Ammonia-oxidizing Archaea Bacteria Research Articles

Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains

Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.

Ammonia-oxidizing archaea bacteria (AOB) and comammox drive the nitrification in alkaline soil under long-term biochar and N fertilizer applications

Ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia oxidizers (comammox) take an essential part in soil nitrogen (N) cycling. In case of 8 years biochar and N fertilizer application, nevertheless, the comparative contribution of comammox, AOA and AOB to nitrification is unclear. Our long-term field study on alkaline soil (pHwater 8.49) investigated the impact of biochar and N fertilizer on nitrification rate and potential ammonia oxidation in terms of the soil properties, both physical and chemical, together with the abundance and diversity of AOA, AOB and comammox. The findings revealed that biochar and N fertilizer did not affect the amoA abundance of AOA but increased it in AOB and commamox clade A and clade B, but decreased the diversity of AOA and comammox. Nitrogen fertilization significantly declined the diversity of AOB. The AOB abundance was controlled mainly by pH, whereas the AOA, AOB and comammox Chao1 index were governed by soil microbial biomass carbon (MBC). Additionally, biochar increased the soil nitrification rate with or without N fertilizer, but N fertilizer decreased the soil nitrification rate and potential ammonia oxidation (with nitrite oxidation inhibited) under the same biochar application. Biochar and/or N fertilizer increased the corresponding contribution of AOA and comammox to ammonia oxidation by 143–156 % and 33–395 %, respectively, but suppressed the contribution of AOB. Although the abundance of AOA amoA was obviously greater than that of AOB and comammox, the highest contribution to ammonia oxidation was by AOB in soil not fertilized by N and by comammox in the N-fertilized soil. Our findings suggest that changes in soil properties brought about by biochar and N fertilizer addition can influence the diversity of AOA, AOB and comammox, affecting potential ammonia oxidation and the nitrification rate. The AOB and comammox make a bigger contribution to nitrification than AOA in the alkaline soil.

Effect of Manure Application on Net Nitrification Rates, Heavy Metal Concentrations and Nitrifying Archaea/Bacteria in Soils.

In this study, we determined the effect of manure application on net nitrification rates (NNRs), heavy metal concentrations (HMCs), and abundance of ammonia-oxidizing archaea (AOA)/bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in soil. HMCs were measured by atomic absorption spectroscopy. Abundance of AOA, AOB, and NOB was enumerated by q-PCR. NNRs ranged from 2.8 to 14.7mgkg-1h-1 and were significantly (p < 0.05) increased in manure soils as compared to control soils. NNRs were affected by pH 7 and temperature 30°C. Cd, Fe and Pb concentrations were classified as excessively polluted, moderate contamination and slight pollution, respectively, in the manure soils. NNRs and concentrations of Fe and Pb were significantly (p < 0.00) positive correlated, but Cu and Cd were significantly (p < 0.00) negative correlated with NNRs. Application of manure significantly (p < 0.05) increased HMCs (Fe, Cu, and Pb), which have indirect and direct effects on NNRs and nitrifying bacteria.

The more important role of archaea than bacteria in nitrification of wastewater treatment plants in cold season despite their numerical relationships

Nitrification failure of wastewater treatment plants (WWTPs) in cold season calls into investigations of the functional ammonia-oxidizing microorganisms (AOMs). In this study, we report the abundance of ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia-oxidizing (comammox) Nitrospira in 23 municipal WWTPs in cold season, and explore the correlations between AOMs abundance and their relative contribution to nitrification. The copy numbers of AOA and AOB amoA gene ranged from 2.42 × 107 to 2.47 × 109 and 5.54 × 106 to 3.31 × 109 copies/g sludge, respectively. The abundance of amoA gene of Candidatus Nitrospira inopinata, an important strain of comammox Nitrospira, was stable with averaged abundance of 8.47 × 106 copies/g sludge. DNA-based stable isotope probing (DNA-SIP) assays were conducted with three typical WWTPs in which the abundance of AOA was lower than, similar to and higher than that of AOB, respectively. The results showed that considerable 13C-assimilation by AOA was detected during active nitrification in all WWTPs, whereas just a much lesser extent of 13C-incorporation by AOB and comammox Nitrospira was found in one WWTP. High-throughput sequencing with 13C-labeled DNA also showed the higher reads abundance of AOA than AOB and comammox Nitrospira. Nitrososphaera viennensis was the dominant active AOA, while Nitrosomonas oligotropha and Nitrosomonas europaea were identified as active AOB. The results obtained suggest that AOA, rather than AOB and comammox Nitrospira, dominate ammonia oxidation in WWTPs in cold season despite the numerical relationships of AOMs.

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.

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.

Influence of edaphic, climatic, and agronomic factors on the composition and abundance of nitrifying microorganisms in the rhizosphere of commercial olive crops.

The microbial ecology of the nitrogen cycle in agricultural soils is an issue of major interest. We hypothesized a major effect by farm management systems (mineral versus organic fertilizers) and a minor influence of soil texture and plant variety on the composition and abundance of microbial nitrifiers. We explored changes in composition (16S rRNA gene) of ammonia-oxidizing archaea (AOA), bacteria (AOB), and nitrite-oxidizing bacteria (NOB), and in abundance of AOA and AOB (qPCR of amoA genes) in the rhizosphere of 96 olive orchards differing in climatic conditions, agricultural practices, soil properties, and olive variety. Majority of archaea were 1.1b thaumarchaeota (soil crenarchaeotic group, SCG) closely related to the AOA genus Nitrososphaera. Most AOB (97%) were identical to Nitrosospira tenuis and most NOB (76%) were closely related to Nitrospira sp. Common factors shaping nitrifiers assemblage composition were pH, soil texture, and olive variety. AOB abundance was positively correlated with altitude, pH, and clay content, whereas AOA abundances showed significant relationships with organic nitrogen content and exchangeable K. The abundances of AOA differed significantly among soil textures and olive varieties, and those of AOB among soil management systems and olive varieties. Overall, we observed minor effects by orchard management system, soil cover crop practices, plantation age, or soil organic matter content, and major influence of soil texture, pH, and olive tree variety.

Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils.

Rice paddy fields are characterized by regular flooding and nitrogen fertilization, but the functional importance of aerobic ammonia oxidizers and nitrite oxidizers under unique agricultural management is poorly understood. In this study, we report the differential contributions of ammonia-oxidizing archaea (AOA), bacteria (AOB) and nitrite-oxidizing bacteria (NOB) to nitrification in four paddy soils from different geographic regions (Zi-Yang (ZY), Jiang-Du (JD), Lei-Zhou (LZ) and Jia-Xing (JX)) that are representative of the rice ecosystems in China. In urea-amended microcosms, nitrification activity varied greatly with 11.9, 9.46, 3.03 and 1.43 μg NO3−-N g−1 dry weight of soil per day in the ZY, JD, LZ and JX soils, respectively, over the course of a 56-day incubation period. Real-time quantitative PCR of amoA genes and pyrosequencing of 16S rRNA genes revealed significant increases in the AOA population to various extents, suggesting that their relative contributions to ammonia oxidation activity decreased from ZY to JD to LZ. The opposite trend was observed for AOB, and the JX soil stimulated only the AOB populations. DNA-based stable-isotope probing further demonstrated that active AOA numerically outcompeted their bacterial counterparts by 37.0-, 10.5- and 1.91-fold in 13C-DNA from ZY, JD and LZ soils, respectively, whereas AOB, but not AOA, were labeled in the JX soil during active nitrification. NOB were labeled to a much greater extent than AOA and AOB, and the addition of acetylene completely abolished the assimilation of 13CO2 by nitrifying populations. Phylogenetic analysis suggested that archaeal ammonia oxidation was predominantly catalyzed by soil fosmid 29i4-related AOA within the soil group 1.1b lineage. Nitrosospira cluster 3-like AOB performed most bacterial ammonia oxidation in the ZY, LZ and JX soils, whereas the majority of the 13C-AOB in the JD soil was affiliated with the Nitrosomona communis lineage. The 13C-NOB was overwhelmingly dominated by Nitrospira rather than Nitrobacter. A significant correlation was observed between the active AOA/AOB ratio and the soil oxidation capacity, implying a greater advantage of AOA over AOB under microaerophilic conditions. These results suggest the important roles of soil physiochemical properties in determining the activities of ammonia oxidizers and nitrite oxidizers.