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1.
As part of a long-term sloped land use experiment established in 1995 at Taoyuan Agro-ecosystem Research Station (111°26′ E, 28°55′ N) in China, soil samples were collected from three land use types, including cropland (CL), natural forest, and tea plantation. Quantitative polymerase chain reaction and terminal restriction fragment length polymorphism were used to determine the abundance and community composition of amoA-containing bacteria (AOB) and archaea (AOA). The results indicate that land use type induced significant changes in soil potential nitrification rate and community composition, diversity, and abundance of AOB and AOA. Both AOB and AOA community compositions were generally similar between upper and lower slope positions (UP and LP), except within CL. The LP soils had significantly (p?<?0.05) higher diversity and abundance of both AOB and AOA than in the UP. Potential nitrification rate was significantly correlated (p?<?0.05) with diversity and abundance of AOA, but not with AOB. Among land use types, the NO3 ? and amoA-containing AOA runoff loss was greatest in CL. Nitrate-N runoff loss was significantly correlated (p?<?0.05) with the loss of AOA amoA copies in the runoff water. Furthermore, relationships between NO3 ?-N runoff loss and abundance of AOA but not of AOB at both slope positions were significantly correlated (p?<?0.05). These findings suggest that AOA are more important than AOB in nitrification and NO3 ?-N runoff loss in acidic soils across sloped land use types.  相似文献   

2.
Ammonia oxidation is a critical step in the soil nitrogen (N) cycle and can be affected by the application of mineral fertilizers or organic manure. However, little is known about the rhizosphere effect on the function and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities, the most important organisms responsible for ammonia oxidation in agricultural ecosystems. Here, the potential nitrification activity (PNA), population size and composition of AOB and AOA communities in both the rhizosphere and bulk soil from a long-term (31-year) fertilizer field experiment conducted during two seasons (wheat and maize) were investigated using the shaken slurry method, quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis. N fertilization greatly enhanced PNA and AOB abundance, while manure application increased AOA abundance. The community structure of AOB exhibited more obvious shifts than that of AOA after long-term fertilization, resulting in more abundant AOB phylotypes similar to Nitrosospira clusters 3 and 4 in the N-fertilized treatments. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than that of AOA among soils during both seasons, indicating that AOB play an active role in ammonia oxidation. Conversely, the PNA and population sizes of AOB and AOA were typically higher in the rhizosphere than the bulk soil, implying a significant rhizosphere effect on ammonia oxidation. Cluster and redundancy analyses further showed that this rhizosphere effect played a more important role in shaping AOA community structure than long-term fertilization. Overall, the results indicate that AOB rather than AOA functionally dominate ammonia oxidation in the calcareous fluvo-aquic soil, and that rhizosphere effect and fertilization regime play different roles in the activity and community structures of AOB and AOA.  相似文献   

3.
全球30%以上陆地面积是酸性土壤(pH5.5),而酸性土壤中氨氧化微生物群落特征研究是破译其硝化过程微生物学机理的基础。尤其随着完全硝化微生物(Complete ammonia oxidizer,comammox)的发现,亟需重新认知酸性土壤中氨氧化微生物类群。以酸性马尾松林为研究对象,综合利用荧光定量PCR(qPCR)、凝胶电泳半定量和宏基因组测序等技术研究土壤中氨氧化古菌(Ammonia-oxidizing archaea,AOA)、氨氧化细菌(Ammonia-oxidizing bacteria,AOB)和Comammox的相对丰度以及群落组成特征。研究发现AOA和AOB amoA基因丰度分别为2.61×106 copies·g~(-1)和1.45×106copies·g~(-1);而comammoxamoA基因qPCR结果存在显著的非特异性扩增,导致其丰度被高估,而经凝胶电泳半定量矫正后,约为(1.38～1.47)×106copies·g~(-1),该结果和土壤宏基因测序揭示的comammox相对丰度基本吻合。此外,宏基因组分析发现经典嗜酸group1.1a-associated仅占AOA总类群的12%,而group1.1b则占88%,尽管目前仍未有嗜酸group 1.1b AOA纯菌株的报道。AOB主要类群为Nitrosospira(约64%),而Nitrosomonas约占36%。Comammox主要类群为clade B(约64%),而clade A仅占36%且均隶属于clade A.1亚枝,这暗示clade B与已报道的嗜中性comammox clade A纯菌株有极大的生理代谢差异。总之,本研究提供了综合利用qPCR、半定量和宏基因组分析土壤氨氧化微生物群落的策略,并建议优化comammox的qPCR引物,同时本研究系统分析了酸性马尾松林土壤中氨氧化微生物的相对丰度和群落组成特征。  相似文献   

4.
Soil surface electrochemical properties may have a strong influence on nitrifying microorganisms, H+ and NH4+ activities, and therefore on the nitrification process. A gradient of surface electrochemical parameters was obtained by amendment of a subtropical acid pine soil (Oxisol) with 0% (control), 3%, 5%, 8%, 10% and 12% pure Ca-Montmorillonite by weight. The H+ and NH4+ activities, the abundance of the ammonia-oxidizing bacterial (AOB) and archaeal (AOA) amoA gene copies, and time-dependent kinetics of net nitrification were investigated. Soil particle surface specific area ranged from 53 to 103 m2 g−1 and increased with increasing montmorillonite application rate. Similar to specific area, surface charge quantity, surface charge density, electric field strength and surface potential increased after montmorillonite amendment. The H+ and NH4+ activities decreased linearly after montmorillonite addition. AOB amoA gene copy number was 1.82 × 105 copies g−1 for unamended soil, and the highest AOB amoA gene copy numbers were found for the 10% montmorillonite amendment (3.11 × 107 g−1 soil), which was more than 150 times higher than unamended soil. AOA amoA gene copy numbers were 9.19 × 103 copies g−1 dry unamended soil, and the highest AOA amoA gene copy numbers were found in the 8% montmorillonite amendment (1.22 × 105 g−1 soil). Although pH significantly decreased during the first three weeks of incubation, no significant difference was observed between the unamended control and different rates of montmorillonite addition treatments during the whole incubation. The largest net nitrification (103 mg N kg−1) was observed in the 10% montmorillonite amendment and the lowest in unamended soil (62 mg N kg−1). While montmorillonite did not change the kinetic patterns of net nitrification, the highest nitrification potential (275 mg N kg−1) for the 10% montmorillonite treatment was more than 3 times higher than unamended soil from simulation of time-dependent kinetics. Nitrification was significantly stimulated after montmorillonite amendment in acid soil mainly due to an increase in the quantity and activity of AOB and AOA. We concluded that soil particle surface parameters can significantly influence nitrification, especially in acid soils.  相似文献   

5.

Purpose

Nitrogen (N) is one of the most important elements that can limit plant growth in forest ecosystems. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are considered as the key drivers of global N biogeochemical cycling. Soil ammonia-oxidizing microbial communities associated with subtropical vegetation remain poorly characterized. The aim of this study was to determine how AOA and AOB abundance and community structure shift in response to four typical forest vegetations in subtropical region.

Materials and methods

Broad-leaved forest (BF), Chinese fir forest (CF), Pinus massoniana forest (PF), and moso bamboo forest (MB) were widely distributed in the subtropical area of southern China and represented typical vegetation types. Four types of forest stands of more than 30 years grew adjacent to each other on the same soil type, slope, and elevation, were chosen for this experiment. The abundance and community structure of AOA and AOB were characterized by using real-time PCR and denaturing gradient gel electrophoresis (DGGE). The impact of soil properties on communities of AOA and AOB was tested by canonical correspondence analysis (CCA).

Results and discussion

The results indicated that AOB dominated in numbers over AOA in both BF and MB soils, while the AOA/AOB ratio shifted with different forest stands. The highest archaeal and bacterial amoA gene copy numbers were detected in CF and BF soils, respectively. The AOA abundance showed a negative correlation with soil pH and organic C but a positive correlation with NO3 ??N concentration. The structures of AOA communities changed with vegetation types, but vegetation types alone would not suffice for shaping AOB community structure among four forest soils. CCA results revealed that NO3 ??N concentration and soil pH were the most important environmental gradients on the distribution of AOA community except vegetation type, while NO3 ??N concentration, soil pH, and organic C significantly affected the distribution of the AOB communities.

Conclusions

These results revealed the differences in the abundance and structure of AOA and AOB community associated with different tree species, and AOA was more sensitive to vegetation and soil chemical properties than AOB. N bioavailability could be directly linked to AOA and AOB community, and these results are useful for management activities, including forest tree species selection in areas managed to minimize N export to aquatic systems.  相似文献   

6.
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are considered as the key drivers of global nitrogen (N) biogeochemical cycling. Responses of the associated microorganisms to global changes remain unclear. This study was to determine if there was a shift in soil AOB and AOA abundances and community structures under free-air carbon dioxide (CO2) enrichment (FACE) and N fertilization in Duke Forest of North Carolina, by using DNA-based molecular techniques, i.e., quantitative PCR, restriction fragment length polymorphism (RFLP) and clone library. The N fertilization alone increased the abundance of bacterial amoA gene, but this effect was not observed under elevated CO2 condition. There was no significant effect of the N fertilization on the thaumarchaeal amoA gene abundance in the ambient CO2 treatments, while such effect increased significantly under elevated CO2. A total of 690 positive clones for AOA and 607 for AOB were selected for RFLP analysis. Analysis of molecular variance (AMOVA) indicated that effects of CO2 enrichment and N fertilization on the community structure of AOA and AOB were not significant. Canonical correspondence analysis also showed that soil pH rather than elevated CO2 or N fertilization shaped the distribution of AOB and AOA genotypes. A negative linear relationship between the δ13C and archaeal amoA gene abundance indicated a positive effect of elevated CO2 on the growth ammonia oxidizing archaea. On the other hand, the community structures of AOB and AOA are determined by the soil niche properties rather than elevated CO2 and N fertilization.  相似文献   

7.

Purpose

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are ubiquitous and important for nitrogen transformations in terrestrial ecosystems. However, the distribution patterns of these microorganisms as affected by the terrestrial environments across a large geographical scale are not well understood. This study was designed to gain insights into the ecological characteristics of AOA and AOB in 65 soils, collected from a wide range of soil and ecosystem types.

Materials and methods

Barcoded pyrosequencing in combination with quantitative PCR was employed to characterize the relative abundance, diversity, and community composition of archaeal 16S rRNA gene, and AOA and AOB amoA genes in 65 soil samples.

Results and discussion

The operational taxonomic unit richness and Shannon diversity of Thaumarchaeota, AOA, and AOB were highly variable among different soils, but their variations were best explained by soil pH. Soil pH was strongly correlated with the overall community composition of ammonia oxidizers, as measured by the pairwise Bray–Curtis dissimilarity across all sites. These findings were further corroborated by the evident pH-dependent distribution patterns of four thaumarchaeal groups (I.1a-associated, I.1b, I.1c, and I.1c-associated) and four AOB clusters (2, 3a.1, 10, and 12). The ratios of AOA to AOB amoA gene copy numbers significantly decreased with increasing pH, suggesting a competitive advantage of AOA over AOB in acidic soils.

Conclusions

These results suggest that the distribution of ammonia oxidizers across large-scale biogeographical settings can be largely predicted along the soil pH gradient, thus providing important indications for the ecological characteristics of AOA and AOB in different soils.  相似文献   

8.
Biochar amendments have frequently been reported to alter microbial communities and biogeochemical processes in soils. However, the impact of biochar application on bacterial (AOB) and archaeal ammonia oxidizers (AOA) remains poorly understood. In this study, we investigated the responses of AOB and AOA to the application of biochar derived from cotton stalk at rates of 5, 10, and 20 % by weight to a coastal alkaline soil during a 12-week incubation. The results showed that the amoA gene of AOB consistently outnumbered that of AOA, whereas only the AOA amoA gene copy number was significantly correlated with the potential ammonia oxidation (PAO) rate (P?<?0.01). The significant decrease of PAO rates in biochar treatments occurred after incubation for 4–6 weeks, which were distinctly longer than that in the control (2 weeks). The PAO rates were significantly different among treatments during the first 4 weeks of incubation (P?<?0.05), with the highest usually in the 10 % treatment. Biochar application significantly increased the abundance of both nitrifiers in the 4 weeks of incubation (P?<?0.05). Biochar amendment also decreased AOA diversity, but increased AOB diversity, which resulted in different community structures of both nitrifiers (P?<?0.01), as shown by the differences between the 5 % biochar and the control treatments. We conclude that biochar application generally enhanced the abundance and altered the composition of ammonia oxidizers; the rate of biochar application also affected the rate and dynamics of nitrification, and the risk for increasing the alkalinity and N leaching of the studied soil was lower with a lower application rate.  相似文献   

9.
Soil microbial habitats are altered by mulching, a common practice in urban areas during which vegetation is removed and soils covered to suppress weeds and retain moisture. Soil microorganisms drive nitrogen-cycling processes in mulched soils, because living plants no longer take up ammonium-N released during decomposition of residual organic matter. Because ammonia oxidizers carry out the first, rate-limiting step of nitrification, we compared ammonia oxidizers in experimental, unfertilized plots of mulched and vegetated soils. We hypothesized that mulched and vegetated soils would support contrasting communities of bacterial and archaeal ammonia oxidizers, as determined by quantitative PCR and primers specific for genes encoding ammonia monooxygenase subunit A (amoA). Clone libraries of archaeal amoA also were constructed to compare diversity in soil cores, duplicate blocked plots, and treatments (bark-mulched, gravel-mulched, and unmanaged old field vegetation). Gene copies from ammonia-oxidizing bacteria (AOB) ranged from 2.2 × 106 to 2.7 × 107 gene copies per gram dry soil and did not differ across treatments. In contrast, gene copies from ammonia-oxidizing archaea (AOA) ranged from 9.1 × 105 to 1.0 × 108 copies per gram dry soil, with bark-mulched soils having significantly lower abundance. Community structure of AOA in gravel-mulched soils was distinct from the other two treatments. At 97% amino acid similarity, 22 operational taxonomic units, or OTUs, were identified, with only one OTU found in all 18 clone libraries. This ubiquitous OTU-1, which was highly similar to published amoA sequences recovered from soils, comprised 55% of all 482 translated sequences. Greater variability in OTU richness was observed among cores from mulched soils than from vegetated soils. Our observations supported our hypothesis that AOA communities differ in mulched and vegetated soils, with mulched soils providing altered and variable microniches for these N cycling microorganisms.  相似文献   

10.
《Applied soil ecology》2010,46(3):193-200
Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) co-exist in soil, but their relative distribution may vary depending on the environmental conditions. Effects of changes in soil organic matter and nutrient content on the AOB and AOA are poorly understood. Our aim was to compare effects of long-term soil organic matter depletion and amendments with labile (straw) and more recalcitrant (peat) organic matter, with and without easily plant-available nitrogen, on the activities, abundances and community structures of AOB and AOA. Soil was sampled from a long-term field site in Sweden that was established in 1956. The potential ammonia oxidation rates, the AOB and AOA amoA gene abundances and the community structures of both groups based on T-RFLP of amoA genes were determined. Straw amendment during 50 years had not altered any of the measured soil parameters, while the addition of peat resulted in a significant increase of soil organic carbon as well as a decrease in pH. Nitrogen fertilization alone resulted in a small decrease in soil pH, organic carbon and total nitrogen, but an increase in primary production. Type and amount of organic matter had an impact on the AOB and AOA community structures and the AOA abundance. Our findings confirmed that AOA are abundant in soil, but showed that under certain conditions the AOB dominate, suggesting niche differentiation between the two groups at the field site. The large differences in potential rates between treatments correlated to the AOA community size, indicating that they were functionally more important in the nitrification process than the AOB. The AOA abundance was positively related to addition of labile organic carbon, which supports the idea that AOA could have alternative growth strategies using organic carbon. The AOB community size varied little in contrast to that of the AOA. This indicates that the bacterial ammonia oxidizers as a group have a greater ecophysiological diversity and potentially cover a broader range of habitats.  相似文献   

11.

Purpose

Boreal forests are considered to be more sensitive to global climate change compared with other terrestrial ecosystems, but the long-term impact of climate change and forest management on soil microbial functional diversity is not well understood. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the most important players in nitrogen (N) cycling-associated processes in terrestrial ecosystems. This study investigated the separate and combined impacts of long-term soil warming and fertilization on soil AOB and AOA community structures and abundances in a Norway spruce stand in northern Sweden.

Materials and methods

The soil-warming experiment was established in the buffer zones of two irrigated plots (I) and complete nutrient solution plots (IL) since 1995. The warming treatment started in April each year by maintaining soil temperature on warmed plots at 5°C above the temperature in unwarmed plots using heating cables. In August 2006, soil samples were collected from eight subplots for molecular analysis. The abundance of bacterial and archaeal amoA genes was determined by quantitative polymerase chain reaction. Similarly, total bacterial and archaeal population sizes have also been determined. The diversity of AOB and AOA was assessed by constructing amoA gene clone libraries, and different genotypes were screened with restriction fragment length polymorphism.

Results and discussion

Results showed that fertilization did not significantly affect the abundance of the bacterial amoA gene under either warming or non-warming conditions; however, warming decreased the abundance under fertilization treatments. No significant effects of fertilization and soil warming were observed on the number of thaumarchaeal amoA gene copies across all treatments. In this study, amoA gene abundance of AOB was significantly higher than that of AOA across all treatments. The community structure of both AOB and AOA was strongly influenced by fertilization. For bacterial amoA genes, Nitrosospira cluster 2 was present across all treatments, but the only genotype was observed in the fertilization treatments while, for thaumarchaeal amoA genes, the relative abundance of soil cluster 5 increased in fertilization treatments. By comparison, soil-warming effects on AOB and AOA community structure were not significant. Canonical correspondence analysis showed a positive correlation between fertilization and both dominant genotypes of AOB and AOA.

Conclusions

These results indicated that the abundance of AOA and AOB was not affected by fertilization or warming alone, but the interaction of fertilization and warming reduced the abundance of AOB. The community composition of ammonia-oxidizers was more affected by the nutrient-optimized fertilization than the soil warming.  相似文献   

12.
The potential nitrification activity (PNA), population size and composition of AOB and AOA communities in both rhizosphere and bulk soil from a long-term (32 year) fertiliser field experiment conducted during early rice and late rice seasons were investigated by using the shaken slurry method and quantitative real-time polymerase chain reaction. The experiment begins in 1986, and including five treatments: without fertiliser input, chemical fertiliser alone, rice straw residue and chemical fertiliser, low organic manure rate and chemical fertiliser and high organic manure rate and chemical fertiliser. The results showed that the application of chemical fertiliser greatly enhanced PNA and AOB abundance, while application of rice straw residue and organic manure increased AOA abundance. Moreover, the results showed that the PNA and population sizes of AOB and AOA were higher in the rhizosphere than in the bulk soil. Cluster and redundancy analyses further indicated that the rhizosphere effect play a more important role in shaping AOA community structure than long-term fertilization. In summary, the results indicated that AOB rather than AOA functionally dominate ammonia oxidation in the double-cropping rice paddy soils, and that rhizosphere effect and fertiliser regime play different roles in the activity and community structures of AOB and AOA.  相似文献   

13.
Ammonia oxidation, the first step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, the relative contributions of AOA and AOB to soil nitrification are not well understood. In this study we used 1-octyne to discriminate between AOA- and AOB-supported nitrification determined both in soil-water slurries and in unsaturated whole soil at field moisture. Soils were collected from stands of red alder (Alnus rubra Bong.) and Douglas-fir (Pseudotsuga menziesii Mirb. Franco) at three sites (Cascade Head, the H.J. Andrews, and McDonald Forest) on acidic soils (pH 3.9–5.7) in Oregon, USA. The abundances of AOA and AOB were measured using quantitative PCR by targeting the amoA gene, which encodes subunit A of ammonia monooxygenase. Total and AOA-specific (octyne-resistant) nitrification activities in soil slurries were significantly higher at Cascade Head (the most acidic soils, pH < 5) than at either the H.J. Andrews or McDonald Forest, and greater in red alder compared with Douglas-fir soils. The fraction of octyne-resistant nitrification varied among sites (21–74%) and was highest at Cascade Head than at the other two locations. Net nitrification rates of whole soil without NH4+ amendment ranged from 0.4 to 3.3 mg N kg−1 soil d−1. Overall, net nitrification rates of whole soil were stimulated 2- to 8-fold by addition of 140 mg NH4+-N kg−1 soil; this was significant for red alder at Cascade Head and the H.J. Andrews. Red alder at Cascade Head was unique in that the majority of NH4+-stimulated nitrifying activity was octyne-resistant (73%). At all other sites, NH4+-stimulated nitrification was octyne-sensitive (68–90%). The octyne-sensitive activity—presumably AOB—was affected more by soil pH whereas the octyne-resistant (AOA) activity was more strongly related to N availability.  相似文献   

14.
Taking two important agricultural soils with different pH, brown soil （Hap-Udic Luvisol） and cinnamon soil （Hap-Ustic Luvisol）, from Northeast China, a pot culture experiment with spring maize （Zea mays L.） was conducted to study the dynamic changes in the abundance and diversity of soil ammonia-oxidizing bacteria （AOB） and ammonia-oxidizing archaea （AOA） populations during maize growth period in response to the additions of nitrification inhibitors dicyandiamide （DCD） and 3,4-dimethylpyrazole phosphate （DMPP） by the methods of real-time polymerase chain reaction （PCR） assay, PCR-denaturing gradient gel electrophoresis （DGGE）, and construction of clone library targeting the amoA gene. Four treatments were established, i.e., no urea （control）, urea, urea plus DCD, and urea plus DMPP. Both DCD and DMPP inhibited growth of AOB significantly, compared to applying urea alone. Soil bacterial amoA gene copies had a significant positive linear correlation with soil nitrate content, but soil archaeal amoA gene copies did not. In both soils, all AOB sequences fell within Nitrosospira or Nitrosospira-like groups, and all AOA sequences belonged to group 1.1b crenaxchaea. With the application of DCD or DMPP, community composition of AOB and AOA in the two soils had less change except that the AOB community composition in Hap-Udic Luvisol changed at the last two growth stages of maize under the application of DCD. AOB rather than AOA likely dominated soil ammonia oxidation in these two agricultural soils.  相似文献   

15.
Nitrogen(N) application may lead to niche segregation of soil ammonia-oxidizing archaea(AOA) and bacteria(AOB), thereby reducing the competitive interactions between AOA and AOB due to higher ammonium substrate availability. However, the adaptive mechanisms of AOA and AOB under N enrichment remain poorly understood. Stable isotope probing(SIP) microcosm incubation was employed to reveal community changes of active AOA and AOB in a loess soil from a field experiment growing potatoes that received no N(control, CK), low N(LN, 75 kg N ha~(-1)), and high N(HN, 375 kg N ha~(-1)). The results showed that the soil potential nitrification rate(PNR) was measured by culturing of the soil samples from the field experiment. Soil PNR was significantly increased in HN by87.5% and 67.5% compared with CK and LN, respectively. Compared with CK, the~(13)C-amoA genes of soil AOA and AOB in HN had 2.58 × 10~4 and 1.55 × 10~6 copies, representing 1.6-and 16.2-fold increase respectively. It was indicated that AOB dominated soil ammonia oxidation. A phylogenetic analysis of the~(13)C-amoA gene showed that N application significantly increased the proportion of54 d9-like AOA up to 90% in HN, while the Nitrososphaera gargensis-like and Nitrososphaera viennensis-like AOA were inhibited and completely disappeared. Nitrogen application also resulted in the community shift of active AOB-dominant group from Nitrosospira briensis-like to Nitrosospira sp. TCH711-like. Our study provides compelling evidence for the emergence and maintenance of active nitrifying communities under the intensified N input to an agricultural ecosystem.  相似文献   

16.
The effects of long-term fertilization of acidic soils on ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities and its ecological implications remain poorly understood. We chose an acidic upland soil site under long-term (27-year) fertilization to investigate ammonia oxidizer communities under four different regimes: mineral N fertilizer (N), mineral NPK fertilizer (NPK), organic manure (OM) and an unfertilized control (CK). Soil net nitrification rates were significantly higher in OM soils than in CK, N or NPK soils. Quantitative analysis of the distribution of amoA genes by DNA-based stable isotope probing revealed that AOA dominate in CK, N and NPK soils, while AOB dominate in OM soils. Denaturing gradient gel electrophoresis and clone library analyses of amoA genes revealed that Group 1.1a-associated AOA (also referred to as Nitrosotalea) were the most dominant active AOA population (>92%), while Nitrosospira Cluster 3 and Cluster 9 were predominant among active AOB communities. The functional diversity of active ammonia oxidizers in acidic soils is affected by long-term fertilization practices, and the responses of active ammonia oxidizers to mineral fertilizer and organic manure are clearly different. Our results provide strong evidence that AOA are more highly adapted to growth at low pH and low substrate availability than AOB, and they suggest that the niche differentiation and metabolic diversity of ammonia oxidizers in acidic soils are more complex than previously thought.  相似文献   

17.
Both arbuscular mycorrhizal (AM) fungi and ammonia oxidizers are important soil microbial groups in regulating soil N cycling. However, knowledge of their interactions, especially the direct influences of AM fungi on ammonia oxidizers is very limited to date. In the present study, a controlled microcosm experiment was established to examine the effects of AM fungi and N supply level on the abundance and community structure of ammonia oxidizing bacteria (AOB) and archaea (AOA) in the rhizosphere of alfalfa plants (Medicago sativa L.) inoculated with AM fungus Glomus intraradices. Effects were studied using combined approaches of quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The results showed that inoculation with AM fungi significantly increased the plant dry weights, total N and P uptake. Concomitantly, AM fungi significantly decreased the amoA gene copy numbers of AOA and AOB in the root compartment (RC) but not in the hyphal compartment (HC). Moreover, AM fungi induced some changes in AOA community structure in HC and RC, while only marginal variations in AOA composition were observed to respond to N supply level in HC. Neither RC nor HC showed significant differences in AOB composition irrespective of experimental treatments. The experimental results suggested that AM fungi could directly shape AOA composition, but more likely exerted indirect influences on AOA and AOB abundance via the plant pathway. In general, AM fungi may play an important role in mediating ammonia oxidizers, but the AOA community appeared to be more sensitive than the AOB community to AM fungi.  相似文献   

18.
Disparities in the substrate affinity and tolerance threshold for ammonia have been believed to play a key role in driving niche differentiation between ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, recent surveys argue that direct competition between AOA and AOB is also important in this phenomenon. Accordingly, it is reasonable to predict that diverse AOA lineages would grow in ammonium (NH4+)-rich alkaline arable soils if AOB growth is suppressed. To test this hypothesis, a microcosm study was established using three different types of alkaline arable soils, in which a high NH4+ concentration (200 μg N g-1 dry soil) was maintained by routinely replenishing urea and the activities of AOB were selectively inhibited by 1-octyne or 3,4-dimethylpyrazole phosphate (DMPP). Compared with amendment with urea alone, 1-octyne partially retarded AOB growth, while DMPP completely inhibited AOB. Both inhibitors accelerated the growth of AOA, with significantly higher ratios of abundance of AOA to AOB observed with DMPP amendment across soils. Nonmetric multidimensional scaling analysis (NMDS) indicated that different treatments significantly altered the community structures of both AOA and AOB and AOA OTUs enriched by high-NH4+ amendment were taxonomically constrained across the soils tested and closely related to Nitrososphaera viennensis EN76 and N. garnensis. Given that these representative strains have been demonstrated to be sensitive to high ammonia concentrations, our results suggest that it is the competitiveness for ammonia, rather than disparities in substrate affinity and tolerance threshold for ammonia, that drives niche differentiation between these phylotypes and AOB in NH4+-rich alkaline soils.  相似文献   

19.
As the first and rate-limiting step of nitrification, ammonia oxidation can be realized either by ammonia-oxidizing bacteria (AOB) or archaea (AOA). However, the key factors driving the abundance, community structure and activity of ammonia oxidizers are still unclear, and the relative importance of AOA and AOB in ammonia oxidation is unresolved. In the present study, we examined the effects of long-term (6 years) nitrogen (N) addition and simulated precipitation increment on the abundance and community composition of AOA and AOB based on a field trial in a typical temperate steppe of northern China. We used combined approaches of quantitative PCR, terminal-restriction fragment length polymorphism (T-RFLP) and clone library analyses of amoA genes. The study objective was to determine (1) AOA and AOB diversity and activity in response to N addition and increased precipitation and (2) the relative contributions of AOA and AOB to soil ammonia oxidation in the typical temperate steppe. The results showed that the potential nitrification rate (PNR) increased with N addition, but decreased with increased precipitation. Both N addition and increased precipitation significantly increased AOB but not AOA abundance, and a significant correlation was only observed between PNR and AOB amoA gene copies. The T-RFLP analysis showed that both N and precipitation were key factors in shaping the composition of AOB, while AOA were only marginally influenced. Phylogenetic analysis indicated that all AOA clones fell within the soil and sediment lineage while all AOB clones fell within the Nitrosospira. The study suggested that AOA and AOB had distinct physiological characteristics and ecological niches. AOB were shown to be more sensitive to N and precipitation than AOA, and the ammonia oxidation process was therefore supposed to be mainly driven by AOB in this temperate steppe.  相似文献   

20.
Increasing lines of evidence have suggested the functional importance of ammonia-oxidizing archaea (AOA) rather than bacteria (AOB) for nitrification in upland soils with low pH. However, it remains unclear whether niche specialization of AOA and AOB occurs in rice paddy wetlands constrained by oxygen availability. Using DNA-based stable isotope probing, we conclude that AOA dominated nitrification activity in acidic paddy soils (pH 5.6) while AOB dominated in alkaline soils (pH 8.2). Nitrification activity was stimulated by urea fertilization and accompanied by a significant increase of AOA in acid soils and AOB in alkaline soils. DNA-based stable isotope probing indicated significant assimilation of 13CO2 for AOA only in acidic paddy soil, while AOB was the solely responsible for ammonia oxidation in the alkaline paddy soil. Phylogenetic analysis further indicated that AOA members within the soil group 1.1b lineage dominated nitrification in acid soils. Ammonia oxidation in the alkaline soil was catalyzed by Nitrosospira cluster 3-like AOB, suggesting that the physiological diversity of AOA is more complicated than previously thought, and soil pH plays important roles in shaping the community structures of ammonia oxidizers in paddy field.  相似文献   

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