Ammonia-oxidizing Bacteria Community Research Articles

Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance

Understanding how microorganisms respond to environmental disturbance is one of the key focuses in microbial ecology. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are responsible for ammonia oxidation which is a crucial step in the nitrogen cycle. Although the physiology, distribution, and activity of AOA and AOB in soil have been extensively investigated, their recovery from a natural disturbance remains largely unknown. To assess the recovery capacities, including resistance and resilience, of AOA and AOB, soil samples were taken from a reservoir riparian zone which experienced periodically water flooding. The samples were classified into three groups (flooding, recovery, and control) for a high-throughput sequencing and quantitative PCR analysis. We used a relative quantitative index of both the resistance (RS) and resilience (RL) to assess the variation of gene abundance, alpha-diversity, and community composition. The AOA generally demonstrated a better recovery capability after the flooding disturbance compared to AOB. In particular, AOA were more resilient after the flooding disturbance. Taxa within the AOA and AOB showed different RS and RL values, with the most abundant taxa showing in general the highest RS indices. Soil NH4+ and Fe2+/Fe3+ were the main variables controlling the key taxa of AOA and AOB and probably influenced the resistance and resilience properties of AOA and AOB communities. The distinct mechanisms of AOA and AOB in maintaining community stability against the flooding disturbance might be linked to the different life-history strategies: the AOA community was more likely to represent r-strategists in contrast to the AOB community following a K-life strategy. Our results indicated that the AOA may play a vital role in ammonia oxidation in a fluctuating habitat and contribute to the stability of riparian ecosystem.

Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop.

Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N2O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N2O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N2O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N2O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N2O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization.

High-methionine soybean has no significant effect on nitrogen-transforming bacteria in rhizosphere soil

Transgenic plants may induce shifts in the microbial community composition that in turn alter microbially-mediated nutrient cycling in soil. Studies of how specific microbial groups respond to genetically modified (GM) planting help predict potential impacts upon processes performed by these groups. This study investigated the effect of transgenic high-methionine soybean cv. ZD91 on nitrogen-fixing and ammonia-oxidizing bacterial populations. A difference in nitrogen-fixing or ammonia-oxidizing bacteria community composition was not found, suggesting that cv. ZD91 does not alter the bacterial populations in rhizosphere soil. This study increases our understanding of the potential effect of transgenic soybean on microbial functional groups within soil by suggesting that nitrogen-transforming bacteria may be useful for future investigations on the GM crops impact in the soil ecosystem.

Reactor performance, biofilm property and microbial community of anaerobic ammonia-oxidizing bacteria under long-term exposure to elevated Cu (II)

In this study, the variation of reactor performance, biofilm property and microbial community in response to the elevated Cu (II) in Anammox system were investigated. The nitrogen removal, extracellular polymeric substance (EPS) and copper content in biofilm, soluble microbial products (SMP), dehydrogenase activity (DHA) and microbial community were evaluated. The self-recovery ability was also investigated after stopping Cu (II) supply. Results showed the long-term feeding of Cu (II) significantly suppressed the nitrogen removal in Anammox system. The nitrogen removal rate (NRR) decreased to 0.210, 0.145 and 0 kg m−3 d−1, respectively in 1, 5 and 10 mg L−1 Cu (II), from the initial 0.50 kg m−3 d−1, with the decreasing ratio of 57.3%, 71.0% and 100%. With the elevation of Cu (II), the SMP, EPS and copper content gradually increased while DHA sharply decreased. Cu (II) improved the microbial diversity and lowered the Candidatus Kuenenia abundance to 1.36% from the initial 6.50%. The self-recovery ability of Anammox system was unsatisfactory, the NRR only recovered to 26.7% after one month operation free from Cu (II). Finally, the mechanism of Cu (II) interacting with Anammox biofilm was analyzed.

Influence of Cu application on ammonia oxidizers in fluvo-aquic soil

Nitrification driving by archaeal and bacterial ammonia oxidizers is an essential step of the global nitrogen cycle. This laboratory study screened toxicity of copper (Cu) stress in the fluvo-aquic system, investigated the ecological niche of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities and analyzed the response of AOA and AOB communities to Cu stress in the system. We added Cu as CuCl2 solution at 0 mg, 100 mg, 300 mg, 600 mg, and 1200 mg Cu per kg soil in the fresh fluvo-aquic soil. Soil samples were incubated for 6 h, 12 h, 1 d, 3 d, 7 d, 14 d, 28 d, and 56 d in lab condition. The soil potential nitrification rates (PNR) were measured at each stage. Denaturing gradient gel electrophoresis (DGGE) analysis of amoA of AOA and AOB were performed at 56 d of Cu incubation. Soil RNA was extracted and the abundance of amoA transcripts was analyzed by real time polymerase chain reaction (real-time PCR) at 1, 3, and 7 d. The amoA gene abundance analysis and DGGE profile analysis showed that the abundance and diversity of AOA were higher than that of AOB in fluvo-aquic soil. However, the correlations between the soil PNR and the number of amoA transcript indicated that the AOB community, rather than AOA community, dominates ammonia oxidation in Cu-polluted fluvo-aquic soil ecosystems. Combining the results of the soil PNR and the abundance and diversity of ammonia oxidizers community, Cu hormetic concentration was identified as a range from 100 to 600 mg kg−1, while the toxic concentration was higher than 600 mg kg−1 in fluvo-aquic soil system. Furthermore, the results of amoA transcript numbers showed that AOA may be resistant to Cu stress and AOB may be more sensitive to Cu stress under our experiment conditions.

Nitrifying activity and ammonia-oxidizing microorganisms in a constructed wetland treating polluted surface water

Ammonia oxidation, performed by both ammonia oxidizing bacteria (AOB) and archaea (AOA), is an important step for nitrogen removal in constructed wetlands (CWs). However, little is known about the distribution of these ammonia oxidizing organisms in CWs and the associated wetland environmental variables. Their relative importance to nitrification in CWs remains still controversial. The present study investigated the seasonal dynamics of AOA and AOB communities in a free water surface flow CW (FWSF-CW) used to ameliorate the quality of polluted river water. Strong seasonality effects on potential nitrification rate (PNR) and the abundance, richness, diversity and structure of AOA and AOB communities were observed in the river water treatment FWSF-CW. PNR was positively correlated to AOB abundance. AOB (6.76×105–6.01×107 bacterial amoA gene copies per gram dry sediment/soil) tended to be much more abundant than AOA (from below quantitative PCR detection limit to 9.62×106 archaeal amoA gene copies per gram dry sediment/soil). Both AOA and AOB abundance were regulated by the levels of nitrogen, phosphorus and organic carbon. Different wetland environmental variables determined the diversity and structure of AOA and AOB communities. Wetland AOA communities were mainly composed of unknown species and Nitrosopumilus-like organisms, while AOB communities were mainly represented by both Nitrosospira and Nitrosomonas.

Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China.

Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001) but not with soil pH (p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048), whereas PNR significantly correlated positively with the richness (p = 0.003), diversity (p = 0.001) and abundance (p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available.

English

For many years, the generation of nitrates from organic sources in order to create nutrient solutions for hydroponics had proved a challenge until lately when microorganisms were introduced to perform this task. The objectives of the current study therefore were to use local microbial consortium to nitrify goat manure in water and to determine microbial diversity in the inoculated consortium. Therefore, microorganisms were sourced from garden soil and natural compost at the Sam Nujoma Marine resources Research Centre (SANUMARC) in Henties Bay Namibia to convert organic nitrogen in goat manure from Utuseb farm near Walvis Bay into nitrates. Results show that microbial consortium from the compost source produced significantly (P&lt; 0.05) more nitrates followed by the garden-soil source, suggesting that it is necessary to add inoculum in order to generate nitrate from goat manure. The ammonia oxidising bacteria (AOB) community from the compost sample&rsquo;s was dominated by uncultured ammonia-oxidising species followed by uncultured bacterium (both not identified), with the least being Nitrosomonas species. The AOB community from the garden source was dominated by uncultured bacterium, followed by uncultured ammonia-oxidising species and the least being Nitrosomonas species. NOB community from the compost source was dominated by uncultured bacterium, followed by Nitrobacter winogradskyi and Nitobacter vulgaris with the least being Nitrococcus mobilis and Nitrospira moscovensis. For the garden soil microbial source, uncultured nitrite-oxidising bacteria dominated followed by uncultured bacterium, whereas the least species were N. moscovensis and Nitrobacter alkalicus. Moreover, community composition of the compost sample was more diverse than the community from the garden sample. These results maintain that there are other unculturable yet important microbes doing the same job if not better than the known ones, in this case suggesting that there may be other local nitrite-oxidizing bacteria responsible for oxidizing ammonia other than the traditionally known Nitrobacter, Nitrospira and Nitrococcus species. &nbsp; Key words: Organic hydroponics, ammonification, nitrification, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria.

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.

Effects of combined application of nitrogen fertilizer and biochar on the nitrification and ammonia oxidizers in an intensive vegetable soil

Soil amended with single biochar or nitrogen (N) fertilizer has frequently been reported to alter soil nitrification process due to its impact on soil properties. However, little is known about the dynamic response of nitrification and ammonia-oxidizers to the combined application of biochar and N fertilizer in intensive vegetable soil. In this study, an incubation experiment was designed to evaluate the effects of biochar and N fertilizer application on soil nitrification, abundance and community shifts of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Hangzhou greenhouse vegetable soil. Results showed that single application of biochar had no significant effect on soil net nitrification rates and ammonia-oxidizers. Conversely, the application of only N fertilizer and N fertilizer + biochar significantly increased net nitrification rate and the abundance of AOB rather than AOA, and only AOB abundance was significantly correlated with soil net nitrification rate. Moreover, the combined application of N fertilizer and biochar had greater effect on AOB communities than that of the only N fertilizers, and the relative abundance of 156 bp T-RF (Nitrosospira cluster 3c) decreased but 60 bp T-RF (Nitrosospira cluster 3a and cluster 0) increased to become a single predominant group. Phylogenetic analysis indicated that all the AOB sequences were grouped into Nitrosospira cluster, and most of AOA sequences were clustered within group 1.1b. We concluded that soil nitrification was stimulated by the combined application of N fertilizer and biochar via enhancing the abundance and shifting the community composition of AOB rather than AOA in intensive vegetable soil.

Responses of soil microbial community to nitrogen fertilizer and precipitation regimes in a semi-arid steppe

Changes of nitrogen (N) cycle caused by N fertilization and precipitation regimes have affected the key ecosystem structure and functions in temperate steppe, which may modify the structure of soil microbial communities involved in N transformation. This paper was designated to examine the response of soil ammonia oxidizers and denitrifiers to the N fertilization and precipitation regimes in a semi-arid steppe where N and water contents are major limiting factors of the grassland productivity. This study was based on a long-term N fertilization and precipitation regimes experiment in Inner Mongolia (116° 17′ 20″ E, 42° 2′ 29″ N). The treatments including CK (control), R (reduced precipitation), W (30% increase in precipitation), N (10 g N m−2 y−1), RN (reduced precipitation and 10 g N m−2 y−1), and WN (30% increase in precipitation and 10 g N m−2 y−1). Soil basic chemical properties and microbial activities were analyzed. Molecular methods were applied to determine the abundance, structure and diversity of ammonia oxidizers and denitrifiers. Statistical analysis detected the main and interactive effect of treatments on soil microbial communities and revealed the relationship between soil microbial community structures and environmental factors. N fertilization significantly increased ammonia-oxidizing bacteria (AOB) abundance. Ammonia-oxidizing archaea (AOA) community structure was markedly changed in N fertilizer treatment and strongly affected by soil pH, while soil nitrate and water content correlated with AOB community structure. Soil nitrate was the key factor influencing nirK gene community structure, while soil pH and water content explained much of the variations of nosZ gene community. AOB-amoA and nosZ gene community diversities were influenced by precipitation regimes and interaction of N fertilization and precipitation regimes, respectively. N fertilization and precipitation regimes had significant influences on the changes of soil properties and microbial functional communities. Soil nitrification was mainly driven by AOB in the semi-arid grassland. Changes of substrate content and soil pH were the key factors in shifting functional microbial communities. The non-synergistic effects of N fertilization and precipitation regimes on the microbial functional groups indicated that the negative effect of lower pH induced by N fertilization would be alleviated by precipitation regimes, which should be well considered in grassland restoration.

Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments

Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1–100 mg kg−1) and copper (Cu, 50–500 mg kg−1) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg−1 BDE 209 with a 100 mg kg−1 Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments.

Short-Term and Long-Term Effects of Tourmaline on Activated Sludge Viability and Performance

The study aimed to explore the short-term and long-term effects of tourmaline on activated sludge viability and biological nutrient removal performance. The experimental results indicated that ultrafine tourmaline particles (1 g/L) promoted sludge viability, the reaction rates, and relative enzyme activities in wastewater nitrogen removal. The difference between short-term and long-term effects of tourmaline was not significant. Although the NH4 +-N removal rate and NO3 −-N formation rate in the presence of 1 g/L ultrafine tourmaline particles were increased to 13.8 and 6.8 mg/L•h, which were higher than those in the control (11.0 and 6.0 mg/L•h), short-term and long-term exposure to 1 g/L ultrafine tourmaline particles did not change the effluent concentrations of ammonia nitrogen, nitrite, and nitrate because the relative substrate concentrations were low in the influent. Denaturing gradient gel electrophoresis (DGGE) analysis results indicated that the microorganism community structures including the whole bacteria community, ammonia-oxidizing bacteria community, or the whole fungi community were not changed after the long-term exposure to 1 g/L ultrafine tourmaline particles, and Shannon diversity indices (H′) assays revealed that the diversities of community structures were not changed after the exposure to 1 g/L ultrafine tourmaline particles.

Role of Ammonia-Oxidizing Archaea in Ammonia Removal of Wetland Under Low-Temperature Condition

Ammonia-oxidizing archaea (AOA) have aroused great attention since it can supplement nitrogen cycle and show extensive existence relative to its bacterial counterpart, ammonia-oxidizing bacteria (AOB). This study compared the abundance and community compositions of AOA and AOB between natural and constructed wetlands under low temperature. More complex community structures were obtained in the constructed wetland, which may be ascribed to the differences in available nutrient contents. Nitrosospira-like organisms predominated AOB communities in both wetlands. Nitrososphaera cluster dominated the AOA community in the constructed wetland, while both Nitrososphaera and Nitrosopumilus clusters were dominant in the natural wetland. AOA dominated over AOB in both the natural and constructed wetlands, and AOA to AOB ratio ranged from 1.47 to 8.13. The natural wetland showed higher nitrification potential at low temperature, mainly due to its higher AOA to AOB ratio. This also explained why a better ammonia treatment performance was observed in the natural wetland even when it had high influent concentrations. The present results provided some new insights to ammonia removal in the wetlands under low temperature.

Principal component analysis for interaction of nitrifiers and wastewater environments at a full-scale activated sludge plant

This study investigated the relationship between wastewater environments and the nitrifiers at a full-scale plant using principal component analysis. Ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were detected by florescent in situ hybridization, polymerase chain reaction, phylogenetic analysis, real-time quantitative polymerase chain reaction. Pyrosequencing was also used in profiling the ammonia monooxygenase locus of ammonia-oxidizing bacteria community. It was found that the dominant ammonia-oxidizing bacteria sequences were related to uncultured ammonia-oxidizing bacterium, uncultured Nitrosomonadaceae bacterium, Nitrosomonas sp., and uncultured bacterium. In addition, Nitrobacter clones were related to uncultured alpha proteobacterium, uncultured bacterium, uncultured Nitrobacter sp., and uncultured Bradyrhizobium sp., whereas Nitrospira clones were similar to uncultured bacterium, Candidatus Nitrospira defluvii, uncultured Nitrospira sp., and uncultured Nitrospirae bacterium. The ammonia-oxidizing bacteria and nitrite-oxidizing bacteria ranged 2.83 × 108–1.33 × 1010 and 1.25 × 1010–1.13 × 1011 copies L−1, respectively, equivalent to nitrite-oxidizing bacteria: ammonia-oxidizing bacteria ratio of 10:1. The first three parts of the principal components analysis accounted for 76.8% of the explained variance. The first principal component (44.4%) designated that ammonia-oxidizing bacteria and Nitrospira were mainly influenced by seasonal variations, followed by chemical oxygen demand concentration and nitrogen species (i.e., ammonia, nitrite, and nitrate). The second principal component (19.1%) showed no information about the nitrifiers’ interaction with environmental factors, whereas Nitrobacter demonstrated a high correlation with ammonia on the third principal component (13.3%). These results revealed that the species of Nitrobacter were less influenced by environmental conditions than ammonia-oxidizing bacteria and Nitrospira spp.

Ammonia-oxidizing archaea and bacteria responding differently to fertilizer type and irrigation frequency as revealed by Illumina Miseq sequencing

Ammonia oxidation, the first and rate-limiting step of nitrification, can be strongly influenced by agricultural practices, but little is known about the effects of fertilization and irrigation combination on ammonia oxidizers in agricultural soils. This study was designed to reveal how fertilizer type and irrigation frequency affect the ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities in a northern Chinese wheat-maize rotation soil. Soil samples were collected from a long-term field experiment under different fertilization and irrigation regimes located in Wuqiao Experimental Station of China Agricultural University in June 2016. The abundance, diversity, and composition of AOA and AOB in the soils were investigated by using real-time PCR and Illumina Miseq sequencing approaches. The abundance of AOA was higher in the irrigated treatments, but lower in the treatments without irrigation, than that of AOB. The AOA abundance was positively correlated with soil moisture, pH, and NO3 −-N, while the AOB abundance was positively correlated with TN and NO3 −-N. Soil potential nitrification activity (PNA) was significantly positively correlated with the AOB abundance. Both fertilizer type and irrigation frequency significantly affected Shannon, ACE, and Chao1 indices of the AOB community, while only irrigation frequency had a significant impact on Shannon index of the AOA community. PCoA analysis results indicated that irrigation frequency greatly affected the AOA community structure, while fertilizer type played a more important role in affecting the AOB community structure. Mantel test and correlation heatmap analysis results indicated that soil moisture, pH, and NH4 +-N were significantly correlated to the AOA community structure, and TN and SOC were significantly correlated to the AOB community structure. This study demonstrated that irrigation frequency greatly influenced the AOA community, while fertilizer type had a stronger effect on the AOB community. It was AOB but not AOA played a more important role in soil nitrification. Moreover, soil moisture, pH, and TN were the main determinants in driving the AOA community and TN and SOC were the main factors in influencing the AOB community.

Research trends and hotspots related to ammonia oxidation based on bibliometric analysis.

Ammonia oxidation is the rate-limiting and central step in global biogeochemistry cycle of nitrogen. A bibliometric analysis based on 4314 articles extracted from Science Citation Index Expanded database was carried out to provide insights into publication performances and research trends of ammonia oxidation in the period 1991-2014. These articles were originated from a wide range of 602 journals and 95 Web of Science Categories, among which Applied and Environmental Microbiology and Environmental Sciences took the leading position, respectively. Furthermore, co-citation analysis conducted with help of CiteSpace software clearly illustrated that ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia oxidation (anammox) were three dominant research themes. A total of 15 landmark works identified with the highest co-citation frequencies at every 8years were extracted, which demonstrated that the establishments of culture-independent molecular biotechnologies as well as the discoveries of anammox and AOA played the most significant roles in promoting the evolution and development of ammonia oxidation research. Finally, word cluster analysis further suggested that microbial abundance and community of AOA and AOB was the most prominent hotspot, with soil and high-throughput sequencing as the most promising ecosystem and molecular biotechnology. In addition, application of anammox in nitrogen removal from wastewater has become another attractive research hotspot. This study provides a basis for better understanding the situations and prospective directions of the research field of ammonia oxidation.

Response of ammonia-oxidizing archaea and bacteria in calcareous soil to mineral and organic fertilizer application and their relative contribution to nitrification

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) co-exist in soils. However, little is known about the effects of fertilization on the AOA and AOB communities and their relative contribution to soil nitrification. The objective of this field study was to determine the effects of four years of mineral and organic fertilizer (i.e., either cattle manure or biofertilizer) application on AOB and AOA in calcareous soil. The combined application of mineral and organic fertilizer (especially cattle manure) significantly increased the species richness (Chao1 and Ace) and α-diversity (Shannon index) of AOB (P < 0.05) but not AOA (P = 0.102). The AOA/AOB ratios were 1.64 and 1.19 in the unfertilized and the mineral fertilizer treatments, respectively. In contrast, the AOA/AOB rations were <1.0 in treatments with both mineral and organic fertilizer. These findings indicated that organic fertilizer increased AOB comparatively to AOA. Fertilizer addition was associated with significant shifts in the community structure of AOB (P < 0.01) but had little effect on AOA. Soil potential nitrification rate were greatly increased by the application of either mineral fertilizer or mineral plus organic fertilizer (P < 0.05). Moreover, potential nitrification rate were positively correlated with AOB abundance (P < 0.001) but not AOA abundance (P = 0.223). Variations in AOB community structure were closely associated with fertilizer-induced changes in soil pH, NH4+ and SOC, whereas AOA community structure was only significantly correlated with SOC (P = 0.040). Our findings suggest (i) that AOB is more sensitive than AOA to different fertilization regimes and (ii) that AOB contribute more than AOA to nitrification in this fertilized calcareous field soil.

PH drives ammonia oxidizing bacteria rather than archaea thereby stimulate nitrification under Ageratina adenophora colonization

Understanding mechanisms of successful colonization by exotic plant species in non-native habitat is critical to meet long-term restoration aims. Overgrowing plants can alter resources, especially soil inorganic nitrogen availability and get benefits from positive feedback. However, comprehensive knowledge on particular mechanisms underlying their successful colonization remains unclear. Here, field examinations and laboratory manipulations were combined to investigate significant impact of overgrowing Ageratina adenophora on soil NO3−-N availability and nitrification. Interestingly, we found significant enhancement in soil total N, NO3−-N, pH, potential nitrification rates, and ammonia oxidizing bacteria (AOB), while reduced abundance of ammonia oxidizing archaea (AOA) under the influence of A. adenophora. Notably, AOB abundance was positively correlated with both pH and soil potential nitrification rates. AOA abundance was negatively correlated with pH and had no significant correlation with soil nitrification potential. Both AOA and AOB communities significantly differed between populated and non-populated soils. pH was the strongest factor contributing to this community difference. We conclude that A. adenophora stimulates nitrification with the help of AOB rather than AOA under relatively higher soil pH condition.

PH rather than nitrification and urease inhibitors determines the community of ammonia oxidizers in a vegetable soil

Nitrification inhibitors and urease inhibitors, such as nitrapyrin and N-(n-butyl) thiophosphoric triamide (NBPT), can improve the efficiencies of nitrogen fertilizers in cropland. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across different soil pH levels are still unclear. In the present work, vegetable soils at four pH levels were tested to determine the impacts of nitrification and urease inhibitors on the nitrification activities, abundances and diversities of ammonia oxidizers at different pHs by real-time PCR, terminal restriction fragment length polymorphism (T-RFLP) and clone sequence analysis. The analyses of the abundance of ammonia oxidizers and net nitrification rate suggested that AOA was the dominate ammonia oxidizer and the key driver of nitrification in acidic soil. The relationships between pH and ammonia oxidizer abundance indicated that soil pH dominantly controlled the abundance of AOA but not that of AOB. The T-RFLP results suggested that soil pH could significantly affect the AOA and AOB community structure. Nitrapyrin decreased the net nitrification rate and inhibited the abundance of bacterial amoA genes in this vegetable soil, but exhibited no effect on that of the archaeal amoA genes. In contrast, NBPT just lagged the hydrolysis of urea and kept low NH4+-N levels in the soil at the early stage. It exhibited no or slight effects on the abundance and community structure of ammonia oxidizers. These results indicated that soil pH, rather than the application of urea, nitrapyrin and NBPT, was a critical factor influencing the abundance and community structure of AOA and AOB.