidation in sponges. PCR-denaturing gradient gel electrophoresis was performed to analyse the taxonomic affiliation of the microbial community associated with these sponges. Archaeal and bacterial amoA genes were found in all 3 sponges. The structure of the phylogenetic trees in relation to temperature and sponge species was analysed using all published amoA sequences retrieved from sponges. Temperature was an important factor influencing the distribution of nitrifiers in sponges. Both archaeal and bacterial amoA sponge sequences tended to cluster with sequences retrieved from habitats of similar temperature. This is the first time that similarity in AOB diversity is described between distantly related species (H. thielei belonging to the class Demospongiae, and N. nodastrella to Hexactinellida). The results described here support the idea of a relatively uniform microbial community between distantly related sponges and suggest that temperature (rather than phylogenetic distance) is determining the diversity of AOA and AOB in sponges.

Lower Abundance of Ammonia-Oxidizing Archaea Than Ammonia-Oxidizing Bacteria Detected in the Subsurface Sediments of the Northern South China Sea

Diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in samples of the northern South China Sea subsurface sediment were assessed by analyzing the amoA gene sequences retrieved from the samples. The microbial diversity was assessed using rarefaction and phylogenetic analyses. The deep-sea subsurface sediments harbored diverse and distinct AOA and AOB communities, but the abundance of AOA was lower than that of AOB, consistent with many other studies about bacteria and archaea in subsurface sediments. Diversity of AOA shown in the OTUs and Shannon index was correlated with the concentration of nitrite in the Pearson analysis, but no obvious relationships between the diversity or abundance of AOB and the physicochemical parameters could be identified in the present study, indicating the concentration of ammonium may not be an important factor to determine the diversity and abundance of ammonia-oxidizing prokaryotes in the subsurface sediments. Additionally, Nitrosomonas-like AOB was found to be dominant in subsurface sediments of the northern South China Sea showing a different adaption strategy comparing with some Nitrosospira-like AOB lineages. Concentration of nitrite was correlated with diversity of AOA, but no correlations between diversity and abundance of AOB and the physicochemical parameters were established in the study. Supplementary materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental files.

Seasonal changes of freshwater ammonia-oxidizing archaeal assemblages and nitrogen species in oligotrophic alpine lakes.

The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% ± 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The amoA gene was detected year round, and seasonal changes in amoA gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal amoA genes were well correlated, suggesting that most freshwater 1.1a Crenarchaeota had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e., amoA) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine amoA gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical amoA-containing ecotypes, which is different from soils and seas. We observed within the freshwater amoA gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.

Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary, California.

Ammonia oxidation-the microbial oxidation of ammonia to nitrite and the first step in nitrification-plays a central role in nitrogen cycling in coastal and estuarine systems. Nevertheless, questions remain regarding the connection between this biogeochemical process and the diversity and abundance of the mediating microbial community. In this study, we measured nutrient fluxes and rates of sediment nitrification in conjunction with the diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing betaproteobacteria (β-AOB). Sediments were examined from four sites in Elkhorn Slough, a small agriculturally impacted coastal California estuary that opens into Monterey Bay. Using an intact sediment core flowthrough incubation system, we observed significant correlations among NO(3)(-), NO(2)(-), NH(4)(+), and PO(4)(3+) fluxes, indicating a tight coupling of sediment biogeochemical processes. (15)N-based measurements of nitrification rates revealed higher rates at the less impacted, lower-nutrient sites than at the more heavily impacted, nutrient-rich sites. Quantitative PCR analyses revealed that β-AOB amoA (encoding ammonia monooxygenase subunit A) gene copies outnumbered AOA amoA gene copies by factors ranging from 2- to 236-fold across the four sites. Sites with high nitrification rates primarily contained marine/estuarine Nitrosospira-like bacterial amoA sequences and phylogenetically diverse archaeal amoA sequences. Sites with low nitrification rates were dominated by estuarine Nitrosomonas-like amoA sequences and archaeal amoA sequences similar to those previously described in soils. This is the first report measuring AOA and β-AOB amoA abundance in conjunction with (15)N-based nitrification rates in estuary sediments.

Seasonal Changes in Abundance of Ammonia-Oxidizing Archaea and Ammonia-Oxidizing Bacteria and Their Nitrification in Sand of an Eelgrass Zone

Seasonal changes in the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) within the sand of an eelgrass (Zostera marina) zone were examined by a quantitative PCR of both crenarchaeotal and betaproteobacterial ammonia monooxygenase alpha subunit (amoA) genes together with temperature and concentrations of ammonium, nitrite, and nitrate from May 2007 to June 2008 at Tanoura Bay, Shizuoka, Japan. The abundance of both amoAs in the sand between May and June 2007 and between January and March 2008 was 1.5 to 2 orders of magnitude higher than the 10(4) copies g(-1) of estimated amoA between September and December. Archaeal amoA was more diverse than betaproteobacterial amoA. Betaproteobacterial amoA clone libraries were dominated by Nitrosospira-like sequence types. An incubation experiment was conducted with sands collected in February 2008 and community structure was analyzed based on reverse-transcribed amoAs. RNA was extracted from sand incubated for 12 days at 30°C, 17 days at 20°C, and 80 days at 10°C. Different amoA clones were detected from in situ sand and incubated sand. This study reveals clear evidence of seasonal change in the abundance of AOA and AOB within the sand of an eelgrass zone.

Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia

Nitrification, the oxidation of NH(4)(+) to NO(2)(-) and subsequently to NO(3)(-), plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. The first and rate-limiting step in nitrification is catalyzed by the enzyme ammonia monooxygenase (AmoA). We evaluate the relationships between the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) amoA genes; potential nitrification rates and environmental variables to identify factors influencing AOA abundance and nitrifier activity in estuarine sediments. Our results showed that potential nitrification rates increased as abundance of AOA amoA increased. In contrast, there was no relationship between potential nitrification rates and AOB amoA abundance. This suggests that AOA are significant in estuarine nitrogen cycling. Surprisingly, more of the variability in potential nitrification rates was predicted by salinity and pore water sulfide than by dissolved oxygen history.