Ammonia-oxidizing Community Composition Research Articles

Nine years of low-dose biochar amendment suppresses nitrification rate in low-yield brown soil

Nitrification is the crucial process of nitrogen (N) transformation and ammonia oxidation is the first and the speed-limited step of nitrification. The one-time amendment of large quantities of biochar has been reported to alter soil fertility. However, it remains unclear how continuous low-dose biochar application affects the abundance and community composition of ammonia oxidizers and the subsequent nitrification and crop production. In this article, we calculate the soil net nitrification rate and the abundance and communities of ammonia-oxidizers across different growth stages of peanuts at 0–20 cm soil layer under four fertilization regimes, namely control with zero fertilization (CK), biochar application (BC), chemical fertilizer application (NPK) and biochar-based fertilizer application (BBF). Results showed that continuous application of low-dose biochar can significantly increase crop yield by 7.8 % compared to unfertilized soil indirectly through regulating the microbial mechanism in the nitrification process. The highest bacterial amoA gene copy numbers were found in the NPK treatment, 2.35-fold higher than the CK treatment. Compared to the single input of NPK chemical fertilizer, biochar-based fertilizer reduced the nitrification rate by reducing the relative abundance of bacteria, especially Nitrosomonas and Nitrosospira. In summary, our findings provide evidence that: (1) sustained low-dose biochar input could also increase the ammonia-oxidizing bacterial abundance, changing soil properties and increasing the crop yield; (2) biochar-based fertilizer could significantly reduce the nitrification rate compared to NPK application by reducing the AOB-amoA gene abundance and the relative abundance of Nitrosomonas and Nitrosospira; (3) soil C/N ratio was also important for the ammonia-oxidizing community.

Long-Term Fertilization Alters Nitrous Oxide Cycling Dynamics in Salt Marsh Sediments.

Salt marsh sediments are known hotspots for nitrogen cycling, including the production and consumption of nitrous oxide (N2O), a potent greenhouse gas and ozone-depleting agent. Coastal eutrophication, particularly elevated nitrogen loading from the application of fertilizers, is accelerating nitrogen cycling processes in salt marsh sediments. Here, we examine the impact of long-term fertilization on nitrogen cycling processes with a focus on N2O dynamics in a New England salt marsh. By combining 15N-tracer experiments with numerical modeling, we found that both nitrification and denitrification contribute to net N2O production in fertilized sediments. Long-term fertilization increased the relative importance of nitrification to N2O production, likely a result of increased oxygen penetration from nutrient-induced increases in marsh elevation. Substrate utilization rates of key nitrogen cycling processes revealed links between functions and the corresponding microbial communities. Higher specific substrate utilization rates leading to N2O production from nitrification in fertilized sediments indicate a shift in the community composition of ammonia oxidizers, whereas the lack of change in specific substrate utilization of N2O production from denitrification under long-term fertilization suggests resilience of the denitrifying communities. Both are consistent with previous studies on the functional gene community composition in these experimental plots.

Nitrification and the ammonia-oxidizing communities in the central Baltic Sea water column

The redoxclines that form between the oxic and anoxic water layers in the central Baltic Sea are sites of intensive nitrogen cycling. To gain better understanding of nitrification, we measured the biogeochemical properties along with potential nitrification rates and analyzed the assemblages of ammonia-oxidizing bacteria and archaea using functional gene microarrays. To estimate nitrification in the entire water column, we constructed a regression model for the nitrification rates and applied it to the conditions prevailing in the area in 2008–2012. The highest ammonia oxidation rates were found in a thin layer at the top of the redoxcline and the rates quickly decreased below detection limit when oxygen was exhausted. This is probably because extensive suboxic layers, which are known to harbor pelagic nitrification, are formed only for short periods after inflows in the Baltic Sea. The nitrification rates were some of the highest measured in the water columns, but the thickness of the layer where conditions were favorable for nitrification, was very small and it remained fairly stable between years. However, the depth of the nitrification layer varied substantially between years, particularly in the eastern Gotland Basin (EGB) due to turbulence in the water column. The ammonia oxidizer communities clustered differently between the eastern and western Gotland Basin (WGB) and the composition of ammonia-oxidizing assemblages correlated with the environmental variables. The ammonia oxidizer community composition was more even in the EGB, which may be related to physical instability of the redoxcline that does not allow predominance of a single archetype, whereas in the WGB, where the position of the redoxcline is more constant, the ammonia-oxidizing community was less even. Overall the ammonia-oxidizing communities in the Baltic Sea redoxclines were very evenly distributed compared to other marine environments where microarrays have been applied previously.

不同放牧强度下土壤氨氧化和反硝化微生物的变化特征

Soil nitrifiers and denitrifiers play key roles in determining soil nitrogen (N) availability, nitrate leaching, and N2O emission, and thus they could be indicative to the effects of grazing intensity on grassland ecosystems as well as grassland degradation. In this study, soil samples were collected from a long-term field experiment with different grazing intensities (low-level, middle-level, and high-level grazing) in arid and semi-arid grasslands in Inner Mongolia. We analyzed the responses of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and denitrifiers, in terms of abundance, community composition, and diversity, at different grazing intensities using real-time PCR and terminal restriction fragment length polymorphism (T-RFLP) approaches. The results showed that soil pH and ammonium content ranged from 7.90-8.18 and 6.37-35.92 mg/kg, respectively. Middle-level grazing significantly increased soil pH (P = 0.03), whereas soil ammonium content was recorded as the highest in the high-level grazing treatment (P =0.02). Soil heterotrophic respiration was markedly lower owing to the effects of grazing intensity than that in the non-grazing treatment (P = 0.02). AOA-amoA and AOB-amoA gene abundances rang ed from (4.94-7.60) × 109 and (0.68-3.75) × 106 copies/g dry soil, respectively. AOA-amoA gene abundance showed no significant change in any of the treatments, whereas middle-level grazing strongly decreased AOB-amoA gene abundance (P =0.04). The abundance of nosZ gene (coding for nitrous oxide reductase) was significantly decreased in the low-level grazing treatment (P = 0. 03). The abundances of AOA and AOB were significantly influenced by ammonium content, whereas nosZ gene abundance was influenced by substrate content and soil aeration. Redundancy analysis showed that the variation in N availability induced by grazing was the major factor influencing the community composition of ammonia oxidizers and denitrifiers.

Population and community structure shifts of ammonia oxidizers after four-year successive biochar application to agricultural acidic and alkaline soils

Long-term studies that advance our mechanistic understanding of biochar (BC)‑nitrogen (N) interactions in agricultural soils are lacking. In this study, soil potential nitrification rates (PNR), the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities following 4-year of BC application were investigated using the shaken-slurry procedure and molecular sequencing techniques for an acidic Oxisol (QU) and an alkaline Cambisol (YU). Soils were obtained from an outdoor soil column experiment with straw-BC application rates of 0 (BC0), 2.25 (BC2.25) and 11.3 (BC11.3) Mgha−1 per cropping season for eight consecutive wheat/millet seasons. Quantitative polymerase chain reaction (qPCR) and 454 high-throughput pyrosequencing techniques were performed to quantify and sequence amoA gene copies and composition of AOA and AOB. Results showed that QU had lower PNR and a higher ratio of amoA gene copies of AOA to AOB than YU, PNR of QU with BC application was significantly associated with the amoA gene of AOB. Similar to previous short-term findings, BC application enhanced QU soil nitrification, which may be explained by the significant increase in AOB abundance and a shift in AOB community structure from Nitrosospira cluster 2 toward cluster 3, along with the disappearance of some obligate acidophile AOA groups, leading to the appearance of ammonia-oxidizers from neutral-alkaline soils in BC-amended acid soils. Canonical correspondence analysis (CCA) showed that soil pH was the most important factor driving shifts in ammonia-oxidizers composition. Although BC application did not have significant effects on PNR in YU, BC11.3 decreased AOA and AOB gene copies and influenced the relative abundance of community structure. Our findings represent the first investigation of long-term BC effects on AOA and AOB communities in agricultural soils using 454 high-throughput pyrosequencing, showing that BC application can alter soil characteristics and influence ammonia oxidizer community composition, abundance, especially in acid soils.

Ammonia Oxidizers in a Grazing Land with a History of Poultry Litter Application.

Poultry litter (PL) is widely applied on grazing lands in Georgia. However, it is not clear how its long-term use affects soil microorganisms and their function. We examined changes in activity and community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a grazing land with a history of PL application and compared it to treatment with urea ammonium nitrate (UAN). Soil samples (0-15 cm) were collected in 2009 (after 15 yr of PL application) and in 2013 (after 2 yr of no application). The abundance and community composition of ammonia oxidizers (AO) were determined with molecular techniques that targeted Nitrification potential (NP) was used for measuring their activity. Abundance of AO was significantly higher in PL (7.41 and 7.10 log copies g soil for AOB and AOA, respectively) than in UAN plots (6.82 and 6.50 log copies g soil for AOB and AOA, respectively) in 2009. This is consistent with NP, which was higher in PL (0.78 mg NO -N kg h) than in UAN (0.50 mg NO-N kg h) plots in 2009. The abundance of AO and NP decreased in 2013. There was no treatment effect on the composition of AO. Correlation analysis suggested that AOB were functionally more important than AOA, indicating the need to target AOB for efficient management of N in PL-receiving soils. Overall, the difference in nitrification between PL and UAN was mainly caused by the change in AO abundance rather than composition, and AO were not negatively affected by an increase in PL-derived trace metal concentrations.

Forest harvest intensity and soil depth alter inorganic nitrogen pool sizes and ammonia oxidizer community composition

Intensive forest harvest techniques have the potential to alter soil carbon and nutrient stocks and biogeochemical processes. We investigated how differing levels of organic matter removal (OMR) during timber harvest influenced the long-term stability of nitrification and the microbes regulating this process. Nitrification is limited by the activity of ammonia oxidizing bacteria (AOB) and archaea (AOA); however, reports on the relative contribution of each of these groups to forest soil nitrification have varied and have not been investigated in response to OMR. The influence of soil depth on the structure and function of the ammonia-oxidizing community has also been underreported and was included in this study. We quantified soil physicochemical properties including concentrations of ammonium (NH4+) and nitrite (NO2−) + nitrate (NO3−), and also coupled next generation sequencing and qPCR of the amoA gene to a whole-soil assay that stimulates nitrification and allows for the discrimination of AOA-from AOB-activity using 1-octyne, which inhibits bacterial ammonia monooxygenase activity. Soils were collected (1 m depth) from replicated loblolly pine (Pinus taeda L.) stands subjected to three different intensities of OMR (i.e., unharvested control, bole-only harvest, and whole-tree harvest + forest floor removal). Increasing intensity of OMR and increasing soil depth lead to significant reductions in concentrations of in situ NH4+ and NO2− + NO3−. Sequencing and subsequent annotation of the ammonia oxidizing community revealed that AOA were dominated by Crenarchaeota and AOB were dominated by Nitrosospira spp. The abundance of both bacterial and archaeal amoA were influenced by OMR and soil depth; furthermore, archaeal amoA was more abundant than bacterial amoA across all soil depths and the ratio of AOA to AOB increased with depth. Community structure of AOA and AOB were influenced by soil depth; however, only AOB were altered by OMR. Soil incubations revealed nitrification was N-limited in these forest soils. Furthermore, AOA- and AOB-contributions to total nitrification were nearly equivalent in surface soils; however, AOA contribution increased to 75% at 1 m. In general, the highest rates of nitrification occurred in the soils taken from unharvested control stands; however, OMR treatment differences were only significant when soils were amended with high levels of ammonia indicating that at ambient levels, intensive OMR may not lead to long-term alterations in nitrification potential.

Emergent macrophytes modify the abundance and community composition of ammonia oxidizers in their rhizosphere sediments.

Ammonia oxidation is a crucial process in global nitrogen cycling, which is catalyzed by the ammonia oxidizers. Emergent plants play important roles in the freshwater ecosystem. Therefore, it is meaningful to investigate the effects of emergent macrophytes on the abundance and community composition of ammonia oxidizers. In the present study, two commonly found emergent macrophytes (Zizania caduciflora and Phragmitas communis) were obtained from freshwater lakes and the abundance and community composition of the ammonia-oxidizing prokaryotes in the rhizosphere sediments of these emergent macrophytes were investigated. The abundance of the bacterial amoA gene was higher in the rhizosphere sediments of the emergent macrophytes than those of bulk sediments. Significant positive correlation was found between the potential nitrification rates (PNRs) and the abundance of bacterial amoA gene, suggesting that ammonia-oxidizing bacteria (AOB) might play an important role in the nitrification process of the rhizosphere sediments of emergent macrophytes. The Nitrosotalea cluster is the dominant ammonia-oxidizing archaea (AOA) group in all the sediment samples. Analysis of AOB group showed that the N. europaeal cluster dominated the rhizosphere sediments of Z. caduciflora and the bulk sediments, whereas the Nitrosospira cluster was the dominant AOB group in the rhizosphere sediments of P. communis.

Effects of 3,4-dimethylpyrazole phosphate (DMPP) on nitrification and the abundance and community composition of soil ammonia oxidizers in three land uses

The application of the nitrification inhibitor, 3,4-dimethylpyrazole-phosphate (DMPP), is considered as an effective strategy to mitigate agricultural nitrogen loss. However, the inhibitory effect of DMPP on nitrification is variable and the importance of the soil microbial community composition to the variability is poorly understood. In this study, nine soils were collected across three land uses to investigate the impact of DMPP on nitrification and associated dynamics of ammonia oxidizers in a 28-day microcosm incubation. The results showed that the efficacy of DMPP at inhibiting net nitrification rates varied highly from no effect to 63.6 % during the first week of incubation. The abundance of ammonia-oxidizing bacteria (AOB), rather than ammonia-oxidizing archaea (AOA), was significantly correlated with nitrate concentrations across three land uses and significantly inhibited by DMPP addition. DMPP had higher efficacy in neutral and alkaline wheat and vegetable soils, compared with pasture soils. Canonical correspondence analysis suggested that soil pH was the most influential factor explaining the community composition of AOB and AOA in the collected soils. However, neither ammonium nitrate nor DMPP addition had a significant effect on the community composition of AOB or AOA during the incubation indicated by non-metric multidimensional scaling ordination. Taken together, our findings indicated that DMPP slowed nitrification by inhibiting the growth of AOB, and DMPP application affected the abundance of AOB more than the ammonia oxidizer community composition.

Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill.

The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain.

Abundance and community composition of ammonia oxidizers in rhizosphere sediment of two submerged macrophytes

ABSTRACTAmmonium oxidation is both the first and a rate-limiting step in the nitrification process that can be catalysed by ammonia-oxidizing archaea (AOA) or ammonia-oxidizing bacteria (AOB). In this study, the abundance and community composition of AOA and AOB in the rhizosphere sediments of two submerged macrophytes (Ceratophyllum demersum and Potamogeton malainus) were investigated. Physicochemical parameters, including pH, total nitrogen, total phosphorus, ammonia nitrogen, nitrate and organic matter, were measured. The number of copies of both the archaeal and bacterial amoA gene was quantified by real-time PCR and clone libraries were constructed for both AOA and AOB. The abundance of archaeal amoA gene ranged from 3.83 × 106 to 4.23 × 106 copies per gram of dry sediment and no significant difference was found among the three treatment groups (one control group and two submerged macrophyte groups). The abundance of bacterial amoA gene ranged from 2.68 × 106 to 8.05 × 107 copies per gram of dry sediment. Bulk sediment maintained significantly higher copy numbers of bacterial amoA gene than those of C. demersum rhizosphere sediment. The diversity of archaeal amoA gene was higher in the rhizosphere sediment of C. demersum; however, the diversity of bacterial amoA gene was relatively lower in rhizosphere sediment of both macrophytes.

Relationships between ammonia-oxidizing communities, soil methane uptake and nitrous oxide fluxes in a subtropical plantation soil with nitrogen enrichment

Ammonia-oxidizers play an essential role in nitrogen (N) transformation and nitrous oxide (N2O) emission in forest soils. It remains unclear if ammonia-oxidizers affect interaction between methane (CH4) uptake and N2O emission. Our specific goal was to test the impacts of changes in ammonia-oxidizing communities elicited by N enrichment on soil CH4 uptake and N2O emission. Based on a field experiment, two-forms (NH4Cl and NaNO3) and two levels (40 and 120 kg N ha−1 yr−1) of N were applied in the subtropical plantation forest of southern China. Soil CH4 and N2O fluxes, the abundance and structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were measured using static chamber-gas chromatography, quantitative PCR (qPCR), and terminal-restriction fragment length polymorphism (T-RFLP). Nitrogen addition tended to inhibit soil CH4 uptake, but significantly promoted soil N2O emission; moreover, these impacts were more significant with NH4+−N than with NO3−−N addition. NH4Cl addition significantly changed ammonia-oxidizer abundance with an increase in AOA and a decrease in AOB. Nitrogen additions significantly decreased the relative abundance of 329 bp and 421 bp of archaeal amoA gene. Negative relationships occurred between soil CH4 uptake and AOA abundance and between soil CH4 uptake and AOA/AOB ratio; however, a positive relationship was found between soil N2O emission and AOA abundance. These results indicate that a shift in abundance and composition of ammonia-oxidizing communities is closely linked to changes in soil CH4 uptake and N2O emission under N enrichment. Furthermore, AOA communities play a contrasting role from AOB communities for regulating the fluctuation between soil CH4 and N2O fluxes.

Ammonia-oxidizing archaea respond positively to inorganic nitrogen addition in desert soils.

In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability.

Abundance and Community Composition of Ammonia-Oxidizers in Paddy Soil at Different Nitrogen Fertilizer Rates

Ammonia oxidation, the first and rate-limiting step of nitrification, is carried out by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). However, the relative importance of AOB and AOA to nitrification in terrestrial ecosystems is not well understood. The aim of this study was to investigate the effect of the nitrogen input amount on abundance and community composition of AOB and AOA in red paddy soil. Soil samples of 10-20 cm (root layer soil) and 0-5 cm (surface soil) depths were taken from a red paddy. Rice in the paddy was fertilized with different rates of N as urea of N1 (75 kg N ha−1 yr−1), N2 (150 kg N ha−1 yr−1), N3 (225 kg N ha−1 yr−1) and CK (without fertilizers) in 2009, 2010 and 2011. Abundance and community composition of ammonia oxidizers was analyzed by real-time PCR and denaturing gradient gel electrophoresis (DGGE) based on amoA (the unit A of ammonia monooxygenase) gene. Archaeal amoA copies in N3 and N2 were significantly (P<0.05) higher than those in CK and N1 in root layer soil or in surface soil under tillering and heading stages of rice, while the enhancement in bacterial amoA gene copies with increasing of N fertilizer rates only took on in root layer soil. N availability and soil NO3−-N content increased but soil NH4+-N content didn't change with increasing of N fertilizer rates. Otherwise, the copy numbers of archaeal amoA gene were higher (P<0.05) than those of bacterial amoA gene in root lary soil or in surface soil. Redundancy discriminate analysis based on DGGE bands showed that there were no obvious differs in composition of AOA or AOB communities in the field among different N fertilizer rates. Results of this study suggested that the abundance of ammonia-oxidizers had active response to N fertilizer rates and the response of AOA was more obvious than that of AOB. Similarity in the community composition of AOA or AOB among different N fertilizer rates indicate that the community composition of ammonia-oxidizers was relatively stable in the paddy soil at least in short term for three years.

Habitat Specialization Along a Wetland Moisture Gradient Differs Between Ammonia-oxidizing and Denitrifying Microorganisms

Gradients in abiotic parameters, such as soil moisture,can strongly influence microbial community structure and function. Denitrifying and ammonia-oxidizing microorganisms,in particular, have contrasting physiological responses to abiotic factors such as oxygen concentration and soil moisture. Identifying abiotic factors that govern the composition and activity of denitrifying and ammonia-oxidizing communities is critical for understanding the nitrogen cycle.The objectives of this study were to (i) examine denitrifier andarchaeal ammonia oxidizer community composition and (ii) assess the taxa occurring within each functional group related to soil conditions along an environmental gradient. Soil was sampled across four transects at four locations along a dry to saturated environmental gradient at a restored wetland. Soil pH and soil organic matter content increased from dry to saturated plots. Composition of soil denitrifier and ammonia oxidizer functional groups was assessed by terminal restriction fragment length polymorphism (T-RFLP) community analysis, and local soil factors were also characterized. Microbial community composition of denitrifiers and ammonia oxidizers differed along the moisture gradient (denitrifier:ANOSIM R = 0.739, P < 0.001; ammonia oxidizers: ANOSIMR = 0.760, P < 0.001). Individual denitrifier taxa were observed over a larger range of moisture levels than individual archaeal ammonia oxidizer taxa (Wilcoxon rank sum, W = 2413, P value = 0.0002). Together, our data suggest that variation in environmental tolerance of microbial taxa have potential to influence nitrogen cycling in terrestrial ecosystems.

Depth distribution of ammonia oxidation rates and ammonia‐oxidizer community composition in the Sargasso Sea

Ammonia oxidation rates and ammonia‐oxidizer community structure were examined in a depth profile (20–2000 m) at the Bermuda Atlantic Time‐Series Study site in December 2009. Ammonia oxidation rates, measured from trace additions of 15 (12–18 nmol L−1), ranged from undetectable at the surface and 2000 m to 2.0 ± 0.1 nmol L−1 d−1 at 120 m, the depth of the primary nitrite maximum (PNM). Nitrification was not detectable in the photic zone in December, perhaps in part due to the density structure of the upper water column at this time. Ammonium oxidation rates varied with ammonium concentration and yielded an estimate for the half‐saturation constant of 65 ± 41 nmol L−1 for the assemblage at 100 m. This value is similar to that reported for the cultivated marine ammonia‐oxidizing archeon Nitrosopumilus maritimus (134 nmol L−1), confirming the high affinity for ammonium of the in situ community in the Sargasso Sea. Ammonia‐oxidizing archaeal (AOA) amoA gene copy numbers were two orders of magnitude higher than ammonia‐oxidizing bacterial (AOB) amoA gene copy numbers at the PNM depth, suggesting that AOA were responsible for most of the ammonium oxidation, which was in turn responsible for the formation of the PNM. AOB abundance exceeded AOA at depths below 140 m, where both groups were much less abundant. Application of an AOA amoA functional gene microarray showed a diverse and even community distribution. A single archetype (AOA24, representing sequences originally from a coral reef) had the highest fluorescence ratio at depths of 0–1000 m.

Effect of agricultural land use change on community composition of bacteria and ammonia oxidizers

Soil microbial communities can be strongly influenced by agricultural practices, but little is known about bacterial community successions as land use changes. The objective of this study was to determine microbial community shifts following major land use changes in order to improve our understanding of land use impacts on microbial community composition and functions. Four agricultural land use patterns were selected for the study, including old rice paddy fields (ORP), Magnolia nursery planting (MNP), short-term vegetable (STV), and long-term vegetable (LTV) cultivation. All four systems are located in the same region with same soil parent material (alluvium), and the MNP, STV, and LTV systems had been converted from ORP for 10, 3, and 30 years, respectively. Soil bacteria and ammonia oxidizer community compositions were analyzed by 454 pyrosequencing and terminal restriction fragment length polymorphism, respectively. Quantitative PCR was used to determine 16S rRNA and amoA gene copy numbers. The results showed that when land use was changed from rice paddy to upland systems, the relative abundance of Chloroflexi increased whereas Acidobacteria decreased significantly. While LTV induced significant shifts of bacterial composition, MNP had the highest relative abundance of genera GP1, GP2, and GP3, which were mainly related to the development of soil acidity. The community composition of ammonia-oxidizing bacteria (AOB) but not ammonia-oxidizing archaea was strongly impacted by the agricultural land use patterns, with LTV inducing the growth of a single super predominant AOB group. The land use changes also induced significant shifts in the abundance of 16S rRNA and bacterial amoA genes, but no significant differences in the abundance of archaea amoA was detected among the four land use patterns. Soil total phosphorous, available phosphorous, NO3 −, and soil organic carbon contents and pH were the main determinants in driving the composition of both bacteria and AOB communities. These results clearly show the significant impact of land use change on soil microbial community composition and abundance and this will have major implications on the microbial ecology and nutrient cycling in these systems, some of which is unknown. Further research should be directed to studying the impacts of these microbial community shifts on nutrient dynamics in these agroecosystems so that improved nutrient management systems can be developed.

Phylogenetic diversity of ammonia-oxidizing archaea and bacteria in biofilters of recirculating aquaculture systems

We constructed ammonia monooxygenase alpha subunit (amoA) gene clone libraries of ammonia-oxidizing archaea (AOA) and bacteria (AOB) from three biofiltration tanks used for closed marine fish culture systems. The number of operational taxonomic units (OTUs) found in any one place was 76%–80% of the total OTUs in each tank for AOA and 100% for AOB when OUTs were defined on the basis of a 5% nucleotide difference. In a phylogenetic tree, all of the AOA amoA sequences fell into a cluster, which contained Candidatus Nitrosopumilus maritimus. All of the AOB amoA sequences were related to the Nitrosospira lineage. These results indicated that different ammonia oxidizers were present in different tanks, but that the dominant phylogenetic types were stable. In a biofiltration tank to which a high concentration of ammonium chloride was added periodically to condition the biofilter materials, most of the AOA amoA sequences were different from the dominant one observed in the fish culture tanks. The AOB amoA sequences were also different, and were similar to those of Nitrosomonas aestuarii. These findings suggest that high concentration ammonia loads have a considerable affect on ammonia-oxidizer community composition.

Relative abundance and diversity of ammonia‐oxidizing archaea and bacteria in the San Francisco Bay estuary

Ammonia oxidation in marine and estuarine sediments plays a pivotal role in the cycling and removal of nitrogen. Recent reports have shown that the newly discovered ammonia-oxidizing archaea can be both abundant and diverse in aquatic and terrestrial ecosystems. In this study, we examined the abundance and diversity of ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) across physicochemical gradients in San Francisco Bay--the largest estuary on the west coast of the USA. In contrast to reports that AOA are far more abundant than beta-AOB in both terrestrial and marine systems, our quantitative PCR estimates indicated that beta-AOB amoA (encoding ammonia monooxygenase subunit A) copy numbers were greater than AOA amoA in most of the estuary. Ammonia-oxidizing archaea were only more pervasive than beta-AOB in the low-salinity region of the estuary. Both AOA and beta-AOB communities exhibited distinct spatial structure within the estuary. AOA amoA sequences from the north part of the estuary formed a large and distinct low-salinity phylogenetic group. The majority of the beta-AOB sequences were closely related to other marine/estuarine Nitrosomonas-like and Nitrosospira-like sequences. Both ammonia-oxidizer community composition and abundance were strongly correlated with salinity. Ammonia-oxidizing enrichment cultures contained AOA and beta-AOB amoA sequences with high similarity to environmental sequences. Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and beta-AOB phylotypes may thrive.

Community composition of ammonia-oxidizing bacteria in the rhizosphere of intercropped wheat (Triticum aestivum L.), maize (Zea mays L.), and faba bean (Vicia faba L.)

Cereal/cereal and cereal/legume intercropping systems are popular in the north, northwest, and southwest of China and often result in yield increases compared to monocropping. Rhizosphere interactions may play a significant role in the yield increases, particularly with respect to nutrient availability. The aim of this study was to investigate the effects of intercropping on N availability and community composition of ammonia-oxidizing bacteria in the rhizosphere of wheat, maize, and faba bean at different growth stages. Denaturing gradient gel electrophoresis (DGGE) based on 16S rRNA genes was used to analyze the community composition of bacterial ammonia oxidizers belonging to β-proteobacteria. The results showed that intercropping with faba bean significantly increased nitrate concentrations in the rhizosphere of wheat and maize at the second sampling time (20 June) compared to monocropping or intercropping between maize and wheat. Intercropping significantly affected the community composition of ammonia-oxidizing bacteria in the rhizosphere compared to monocropping, and the effects were most pronounced in the maize/faba bean and wheat/maize intercropping systems when faba bean and wheat were at anthesis and maize was in seedling stage. In wheat/faba bean intercropping, the effects of intercropping on community composition of ammonia-oxidizing bacteria were less pronounced at the seedling stage of the two species but were significant at anthesis.