Diversity Of Ammonia-oxidizing Bacteria Research Articles

Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean.

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is performed by nitrifying microbes including ammonia-oxidizing bacteria (AOB) and archaea (AOA). In the current study, the phylogenetic diversity and abundance of AOB and AOA in deep-sea sediments of the Pacific Ocean were investigated using ammonia monooxygenase subunit A (amoA) coding genes as molecular markers. The study uncovered 3 AOB unique operational taxonomic units (OTUs, defined at sequence groups that differ by ≤5 %), which indicates lower diversity than AOA (13 OTUs obtained). All AOB amoA gene sequences were phylogenetically related to amoA sequences similar to those found in marine Nitrosospira species, and all AOA amoA gene sequences were affiliated with the marine sediment clade. Quantitative PCR revealed similar archaeal amoA gene abundances [1.68 × 10(5)-1.89 × 10(6) copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 10(3) to 2.29 × 10(6) copies/g sediment (wet weight). The AOA/AOB amoA gene abundance ratios ranged from 0.012 to 162 and were negatively correlated with total C and C/N ratio. These results suggest that organic loading may be a key factor regulating the relative abundance of AOA and AOB in deep-sea environments of the Pacific Ocean.

Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils.

Ammonia-oxidizing bacteria (AOB) are essential in the biogeochemical cycling of nitrogen as they catalyze the rate-limiting oxidation of ammonia into nitrite. Since their first isolation in the late 19th century, chemolithoautotrophic AOBs have been identified in a wide range of natural (e.g., soils, sediments, estuarine, and freshwaters) and man created or impacted habitats (e.g., wastewater treatment plants and agricultural soils). However, little is known on the plant-species association of AOBs, particularly in the nutrient-starved fynbos terrestrial biome. In this study, we evaluated the diversity of AOBs in the plant canopy of three South African fynbos-specific plant species, namely Leucadendron xanthoconus, Leucospermum truncatulum and Leucadendron microcephalum, through the construction of amoA-gene clone libraries. Our results clearly demonstrate that plant-species specific and monophyletic AOB clades are present in fynbos canopy soils.

Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil.

The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers’ fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers’ sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 105–9.2 × 106 and 1.7 × 106–5.3 × 107 gene copies g dry soil−1, respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.

Diversity of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during composting of municipal sludge

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) play an important role in the oxidation of ammonia. The diversity and relative abundance of AOA and AOB in compost samples from four composting stages [initial (day 0), heating (day 3), thermophilic (day 12), and cooling (day 28) stage ] were analyzed using the amoA gene as a functional marker. The number of operational taxonomic units (OTUs) found in each stage during sewage sludge composting was 33.3 % to 66.6 % of the total OTUs for AOB and 43.8 % to 62.5 % for AOA, with OTUs defined on the basis of a 5 % difference in nucleotides. Phylogenetic analysis showed that the AOB amoA sequences related to the Nitrosomonas lineage were dominant throughout the entire composting process. Most of the AOA amoA sequences fell into a soil/sediment cluster containing “Candidatus Nitrososphaera gargensis”. These results indicate that different ammonia oxidizers were present in different stages during composting, but that the dominant phylogenetic types were stable.

Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.

Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4–5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥81–86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.

The influence of land use on the abundance and diversity of ammonia oxidizers.

Nitrification plays a significant role in soil nitrogen cycling, a process in which the first step can be catalyzed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). In this study, six soil samples with distinct land-use regimes (forestland soil, paddy soil, wheat-planted soil, fruit-planted soil, grassland soil, and rape-planted soil) were collected from Chuzhou city in the Anhui province to elucidate the effects of land use on the abundance and diversity of AOA and AOB. The abundance of the archaeal amoA gene ranged from 2.12 × 10(4) copies per gram of dry soil to 2.57 × 10(5) copies per gram of dry soil, while the abundance of the bacterial amoA gene ranged from 5.58 × 10(4) copies per gram of dry soil to 1.59 × 10(8) copies per gram of dry soil. The grassland and the rape-planted soil samples maintained the highest abundance of the bacterial and archaeal amoA genes, respectively. The abundance of the archaeal amoA gene was positively correlated with the pH (P < 0.05). The ammonia concentrations exhibited a significantly positive relation with the abundance of the bacterial amoA gene (P < 0.01) and the number of OTUs of AOB (P < 0.05). The community composition of AOB was more sensitive to the land-use regimes than that of AOA. The data obtained in this study may be useful to better understand the nitrification process in soils with different land-use regimes.

AmoA Gene abundances and nitrification potential rates suggest that benthic ammonia-oxidizing bacteria and not Archaea dominate N cycling in the Colne Estuary, United Kingdom.

Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw](-1) day(-1) in June, increasing to 37.4 μmol N gdw(-1) day(-1) in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw(-1) day(-1) in June, increasing to 11.7 μmol N gdw(-1) day(-1) in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification.

Effects of intercropping and Rhizobial inoculation on the ammonia-oxidizing microorganisms in rhizospheres of maize and faba bean plants

To clarify whether intercropping and the Rhizobium leguminosarum inoculation affected the nitrification and subsequent nitrate leaching in soil, quantitative and qualitative analyses of total bacteria (TB), total archaea (TA), ammonia-oxidizing bacteria (AOB) and archaea (AOA) in the rhizospheres of maize and faba bean were performed. The greater abundances of TB than TA and of AOA than AOB were observed in all the samples, with ratios of TB:TA 21.1 and 8.0; and AOA:AOB 24.5 and 2.3, at the anthesis and pod-bearing stages, respectively. In faba bean rhizosphere, the intercropping and/or inoculation of rhizobia decreased the abundances of TB, TA, AOB and AOA at the anthesis stage; and inoculation of rhizobia alone decreased AOA at the pod-bearing stage. In maize rhizosphere, intercropping alone only enhanced the AOA at the pod bearing stage; while the combination of intercropping and rhizobial inoculation decreased the TA at the anthesis stage, and enhanced TB, AOB and AOA at the pod-bearing stage. The diversity of AOB and AOA were pronounced by intercropping and rhizobial inoculation treatments: at the anthesis stage for AOB and at the pod-bearing stage for AOA. However, Nitrosospira always remained as the predominant AOB in all the treatments. Conclusively, intercropping and rhizobial inoculation brought various shifts in microbial abundance and community compositions in rhizosphere depending on the plants and growth stages, which may decrease the nitrification in rhizosphere. Furthermore, the combination of intercropping and rhizobial inoculation presented stronger effects in most cases than the separated treatments.

Impact of TiO₂ and ZnO nanoparticles at predicted environmentally relevant concentrations on ammonia-oxidizing bacteria cultures under ammonia oxidation.

Increased application of titanium dioxide and zinc oxide nanoparticles (nano-TiO2 and nano-ZnO) raises concerns related to their environmental impacts. The effects that such nanoparticles have on environmental processes and the bacteria that carry them out are largely unknown. In this study, ammonia-oxidizing bacteria (AOB) enrichment cultures, grown from surface sediments taken from an estuary wetland in Fujian Province, China, were spiked with nano-TiO2 and nano-ZnO (with an average size of 32 and 43 nm, respectively) at predicted environmentally relevant concentrations (≤2 mg L(-1)) to determine their impacts on ammonia oxidation and the mechanisms involved. Results showed that higher nano-TiO2 concentrations significantly inhibited ammonia oxidation in enrichment cultures. It is noteworthy that the average ammonia oxidation rate was significantly correlated to the Shannon index, the Simpson's index, and AOB abundance. This suggested that ammonia oxidation inhibition primarily resulted from a reduction of AOB biodiversity and abundance. However, AOB biodiversity and abundance as well as the average ammonia oxidation rate were not inhibited by nano-ZnO at predicted environmentally relevant concentrations. Accordingly, an insignificant correlation was established between biodiversity and abundance of the AOB amoA gene and the average ammonia oxidation rate under nano-ZnO treatments. AOB present in samples belonged to the β-Proteobacteria class with an affinity close to Nitrosospira and Nitrosomonas genera. This suggested that identified impacts of nano-TiO2 and nano-ZnO on ammonia oxidation processes can be extrapolated to some extent to natural aquatic environments. Complex impacts on AOB may result from different nanomaterials present in aquatic environments at various ambient conditions. Further investigation on how and to what extent different nanomaterials influence AOB diversity and abundance and their subsequent ammonia oxidation processes is therefore required.

Removal of bisphenol A (BPA) in a nitrifying system with immobilized biomass

The potential for bisphenol A (BPA) removal by mixed consortia of immobilized microorganisms with high nitrification activity was investigated with BPA concentrations in the influent from 2.5 to 10.0mg/L. The presence of BPA limited ammonium oxidation; nitrification efficiency decreased from 91.2±1.3% in the control series to 47.4±9.4% when BPA concentration in wastewater was the highest. The efficiency of BPA removal rose from 87.1±5.5% to 92.9±2.9% with increased BPA concentration in the influent. Measurement of oxygen uptake rates by biomass exposed to BPA showed that BPA was mainly removed by heterotrophic bacteria. A strong negative correlation between the BPA removal efficiency and nitrification efficiency indicated the limited contribution of ammonia-oxidizing bacteria (AOB) to BPA biodegradation. Exposure of biomass to BPA changed the quantity and diversity of AOB in the biomass as shown by real-time PCR and denaturing gradient gel electrophoresis.

Differential sensitivity of nitrifying bacteria to silver nanoparticles in activated sludge.

Nitrification is known as one of the most sensitive processes affected when activated sludge is exposed to antimicrobial silver nanoparticles (AgNPs). The impact of AgNPs and their released silver ions (Ag(+) ) on the abundance, activity, and diversity of different nitrifying bacteria in wastewater treatment plants (WWTPs), however, is poorly understood. The present study investigated the impacts of 2 sizes of AgNPs (5 nm and 35 nm) and Ag(+) ions on the nitrifier community in activated sludge, including both ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). Ammonia-oxidizing bacteria were more sensitive to AgNPs than the NOB; a 5-d and 7-d exposure of activated sludge to 35 nm AgNPs (40 ppm) significantly reduced AOB abundance to 24% and 19%, respectively. This finding was confirmed further by a decrease in activated sludge ammonia oxidation activity measured by (14) C-labeled bicarbonate uptake. In contrast, neither AgNPs (up to 40 ppm) nor Ag(+) (1 ppm) affected the abundance of NOB. Both 5 nm and 35 nm AgNPs decreased the diversity of AOB, as indicated by denaturing gradient gel electrophoresis with ammonia monooxygenase gene (amoA) primers, although some unknown Nitrosomonas species were relatively resistant to AgNPs. The generally greater resistance of NOB than AOB to AgNPs suggests that the accumulation of bacteriostatic nitrite in WWTPs is unlikely to be exacerbated due to the accidental or incidental release of AgNPs.

Community structure of ammonia-oxidizing microorganisms in the Grand Canal, Zhenjiang, of Jiangsu Province, China.

In this study, we simultaneously investigated the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the Grand Canal (the Zhenjiang section). Both clone library and qPCR (quantitative polymerase chain reaction) indicated that the abundance and diversity of AOB were higher than AOA in the Grand Canal for all four seasons. Among the 109 archaeal amoA sequences retrieved, 62.39 and 37.61% fell within the Nitrosopumilus and Nitrososphaera clusters, respectively. The 128 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 81.25 and 18.75% of the AOB group, respectively. The AOA abundance was significantly and positively correlated with the NH4-N. The AOB abundance did not show significant correlations with the measured parameters. Obvious differences were observed for the AOA community compositions obtained from different seasons. The community structure of AOB changed slightly. It indicated that AOB seemed to play a more important role for the nitrification process than AOA in this environment, and was more adapted to this environment.

Bacteria dominate the ammonia-oxidizing community in a hydrothermal vent site at the Mid-Atlantic Ridge of the South Atlantic Ocean.

Ammonia oxidation is the first and rate-limiting step of nitrification, which is carried out by two groups of microorganisms: ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). In this study, diversity and abundance of AOB and AOA were investigated in five rock samples from a deep-sea hydrothermal vent site at the Mid-Atlantic Ridge (MAR) of the South Atlantic Ocean. Both bacterial and archaeal ammonia monooxygenase subunit A (amoA) gene sequences obtained in this study were closely related to the sequences retrieved from deep-sea environments, indicating that AOB and AOA in this hydrothermal vent site showed typical deep ocean features. AOA were more diverse but less abundant than AOB. The ratios of AOA/AOB amoA gene abundance ranged from 1/3893 to 1/242 in all investigate samples, indicating that bacteria may be the major members responding to the aerobic ammonia oxidation in this hydrothermal vent site. Furthermore, diversity and abundance of AOA and AOB were significantly correlated with the contents of total nitrogen and total sulfur in investigated samples, suggesting that these two environmental factors exert strong influences on distribution of ammonia oxidizers in deep-sea hydrothermal vent environment.

Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland

Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) might be the key microorganisms in ammonia conversion in ecosystems. However, the depth-related change of AOA and AOB in sediment ecosystem is still not clear. The relative contribution of AOA and AOB to nitrification in wetland sediment remains also unclear. Moreover, information about ammonia-oxidizing microorganisms in high-altitude freshwater wetland is still lacking. The present study investigated the relative abundances and community structures of AOA and AOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China). Variations of the relative abundances and community structures of AOA and AOB were found in the wetland sediments, dependent on both sampling site and sediment depth. The relative abundances of AOA and AOB (0.04-3.84 and 0.01-0.52 %) and the AOA/AOB ratio (0.12-4.65) showed different depth-related change patterns. AOB community size was usually larger than AOA community size. AOB diversity was usually higher than AOA diversity. AOA diversity decreased with the increase of sediment depth, while AOB diversity showed no obvious link with the sediment depth. Pearson's correlation analysis showed that AOA diversity had a positive significant correlation with available phosphorus. Nitrosospira-like sequences, with different compositions, predominated in the wetland sediment AOB communities. This work could provide some new insights toward nitrification in freshwater sediment ecosystems.

Bacteria dominate ammonia oxidation in soils used for outdoor cattle overwintering

In areas used for cattle overwintering detrimental effects normally associated with grazing are intensified. Among the alterations observed, increases on the N availability and soil pH may highly influence structure of ammonia oxidizing microbes and thus influence nitrification pattern in soil. To evaluate this assumption, we assessed the abundance and diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in three sites with different degrees of animal impact (severe, moderate or no impact) of an overwintering pasture by means of qPCR and T-RFLP of amoA genes. In areas where no animal impact could be identified AOA was dominating over AOB. However, AOB abundance increased as the degree of animal impact enhances, becoming most dominant in the severely impacted site. Interestingly, the diversity of AOB was the highest in the severely impacted area, where AOA diversity was the lowest. Obviously the pressure imposed by altered environmental conditions created by cattle husbandry lead to the selection of AOB and AOA populations, adapted to alkaline pH and higher ammonia concentration.

Introduction to Establish the Comparative Analysis of 16S rRNA Gene Sequences with amoA and nxrA for Nitrifying Bacteria Isolated from East Kolkata Wetland: an International Ramsar Site

The nitrogen cycle is most complex and very important for the life on earth. Nitrifying bacteria which carried out nitrogen cycling process play a vital role in water quality control, thus creating a genomic fingerprint database for surveillance and monitoring of genetic variability of nitrifying bacteria is very important and also to establish a Biosecurity protocol for the Bheries located in different areas of West Bengal. The currently evolutionary relationships and the natural diversity of Ammonia Oxidizing Bacteria (AOB) and Nitrite Oxidizing Bacteria (NOB) is mainly based on comparative sequence analyses of their genes encoding the 16S rRNA and the active site polypeptide of the ammonia monooxygenase (AmoA) and Nitrite oxidoreductase (NxrA) in the East Kolkata Wetland. This study extended significantly the 16S rRNA and amoA databases for AOB, nxrA databases for NOB. Therefore, either of the functional markers (amoA or nxrA) can be used to trace ammonia oxidizers or structural marker (16S rDNA) can be used to trace specific species in environmental studies. These techniques included the use of 16S rDNA genes to characterize natural AOB and NOB populations and to analyze their taxonomic and phylogenetic features. The current perception of AOB and NOB phylogeny established by comparative 16S rRNA sequence analysis could be confirmed independently by exploiting the gene amoA and nxrA genes and proved as an alternative phylogenetic marker. The aim of our work is to investigate the potential of the ammonia monooxygenase subunit A gene (amoA) and Nitrite oxidoreductase (nxrA) gene as functional markers for AOBs and NOBs along with 16S rDNA sequence analysis in EKW. For ecological surveillance, genes like amoA and nxrA specific for the nitrifying bacteria under present research work could be a more reliable tool.

Diversity, Abundance, and Spatial Distribution of Ammonia-Oxidizing β-Proteobacteria in Sediments from Changjiang Estuary and Its Adjacent Area in East China Sea

Changjiang Estuary, the largest estuary in China, encompasses a wide range of nutrient loading and trophic levels from the rivers to the sea, providing an ideal natural environment to explore relationships between functional diversity, physical/chemical complexity, and ecosystem function. In this study, molecular biological techniques were used to analyze the community structure and diversity of ammonia-oxidizing bacteria (AOB) in the sediments of Changjiang Estuary and its adjacent waters in East China Sea. The amoA gene (encoding ammonia monooxygenase subunit A) libraries analysis revealed extensive diversity within the β-Proteobacteria group of AOB, which were grouped into Nitrosospira-like and Nitrosomonas-like lineages. The majority of amoA gene sequences fell within Nitrosospira-like clade, and only a few sequences were clustered with the Nitrosomonas-like clade, indicating that Nitrosospira-like lineage may be more adaptable than Nitrosomonas-like lineage in this area. Multivariate statistical analysis indicated that the spatial distribution of the sedimentary β-Proteobacterial amoA genotype assemblages correlated significantly with nitrate, nitrite, and salinity. The vertical profile of amoA gene copies in gravity cores showed that intense sediment resuspension led to a deeper mixing layer. The horizontal distribution pattern of amoA gene copies was nearly correlated with the clayey mud belt in Changjiang Estuary and its adjacent area in East China Sea, where higher β-Proteobacteria phylogenetic diversity was observed. Meanwhile, those areas with high amoA copies in the surface sediments nearly matched those with low concentrations of dissolved oxygen and ammonium in the bottom water.

The response of ammonia-oxidizer activity and community structure to fertilizer amendment of orchard soils

Soil microorganisms have a significant role in determining the relative loss and retention of plant available nitrogen (N) and thus relative efficiency in the use of fertility inputs to agricultural production systems. Although the effect of management system on activity of the N-cycling microbial communities has been evaluated in certain annual cropping systems, results have been variable and there have been few studies conducted in perennial crops, such as apple. We examined the effect of organic and mineral fertility inputs to organic and conventional orchard soils on the overall activity, abundance and diversity of ammonia-oxidizing bacteria and archaea. Apple rootstocks were cultivated in orchard soils receiving one of five fertility treatments: Brassica napus seed meal, plant-based compost, urea, urea with plant-based compost, and a no-treatment control. Based on analysis of the ammonia monooxygenase gene (amoA), ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) in both untreated conventionally and organically managed orchard soils. However, AOB abundance was significantly different in both organically and conventionally managed soils with fertilizer amendments. The microbial community of the conventional orchard soil appeared to be limited by inorganic N since a response in potential activity to N input was only observed in treatments with urea. In the organic orchard soil, an increase in AOB gene abundance was detected only in response to the urea plus compost fertility treatment. Soil management and fertilizer additions had little effect on AOA gene abundance compared to the no-treatment control. Although composition of the AOB community was similar between the conventional and organically managed soils, AOA communities were significantly different. The different responses of the bacterial and archaeal ammonia-oxidizer communities to organic and conventional management and fertilizer amendments highlight the need for an increased focus in agricultural research to understand and improve the specificity of fertilizer application for orchard production systems.

Ammonia oxidizers are pioneer microorganisms in the colonization of new acidic volcanic soils from South of Chile

Ammonia oxidation, performed by specialized microorganisms belonging to the Bacteria and Archaea, is the first and most limiting step of soil nitrification. Nitrification has not yet been examined in young volcanic soils. The aim of the present work was to evaluate the abundance and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in acidic volcanic soils (andisols) of different defined ages to determine their relative contribution to nitrification and soil colonization. Soil was collected from three vegetated sites on Llaima Volcano (Chile) recolonized after lava eruptions in 1640, 1751 and 1957. Quantitative polymerase chain reaction, terminal restriction fragment length polymorphism and clone sequence analyses of the amoA gene were performed for the AOA and AOB communities. All soils showed high nitrification potentials, but they were highest in the younger soils. Archaeal amoA genes outnumbered bacterial amoA genes at all sites, and AOA abundances were found to be proportional to the nitrification potentials. Sequencing indicated the presence of AOA related to Nitrososphaera and Nitrosotalea, and AOB related primarily to Nitrosospira and sporadically to Nitrosomonas. The study showed that both AOA and AOB are early colonizers of andisols, but that AOA outnumber AOB and play an important role in nitrification.

Influence of Land Use Intensity on the Diversity of Ammonia Oxidizing Bacteria and Archaea in Soils from Grassland Ecosystems

In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira. The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominating all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates.