Archaeal amoA Genes Research Articles

Nitrification of archaeal ammonia oxidizers in a high- temperature hot spring

Abstract. The oxidation of ammonia by microbes has been shown to occur in diverse natural environments. However, the link of in situ nitrification activity to taxonomic identities of ammonia oxidizers in high-temperature environments remains poorly understood. Here, we studied in situ ammonia oxidation rates and the diversity of ammonia-oxidizing Archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3− pool dilution technique in the surface and bottom sediments were 4.80 and 5.30 nmol N g−1 h−1, respectively. Real-time quantitative polymerase chain reaction (qPCR) indicated that the archaeal 16S rRNA genes and amoA genes were present in the range of 0.128 to 1.96 × 108 and 2.75 to 9.80 × 105 gene copies g−1 sediment, respectively, while bacterial amoA was not detected. Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic Candidatus Nitrosocaldus yellowstonii, which represented the most abundant operational taxonomic units (OTU) in both surface and bottom sediments. The archaeal predominance was further supported by fluorescence in situ hybridization (FISH) visualization. The cell-specific rate of ammonia oxidation was estimated to range from 0.410 to 0.790 fmol N archaeal cell−1 h−1, higher than those in the two US Great Basin hot springs. These results suggest the importance of archaeal rather than bacterial ammonia oxidation in driving the nitrogen cycle in terrestrial geothermal environments.

Differential response of ammonia-oxidizing archaea and bacteria to the wetting of salty arid soil.

Ammonia-oxidizing archaea and bacteria (AOA, AOB) catalyze the first and rate-limiting step of nitrification. To examine their differential responses to the wetting of dry and salty arid soil, AOA and AOB amoA genes (encoding subunit A of the ammonia monooxygenase) and transcripts were enumerated in dry (summer) and wet (after the first rainfall) soil under the canopy of halophytic shrubs and between the shrubs. AOA and AOB were more abundant under shrub canopies than between shrubs in both the dry and wetted soil. Soil wetting caused a significant decrease in AOB abundance under the canopy and an increase of AOA between the shrubs. The abundance of the archaeal amoA gene transcript was similar for both the wet and dry soil, and the transcript-to-gene ratios were < 1 independent of niche or water content. In contrast, the bacterial amoA transcript-to-gene ratios were between 78 and 514. The lowest ratio was in dry soil under the canopy and the highest in the soil between the shrubs. The results suggest that the AOA are more resilient to stress conditions and maintain a basic activity in arid ecosystems, while the AOB are more responsive to changes in the biotic and abiotic conditions.

Soil physicochemical properties impact more strongly on bacteria and fungi than conversion of grassland to oil palm

The conversion of grassland to oil palm is expected to increase throughout tropical regions where oil palm grows. Given the extent of land use change, there are concerns associated with impacts on ecosystem function and nutrient cycling. For this work, soil samples were collected in Papua New Guinea from 15 sites with oil palm (planted on grassland) and adjacent remnant grassland. Using DNA-based approaches, bacterial and fungal community composition was assessed in each sample, along with abundance of genes involved in key nitrogen cycling steps: nitrification (bacterial and archaeal amoA genes), nitrite reduction (nirS gene), and nitrous oxide reduction (nosZ gene). Across all microbial properties measured, variation among sites was greater than variation due to land use change. This was driven by among-site variation in soil physicochemical properties, particularly total soil organic carbon content and δ13C, electrical conductivity, exchangeable calcium, potassium and magnesium content, and extractable phosphorus content. The results suggest that in this environment, routinely measured soil properties such as soil pH, organic carbon, and exchangeable cation contents may serve as indicators for the effects of land use and management on soil microbial community composition and functioning.

Revisiting nitrification in the Eastern Tropical South Pacific: A focus on controls

AbstractNitrification, the oxidation of ammonium ( ) to nitrite ( ) and to nitrate ( ), is a component of the nitrogen (N) cycle internal to the fixed N pool. In oxygen minimum zones (OMZs), which are hotspots for oceanic fixed N loss, nitrification plays a key role because it directly supplies substrates for denitrification and anaerobic ammonia oxidation (anammox), and may compete for substrates with these same processes. However, the control of oxygen and substrate concentrations on nitrification are not well understood. We performed onboard incubations with 15N‐labeled substrates to measure rates of and oxidation in the eastern tropical South Pacific (ETSP). The spatial and depth distributions of and oxidation rates were primarily controlled by and availability, oxygen concentration, and light. In the euphotic zone, nitrification was partially photoinhibited. In the anoxic layer, oxidation was negligible or below detection, but high rates of oxidation were observed. oxidation displayed extremely high affinity for both and oxygen. The positive linear correlations between oxidation rates and in situ concentrations and ammonia monooxygenase subunit A (amoA) gene abundances in the upper oxycline indicate that the natural assemblage of ammonia oxidizers responds to in situ concentrations or supply by adjusting their population size, which determines the oxidation potential. The depth distribution of archaeal and bacterial amoA gene abundances and N2O concentration, along with independently reported simultaneous direct N2O production rate measurements, suggests that AOA were predominantly responsible for oxidation, which was a major source of N2O production at oxygen concentrations &gt; 5 µM.

Effects of polybrominated diphenyl ethers and plant species on nitrification, denitrification and anammox in mangrove soils

Little is known about polybrominated diphenyl ethers (PBDEs) and planting affect biogeochemical processes, and their impact on microbial nitrogen (N) transformation in soil. A 12-month microcosm experiment was conducted to understand the effects of a mixture of PBDEs at two contamination levels, 2 and 20mgkg−1dry weight representing low and high soil contamination, respectively, using two mangrove plant species, namely Kandelia obovata (Ko) and Bruguiera gymnorrhiza (Bg), on nitrification, denitrification and anammox in mangrove soils. No significant changes in these N transformation processes were found at month 3 and at a low level of PBDEs in both plant species, suggesting that short-term exposure to 2mgkg−1 contamination did not affect microbial N transformation. At month 12, a high level of PBDE contamination significantly decreased the nitrification potential activity and the copy numbers of archaeal amoA and bacterial amoA gene in Ko soil, but such inhibitory effect was not significant in Bg soil. On the contrary, the denitrification-related parameters, including the activities of nitrate reductase and nitrite reductase, potential denitrification activity and copy numbers of nirK, nirS and nosZ gene, were stimulated by a high level of PBDE contamination in both Ko and Bg soils, and the stimulation was higher in the more anaerobic Bg soil. Different from denitrification, a high level of PBDE contamination decreased the copy numbers of anammox bacterial 16S rRNA gene in Bg soil but not in Ko soil; this was possibly related to the lower nitrate concentration in Bg soil that might inhibit the growth of anammox bacteria. These results indicated that the effects of PBDEs on microbial N transformation were plant species-specific, with the nitrifying microorganisms in Ko soil more susceptible to PBDE contamination, while denitrification and anammox in Bg soil were more sensitive.

Diversity, abundance and community structure of ammonia-oxidizing archaea and bacteria in riparian sediment of Zhenjiang ancient canal

Ammonia-oxidizing microorganisms play an important role in the nitrification process. In this study, the abundance, diversity and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in riparian sediment of Zhenjiang ancient canal were investigated using amoA gene as a molecular biomarker. Clone libraries and qPCR (quantitative polymerase chain reaction) results indicated both abundance and diversity of AOB were higher than that of AOA, suggesting that AOB may play a more important role than AOA in nitrification process. The abundances, diversity and community structure of AOA and AOB had an obvious spatial variation in six different sampling sites, which may be attributed to the differences in sediment physico-chemical characteristics. 66.7%, 26.5% and 6.8% of the total 117 AOA gene sequences fell into the Nitrososphaera, Nitrosopumilus and Nitrosotalea cluster, whereas, 52.2% and 47.8% of the total 134 AOB amoA gene sequences belonged to the Nitrosomonas and Nitrosospira cluster. There was a strong positive relationship between the potential nitrification rates (PNRs) without ampicillin and bacterial amoA gene copy numbers, whereas no significant correlation between the archaeal amoA gene copy numbers and the PNRS without ampicillin. In addition, when ampicillin was added into the cultured systems in order to inhibit the bacteria, the values of PNRs decreased by 21.71%, 39.62%, 46.04%, 27.06%, 39.26% and 7.24%, respectively, for the C1, C2, C3, C4, G5 and G6 samples sites, indicating that PNRs were apparently affected by ammonia-oxidizing bacteria. These results further indicate that nitrification is more related to AOB than AOA in the riparian sediment of Zhenjiang ancient canal.

Relationships between ammonia-oxidizing communities, soil methane uptake and nitrous oxide fluxes in a subtropical plantation soil with nitrogen enrichment

Ammonia-oxidizers play an essential role in nitrogen (N) transformation and nitrous oxide (N2O) emission in forest soils. It remains unclear if ammonia-oxidizers affect interaction between methane (CH4) uptake and N2O emission. Our specific goal was to test the impacts of changes in ammonia-oxidizing communities elicited by N enrichment on soil CH4 uptake and N2O emission. Based on a field experiment, two-forms (NH4Cl and NaNO3) and two levels (40 and 120 kg N ha−1 yr−1) of N were applied in the subtropical plantation forest of southern China. Soil CH4 and N2O fluxes, the abundance and structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were measured using static chamber-gas chromatography, quantitative PCR (qPCR), and terminal-restriction fragment length polymorphism (T-RFLP). Nitrogen addition tended to inhibit soil CH4 uptake, but significantly promoted soil N2O emission; moreover, these impacts were more significant with NH4+−N than with NO3−−N addition. NH4Cl addition significantly changed ammonia-oxidizer abundance with an increase in AOA and a decrease in AOB. Nitrogen additions significantly decreased the relative abundance of 329 bp and 421 bp of archaeal amoA gene. Negative relationships occurred between soil CH4 uptake and AOA abundance and between soil CH4 uptake and AOA/AOB ratio; however, a positive relationship was found between soil N2O emission and AOA abundance. These results indicate that a shift in abundance and composition of ammonia-oxidizing communities is closely linked to changes in soil CH4 uptake and N2O emission under N enrichment. Furthermore, AOA communities play a contrasting role from AOB communities for regulating the fluctuation between soil CH4 and N2O fluxes.

Dynamics of bacterial and archaeal amoA gene abundance after additions of organic inputs combined with mineral nitrogen to an agricultural soil

Dynamics of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) abundance was assayed in a tropical Humic Nitisol during two cropping seasons of a long-term field experiment situated in the central highlands of Kenya. Since 2002, soils were treated yearly with biochemically contrasting organic inputs (4 Mg C ha−1 year−1) of Tithonia diversifolia (TD; C/N ratio: 13; lignin: 8.9 %; polyphenols: 1.7 %), Calliandra calothyrsus (CC; 13; 13; 9.4) and Zea mays (ZM; 59; 5.4; 1.2) combined with and without 120 kg CaNH4NO3 ha−1 season−1. In 2012 and 2013, soils (0–15 cm) were sampled at young growth (EC30) and flowering (EC60) stages of maize and subjected to DNA-based amoA gene quantification. ZM and TD increased AOB abundance by 9 and 19 %, respectively, compared to CC, while AOA remained unaffected. This was ascribed to high organic N in TD and lower lignin and polyphenol contents in ZM than in CC. In CC, formation of polyphenol-protein complexes limited microbial access to N. Sole use of mineral N or its combination with organic inputs decreased AOA abundance by 35 % but not AOB as a consequence of pH reduction by mineral N. Overall, AOB was more responsive than AOA to input quality that became most pronounced under optimal soil moisture conditions found in 2013 and at EC60 in 2012. We recommend prolonged study periods, considering also rRNA-based analyses to explore the dynamics of active nitrifying communities as a consequence of interrelations of contrasting organic inputs, crop growth stages and seasonality in agricultural soils.

Bioturbation of Tubificid worms affects the abundance and community composition of ammonia-oxidizing archaea and bacteria in surface lake sediments

To better understand the effects of Tubificid worm bioturbation on ammonia-oxidizing microorganisms in surface lake sediment, sediment-water microcosms with different densities of Tubificid worms were constructed. Clone libraries and real-time PCR were applied to analyze the community composition and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in surface sediments. The results suggest that bioturbation of Tubificid worms promote the release of nitrogen and phosphorus in surface sediment. The abundance of the bacterial amoA gene was higher than that of the archaeal amoA gene in all groups. Nitrosopumilus (93.7 % identity) was the main AOA in all groups, whereas no Nitrosotalea sequence was detected in the three treatment groups. All AOB in the surface sediments belonged to two populations of β-Proteobacteria subclasses, Nitrosomonas (92.7 % identity) and Nitrosospira (97.8 % identity), except those in the surface sediments of the low-density treatment group, which contained only Nitrosomonas. Moreover, the diversities of AOA and AOB were reduced in Tubificid worms containing microcosms. In conclusion, the bioturbation of Tubificid worms affects the abundance and community composition of ammonia-oxidizing microorganisms in surface sediments.

Effects of fertilization on microbial abundance and emissions of greenhouse gases (CH4 and N2O) in rice paddy fields

This study is to explore effects of nitrogen application and straw incorporation on abundance of relevant microbes and CH 4 and N2O fluxes in a midseason aerated rice paddy field. Fluxes of CH 4 and N2O were recorded, and abundance of relevant soil microbial functional genes was determined during rice-growing season in a 6-year-long fertilization experiment field in China. Results indicate that application of urea significantly changed the functional microbial composition, while the influence of straw incorporation was not significant. Application of urea significantly decreased the gene abundances of archaeal amoA and mcrA, but it significantly increased the gene abundances of bacterial amoA. CH 4 emission was significantly increased by fresh straw incorporation. Incorporation of burnt straw tended to increase CH 4 emission, while the urea application had no obvious effect on CH 4 emission. N2O emission was significantly increased by urea application, while fresh or burnt straw incorporation tended to decrease N2O emission. The functional microbial composition did not change significantly over time, although the abundances of pmoA, archaeal amoA, nirS, and nosZ genes changed significantly. The change of CH 4 emission showed an inverse trend with the one of the N2O emissions over time. To some extent, the abundance of some functional genes in this study can explain CH 4 and N2O emissions. However, the correlation between CH 4 and N2O emissions and the abundance of related functional genes was not significant. Environmental factors, such as soil Eh, may be more related to CH 4 and N2O emissions.

Sedimentary archaeal amoA gene abundance reflects historic nutrient level and salinity fluctuations in Qinghai Lake, Tibetan Plateau.

Integration of DNA derived from ancient phototrophs with their characteristic lipid biomarkers has been successfully employed to reconstruct paleoenvironmental conditions. However, it is poorly known that whether the DNA and lipids of microbial functional aerobes (such as ammonia-oxidizing archaea: AOA) can be used for reconstructing past environmental conditions. Here we identify and quantify the AOA amoA genes (encoding the alpha subunit of ammonia monooxygenases) preserved in a 5.8-m sediment core (spanning the last 18,500 years) from Qinghai Lake. Parallel analyses revealed that low amoA gene abundance corresponded to high total organic carbon (TOC) and salinity, while high amoA gene abundance corresponded to low TOC and salinity. In the Qinghai Lake region, TOC can serve as an indicator of paleo-productivity and paleo-precipitation, which is related to historic nutrient input and salinity. So our data suggest that temporal variation of AOA amoA gene abundance preserved in Qinghai Lake sediment may reflect the variations of nutrient level and salinity throughout the late Pleistocene and Holocene in the Qinghai Lake region.

Nitrification and ammonia-oxidizing bacteria shift in response to soil moisture and plant litter quality in arid soils from the Patagonian Monte

We aimed to evaluate the effects of both plant litter quality, characteristic of sites with different histories of grazing disturbance, and soil water content on nitrification in soils from an arid ecosystem of Patagonia. To reach this goal, soil microcosms covered by plant litter of different quality and subjected to different soil water conditions were sampled at different times to analyze: (i) the nitrifying enzyme activity; (ii) the concentration of inorganic forms of nitrogen; and (iii) the abundance of bacterial (AOB) and archaeal (AOA) amoA genes. Soil water enhanced nitrifying activity in average 16% during the period of highest nitrification rates, and nitrate concentration in average 733% after 70 days of incubation. Microcosms amended with high litter quality showed the highest ammonium and the lowest phenolics concentrations, and higher or equal nitrification rates than microcosms amended with poor litter quality. After one week of incubation, the combination of both high litter quality and soil water significantly enhanced amoA gene abundance from AOB (p<0.05). The AOB:AOA amoA genes ratio ranged from 12 to 3170. Altogether, our results suggest that high soil water and litter quality exerted positive effects over the nitrifying activity and the abundance of AOB but not AOA in these arid soils.

Diversity of ammonia-oxidising bacteria and archaea in seven different estuarine sediments from Poyang Lake

In the present study, we used a culture-independent method based on library construction and sequencing to analyse the genetic diversity of the ammonia monooxygenase genes (amoA) of ammonia-oxidising archaea and bacteria in seven different estuarine sediments of Poyang Lake. The total of 67 and 38 operational taxonomic units (OTUs) (similarity &lt;95%) of archaeal (AOA) and bacterial (AOB) amoA genes were retrieved respectively. AOA had higher diversity of amoA genes than did AOB. Phylogenetic analysis showed that AOA amoA sequences were closely related to amoA sequences from Crenarchaeota, Thaumarchaeota and some other uncultured archaea. Fragments from AOB were most associated with sequences from betaproteobacteria and some other uncultured bacteria. On the basis of Kendall’s correlation coefficient, there was a significant positive correlation between AOA amoA gene diversity and temperature, and the AOB diversity was positively correlated with total nitrogen and nitrate nitrogen concentration, and negatively correlated with pH in the sediments, suggesting that AOA and AOB were probably sensitive to several environmental factors. Our work could enhance our understanding of the roles of ammonia-oxidising microorganisms in these seven estuarine sediments from Poyang Lake.

Ammonia and nitrite oxidation in the Eastern Tropical North Pacific

AbstractNitrification plays a key role in the marine nitrogen (N) cycle, including in oceanic oxygen minimum zones (OMZs), which are hot spots for denitrification and anaerobic ammonia oxidation (anammox). Recent evidence suggests that nitrification links the source (remineralized organic matter) and sink (denitrification and anammox) of fixed N directly in the steep oxycline in the OMZs. We performed shipboard incubations with 15N tracers to characterize the depth distribution of nitrification in the Eastern Tropical North Pacific (ETNP). Additional experiments were conducted to investigate photoinhibition. Allylthiourea (ATU) was used to distinguish the contribution of archaeal and bacterial ammonia oxidation. The abundance of archaeal and β‐proteobacterial ammonia monooxygenase gene subunit A (amoA) was determined by quantitative polymerase chain reaction. The rates of ammonia and nitrite oxidation showed distinct subsurface maxima, with the latter slightly deeper than the former. The ammonia oxidation maximum coincided with the primary nitrite concentration maximum, archaeal amoA gene maximum, and the subsurface nitrous oxide maximum. Negligible rates of ammonia oxidation were found at anoxic depths, where high rates of nitrite oxidation were measured. Archaeal amoA gene abundance was generally 1 to 2 orders of magnitude higher than bacterial amoA gene abundance, and inhibition of ammonia‐oxidizing bacteria with 10 μM ATU did not affect ammonia oxidation rates, indicating the dominance of archaea in ammonia oxidation. These results depict highly dynamic activities of ammonia and nitrite oxidation in the oxycline of the ETNP OMZ.

Long-term organic and inorganic fertilization alters temperature sensitivity of potential N2O emissions and associated microbes

Emissions of the greenhouse gas nitrous oxide (N2O) from soil are sensitive to many factors including temperature, nutrient status, pH and bulk-density. Interactions among these are complex, particularly in agricultural systems where fertilizer-addition has interactive influences across many soil properties. Under laboratory conditions, the temperature sensitivity of N2O emissions, as measured by Q10 values (fractional change in rate with a 10 °C increase in temperature), was higher in soils receiving long-term fertilizer addition compared with control. Different fertilization regimes significantly influenced the emission pathways. Application of manure increased the proportion of potential N2O derived from denitrification although the incubation condition used in the present study might not be favorable for anaerobic denitrification. The abundance of archaeal amoA gene copies increased under all fertilizer treatments, but that of bacterial amoA only increased under mineral (NPK) fertilization. Meanwhile, abundance of nirS, nirK and nosZ only increased under OM and MNPK fertilization. T-RFLP analyses showed that both ammonia oxidizing and denitrifier community structures were altered by fertilization, but only the nirS community structure was sensitive to temperature change. Furthermore, a strong correlation was observed between nirS gene abundance and potential N2O emissions. Relationships between AOA, nirK gene abundances and potential N2O emission were significant but relatively weak. PLS path model revealed that besides direct effect, potential N2O emission was also indirectly influenced by temperature through mediation of NH4+ concentration and nirS-type denitrifier. Our work suggests that warming-induced elevation of potential N2O emission could be strengthened by long-term application of fertilizers, especially organic manure, via shifting community abundance and structure of nirS-type denitrifier.

Nitrogen fertilization induced changes in ammonia oxidation are attributable mostly to bacteria rather than archaea in greenhouse-based high N input vegetable soil

Little is known about the effects of nitrogen (N) fertilization rates on ammonia-oxidizing bacteria (AOB) and archaea (AOA) and their differential contribution to ammonia oxidation, particularly in greenhouse-based high N input vegetable soils. Potential ammonia oxidation (PAO) of these vegetable soils was evaluated under five levels of N fertilization (with urea) in the presence or absence of the bacterial protein synthesis inhibitors kanamycin and gentamicin. Abundance and community composition of AOB and AOA were evaluated by quantitative polymerase chain reaction (PCR) and clone libraries. The five annual N fertilization rates studied were 100% (N870: 300, 270 and 300 kg N ha−1 for tomato, cucumber and celery, respectively), 80% (N696), 60% (N522), 40% (N348) and 0% (N0) of the conventional N rate. The PAO decreased significantly with increasing N fertilization rates irrespective of the presence of kanamycin plus gentamicin. PAO was significantly lower in the presence than in the absence of kanamycin plus gentamicin, and was decreased by 71.9% under N0, 77.2% under N348, 54.9% under N522, 49.9% under N696, and 51.6% under N870. The abundance of bacterial and archaeal amoA genes was significantly decreased at the highest N fertilization rate. The clone sequences of AOB and AOA were mostly affiliated with the genus Nitrosospira and group 1.1b thaumarchaeota. Changes in community composition were more pronounced in AOB than in AOA after long-term (6-year) N fertilization. Our results suggest that AOB may play a more important role than AOA in NH3 oxidation in such high N input vegetable soils.

Macrophyte landscape modulates lake ecosystem-level nitrogen losses through tightly coupled plant-microbe interactions

Root functional diversity of submerged vegetation exerts a major effect on nitrogen (N) cycling in lake sediments. This fact, however, is neglected in current N-balance models because the links between the engineering role of plants and in situ microbial N cycling are poorly understood. We hypothesized that macrophyte species with high root oxygen loss (ROL) capacity promote the highest denitrification because of a higher abundance of ammonia oxidizers and tighter coupling between nitrifiers and denitrifier communities. We sampled five small ultraoligotrophic shallow lakes with abundant macrophyte cover including sediments dominated either by Isoetes spp. (high ROL), mixed communities of natopotamids (low ROL), and unvegetated sandy sediments. At each site, we quantified denitrification (DNT) rates and proxies for the abundance of denitrifiers (nirS and nirK genes), and both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) and the diversity of nirS-harboring bacteria. Vegetated sediments showed significantly higher abundances of N-cycling genes than bare sediments. Plant communities dominated by Isoetes generated sediments with higher redox and NO3− concentrations and significantly higher DNT rates than natopotamids-dominated landscapes. Accordingly, increasing DNT rates were observed along the gradient from low ROL plants-bare sediments-high ROL plants. Significantly higher abundance of the archaeal amoA gene was recorded in sediments colonized by high ROL plants unveiling a key biogeochemical role for AOA in coupling macrophyte landscape and ecosystem denitrification.

Abundance and diversity of ammonia-oxidizing archaea and bacteria on granular activated carbon and their fates during drinking water purification process.

Ammonia is a precursor to trichloramine, which causes an undesirable chlorinous odor. Granular activated carbon (GAC) filtration is used to biologically oxidize ammonia during drinking water purification; however, little information is available regarding the abundance and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) associated with GAC. In addition, their sources and fates in water purification process remain unknown. In this study, six GAC samples were collected from five full-scale drinking water purification plants in Tokyo during summer and winter, and the abundance and community structure of AOA and AOB associated with GAC were studied in these two seasons. In summer, archaeal and bacterial amoA genes on GACs were present at 3.7 × 10(5)-3.9 × 10(8) gene copies/g-dry and 4.5 × 10(6)-4.2 × 10(8) gene copies/g-dry, respectively. In winter, archaeal amoA genes remained at the same level, while bacterial amoA genes decreased significantly for all GACs. No differences were observed in the community diversity of AOA and AOB from summer to winter. Phylogenetic analysis revealed high AOA diversity in group I.1a and group I.1b in raw water. Terminal-restriction fragment length polymorphism analysis of processed water samples revealed that AOA diversity decreased dramatically to only two OTUs in group I.1a after ozonation, which were identical to those detected on GAC. It suggests that ozonation plays an important role in determining AOA diversity on GAC. Further study on the cell-specific activity of AOA and AOB is necessary to understand their contributions to in situ nitrification performance.

Nitrogen losses, uptake and abundance of ammonia oxidizers in soil under mineral and organo-mineral fertilization regimes.

A laboratory incubation experiment and greenhouse studies investigated the impact of organo-mineral (OM) fertilization as an alternative practice to conventional mineral (M) fertilization on nitrogen (N) uptake and losses in perennial ryegrass (Lolium perenne) as well as on soil microbial biomass and ammonia oxidizers. While no significant difference in plant productivity and ammonia emissions between treatments could be detected, an increase in soil total N content and an average 17.9% decrease in nitrates leached were observed in OM fertilization compared with M fertilization. The microbial community responded differentially to treatments, suggesting that the organic matter fraction of the OM fertilizer might have influenced N immobilization in the microbial biomass in the short-medium term. Furthermore, nitrate contents in fertilized soils were significantly related to bacterial but not archaeal amoA gene copies, whereas in non-fertilized soils a significant relationship between soil nitrates and archaeal but not bacterial amoA copies was found. The application of OM fertilizer to soil maintained sufficient productivity and in turn increased N use efficiency and noticeably reduced N losses. Furthermore, in this experiment, ammonia-oxidizing bacteria drove nitrification when an N source was added to the soil, whereas ammonia-oxidizing archaea were responsible for ammonia oxidation in non-fertilized soil. © 2015 Society of Chemical Industry.

The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments.

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.