Ammonia-oxidizing Archaea amoA Genes Research Articles

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts.

Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

Do biodegradable microplastics cause soil inorganic carbon loss in calcareous soils?

The presence of biodegradable microplastics (MPs) has the potential to affect soil pH, and possibly accelerate or inhibit the loss of soil inorganic carbon (SIC) in calcareous soils. However, most researchers have focused on the release of biotic carbon dioxide (CO2) from soils following MP amendments, and few studies have investigated SIC-derived CO2. In this experiment, three typical biodegradable MPs were applied to three calcareous soils amended with 1 % 13C-labeled (99 % atom) carbonate, and the release of CO2 originating from SIC was quantified. The total CO2 emissions, soil pH, and microbial functional genes involved in soil nitrification and denitrification were also detected. Throughout the experiment, the contribution of 13C-labeled carbonate to total CO2 emissions ranged from 0.42 % to 3.31 %. The impact of biodegradable MPs on SIC-derived CO2 varied with incubation period. At the early stage (≤20 days), the amendment of three biodegradable MPs increased the abiotic CO2 in some cases, and the CO2 emissions from 13C-labeled SIC were positively correlated with the total CO2 originating from the decomposition of SOC and MPs. At the late stage (20–70 days), the presence of biodegradable MPs inhibited the release of CO2 from 13C-labeled carbonate in most treatments. Moreover, there were negative relationships of SIC-derived CO2 with soil pH and the amoA gene of ammonia-oxidizing archaea (AOA), but positive correlations of SIC-derived CO2 with amoA of ammonia oxidizing bacteria (AOB) and nirK and nirS genes encoding nitrate reductase in denitrification. Our results indicate that long-term exposure to biodegradable MPs probably regulates the release of H+ in the nitrification process by controlling AOB, and then controlling the dynamics of SIC in calcareous soils.

Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.

Dichlorodiphenyltrichloroethane inhibits soil ammonia oxidation by altering ammonia-oxidizing archaeal and bacterial communities

Dichlorodiphenyltrichloroethane (DDT), a persistent organic pollutant, has known effects on natural microbes. However, its effects on soil ammonia-oxidizing microbes, significant contributors to soil ammoxidation, remain unexplored. To address this, we conducted a 30-day microcosm experiment to systematically study the effects of DDT contamination on soil ammonia oxidation and the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings revealed that DDT inhibited soil ammonia oxidation in the early stage (0–6 days), but it gradually recovered after 16 days. The copy numbers of amoA gene of AOA decreased in all DDT-treated groups from 2 to 10 days, while that of AOB decreased from 2 to 6 days but increased from 6 to 10 days. DDT influenced the diversity and community composition of AOA but had no significant effect on AOB. Further, the dominant AOA communities comprised uncultured_ammonia-oxidizing_crenarchaeote and Nitrososphaera sp. JG1: while the abundance of the latter significantly and negatively correlated with NH 4+-N (P ≤ 0.001), DDT (0.001 < P ≤ 0.01), and DDD (0.01 < P ≤ 0.05) and positively correlated with NO3−-N (P ≤ 0.001), that of the former significantly and positively correlated with DDT (P ≤ 0.001), DDD (P ≤ 0.001), and NH 4+-N (0.01 < P ≤ 0.05) and negatively correlated with NO3−-N (P ≤ 0.001). Among AOB, the dominant group was the unclassified Nitrosomonadales in Proteobacteria, which showed significant negative correlation with NH 4+-N (0.01 < P ≤ 0.05) and significant positive correlation with NO3−-N (0.001 < P ≤ 0.01). Notably, among AOB, only Nitrosospira sp. III7 exhibited significant negative correlations with DDE (0.001 < P ≤ 0.01), DDT (0.01 < P ≤ 0.05), and DDD (0.01 < P ≤ 0.05). These results indicate that DDT and its metabolites affect soil AOA and AOB, consequently affecting soil ammonia oxidation.

Accelerated nitrification and altered community structure of ammonia-oxidizing microorganisms in the saline-alkali tolerant rice rhizosphere of coastal solonchaks

Plantations of saline-alkali tolerant rice in coastal areas are proposed as a strategy to improve rice yield and ensure global food security. The soil nitrification process driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is an integral part of the soil nitrogen cycle and correlates with the quality of coastal solonchak. However, little is known about the effects of saline-alkali tolerant rice cultivation on the soil nitrification process in coastal solonchaks. In this study, we investigated the community structures of AOA/AOB and the nitrification rate in the rice rhizosphere along salinity gradients. The abundance and nitrification rates of AOA and AOB declined with increasing salinity. Saline-alkali-tolerant rice cultivation significantly increased the abundance of AOA and AOB amoA genes from (3.09–11.5) × 106 and (7.76–52.0) × 105 copies g−1 in soils to (16.2–50.9) × 106 and (69.2–423) × 105 copies g−1 in the rhizosphere, respectively. Compared with bulk soils, the nitrification rate of AOA and AOB in the rhizosphere increased significantly with salinity. Saline-alkali-tolerant rice cultivation enhanced the nitrification process of saline-alkali tolerant soil by increasing the nitrification contribution of AOB. Our findings offer new clues on the accelerated nitrification process in the saline-alkali tolerant rice rhizosphere in coastal solonchaks and reveal its roles in shaping AOA/AOB communities, providing suggestions for saline-alkali tolerant rice plantations in coastal solonchaks.

Effects of common afforestation tree species on soil bacterial community and microbial functional guilds in subtropical forests.

To understand the effects of common afforestation tree species on soil microbial community in subtropical forests, seven different tree species were selected as the research object, including Pinus massoniana, Mytilaria laosensis, Liquidambar formosana, Ilex chinensis, Michelia macclurei, Quercus acutissima and Betula luminifera. Based on 16S rRNA high-throughput sequencing and real-time quantitative PCR techniques, we explored the effects of different tree species on soil bacterial community composition, diversity and microbial functional guilds. The results showed that Acidobacteria, Proteobacteria, and Actinobacteria were the dominant bacterial phyla, and that there was no significant difference in bacterial diversity or richness index among different tree species. Results of redundancy analysis suggested that soil bulk density, soil C/N, litter nitrogen content, and litter C/N were the predominant factors determining soil bacterial community composition. The afforestation tree species had significant effects on functional gene abundances of ammonia oxidizing archaea, ammonia oxidizing bacteria and complete ammonia oxidation. Comammox were dominant in abundance. Ammonia oxidizing archaea amoA gene was the only type whose abundance showed significant correlation with soil nitrate content, suggesting that ammonia oxidizing archaea could play a dominant role in the autotrophic nitrification in the acidic subtropical forest soils. The afforestation tree species had significant effects on functional gene abundances of ammonia oxidizing microorganisms. Results of correlation analysis showed that litter nitrogen content was the driving factor for the abundance of ammonia oxidizing microorganisms. Our study provided strong evidence that the responses of soil microbial functional guilds to tree species were more sensitive than bacterial community composition. Future studies should explore the mechanisms of tree plantations on forest ecosystem functioning from the perspective of microbial functional guilds.

Characteristics of soil N2O emission and N2O-producing microbial communities in paddy fields under elevated CO2 concentrations

The effects of elevated carbon dioxide (CO2) concentration (e[CO2]) on nitrous oxide (N2O) emissions from paddy fields and the microbial processes involved in N2O emissions have recently received much attention. Ammonia-oxidizing microorganisms and denitrifying bacteria dominate the production of N2O in paddy soils. To better understand the dynamics of N2O production under e[CO2], a field experiment was conducted after five years of CO2 fumigation based on three treatments: CK (ambient atmospheric CO2), T1 (CK + increase of 40 ppm per year until 200 ppm), and T2 (CK + 200 ppm). N2O fluxes, soil physicochemical properties, and N2O production potential were quantified during the rice-growth period. The functional gene abundance and community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed using quantitative polymerase chain reaction (qPCR) and those of ammonia-denitrifying bacteria (nirS- and nirK-type) were analyzed using Illumina MiSeq sequencing. N2O emissions decreased by 173% and 41% under the two e[CO2] treatments during grain filling and milk ripening, respectively (P < 0.05). N2O emissions increased by 279% and 172% in the T2 treatment compared with T1 during the tillering and milk-ripening stages, respectively (P < 0.05). Furthermore, the N2O production potential was significantly higher in the CK treatment than in T1 and T2 during the elongation stage. The N2O production potential and abundance of AOA amoA genes in T1 treatment were significantly lower than those in CK treatment during the high N2O emission phase caused by mid-season drainage (P < 0.05). Although nirK- and nirS-type denitrifying bacteria community structure and diversity did not respond significantly (P > 0.05) to e[CO2], the abundance of nirK-type denitrifying bacteria significantly affected the N2O flux (P < 0.05). Linear regression analysis showed that the N2O production potential, AOA amoA gene abundance, and nirK gene abundance explained 47.2% of the variation in N2O emissions. In addition, soil nitrogen (N) significantly affected the nirK- and nirS-type denitrifier communities. Overall, our results revealed that e[CO2] suppressed N2O emissions, which was closely associated with the abundance of AOA amoA and nirK genes (P < 0.05).

Manure combined with biochar reduces rhizosphere nitrification potential and amoA gene abundance of ammonia-oxidizing microorganisms in acid purple soil

Fertilization and soil environmental factors determine the niche differentiation of ammonia-oxidizing microorganisms, thereby affecting the ammonia-oxidation process. However, the characteristics of rhizosphere potential nitrification rate (PNR), ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) population under manure combined biochar are unclear. In this study, a pot experiment growing lemon was conducted, setting up six treatments, namely no fertilization (CK), chemical fertilizer (CF), manure (M), chemical fertilizer combined with biochar (CFBC), manure combined with biochar (MBC), fresh manure combined with biochar (FMBC). We investigated the effects of manure, chemical fertilizer and manure combined with biochar on soil physical-chemical properties, PNR, and the amoA gene abundance, diversity and structure of AOA and AOB in the rhizosphere. Our results showed that compared with CK treatment, CF and CFBC increases PNR by 19.3–34.7 % in the rhizosphere, M, MBC and FMBC decrease PNR about 60.0 %; CF and CFBC increased AOA amoA gene copies by 40.2–101.7 %, while M, MBC and FMBC treatments decreased it by 66.5–81.9 %, five fertilization treatments decreased the AOB amoA gene copy by 33.1–81.9 %. The redundancy analysis showed that chemical fertilizer and manure combined with biochar affects the population structure of AOA and AOB by pH, available phosphorus (AP), ratio of carbon to nitrogen (C/N), soil moisture content (SMC), nitrate nitrogen (NO3−-N) and ammonium nitrogen (NH4+-N) in the rhizosphere. The results of partial least squares indicated that pH, total nitrogen (TN), AOA amoA gene copy and AOA Shannon index were main factors affecting nitrification potential in the rhizosphere. Therefore, AOA dominates the ammonia oxidation process in the acid purple soil under the condition of chemical fertilizer and pig manure combined with rice husk biochar. Meanwhile, fertilization affected ammonia oxidation process by regulating soil pH and TN in lemon rhizosphere soil.

A meta-analysis to examine whether nitrification inhibitors work through selectively inhibiting ammonia-oxidizing bacteria.

Nitrification inhibitor (NI) is often claimed to be efficient in mitigating nitrogen (N) losses from agricultural production systems by slowing down nitrification. Increasing evidence suggests that ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) have the genetic potential to produce nitrous oxide (N2O) and perform the first step of nitrification, but their contribution to N2O and nitrification remains unclear. Furthermore, both AOA and AOB are probably targets for NIs, but a quantitative synthesis is lacking to identify the “indicator microbe” as the best predictor of NI efficiency under different environmental conditions. In this present study, a meta-analysis to assess the response characteristics of AOB and AOA to NI application was conducted and the relationship between NI efficiency and the AOA and AOB amoA genes response under different conditions was evaluated. The dataset consisted of 48 papers (214 observations). This study showed that NIs on average reduced 58.1% of N2O emissions and increased 71.4% of soil concentrations, respectively. When 3, 4-dimethylpyrazole phosphate (DMPP) was applied with both organic and inorganic fertilizers in alkaline medium soils, it had higher efficacy of decreasing N2O emissions than in acidic soils. The abundance of AOB amoA genes was dramatically reduced by about 50% with NI application in most soil types. Decrease in N2O emissions with NI addition was significantly correlated with AOB changes (R2 = 0.135, n = 110, P < 0.01) rather than changes in AOA, and there was an obvious correlation between the changes in concentration and AOB amoA gene abundance after NI application (R2 = 0.037, n = 136, P = 0.014). The results indicated the principal role of AOB in nitrification, furthermore, AOB would be the best predictor of NI efficiency.

Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea

SummaryThe significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.

Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils

The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted field plots under contrasting management regimes—permanent bare fallow, grassland, and arable (wheat) cultivation maintained for more than 50 years. Metagenome and metatranscriptome analysis indicated nitrite oxidizing bacteria (NOB) were more abundant than ammonia oxidizing archaea (AOA) and bacteria (AOB) in all soils. The most abundant AOA and AOB in the metagenomes were, respectively, Nitrososphaera and Ca. Nitrososcosmicus (family Nitrososphaeraceae) and Nitrosospira and Nitrosomonas (family Nitrosomonadaceae). The most abundant NOB were Nitrospira including the comammox species Nitrospira inopinata, Ca. N. nitrificans and Ca. N. nitrosa. Anammox bacteria were also detected. Nitrospira and the AOA Nitrososphaeraceae showed most transcriptional activity in arable soil. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome; AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Nitrification potential assessed in soil from the experimental sites (microcosms amended or not with DCD at concentrations inhibitory to AOB but not AOA), was highest in arable samples and lower in all assays containing DCD, indicating AOB were responsible for oxidizing ammonium fertilizer added to these soils.

Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (PN) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and PN values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH3 and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.

Ammonia-oxidizing archaea are dominant over comammox in soil nitrification under long-term nitrogen fertilization

The complete ammonia oxidizers (comammox) capable of catalyzing nitrification, oxidizing ammonia to nitrate, via activity of only one type of microbes were recently discovered which has updated our knowledge of traditional two-step nitrification. The extent of contribution of comammox and canonical ammonia oxidizers including ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to soil nitrification, especially in soils with long-term input of nitrogen (N) fertilizers, remains unknown. The transcriptional abundance of amoA gene from comammox, AOA, and AOB in soils fertilized for 29 years was investigated in different seasons and soil layers via quantitative PCR. The results showed that comammox were detected in all soil samples; however, AOA and AOB had significantly higher transcriptional abundance of amoA gene than comammox. Nitrification activity was most significantly correlated with the transcriptional abundance of AOA amoA gene (Pearson correlation, r = 0.217, P < 0.05) suggesting AOA were the dominant contributors to soil potential nitrification. Lower abundances of amoA gene transcripts were observed in July than in April and November. The application of high level of mineral N fertilizer decreased the abundance of both AOA and AOB; however, long-term input of organic manure combined with mineral N fertilizer stabilized the abundances of ammonium-oxidizing microbes in soils. Seasonal variation and fertilization regimes substantially affected the abundance of both AOA and AOB, but AOB were not as sensitive in responding to the seasonal variation and fertilization as AOA. The analysis of RDA and VPA demonstrated that sampling month, soil depth, and fertilization regime explained 30.20%, 11.46%, and 5.40% of the variation in nitrification microorganism amoA gene composition, respectively. Seasonal variation exerted the most influences on the nitrifiers’ composition, and soil depth and fertilization regime were also important factors in shaping the nitrifier communities. According to the correlation analysis, NO3−–N content was the most important soil property in impacting the transcriptional abundance of amoA gene, and the amoA gene transcript abundance decreased with increasing NO3−–N content. The results suggest that the activity of comammox may be more inhibited by the long-term nitrogen fertilization than canonical ammonia oxidizers in agricultural soils. This study provides insights into the different responses of comammox and canonical ammonia oxidizers to fertilization, seasonal variation, and soil depth and their relative contributions to nitrification in agricultural soil.

Molecular analysis of microbial nitrogen transformation and removal potential in mangrove wetlands under anthropogenic nitrogen input

Mangrove ecosystems are natural nitrogen removal systems that are primarily mediated by nitrogen cycle microorganisms, but their relative contributions to nitrogen transformation and removal in mangrove sediments under anthropogenic nitrogen input needs further resolution and characterization. Here, we investigated the responses and the relative contributions of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), anaerobic ammonium oxidizing (anammox) bacteria and denitrifying bacteria after spiking urea into mangrove sediments incubated in a laboratory microcosm experiment for four weeks. During incubation, the diversity, abundances and transcription levels of the hzo genes for anammox bacteria, amoA genes for AOA and AOB, and nirS genes for denitrifying bacteria were monitored using targeted gene clone library analyses and quantitative PCR assays at the DNA and RNA levels. The results showed that mangrove sediments harbour habitat-specific anammox bacteria which related to Candidatus Scalindua and Candidatus Kuenenia clades. Mangrove specific AOA related to deep branched clades within Candidatus Nitrososphaera and Candidatus Nitrosotalea, and AOB related to Nitrosomonas and Nitrosospira were also detected in the collected sediment samples. Growth and activity of AOA were detected at all levels of amendment of nitrogen input, whereas AOB growth was detectable only at the high-level nitrogen input (1.5 mg urea per gram of dry sediment) with no amoA transcripts and lower abundance than AOA. The abundance and transcription levels of the nirS gene were higher (~1000 times) than those of the hzo gene in all groups. Pearson correlation analysis demonstrated that the abundance of both AOA and AOB amoA genes had a significant positive correlation with the nirS gene (p < 0.01). These results indicated that nitrification (primarily mediated by the AOA)-denitrification process played the most important role in nitrogen removal from the amendment of nitrogen short-term input in the mangrove sediments.

Monthly distribution of ammonia-oxidizing microbes in a tropical bay.

Ammonia oxidation, performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), plays a critical role in the cycle of nitrogen in the ocean. For now, environmental variables controlling distribution of ammonia-oxidizing microbes are still largely unknown in oceanic environments. In this study, we used real-time quantitative PCR and high-throughput sequencing methods to investigate the abundance and diversity of AOA and AOB from sediment and water in Zhanjiang Bay. Phylogenic analysis revealed that the majority of AOA amoA sequences in water and sediment were affiliated with the genus Nitrosopumilus, whereas the Nitrosotalea cluster was only detected with low abundance in water. Nitrosomonas and Nitrosospira dominated AOB amoA sequences in water and sediment, respectively. The amoA copy numbers of both AOA and AOB varied significantly with month for both sediment and water. When water and sediment temperature dropped to 17-20°C in December and February, respectively, the copy number of AOB amoA genes increased markedly and was much higher than for AOA amoA genes. Also, AOA abundance in water peaked in December when water temperature was lowest (17-20°C). Stepwise multiple regression analyses revealed that temperature was the most key factor driving monthly changes of AOA or AOB abundance. It is inferred that low water temperature may inhibit growth of phytoplankton and other microbes and so reduce competition for a common substrate, ammonium.

Abundance and community structure of ammonium monooxygenase (amoA) genes in the wet season of liaohe estuary sediments

Ammonia oxidation is an important part of the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are important players in the ammoxidation process. In this study, 13 sediment samples from the Liaohe estuary were collected in the wet season. The abundances of 16S rRNA and amoA genes were detected by real-time fluorescence quantitative PCR. The diversity and community structure of AOA and AOB were investigated by constructing clone libraries. The AOA and AOB amoA gene abundances ranged from 3.10 × 106–2.85 × 107 and 6.59 × 105–1.20 × 107 copies/g wet deposit, respectively. At all sites, AOA abundance was greater than AOB (AOA: AOB = 2.2–86.5). The ratio of AOA: archaeal 16S rRNA gene abundances and AOB: bacterial 16S rRNA gene abundances were 4.6 × 10−3–1.5 × 10−2 and 1.5 × 10−6–1.0 × 10−4. Phylogenetic analysis showed that the AOA amoA sequences were mainly Nitrosophaera and Nitrosopumilus, and most of the AOB amoA sequences belong to unclassified bacteria, which mainly were detected in estuarine sediments and wetland soils. AOA and AOB community had an obvious spatial heterogeneity. In addition, canonical correspondence analysis showed that the salinity, ammonia, total phosphorus, total organic carbon, sand, and silt content were the main driven factors of AOA and AOB community structure, in which the sand and silt content had a significant contribution.

Distribution and Potential Nitrification Rates of Aerobic Ammonia-Oxidizing Microorganisms in Surface Sediments of Mangrove in Sanya River

The ammonia oxidation process is a rate-limiting step in nitrification. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are the major drivers of ammonia oxidation. Their distribution and relative contributions to nitrification are the research highlights in the nitrogen cycle. Real-time quantitative polymerase chain reaction (qPCR) was used to study the distribution of aerobic ammonia-oxidizing microorganisms in the surface sediments of mangrove in the Sanya River, and the relative contribution rates of AOB and AOA to nitrification were calculated through the determination of the potential nitrification rates (PNR). The results showed that, in most sampling sites, the abundance of AOA amoA genes was higher than that of AOB amoA genes. The abundance of AOB was higher during the winter, whereas that of AOA was higher during the summer, and the ratio of AOA to AOB abundance was lower during the winter. The dissolved oxygen (DO) content, pH, total organic carbon (TOC) content, and nitrate concentration greatly influenced the abundance of AOB and AOA. The potential nitrification rates of AOB and AOA were both higher during the summer than during the winter, and the relative contribution rate of AOA to nitrification was higher during the winter, whereas that of AOB was higher during the summer. There were no significant correlations between the PNR and amoA genes abundance of AOB and AOA.

Green manuring inhibits nitrification in a typical paddy soil by changing the contributions of ammonia-oxidizing archaea and bacteria

Rice–rice–green manure rotations in south China are characterized by high efficiency and good environmental performance, and the application of green manure plays an important role in N management. Nitrification is a key process in N cycling and is highly correlated with the N utilization of crops and with leaching losses. As a potential N loss pathway, the nitrification process and nitrifiers as affected by green manuring are of critical importance. A pot experiment covering green manure-double rice rotation was conducted to evaluate the effects of green manure and N fertilizer on soil nitrification and to achieve a mechanistic understanding of underlying processes in an alkaline paddy soil. Soil nitrification potential (NP) and the recovered nitrification potential (RNP) were measured. Relative contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil nitrification were studied using specific bacterial inhibitors. In the alkaline paddy soil, soil NP and nitrate concentrations were significantly decreased by green manuring but increased with increasing N fertilization. Soil nitrification was dominated by AOB and that the relative contributions of AOB to RNP ranged from 65% to 79% at different sampling stages despite the larger abundance of AOA amoA gene numbers. RNP and the contribution of AOB to RNP were significantly increased by N fertilizer, whereas the contribution of AOA was decreased by green manuring. We concluded that the application of inorganic N enhanced NP while green manures reduced it, which is consistent with the variation of observed soil nitrate concentrations. These results indicate that the utilization of winter green manure is an effective practice to improve N management in paddy rice.

Composition, diversity, and activity of aerobic ammonia-oxidizing Bacteria and Archaea in the intertidal sands of a grand strand South Carolina beach.

Aerobic ammonia oxidation to nitrite has been established as an important ecosystem process in regulating the level of nitrogen in marine ecosystems. This process is carried out by ammonia‐oxidizing bacteria (AOB) within the classes Betaproteobacteria and Gammaproteobacteria and ammonia‐oxidizing Archaea (AOA) from the phylum Thaumarchaeota, and the latter of which has been established as more prevalent in marine systems. This study investigated the presence, abundance, and activity of these groups of microbes at a beach near Springmaid Pier in Myrtle Beach, South Carolina, through the implementation of next generation sequencing, quantitative PCR (qPCR), and microcosm experiments to monitor activity. Sequencing analysis revealed a diverse community of ammonia‐oxidizing microbes dominated by AOA classified within the family Nitrosopumilaceae, and qPCR revealed the abundance of AOA amoA genes over AOB by at least an order of magnitude in most samples. Microcosm studies indicate that the rates of potential ammonia oxidation in these communities satisfy Michaelis–Menten substrate kinetics and this process is more active at temperatures corresponding to summer months than winter. Potential rates in AOA medium were higher than that of AOB medium, indicating a potentially greater contribution of AOA to this process in this environment. In conclusion, this study provides further evidence of the dominance of AOA in these environments compared with AOB and highlights the overall efficiency of this process at turning over excess ammonium that may be present in these environments.

Responses of AOA and AOB activity and DNA/cDNA community structure to allylthiourea exposure in the water level fluctuation zone soil.

Ammonia oxidation is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Allylthiourea (ATU) has been found to specifically inhibit ammonia oxidation. However, the effect of ATU on AOA and AOB transcription has been infrequently studied. In the present study, we examined the responses of AOA and AOB activity and DNA/cDNA community structure to ATU exposure. The ammonia oxidation activity in the 100-mg/L ATU group was 4.3% ofthat in the control group after 7days. When exposed to ATU, the gene abundance of AOA was favored compared with that of AOB, and there were no statistically significant differences in the abundance of AOB amoA in DNA and cDNA between the two groups. Compared with the control group, the gene abundance of AOA significantly increased by 5.23 times, while the transcription of AOA significantly decreased by 0.70 times. Moreover, the transcriptional ratio of AOA in the ATU group was only 0.05 times as highasthat in the control group. ATU selectively affected AOB and completely inhibited Nitrosomonas europaea and Bacterium amoA.22.HaldeII.kultur at the genetic level. Under ATU exposure, all AOA clusters were transcribed, but three AOB clusters were not transcribed. Our results indicated that the ammonia oxidation potential of the soil of water level fluctuation areas, based on ATU inhibition, was associated mainly with AOA amoA gene abundance and AOB community shifts in DNA and cDNA.