Purpose
The nitrification inhibitor 3,4-dimethylpyrazol-phosphate (DMPP) and the urease inhibitor N-(n-butyl) thiophosphoric triamide (nBTPT) can mitigate N losses through reducing nitrification and ammonia volatilization, respectively. However, the impact of repeated applications of these inhibitors on nitrogen cycling microorganisms is not well documented. This study aimed to investigate the changes in the abundance and community structure of the functional microorganisms involved in nitrification and denitrification in Australian pasture soils after repeated applications of DMPP and nBTPT.Materials and methods
Soil was collected in autumn and spring, 2014 from two pasture sites where control, urea, urea ammonium nitrate, and urea-coated inhibitors had been repeatedly applied over 2 year. Soil samples were analyzed to determine the potential nitrification rates (PNRs), the abundances of amoA, narG, nirK and bacterial 16S rRNA genes, and the community structure of ammonia oxidizers.Results and discussion
Two years of urea application resulted in a significantly lower soil pH at Terang and a significant decrease in total bacterial 16S rRNA gene abundance at Glenormiston and led to significantly higher PNRs and abundances of ammonia oxidizers compared to the control. Amendment with either DMPP or nBTPT significantly decreased PNRs and the abundance of amoA and narG genes. However, there was no fertilizer- or inhibitor-induced change in the community structure of ammonia oxidizers.Conclusions
These results suggest that there were inhibitory effects of DMPP and nBTPT on the functional groups mediating nitrification and denitrification, while no significant impact on the community structure of ammonia oxidizers was observed. The application of nitrification or urease inhibitor appears to be an effective approach targeting specific microbial groups with minimal effects on soil pH and the total bacterial abundance.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Purpose
Global climate change, in particular temperature variation, is likely to alter soil microbial abundance and composition, with consequent impacts on soil biogeochemical cycling and ecosystem functioning. However, responses of belowground nitrogen transformation microorganisms to temperature changes in high-elevation terrestrial ecosystems are not well understood.Materials and methods
Here, the effects of simulated cooling and warming on the abundance and community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as the abundance of denitrifiers, were investigated using quantitative polymerase chain reaction and clone library approaches, on the basis of a 2-year reciprocal elevation translocation experiment along an elevation gradient from 3,200 to 3,800 m above sea level on the Tibetan Plateau.Results and discussion
We found that, compared with the temperature variations caused by elevation translocation, the soil origin exerted a much stronger influence on AOA abundance. There were significant effects of both soil origin and elevation translocation on AOB abundance, which was particularly decreased by elevation-enhanced (simulated cooling) and increased by elevation-decreased (simulated warming) treatments. Altered temperature affected the abundance of nirK rather than nirS and nosZ genes, and the latter two seemed to be associated tightly with the soil origin. Furthermore, the results showed that temperature changes had obvious influences on the community structure and diversity of AOB, but not AOA. More apparent response of AOB to warming than in other studies on grassland and forest ecosystems may be attributed to higher elevation and lower mean annual temperature in this study.Conclusions
Our findings thus suggest that, in comparison with AOA and denitrifying populations, AOB may respond more sensitively to natural temperature variation caused by elevation translocation in this alpine grassland ecosystem on the Tibetan Plateau. 相似文献Purpose
Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, is a pivotal component of the biogeochemical nitrogen cycle. Nitrification was conventionally assumed as a two-step process in which ammonia oxidation was thought to be catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nitrite oxidation by nitrite-oxidizing bacteria (NOB). This long-held assumption of labour division between the two functional groups, however, was challenged by the recent unexpected discovery of complete ammonia oxidizers within the Nitrospira genus that are capable of converting ammonia to nitrate in a single organism (comammox). This breakthrough raised fundamental questions on the niche specialization and differentiation of comammox organisms with other canonical nitrifying prokaryotes in terrestrial ecosystems.Materials and methods
This article provides an overview of the recent insights into the genomic analysis, physiological characterization and environmental investigation of the comammox organisms, which have dramatically changed our perspective on the aerobic nitrification process. By using quantitative PCR analysis, we also compared the abundances of comammox Nitrospira clade A and clade B, AOA, AOB and NOB in 300 forest soil samples from China spanning a wide range of soil pH.Results and discussion
Comammox Nitrospira are environmentally widespread and numerically abundant in natural and engineered habitats. Physiological data, including ammonia oxidation kinetics and metabolic versatility, and comparative genomic analysis revealed that comammox organisms might functionally outcompete other canonical nitrifiers under highly oligotrophic conditions. These findings highlight the necessity in future studies to re-evaluate the niche differentiation between ammonia oxidizers and their relative contribution to nitrification in various terrestrial ecosystems by including comammox Nitrospira in such comparisons.Conclusions
The discovery of comammox and their broad environmental distribution added a new dimension to our knowledge of the biochemistry and physiology of nitrification and has far-reaching implications for refined strategies to manipulate nitrification in terrestrial ecosystems and to maximize agricultural productivity and sustainability.The discovery of comammox Nitrospira being capable of complete oxidising ammonia to nitrate radically challenged the conventional concept of two-step nitrification. However, the response of comammox Nitrospira to nitrification inhibitors (NIs) and their role in soil nitrification remain largely unknown, which has hindered our ability to predict the efficiency of NIs in agroecosystems.
Materials and methodsWe evaluated the effect of four NIs, 2-chloro-6-(trichloromethyl) pyridine (nitrapyrin), 3,4-dimethylpyrazole phosphate (DMPP), allylthiourea (ATU) and dicyandiamide (DCD) on the growth of comammox Nitrospira, ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in two pasture and arable soils.
Results and discussionThe amendment of nitrogen fertiliser significantly increased soil nitrate concentrations over time, indicating a sustaining nitrification activity in both soils. The addition of all the four NIs effectively reduced the production of nitrate in both soils, but to varying degrees during incubation. The abundances of comammox Nitrospira clade A were significantly increased by addition of nitrogen fertilisers and significantly impeded by the four NIs in the pasture soil, but their abundances were only remarkably hindered by nitrapyrin in the arable soil. All the four NIs obviously inhibited the AOB abundances in both soils. Except for DMPP, the other three NIs effectively suppressed the AOA abundances in both soils.
ConclusionsWe provided new evidence that growth of comammox Nitrospira clade A can be stimulated by nitrogen fertilisers and inhibited by various nitrification inhibitors, suggesting their potential role in nitrification of agricultural soils.
相似文献The aim of this study is to investigate the abundance, diversity, and distribution of archaea and bacteria as affected by environment parameters in paddy soils, with focus on putative functional microbial groups related to redox processes. Because there is generally a high iron content in the soil, we also want to test a hypothesis that soil iron concentration significantly affects microbial diversity and distribution.
Materials and methodsQuantitative PCR and barcoded pyrosequencing of 16S ribosomal RNA genes were employed to investigate the abundance and community composition of archaeal and bacterial communities in 27 surface paddy soil samples. Pearson’s correlation, analysis of variance, partial least squares regression, principal coordinates analysis, and structural equation models were performed for the analyses of gene copy numbers, α-diversity, β-diversity, and relative abundances of archaea and bacteria and their relationships with environmental factors.
Results and discussionArchaeal abundance was correlated greatest with temperature, but bacterial abundance was affected mainly by soil organic matter and total nitrogen content. Soil pH and concentrations of different ions were associated with archaeal and bacterial β-diversity. The relative abundances of Euryarchaeota and Thaumarchaeota were 61.3 and 13.1% of archaea and correlated with soil pH, which may affect the availability of substrates to methanogens and ammonia oxidizers. Dominant bacterial phyla were Proteobacteria (32.4%), Acidobacteria (17.8%), Bacteroidetes (9.3%), and Verrucomicrobia (6.0%). The relative abundances of putative bacterial reducers of nitrate, Fe(III), sulfate, and sulfur, and oxidizers of ammonia, nitrite, reduced sulfur, and C1 compounds had positive, negative, or non-significant correlations with the concentrations of their substrates. Soil iron concentration was correlated only with the distributions of some putative iron-reducing bacteria.
ConclusionsIn paddy soils characterized by dynamic redox processes, archaea and bacteria differ in relationships of abundance, diversity, and distribution with environmental factors. Especially, the concentrations of electron donors or acceptors can explain the distributions of some but not all the putative functional microbial groups related to redox processes. Depending on pH range, soil pH has a strong impact on microbial ecology in paddy soils.
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