Abundance Of Ammonia-oxidizing Bacteria amoA Gene Research Articles

Divergent response of ammonia oxidizers to various amino acids

Amino acids (AAs) have an important role on the biogeochemical cycle of N in terrestrial environments. However, the effect of AAs on chemolithotrophic ammonia-oxidizing bacteria (AOB) and archaea (AOA) and nitrification rate has not been elucidated. Supplying soil microcosms with three AAs (asparagine, glutamate, and phenylalanine) with distinct intrinsic properties and equivalent amount of ammonium (NH4+), we investigated their effect on AOB and AOB amoA gene abundances and on nitrification rate. A parallel experiment was also performed in which nitrification was inhibited, using dicyandiamide (DCD), to get insights on amoA-dependent nitrification activity and the mineralization of AAs. The source of N strongly affected nitrification with the highest rate to be observed in NH4+-treated soils followed by asparagine, glutamate, and phenylalanine. Nitrate accumulation was associated with an increase in the abundance of AOB amoA genes suggesting a stronger contribution of AOB in the regulation of nitrification compared to AOA. Differences in N-mineralization rate of AAs appear as the main driver of the divergent nitrification rates is soils treated with various sources of N, which probably was driven by their different properties. Moreover in the case of phenylalanine, inhibitory effects on nitrification were documented. Nitrification was completely inhibited by DCD, indicating amoA-dependent nitrification activity. The present study demonstrates the crucial role of AAs on performance of ammonia oxidizers and nitrification, particularly in neutral or slightly alkaline soils with low organic matter content.

Effects of the nitrification inhibitor dicyandiamide (DCD) on N2Oemissions and the abundance of nitrifiers and denitrifiers in two contrasting agricultural soils

Nitrous oxide (N2O) is a trace gas and is mainly produced through the microbial-mediated nitrification and denitrification processes in agricultural soils. Dicyandiamide (DCD) is a powerful nitrification inhibitor (NI) which can mitigate N2O production from soil. However, it remains poorly understood how N2O emission and associated microbes are affected by DCD application across different agricultural soils. Here, we carried out a 21-day laboratory microcosm incubation experiment to examine the impact of ammonium sulfate and DCD applications on N2O production and the abundance of nitrifiers and denitrifiers in two contrasting agricultural soils. The abundance of the functional genes was quantified by quantitative PCR to investigate the population changes in response to ammonium sulfate and DCD addition. Higher N2O production emitted followed the application of ammonium sulfate (287.9 ng N2O–N g−1 soil) in the alluvial soil was obtained compared to that (84.9 ng N2O–N g−1 soil) in the red soil. The average N2O emission rate in the NH4 + treatment from the alluvial soil was significantly higher than that from the red soil, and DCD addition remarkably reduced N2O emission rates in both soils during the 21-day incubation. We also observed that the abundance of ammonia-oxidizing bacteria (AOB) amoA gene and the nirK gene was positively correlated with total N2O emissions in the alluvial soil, but only AOB amoA gene abundance was significantly related to the total N2O emissions in the red soil. These results suggested that DCD was more effective in inhibiting N2O production in the alluvial soil than in the red soil. DCD could effectively reduce N2O emission by suppressing the growth of microorganisms containing AOB amoA gene and the nirK gene in the alluvial soil.

Diversity and abundance of ammonia-oxidizing bacteria (AOB) revealed by PCR amplification of amoA gene in a polyacrylamide transportation system of an oilfield

Microorganisms were detected in the hydrolyzed high-molecular-weight polyacrylamide (HPAM) transportation system. The diversity of both general bacteria and ammonia-oxidizing bacteria (AOB) in the online distribution system was further analyzed using 16S rRNA and the functional amoA genes through PCR amplification and clone library methods together with the physicochemical properties and environmental factors of samples. In total, twenty-four families of bacteria were identified in the system; biofilm sample showed higher diversity and production water showed lower diversity than the other samples. The AOB-like phylotypes in sample S6 mainly showed high alignment to Nitrosospira briensis while others in samples showed low alignment to the known uncultrued AOB, indicative of new AOB phylotypes possibly. The abundance of AOB amoA gene abundance ranged from 3.54 × 102 to 2.04 × 103 copies·ml−1, where were significantly lower than those of bacterial 16S rRNA gene copies from 2.94 × 106 to 6.33 × 108 copies·ml−1 in samples S4–S6. The RDA analysis showed that the AOB amoA gene was positively related to the concentration of NH4+, NO2−, NO3−, SO42− and S2−. The results showed the distribution of bacterial amoA gene for nitrification in this polyacrylamide transporting system and the information enriches our knowledge of microbial community diversity in the nitrogen cycle of the polyacrylamide transportation system.

Tillage effects on soil nitrification and the dynamic changes in nitrifying microorganisms in a subtropical rice-based ecosystem: A long-term field study

The dynamics of N mineralization and nitrification may be altered by tillage, which ultimately affects crop growth and yield. This study investigated effects of tillage on soil nitrogen dynamics in a subtropical rice (Oryza sativa L.) soil (Hydragric Anthrosols, WRB classification) under combination ridge with no-tillage (RNT) and conventional tillage (CT) for 22 years in Chongqing, China. Soil mineralization, nitrification and changes in abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were investigated to test the hypothesis that RNT decreases nitrification in the rice-based ecosystem. Soil mineralization and nitrification rates decreased after 22 years of RNT compared with CT. Soil pH decreased about 0.5 units after 22 years of RNT, and this difference may be responsible for the decrease of N mineralization and nitrification rates observed under RNT. The nitrification process was best fitted by a first-order kinetic model for both CT and RNT. While the nitrification rate was significantly lower for RNT (2.96mgNkg−1day−1) than CT (3.40mgNkg−1day−1), AOB and AOA amoA gene copies were significantly higher for RNT than CT. This suggested that the functional expression (i.e., nitrification) may not be closely related to numbers of microorganisms that have the ability to nitrify. The AOA dominated in abundance over the AOB for both CT and RNT paddy soils, with AOA to AOB ratios ranging from 13 to 52, and the AOA abundance showed similar changes with AOB, suggesting that AOA may also play an important role in soil nitrification. Results implied that RNT may increase soil N retention by keeping N longer in the NH4+ state, thus decreasing the potential for N loss from leaching.

长期施加氮肥及氧化钙调节对酸性土壤硝化作用及氨氧化微生物的影响

High levels of N fertilization and acid deposition could cause soil acidification directly and indirectly. The nitrogen cycle, especially nitrification, makes a great contribution to the acidification of agricultural soils across China, which further leads to the mobilization of potentially toxic metals such as aluminum (Al) and manganese (Mn) and decerases crop yields. Chemicals (e.g., CaO) are amended as soil conditioners to relieve soil acidification. Ammonia oxidation, the rate-limiting step in the nitrification process, is driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Increasing evidence demonstrates that pH is one of the most important factors determining the niche separation of AOA and AOB, and AOA play the more important role in nitrification of acidic soils. However, abundant AOB have been detected in acidic soils but little is known about their ecological function. In this study, the effects of long-term N fertilization practices and liming on nitrification and ammonia oxidizers in acidic soils were investigated using quantitative PCR and DGGE methods combined with soil physiochemical analysis. Compared with a previous study conducted 6 years ago at the same site, N fertilizer application without liming further decreased soil pH (3.35—3.47) and potential nitrification rate (PNR) (0.02—0.14 µg NO-2 -N g-1 soil h-1), while 2 years liming alleviated soil acidification (pH 4.10—4.46) and increased PNR (0.22—0.34 µg NO-2 -N g-1 soil h-1) significantly. There was a significantly positive correlation between soil pH and PNR, indicating the increase in soil pH via liming had positive effects on nitrification in acidic soils. AOA amoA gene copy numbers (7.40 ×107—4.08 ×108 copies/ g) were significantly higher than their counterpart AOB (1.67 ×106—2.57 ×107 copies/ g) in soils that received different chemical N fertilizers. Ratios of AOA and AOB amoA gene abundance ranged between 10.9 and 44.3. After amending lime for two years in the N fertilizers treatment plots, AOA amoA gene copy numbers (8.23 ×106—4.89 ×107 copies/ g) decreased to a certain degree but AOB amoA gene copy numbers (1.99 ×107—5.42 ×107 copies/ g) increased significantly compared to their corresponding fertilization treatments without liming,resulting in lower ratios of AOA to AOB amoA gene abundance (0.83—1.94). Moreover, liming showed no clear influence on AOA community structure, but significantly increased AOB community diversity. Taken together, these results indicate that although the activity and abundance of AOA was generally greater than those of AOB in acidic soils, both AOA and AOB actively responded to disturbance in acidic soils based on their niche differentiation and had different effects on nitrification of acidic soils.

Abundance and Diversity of Ammonia-Oxidizing Bacteria and Archaea in Cold Springs on the Qinghai-Tibet Plateau

The cold springs underlain by gas hydrates on the Qinghai-Tibet Plateau (QTP) are similar to deep-sea cold seeps with respect to methane biogeochemistry. Previous studies have shown that ammonia oxidizing bacteria (AOB) and archaea (AOA) are actively present and play important roles in the carbon/nitrogen cycles in cold seeps. Studying AOA and AOB communities in the QTP cold springs will be of great importance to our understanding of carbon and nitrogen cycling dynamics related to the underlying gas hydrates on the QTP. Thus, the abundance and diversity of AOB and AOA in sediments of four cold springs underlain by gas hydrates on the QTP were determined by using quantitative polymerase chain reaction and amoA gene (encoding ammonia monooxygenase involved in ammonia oxidation) phylogenetic analysis. The results showed that the AOB and AOA amoA gene abundances were at 103–104 copies per gram of the sediments in the investigated cold springs. The AOB population consisted of Nitrosospira and Nitrosomonas in contrast with the mere presence of Nitrosospira in marine cold seeps. The AOB diversity was higher in cold springs than in cold seeps. The AOA population was mainly composed of Nitrososphaera, in contrast with the dominance of Nitrosopumilus in cold seeps. The terrestrial origin and high level of dissolved oxygen of the cold springs may be the main factors accounting for the observed differences in AOB and AOA populations between the QTP cold springs and marine cold seeps.

Abundance and diversity of ammonia-oxidizing archaea in response to various habitats in Pearl River Delta of China, a subtropical maritime zone

Ammonia-oxidizing archaea (AOA) are widely considered key to ammonia oxidation in various environments. However, little work has been conducted to simultaneously investigate the abundance and diversity of AOA as well as correlations between archaeal amoA genotypes and environmental parameters of different ecosystems at one district. To understand the abundance, diversity, and distribution of AOA in Pearl River Delta of China in response to various habitats, the archaeal amoA genes in soil, marine, river, lake, hot spring and wastewater treatment plant (WWTP) samples were investigated using real-time fluorescent quantitative PCR and clone libraries. Our analyses indicated that the diversity of AOA in various habitats was different and could be clustered into five major clades, i.e., estuary sediment, marine water/sediment, soil, hot spring and Cluster 1. Phylogenetic analyses revealed that the structure of AOA communities in similar ecological habitats exhibited strong relation. The canonical correspondence method indicated that the AOA community structure was strongly correlated to temperature, pH, total organic carbon, total nitrogen and dissolved oxygen variables. Assessing AOA amoA gene copy numbers, ranging from 6.84 × 106 to 9.45 × 107 copies/g in dry soil/sediment, and 6.06 × 106 to 2.41 × 107 copies/L in water samples, were higher than ammonia-oxidizing bacteria (AOB) by 1–2 orders of magnitude. However, AOA amoA copy numbers were much lower than AOB in WWTP activated sludge samples. Overall, these studies suggested that AOA may be a major contributor to ammonia oxidation in natural habitats but play a minor role in highly aerated activated sludge. The result also showed the ratio of AOA to AOB amoA gene abundance was positively correlated with temperature and less correlated with other environmental parameters. New data from our study provide increasing evidence for the relative abundance and diversity of ammonia-oxidizing archaea in the global nitrogen cycle.

Effects of chlorimuron-ethyl application with or without urea fertilization on soil ammonia-oxidizing bacteria and archaea

Chlorimuron-ethyl (CE) has been widely used in modern agriculture, but little is known regarding the influence of CE on ammonia-oxidizing bacteria (AOB) and archaea (AOA) populations in soils. In this study, microcosm incubation of aquic brown soil was conducted for 60 d. Associated changes in the population sizes of AOB and AOA in response to CE application with or without urea fertilization were examined via quantitative real-time PCR (qPCR) assays of the ammonia monooxygenase gene (amoA). The half-life of CE ranged from 11.80 d to 14.54 d in the tested soil. Compared to the untreated control, the application of CE alone had no strong effects on soil pH, and urea fertilization temporarily increased soil pH in the first 7 days. The abundance of the AOA amoA gene was greater than the abundance of the AOB amoA gene in all treatments, but both were significantly suppressed by CE application in a dose-dependent manner. Urea fertilization generally increased AOB and AOA amoA gene abundances, except that the AOA amoA gene level was slightly reduced at the early stage of the incubation period. AOB and AOA preferred different N levels for growth, with AOB only growing significantly at high NH4+ levels and AOA growing substantially at low NH4+ levels. The stimulation effects of urea fertilization on AOA and AOB amoA gene abundances were strongly suppressed by the CE application. This study indicated that the CE application substantially suppressed soil nitrification via inhibiting the AOB and AOA population regardless of urea fertilization, which resulted in significant changes in the soil NH4+-N and NO3−-N levels. Furthermore, AOB and AOA inhabiting separate ecological niches with different NH4+ levels played various roles in N cycling.

Soil N mineralization, nitrification and dynamic changes in abundance of ammonia-oxidizing bacteria and archaea along a 2000 year chronosequence of rice cultivation

Soil mineralization, nitrification, and dynamic changes in abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were studied to validate our hypothesis that soil mineralization and nitrification decreased along the chronosequence of rice cultivation. Paddy soils with a 300, 700 and 2000-year cultivation history (P300, P700 and P2000) were selected to study net mineralization and nitrification processes. Dynamic abundance of AOB and AOA was estimated by quantifying their respective amoA gene copies. The net mineralization rate was higher for P300 than P700 and P2000. Potential nitrification (N p ) and average nitrification rates (V a ) were similar for P300 and P700 soils, but the simulated potential nitrification rate (V p ) and nitrification rate (k1) was 72 % and 88 % higher for P300 than P700, respectively. V a was about 70 % lower than for P2000 than P300 and P700. AOB amoA gene copies were higher for P300 than P700 and P2000, whereas AOA abundance did not show significant differences. AOB abundance showed a positive response to NH4 supply but AOA did not. Both N mineralization and nitrification were depressed with increased cultivation time. Archaea responded to mineralization positively rather than nitrification, which suggested that readily mineralized organic matter may play an important role in AOA.

Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management

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.

Succession and community composition of ammonia-oxidizing archaea and bacteria in bulk soil of a Japanese paddy field

The present study describes succession in the abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the upland and flooded bulk soils of a Japanese rice paddy field over 2 years using a quantitative polymerase chain reaction of both crenarchaeotal and betaproteobacterial ammonia monooxygenase alpha subunit (amoA) genes. A marked increase in the abundance of AOA amoA gene was observed in upland bulk soil after plowing, drainage and rice harvesting. A marked increase was also observed in the abundance of AOB amoA gene after plowing. The abundances of both AOA and AOB amoA genes in flooded bulk soil decreased immediately after flooding. During the middle period of flooding, the abundance of AOA amoA gene increased slightly in the flooded bulk soil. As the flooding subsided, the abundance of AOA amoA gene decreased, whereas that of AOB amoA gene increased. The AOA amoA gene sequences were affiliated with two phylogenetic clusters previously found in marine and soil environments. Both Nitrosospira-like and Nitrosomonas-like clones were detected. Our results revealed that there was a difference in the succession of abundances between AOA and AOB amoA genes in Japanese bulk paddy soil.