Ammonia-oxidizing Archaea Community Structure Research Articles

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 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.

Abundance and diversity of ammonia-oxidizing archaea in a biological aerated filter process

Ammonia-oxidizing archaea (AOA) represent an important group of ammonia-oxidizing microorganisms that are able to convert ammonia to nitrite, a function which is crucial for the removal of nitrogen from wastewater. In this study, we investigated the abundance and diversity of AOA in a full-scale wastewater treatment plant (WWTP) which used a biological aerated filter (BAF) as the main processing mode. According to the quantitative PCR results, AOA clearly outnumbered ammonia-oxidizing bacteria (AOB) during the whole process. The abundance of AOA amoA genes in the filter layer of BAF was highest with the value varied from 6.32 × 103 to 3.8 × 104 copies/ng DNA. The highest abundance of AOB amoA genes was 1.32 × 102 copies/ng DNA, recorded in the effluent of the ACTIFLO® settling tank. The ratios of AOA/AOB in the WWTP were maintained at two or three orders of magnitude. Most AOA obtained from the WWTP fell within the Nitrosopumilus cluster. The abundance of AOA and AOB was significantly correlated with ammonium nitrogen concentrations and pH value. The community structure of AOA was significantly influenced by dissolved oxygen concentrations, pH value and chemical oxygen demand.

Effect of Dicyandiamide on N2O Emission in Fallow Paddy Field and Rape Cropping

The emissions of greenhouse gas in winter are often neglected, and the latest research results showed that N2O emissions in fallow paddy field and winter oilseed rape are still large, research on mitigating the N2O flux and the mechanism behind them is of significance for mitigating N2O emissions from agricultural soil. By using static chamber techniques and molecular biology techniques, the N2O emission as well as the community composition and abundance of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) from fallow paddy field, rape cropping with and without DCD treatment in Taoyuan agricultural ecological experiment station of the Chinese Academy of sciences were measured. The results showed that the addition of DCD significantly inhibited N2O emissions in fallow paddy field and rape cropping by 36.7% and 23.6%, respectively. The application of DCD in fallow paddy field inhibited the abundance of AOA and AOB by 59.3% and 73.7%, respectively, but only changed the community structure of AOA. The addition of DCD in rape cropping only changed the community structure and inhibited the abundance of AOB. This research showed that DCD application could effectively mitigate the N2O emissions in fallow paddy field and winter rape cropping under different mitigation mechanisms.

Legacy effects of simulated short-term climate change on ammonia oxidisers, denitrifiers, and nitrous oxide emissions in an acid soil.

Although the effect of simulated climate change on nitrous oxide (N2O) emissions and on associated microbial communities has been reported, it is not well understood if these effects are short-lived or long-lasting. Here, we conducted a field study to determine the interactive effects of simulated warmer and drier conditions on nitrifier and denitrifier communities and N2O emissions in an acidic soil and the longevity of the effects. A warmer (+2.3°C) and drier climate (-7.4% soil moisture content) was created with greenhouses. The variation of microbial population abundance and community structure of ammonia-oxidizing archaea (AOA), bacteria (AOB), and denitrifiers (nirK/S, nosZ) were determined using real-time PCR and high-throughput sequencing. The results showed that the simulated warmer and drier conditions under the greenhouse following urea application significantly increased N2O emissions. There was also a moderate legacy effect on the N2O emissions when the greenhouses were removed in the urea treatment, although this effect only lasted a short period of time (about 60days). The simulated climate change conditions changed the composition of AOA with the species affiliated to marine group 1.1a-associated lineage increasing significantly. The abundance of all the functional denitrifier genes decreased significantly under the simulated climate change conditions and the legacy effect, after the removal of greenhouses, significantly increased the abundance of AOB, AOA (mainly the species affiliated to marine group 1.1a-associated lineage), and nirK and nosZ genes in the urea-treated soil. In general, the effect of the simulated climate change was short-lived, with the denitrifier communities being able to return to ambient levels after a period of adaptation to ambient conditions. Therefore, the legacy effect of simulated short-time climate change conditions on the ammonia oxidizer and denitrifier communities and N2O emissions were temporary and once the conditions were removed, the microbial communities were able to adapt to the ambient conditions.

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland

Ammonia oxidation is carried out by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The Ebinur Lake wetland is the best example of a temperate arid zone wetland ecosystem in China. Soil samples were collected from rhizosphere and non-rhizosphere soil containing Halocnemum strobilaceum (samples H and H'), Phragmites australis (samples R and R'), and Karelinia caspia (samples K and K') to study the relationship between environmental factors and the community structure of AOB and AOA. Phylogenetic analysis showed that the AOA sequences belonged to the Nitrosopumilus and Nitrososphaera clusters. AOB were grouped into Nitrosospira sp. and Nitrosomonas sp. Quantitative polymerase chain reaction results showed that the AOA abundance ranged from 2.09 × 104 to 2.94 × 105 gene copies/g soil. The highest number of AOA was detected in sample K, followed by samples R and H. AOB abundance varied between 2.91 × 105 and 1.05 × 106 gene copies/g soil, which was higher than that of AOA. Redundancy analysis indicated that electrical conductivity, pH, and NH4+-N might influence the community structure of AOA and AOB. AOB might play a more crucial role than AOA in ammonia oxidation based on AOB's higher diversity and abundance in the Ebinur Lake wetland in Xinjiang.

Contrasting effects of nitrogen forms and soil pH on ammonia oxidizing microorganisms and their responses to long-term nitrogen fertilization in a typical steppe ecosystem

Ammonia-oxidizing microorganisms, i.e. ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), are the primary agents responsible for soil nitrification. Few studies, however, have evaluated how AOA and AOB responses to long-term N fertilization are affected by soil pH and different forms of nitrogen (N). We examined the effects of soil acidification and different forms of N (NH4+ and NO3−) on abundances and community structure of AOA and AOB based on a field acid addition experiment and a short-term microcosm N addition experiment. The field acid addition experiment demonstrated that, with decreasing soil pH, AOB abundance decreased while AOA abundance mostly increased except for an extremely low pH treatment. Relationships between soil pH and abundance of ammonia oxidizers in the acid addition experiment conflict with those in the long-term N fertilization experiment, indicating a predominant role of N rather than soil pH on responses of AOB and AOA under N inputs. The short-term N addition experiment confirmed the general positive effect of NH4+ on AOB and the negative effect of NO3−on AOA which help explain the responses of AOB and AOA abundance to long-term N fertilization. Community structure of ammonia oxidizers, in contrast, showed little response to acid addition and short-term N additions. The positive responses of AOB and not AOA to various N additions revealed a dominant role of AOB in nitrification with broad ranges of soil pH and N availability. We found a negative effect of NO3− addition on AOA abundance, which may be a key factor limiting contributions of AOA to nitrification in many soils.

Effects of copper on the abundance and diversity of ammonia oxidizers during dairy cattle manure composting

This study investigated the effects of adding Cu(II) at two exposure levels (50 and 500mgkg−1, i.e., Cu50 and Cu500 treatments, respectively) on the activity of ammonia-oxidizing microorganisms during dairy cattle manure composting. The results showed that the pH, NH4+-N, NO3−-N, and potential ammonia oxidation values were inhibited significantly by the addition of Cu(II). Furthermore, the abundances of the ammonia-oxidizing archaea (AOA) amoA gene and ammonia-oxidizing bacteria (AOB) amoA gene were determined by quantitative PCR, and their compositions were evaluated by denaturing gradient gel electrophoresis (DGGE). AOA was the dominant ammonia oxidizing microorganism, of which the abundance was much higher than AOB during composting. Cu50 and Cu500 had significant inhibitory effects on the abundance of the amoA gene. The DGGE profile and statistical analysis showed that Cu(II) changed the AOA and AOB community structure and diversity, where Nitrosomonas and Crenarchaeota dominated throughout the composting process.

Warmer and drier conditions alter the nitrifier and denitrifier communities and reduce N2O emissions in fertilized vegetable soils

Nitrous oxide (N2O) is a potent greenhouse gas and is mainly produced from agricultural soils especially vegetable soils with large N fertilizer input. How future projected climate change may impact on the N2O emissions and the related key (de)nitrifier communities in such ecosystem is poorly understood. The aim of this field study was to determine the interactive effects of a simulated warmer and drier climate on (de)nitrifier communities and N2O emissions in a vegetable soil. A warmer (+3.3°C) and drier climate (−14.4% soil moisture content) was created with greenhouses with or without urea N fertilizer application. The variation of microbial population abundance and community structure of Ammonia-oxidizing archaea (AOA), bacteria (AOB) and denitrifiers (nirK/S, nosZ) were determined using Real time-PCR and sequencing. The results showed a strong interactive effect of simulated climate change with N fertilizer applications, whereby the impacts of warmer and drier conditions on the microbial communities and N2O emissions were more evident when N fertilizer was applied. The simulated warmer and drier conditions in the greenhouses significantly decreased N2O emissions largely due to the drier soil conditions. The abundance and community structure of AOB showed more rapid responses than AOA under the simulated climate conditions when N fertilizer was applied. Changes of AOB community structure were significantly correlated with soil moisture content and NH4+-N concentration. The simulated climate change did not affect the nirS gene abundance, but significantly increased nirK gene abundance, and significantly decreased nosZ gene abundance with urea application. N2O emissions were positively correlated with the bacterial amoA abundance and with the ratio of nirK/nosZ gene abundance. Therefore, bacterial amoA, nirK- and nosZ-type denitrifiers are the dominant microbial communities which were affected by the simulated climate conditions and are thus critically important for N cycling in vegetable soils under a changing climate.

Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants' receiving area in Hangzhou Bay.

The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River's estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 10(5)-10(7) gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39-5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4 (+)-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge.

Diversity, abundance and community structure of ammonia-oxidizing archaea and bacteria in riparian sediment of Zhenjiang ancient canal

Ammonia-oxidizing microorganisms play an important role in the nitrification process. In this study, the abundance, diversity and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in riparian sediment of Zhenjiang ancient canal were investigated using amoA gene as a molecular biomarker. Clone libraries and qPCR (quantitative polymerase chain reaction) results indicated both abundance and diversity of AOB were higher than that of AOA, suggesting that AOB may play a more important role than AOA in nitrification process. The abundances, diversity and community structure of AOA and AOB had an obvious spatial variation in six different sampling sites, which may be attributed to the differences in sediment physico-chemical characteristics. 66.7%, 26.5% and 6.8% of the total 117 AOA gene sequences fell into the Nitrososphaera, Nitrosopumilus and Nitrosotalea cluster, whereas, 52.2% and 47.8% of the total 134 AOB amoA gene sequences belonged to the Nitrosomonas and Nitrosospira cluster. There was a strong positive relationship between the potential nitrification rates (PNRs) without ampicillin and bacterial amoA gene copy numbers, whereas no significant correlation between the archaeal amoA gene copy numbers and the PNRS without ampicillin. In addition, when ampicillin was added into the cultured systems in order to inhibit the bacteria, the values of PNRs decreased by 21.71%, 39.62%, 46.04%, 27.06%, 39.26% and 7.24%, respectively, for the C1, C2, C3, C4, G5 and G6 samples sites, indicating that PNRs were apparently affected by ammonia-oxidizing bacteria. These results further indicate that nitrification is more related to AOB than AOA in the riparian sediment of Zhenjiang ancient canal.

Distribution characteristics of ammonia oxidizing microorganisms in rhizosphere sediments of cattail

The abundance, diversity and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated, using amoA gene as a molecular biomarker, to examine how cattail (Typha orientalis) growth affects the abundances and communities of AOB and AOA in the rhizosphere sediment. Clone libraries and qPCR (quantitative polymerase chain reaction) results indicated the amoA gene copies numbers, relative abundance of AOA and AOB amoA gene clone libraries were highest in rhizosphere sediment, followed by non-rhizosphere sediment and control, indicating that cattail growth has a remarkable effect on the abundance and community structure of ammonia oxidizing microorganisms. Diversity index (Chao1 and Shannon H) have an obvious variation in cattail rhizosphere, non-rhizosphere and control sediments. The average values of Shannon H of AOA and AOB in the rhizosphere sediment were higher than the non-rhizosphere sediment and control. The average value of Chao1 was highest in non-rhizosphere sediment for AOA, whereas, was highest in the rhizosphere sediment for AOB. The abundance, diversity and community structure of AOA and AOB were obvious different in the cattail's three developmental stages, and higher abundances and more complex community structure were obtained in the maturity stage, which may be attributable to the higher root exudation owing to fast growth rates and strong metabolisms in the maturity stage. In addition, despite higher abundant of AOA versus AOB was demonstrated in the cattail rhizosphere, non-rhizosphere sediment and control, bacteria, not archaeal, have more ecosystem functions and play a more important role in dominating ammonia oxidation under the conditions of this study according to the two findings from the present study. One is that AOB had a more diverse and more complex community structure than AOA; the other is that the average value of potential nitrification rates (PNRs) significantly decreased (by 49.08%, 53.69% and 10.39%, respectively) in rhizosphere, non-rhizosphere sediment and control, as compared to PNRs without the ampicillin, when ammonia-oxidizing bacteria were inhibited by ampicillin.

Effect of chemical fertilization and green manure on the abundance and community structure of ammonia oxidizers in a paddy soil

Ammonia oxidization is a critical step in the soil N cycle and can be affected by the fertilization regimes. Chinese milk-vetch (Astragalus sinicus L., MV) is a major green manure of rice (Oryza sativa L.) fields in southern China, which is recommended as an important agronomic practice to improve soil fertility. Soil chemical properties, abundance and community structures of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in a MV-rice rotation field under different fertilization regimes were investigated. The field experiment included six treatments: control, without MV and chemical fertilizer (CK); 100% chemical fertilizer (NPK); 18 000 kg MV ha-1 plus 100% chemical fertilizer (NPKM1); 18 000 kg MV ha-1 plus 40% chemical fertilizer (NPKM2); 18 000 kg MV ha-1 alone (MV); and 18 000 kg MV ha-1 plus 40% chemical fertilizer plus straw (NPKMS). Results showed that NPKMS treatment could improve the soil fertility greatly although the application of 60% chemical fertilizer. The abundance of AOB only in the MV treatment had significant difference with the control; AOA were more abundant than AOB in all corresponding treatments. The NPKMS treatment had the highest AOA abundance (1.19 x 108 amoA gene copies g-1) and the lowest abundance was recorded in the CK treatment (3.21 x 107 amoA gene copies g-1). The abundance of AOA was significantly positively related to total N, available N, NH4+-N, and NO3--N. The community structure of AOA exhibited little variation among different fertilization regimes, whereas the community structure of AOB was highly responsive. Phylogenetic analysis showed that all AOB sequences were affiliated with Nitrosospira or Nitrosomonas and all AOA denaturing gradient gel electrophoresis (DGGE) bands belonged to the soil and sediment lineage. These findings could be fundamental to improve our understanding of AOB and AOA in the N cycle in the paddy soil.

Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China.

Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to −25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g−1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.

Abundance and diversity of ammonia-oxidizing archaea and bacteria on granular activated carbon and their fates during drinking water purification process.

Ammonia is a precursor to trichloramine, which causes an undesirable chlorinous odor. Granular activated carbon (GAC) filtration is used to biologically oxidize ammonia during drinking water purification; however, little information is available regarding the abundance and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) associated with GAC. In addition, their sources and fates in water purification process remain unknown. In this study, six GAC samples were collected from five full-scale drinking water purification plants in Tokyo during summer and winter, and the abundance and community structure of AOA and AOB associated with GAC were studied in these two seasons. In summer, archaeal and bacterial amoA genes on GACs were present at 3.7 × 10(5)-3.9 × 10(8) gene copies/g-dry and 4.5 × 10(6)-4.2 × 10(8) gene copies/g-dry, respectively. In winter, archaeal amoA genes remained at the same level, while bacterial amoA genes decreased significantly for all GACs. No differences were observed in the community diversity of AOA and AOB from summer to winter. Phylogenetic analysis revealed high AOA diversity in group I.1a and group I.1b in raw water. Terminal-restriction fragment length polymorphism analysis of processed water samples revealed that AOA diversity decreased dramatically to only two OTUs in group I.1a after ozonation, which were identical to those detected on GAC. It suggests that ozonation plays an important role in determining AOA diversity on GAC. Further study on the cell-specific activity of AOA and AOB is necessary to understand their contributions to in situ nitrification performance.

Effects of climate warming and elevated CO2 on autotrophic nitrification and nitrifiers in dryland ecosystems

Global climate change is predicted to enhance atmospheric temperature and CO2, with important consequences on biogeochemical nitrogen cycling in dryland ecosystems, which are highly vulnerable and characterized by extremely low nutrient availability. Belowground nitrification processes, predominantly mediated by ammonia-oxidizing archaea (AOA) and bacteria (AOB), are central to plant nitrogen availability and soil N2O emissions, but their responses to future climatic scenarios in drylands remain largely unknown. Here we investigated the impact of factorial combinations of elevated CO2 (+200 ppm) and elevated temperature (+3 °C) on dynamics of ammonia oxidizers and nitrification in three dryland soils planted with Eucalyptus tereticornis. Soil properties (including total carbon, H2O%, and nitrate) and potential nitrification rates were strongly impacted by elevated temperature after nine months, accompanied by significantly higher AOA abundance in two soils and a gradual decrease in AOB abundance under elevated temperature. DNA-stable isotope probing showed increased assimilation of 13CO2 by AOA, but not AOB, under warming, indicating that AOA were actively growing and utilizing the 13CO2 substrates, which was coupled with significantly higher net nitrogen mineralization and nitrification rates. High-throughput microarray analysis revealed temperature selections of particular AOA assemblages and a significant reduction in diversity and co-occurrence of the metabolically active AOA phylotypes. Although these responses were soil specific, structural equation modelling by compiling all the data together showed that warming had significant direct and indirect impacts on soil nitrification which were driven by changes in AOA community structure, but no obvious effects of elevated CO2 could be identified. Our findings suggest that warming has stronger effects than elevated CO2 on autotrophic nitrification, and AOA are more responsive to elevated temperature than AOB in the tested dryland ecosystems.

Fungal endophyte Phomopsis liquidambari affects nitrogen transformation processes and related microorganisms in the rice rhizosphere.

The endophytic fungus Phomopsis liquidambari performs an important ecosystem service by assisting its host with acquiring soil nitrogen (N), but little is known regarding how this fungus influences soil N nutrient properties and microbial communities. In this study, we investigated the impact of P. liquidambari on N dynamics, the abundance and composition of N cycling genes in rhizosphere soil treated with three levels of N (urea). Ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and diazotrophs were assayed using quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis at four rice growing stages (S0: before planting, S1: tillering stage, S2: grain filling stage, and S3: ripening stage). A significant increase in the available nitrate and ammonium contents was found in the rhizosphere soil of endophyte-infected rice under low N conditions. Moreover, P. liquidambari significantly increased the potential nitrification rates, affected the abundance and community structure of AOA, AOB, and diazotrophs under low N conditions in the S1 and S2 stages. The root exudates were determined due to their important role in rhizosphere interactions. P. liquidambari colonization altered the exudation of organic compounds by rice roots and P. liquidambari increased the concentration of soluble saccharides, total free amino acids and organic acids in root exudates. Plant-soil feedback mechanisms may be mediated by the rice-endophyte interaction, especially in nutrient-limited soil.

Effects of 44 years of chronic nitrogen fertilization on the soil nitrifying community of permanent grassland

Chronic nutrient addition to grassland soils can strongly influence the composition and abundance of nitrifying microbial communities. Despite the fact that nitrifying microbes play a crucial role in regulating ecosystem nitrogen (N) cycling, our understanding of how long-term N fertilization might influence nitrifying microbial groups is still limited. Here we used soil from a 44-year-old grassland fertilization experiment and performed high-throughput pyrosequencing analyses (and real-time quantitative PCR) to determine whether and how the identity and abundance of nitrifying microbes has changed in response to chronic inorganic (chemical fertilizer) and organic (cattle slurry) N additions. We found that the amoA genes of ammonia-oxidizing archaea (AOA) significantly increased under organic N additions, whereas ammonia-oxidizing bacteria (AOB) increased with the addition of inorganic N. Proportional changes of AOA, AOB and nitrite-oxidizing bacteria (NOB) demonstrate that nitrifying phylotypes are influenced by chronic N additions. We also found that AOA/AOB ratios increased with higher application rates of cattle slurry suggesting that AOA may affect N cycling more in soils receiving animal manures, whereas AOB are functionally more important in chemically fertilized soils. Phylogenetic analysis shows that shifts in AOA and AOB community structure occurred through time across N fertilization treatments. For example, (a) fosmid 29i4-like AOA, (b) Nitrosospira cluster 3-like AOB, and (c) Nitrospira-like NOB dominated nitrifying communities in fertilized soils. Finally, high-throughput pyrosequencing of 16S rRNA genes show that N fertilization (either inorganic or organic) increased the abundance of Actinobacteria in soils while it decreased the abundance of Proteobacteria. Our study is one of the first to show that long-term N additions to soils can greatly affect nitrifying communities, and that phylogenetically and functionally distinct nitrifiers have developed through time in response to chronic N fertilization.

Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can be involved in biotransformation of ammonia to nitrite in soil ecosystems. However, the distribution of AOA and AOB in plateau soils and influential factors remain largely unclear. In the present study, the activity, abundance and structure of ammonia oxidizers in different soils on the Yunnan Plateau were assessed using potential nitrification rates (PNRs), quantitative PCR assay and clone library analysis, respectively. Wide variation was found in both AOA and AOB communities in plateau soils. PNRs showed a significant positive correlation with AOB abundance. Both were determined by the ratio of organic carbon to nitrogen (C/N) and total phosphorous (TP). AOB could play a more important role in ammonia oxidation. AOB community diversity was likely affected by soil total nitrogen (TN) and total organic carbon (TOC) and was usually higher than AOA community diversity. Moreover, Nitrososphaera- and Nitrosospira-like organisms, respectively, were the dominant AOA and AOB in plateau soils. AOA community structure was likely shaped by TP and C/N, while AOB community structure was determined by pH.

Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States.

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can contribute to ammonia biotransformation in freshwater lake ecosystems. However, the factors shaping the distribution of sediment AOA and AOB in plateau freshwater lake remains unclear. The present study investigated sediment AOA and AOB communities in two freshwater lakes (hypertrophic Dianchi Lake and mesotrophic Erhai Lake) on the Yunnan Plateau (China). A remarkable difference in the abundance, diversity, and composition of sediment AOA and AOB communities was observed between Dianchi Lake and Erhai Lake. AOB usually outnumbered AOA in Dianchi Lake, but AOA showed the dominance in Erhai Lake. Organic matter (OM), total nitrogen (TN), and total phosphorus (TP) might be the key determinants of AOB abundance, while AOA abundance was likely influenced by the ration of OM to TN (C/N). AOA or AOB community structure was found to be relatively similar in the same lake. TN and TP might play important roles in shaping sediment AOA and AOB compositions in Dianchi Lake and Erhai Lake. Moreover, Nitrososphaera-like AOA were detected in Dianchi Lake. Nitrosospira- and Nitrosomonas-like AOB were dominant in Dianchi Lake and Erhai Lake, respectively. Sediment AOA and AOB communities in Dianchi Lake and Erhai Lake were generally regulated by trophic state.