AOA) And Bacteria Community Research Articles

Direct and indirect influence of arbuscular mycorrhizal fungi on abundance and community structure of ammonia oxidizing bacteria and archaea in soil microcosms

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.

Distribution and Abundance of Archaeal and Bacterial Ammonia Oxidizers in the Sediments of the Dongjiang River, a Drinking Water Supply for Hong Kong

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrification. However, limited information about the characteristics of AOA and AOB in the river ecosystem is available. The distribution and abundance of AOA and AOB in the sediments of the Dongjiang River, a drinking water source for Hong Kong, were investigated by clone library analysis and quantitative real-time PCR. Phylogenetic analysis showed that Group 1.1b-and Group 1.1b-associated sequences of AOA predominated in sediments with comparatively high carbon and nitrogen contents (e.g. total carbon (TC) >13 g kg−1 sediment, NH4+-N >144 mg kg−1 sediment), while Group 1.1a- and Group 1.1a-associated sequences were dominant in sediments with opposite conditions (e.g. TC <4 g kg−1 sediment, NH4+-N <93 mg kg−1 sediment). Although Nitrosomonas- and Nitrosospira-related sequences of AOB were detected in the sediments, nearly 70% of the sequences fell into the Nitrosomonas-like B cluster, suggesting similar sediment AOB communities along the river. Higher abundance of AOB than AOA was observed in almost all of the sediments in the Dongjiang River, while significant correlations were only detected between the distribution of AOA and the sediment pH and TC, which suggested that AOA responded more sensitively than AOB to variations of environmental factors. These results extend our knowledge about the environmental responses of ammonia oxidizers in the river ecosystem.

Effects of temperatures near the freezing point on N2O emissions, denitrification and on the abundance and structure of nitrifying and denitrifying soil communities

Climate warming in temperate regions may lead to decreased soil temperatures over winter as a result of reduced snow cover. We examined the effects of temperatures near the freezing point on N(2)O emissions, denitrification, and on the abundance and structure of soil nitrifiers and denitrifiers. Soil microcosms supplemented with NO3 - and/or NO3 - plus red clover residues were incubated for 120 days at -4 °C, -1 °C, +2 °C or +5 °C. Among microcosms amended with residues, N(2)O emission and/or denitrification increased with increasing temperature on Days 2 and 14. Interestingly, N(2)O emission and/or denitrification after Day 14 were the greatest at -1 °C. Substantial N(2) O emissions were only observed on Day 2 at +2 °C and +5 °C, while at -1 °C, N(2)O emissions were consistently detected over the duration of the experiment. Abundances of ammonia oxidizing bacteria (AOB) and archaea (AOA), Nitrospira-like bacteria and nirK denitrifiers were the lowest in soils at -4 °C, while abundances of Nitrobacter-like bacteria and nirS denitrifiers did not vary among temperatures. Community structures of nirK and nirS denitrifiers and Nitrobacter-like bacteria shifted between below-zero and above-zero temperatures. Structure of AOA and AOB communities also changed but not systematically among frozen and unfrozen temperatures. Results indicated shifts in some nitrifier and denitrifier communities with freezing and a surprising stimulation of N(2)O emissions at -1 °C when NO3 - and C are present.

Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials.

It is well known that the ratio of ammonia-oxidizing archaea (AOA) and bacteria (AOB) ranges widely in soils, but no data exist on what might influence this ratio, its dynamism, or how changes in relative abundance influences the potential contributions of AOA and AOB to soil nitrification. By sampling intensively from cropped-to-fallowed and fallowed-to-cropped phases of a 2-year wheat/fallow cycle, and adjacent uncultivated long-term fallowed land over a 15-month period in 2010 and 2011, evidence was obtained for seasonal and cropping phase effects on the soil nitrification potential (NP), and on the relative contributions of AOA and AOB to the NP that recovers after acetylene inactivation in the presence and absence of bacterial protein synthesis inhibitors. AOB community composition changed significantly (P0.0001) in response to cropping phase, and there were both seasonal and cropping phase effects on the amoA gene copy numbers of AOA and AOB. Our study showed that the AOA:AOB shifts were generated by a combination of different phenomena: an increase in AOA amoA abundance in unfertilized treatments, compared with their AOA counterparts in the N-fertilized treatment; a larger population of AOB under the N-fertilized treatment compared with the AOB community under unfertilized treatments; and better overall persistence of AOA than AOB in the unfertilized treatments. These data illustrate the complexity of the factors that likely influence the relative contributions of AOA and AOB to nitrification under the various combinations of soil conditions and NH(4)(+)-availability that exist in the field.

The influence of salinity and ammonium levels on amoA mRNA expression of ammonia-oxidizing prokaryotes

This study investigated the influence of salinity and ammonium levels on ammonia-oxidizing bacteria (AOB) and archaea (AOA) by monitoring their amo subunit A (amoA) messenger RNA (mRNA) expression. The aerobic mini-continuous stirred-tank reactors (mini-CSTRs) were operated for 48 h under different salinity or ammonium levels. Quantification of archaeal and bacterial amoA mRNA levels using real-time reverse transcription polymerase chain reaction, combined with terminal restriction fragment length polymorphism (T-RFLP) analysis, was applied to investigate the differential transcriptional responses among AOA species. High salinity levels repressed both archaeal and bacterial amoA mRNA expressions. On the other hand, high ammonium levels repressed only archaeal mRNA expression, suggesting that ammonium is a significant environmental factor shaping abundance of AOA and AOB. T-RFLP results indicated that the impacts of salinity and ammonium levels were different among AOA species. Although further study is necessary to add significance to our findings, the combination of the short-term mini-CSTR operations and amoA mRNA-based analyses allow a preliminary study on the influences of environmental factors on competition between the AOA and AOB communities.

Impact of Fungicides on the Diversity and Function of Non-target Ammonia-Oxidizing Microorganisms Residing in a Litter Soil Cover

Litter soil cover constitutes an important micro-ecosystem in sustainable viticulture having a key role in nutrient cycling and serving as a habitat of complex microbial communities. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are known to regulate nitrification in soil while little is known regarding their function and diversity in litter. We investigated the effects of two fungicides, penconazole and cyprodinil, commonly used in vineyards, on the function and diversity of total and active AOB and AOA in a microcosm study. Functional changes measured via potential nitrification and structural changes assessed via denaturating gradient gel electrophoresis (DGGE) at the DNA and RNA levels were contrasted with pesticide dissipation in the litter layer. The latter was inversely correlated with potential nitrification, which was temporarily inhibited at the initial sampling dates (0 to 21 days) when nearly 100 % of the applied pesticide amounts was still present in the litter. Fungicides induced changes in AOB and AOA communities with RNA-DGGE analysis showing a higher sensitivity. AOA were more responsive to pesticide application compared to AOB. Potential nitrification was less sensitive to the fungicides and was restored faster than structural changes, which persisted. These results support the theory of microbial redundancy for nitrification in a stressed litter environment.

Abundance and community structure of ammonia oxidizing bacteria and archaea in a Sweden boreal forest soil under 19-year fertilization and 12-year warming

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.

Abundance and community structure of ammonia-oxidizing bacteria and archaea in a temperate forest ecosystem under ten-years elevated CO 2

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 (CO 2) 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 CO 2 condition. There was no significant effect of the N fertilization on the thaumarchaeal amoA gene abundance in the ambient CO 2 treatments, while such effect increased significantly under elevated CO 2. 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 CO 2 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 CO 2 or N fertilization shaped the distribution of AOB and AOA genotypes. A negative linear relationship between the δ 13C and archaeal amoA gene abundance indicated a positive effect of elevated CO 2 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 CO 2 and N fertilization.

Nitrogen loading levels affect abundance and composition of soil ammonia oxidizing prokaryotes in semiarid temperate grassland

Global nitrogen deposition has profound impact on the terrestrial ecosystem including the semiarid temperate grassland, causing vegetation community shifts and soil acidification. Little is known regarding the effect of nitrogen (N) deposition on the belowground microbial communities. This study aimed to examine the response of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to added N in semiarid temperate grassland. We studied the changes of AOB and AOA by using molecular techniques targeting amoA genes along a urea fertilization gradient, i.e., 0, 1, 2, 4, 8, 16, 32, 64 g N m−2 year−1, in a 6-year field experiment of semiarid temperate grassland, Inner Mongolia of China. AOB community responded to urea–N substrate clearly, and N addition rates 2–4 g N m−2 year−1 induced an increase in its abundances and the shift of its composition. However, AOA community remained unchanged and the highest N loading at 64 g N m−2 year−1 even decreased its abundance. Moreover, higher N loading rates (more than 16 g N m−2 year−1) significantly decreased the diversity of AOB but not AOA, as indicated by the decrease of its Shannon and Evenness indices. The relative long-term nitrogen loading of more than 2–4 g N m−2 year−1 resulted in diversity loss of AOB in this semiarid temperate grassland. Increasing N loading altered AOB abundance and composition, but AOA showed nonsignificant changes.

Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils

Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches.

Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning.

Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms of nitrate leaching were determined. All measured community components for both AOB and AOA exhibited spatial patterns at the hectare scale. The patchy patterns of community structures did not reflect the farming systems, but the AOB community was weakly related to differences in soil pH and moisture, whereas the AOA community to differences in soil pH and clay content. Soil properties related differently to the size of the communities, with soil organic carbon and total nitrogen correlating positively to AOB abundance, while clay content and pH showed a negative correlation to AOA abundance. Contrasting spatial patterns were observed for the abundance distributions of the two groups indicating that the AOB and AOA may occupy different niches in agro-ecosystems. In addition, the two communities correlated differently to community and ecosystem functions. Our results suggest that the AOA, not the AOB, were contributing to nitrate leaching at the site by providing substrate for the nitrite oxidizers.

Characterization and quantification of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a nitrogen-removing reactor using T-RFLP and qPCR

Using ammonia monooxygenase α-subunit (amoA) gene and 16S rRNA gene, the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in a nitrogen-removing reactor, which was operated for five phases, were characterized and quantified by cloning, terminal restriction fragment length polymorphism (T-RFLP), and quantitative polymerase chain reaction (qPCR). The results suggested that the dominant AOB in the reactor fell to the genus Nitrosomonas, while the dominant AOA belonged to Crenarchaeotal Group I.1a in phylum Crenarchaeota. Real-time PCR results demonstrated that the levels of AOB amoA varied from 2.9 × 103 to 2.3 × 105 copies per nanogram DNA, greatly (about 60 times) higher than those of AOA, which ranged from 1.7 × 102 to 3.8 × 103 copies per nanogram DNA. This indicated the possible leading role of AOB in the nitrification process in this study. T-RFLP results showed that the AOB community structure significantly shifted in different phases while AOA only showed one major peak for all the phases. The analyses also suggested that the AOB community was more sensitive than that of AOA to operational conditions, such as ammonia loading and dissolved oxygen.

Community composition of ammonia-oxidizing bacteria and archaea in rice field soil as affected by nitrogen fertilization

Little information is available on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in flooded rice soils. Consequently, a microcosm experiment was conducted to determine the effect of nitrogen fertilizer on the composition of AOB and AOA communities in rice soil by using molecular analyses of ammonia monooxygenase gene ( amoA) fragments. Experimental treatments included three levels of N (urea) fertilizer, i.e. 50, 100 and 150 mg N kg −1 soil. Soil samples were operationally divided into four fractions: surface soil, bulk soil deep layer, rhizosphere and washed root material. NH 4 +-N was the dominant form of N in soil porewater and increased with N fertilization. Cloning and sequencing of amoA gene fragments showed that the AOB community in the rice soil consisted of three major groups, i.e. Nitrosomonas communis cluster, Nitrosospira cluster 3a and cluster 3b. The sequences related to Nitrosomonas were predominant. There was a clear effect of N fertilizer and soil depth on AOB community composition based on terminal restriction fragment length polymorphism fingerprinting. Nitrosomonas appeared to be more abundant in the potentially oxic or micro-oxic fractions, including surface soil, rhizosphere and washed root material, than the deep layer of anoxic bulk soil. Furthermore, Nitrosomonas increased relatively in the partially oxic fractions and that of Nitrosospira decreased with the increasing application of N fertilizer. However, AOA community composition remained unchanged according to the denaturing gradient gel electrophoresis analyses.

Ammonia‐oxidizing archaea: important players in paddy rhizosphere soil?

The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in paddy soil with different nitrogen (N) fertilizer amendments for 5 weeks were investigated using quantitative real-time polymerase chain reaction, denaturing gradient gel electrophoresis (DGGE) jand clone library analysis based on the ammonia monooxygenase alpha-subunit (amoA) gene. Ammonia-oxidizing archaea predominated among ammonia-oxidizing prokaryotes in the paddy soil, and the AOA:AOB DNA-targeted amoA gene ratios ranged from 1.2 to 69.3. Ammonia-oxidizing archaea were more abundant in the rhizosphere than in bulk soil. Rice cultivation led to greater abundance of AOA than AOB amoA gene copies and to differences in AOA and AOB community composition. These results show that AOA is dominant in the rhizosphere paddy soil in this study, and we assume that AOA were influenced more by exudation from rice root (e.g. oxygen, carbon dioxide) than AOB.