Community Structure Of AOB) And Archaea Research Articles

Increases in the soil ammonia oxidizing phylotypes and their rechange due to long-term irrigation with wastewater.

Wastewater irrigation is a common practice for agricultural systems in arid and semiarid zones, which can help to overcome water scarcity and contribute with nutrient inputs. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are key in the transformation of NH4+-N in soil and can be affected by variations in soil pH, EC, N and C content, or accumulation of pollutants, derived from wastewater irrigation. The objective of this study was to determine the changes in the ammonia oxidizing communities in agricultural soils irrigated with wastewater for different periods of time (25, 50, and 100 years), and in rainfed soils (never irrigated). The amoA gene encoding for the catalytic subunit of the ammonia monooxygenase was used as molecular reporter; it was quantified by qPCR and sequenced by high throughput sequencing, and changes in the community composition were associated with the soil physicochemical characteristics. Soils irrigated with wastewater showed up to five times more the abundance of ammonia oxidizers (based on 16S rRNA gene relative abundance and amoA gene copies) than those under rainfed agriculture. While the amoA-AOA: amoA-AOB ratio decreased from 9.8 in rainfed soils to 1.6 in soils irrigated for 100 years, indicating a favoring environment for AOB rather than AOA. Further, the community structure of both AOA and AOB changed during wastewater irrigation compared to rainfed soils, mainly due to the abundance variation of certain phylotypes. Finally, the significant correlation between soil pH and the ammonia oxidizing community structure was confirmed, mainly for AOB; being the main environmental driver of the ammonia oxidizer community. Also, a calculated toxicity index based on metals concentrations showed a correlation with AOB communities, while the content of carbon and nitrogen was more associated with AOA communities. The results indicate that wastewater irrigation influence ammonia oxidizers communities, manly by the changes in the physicochemical environment.

Biochar Addition Inhibits Nitrification by Shifting Community Structure of Ammonia-Oxidizing Microorganisms in Salt-Affected Irrigation-Silting Soil.

Biochar has been widely recognized as an effective and eco-friendly ameliorant for saline soils, but information about the mechanism of how biochar influences nitrification in salt-affected agroecosystem remains fragmented. An incubation experiment was performed on the salt-affected soil collected from a three-consecutive-year experiment at biochar application gradients of 7.5 t⋅ha−1, 15 t⋅ha−1 and 30⋅t ha−1 and under nitrogen (N) fertilization. Responses of the nitrification rate (NR), numbers of ammonia monooxygenase (amoA) gene copies, and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to biochar application were investigated. The results indicated that, under N fertilization, the NR and numbers of amoA-AOB and amoA-AOA gene copies negatively responded to biochar addition. Biochar application increased the community diversity of AOB but decreased that of AOA. Biochar addition and N fertilization shifted the AOB community from Nitrosospira-dominated to Nitrosospira and Nitrosomonas-dominated, and altered the AOA community from Nitrososphaera-dominated to Nitrososphaera and Nitrosopumilus-dominated. The relative abundance of Nitrosospira, Nitrosomonas and Nitrosopumilus decreased, and that of Nitrosovibrio and Nitrososphaera increased with biochar application rate. Soil SOC, pH and NO3−-N explained 87.1% of the variation in the AOB community, and 78.1% of the variation in the AOA community was explanatory by soil pH and SOC. The SOC and NO3−-N influenced NR through Nitrosovibrio, Nitrosomonas, Norank_c_environmental_samples_p_Crenarchaeota and amoA-AOB and amoA-AOA gene abundance. Therefore, biochar addition inhibited nitrification in salt-affected irrigation-silting soil by shifting the community structures of AOB and AOA and reducing the relative abundance of dominant functional ammonia-oxidizers, such as Nitrosospira, Nitrosomonas and Nitrosopumilus.

Active ammonia-oxidizing bacteria and archaea in wastewater treatment systems

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two microbial groups mediating nitrification, yet little is presently known about their abundances and community structures at the transcriptional level in wastewater treatment systems (WWTSs). This is a significant issue, as the numerical abundance of AOA or AOB at the gene level may not necessarily represent their functional role in ammonia oxidation. Using amoA genes as molecular markers, this study investigated the transcriptional abundance and community structure of active AOA and AOB in 14 WWTSs. Quantitative PCR results indicated that the transcriptional abundances of AOB amoA (averaged: 1.6 × 108 copies g−1 dry sludge) were higher than those of AOA (averaged: 3.4 × 107 copies g−1 dry sludge) in all WWTSs despite several higher abundances of AOA amoA at the gene level. Moreover, phylogenetic analysis demonstrated that Nitrosomonas europaea and unknown clusters accounted for 37.66% and 49.96% of the total AOB amoA transcripts, respectively, suggesting their dominant role in driving ammonia oxidation. Meanwhile, AOA amoA transcripts were only successfully retrieved from 3 samples, and the Nitrosospaera sister cluster dominated, accounting for 83.46%. Finally, the substrate utilization kinetics of different AOA and AOB species might play a fundamental role in shaping their niche differentiation, community composition, and functional activity. This study provides a basis for evaluating the relative contributions of ammonia-oxidizing microorganisms (AOMs) to nitrogen conversions in WWTSs.

Response of ammonia-oxidizing Bacteria and Archaea to long-term saline water irrigation in alluvial grey desert soils

Soil nitrification via ammonia oxidation is a key ecosystem process in terrestrial environments, but little is known of how increasing irrigation of farmland soils with saline waters effects these processes. We investigated the effects of long-term irrigation with saline water on the abundances and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Irrigation with brackish or saline water increased soil salinity (EC1:5) and NH4-N compared to irrigation with freshwater, while NO3-N, potential nitrification rates (PNR) and amoA gene copy numbers of AOA and AOB decreased markedly under irrigation regimes with saline waters. Moreover, irrigation with brackish water lowered AOA/AOB ratios. PNR was positively correlated with AOA and AOB amoA gene copy numbers across treatments. Saline and brackish water irrigation significantly increased the diversity of AOA, as noted by Shannon index values, while saline water irrigation markedly reduced AOB diversity. In addition, irrigation with brackish or fresh waters resulted in higher proportions of unclassified taxa in the AOB communities. However, irrigation with saline water led to higher proportions of unclassified taxa in the AOA communities along with the Candidatus Nitrosocaldus genus, as compared to soils irrigated with freshwater. AOA community structures were closely associated with soil salinity, NO3−N, and pH, while AOB communities were only significantly associated with NO3−N and pH. These results suggest that salinity was the dominant factor affecting the growth of ammonia-oxidizing microorganisms and community structure. These results can provide a scientific basis for further exploring the response mechanism of ammonia-oxidizing microorganisms and their roles in nitrogen transformation in alluvial grey desert soils of arid areas.

Distinct responses of ammonia-oxidizing bacteria and archaea to green manure combined with reduced chemical fertilizer in a paddy soil

Ammonia oxidation is the rate-limiting step in nitrification. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the key drivers of the nitrogen cycle. Chinese milk vetch (MV) has the potential to substitute for part of chemical fertilizer, but it remains unclear how MV is able to replace N fertilizer. The purpose of this study was to investigate the rice yield, soil properties, potential nitrification activity (PNA), abundances, and community structures of ammonia oxidizers in a paddy soil under MV combinations of different rates of chemical fertilizer. This study was conducted at a long-term Experimental Station of the Fujian Academy of Agricultural Sciences, Fuzhou, China. The treatments included a control (without fertilization), NPK (chemical fertilizer), MF80 (MV plus 80% NPK), MF60 (MV plus 60% NPK), and MF40 (MV plus 40% NPK). Soil samples were collected after the rice harvest. We determined the soil physico-chemical properties and PNA. The abundances and community structures of AOB and AOA were assessed using their ammonia monooxygenase (amoA) genes. Quantitative PCR was used to determine the gene abundance, and Illumina Miseq sequencing was used to explore the diversity of AOB and AOA. MV significantly increased the soil organic matter and PNA in comparison to the NPK. The available nitrogen content was higher in the MV treatments than in the control and NPK. Compared to the NPK, the application of MV increased the AOB abundance but decreased that of AOA. The abundance of AOA was higher in the control and NPK, but lower in the MV treatments than that of AOB. PNA was significantly positively correlated with the AOB abundance. The primary dominant OTU of the AOB group was Nitrosospira. MV significantly affected the AOB community, while no impact on the AOA community was observed. Principal coordinate analysis showed that the MV treatments were significantly distinct from those of the control and NPK. Redundancy analysis indicated that the soil OM, TN, AN, pH, and PNA were significantly correlated to the AOB community structure. This study demonstrated that MV combined with reduced chemical fertilizer would contribute to the improvement of soil fertility and PNA, resulting in rice yield comparable to that of the NPK. MV had a stronger effect on the AOB community than did chemical fertilizer. AOB played a more important role than AOA in the ammonia oxidation in this soil.

Organic Matter Regulates Ammonia-Oxidizing Bacterial and Archaeal Communities in the Surface Sediments of Ctenopharyngodon idellus Aquaculture Ponds.

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play important roles in nitrogen removal in aquaculture ponds, but their distribution and the environmental factors that drive their distribution are largely unknown. In this study, we collected surface sediment samples from Ctenopharyngodon idellus ponds in three different areas in China that practice aquaculture. The community structure of AOB and AOA and physicochemical characteristics in the ponds were investigated. The results showed that AOA were more abundant than AOB in all sampling ponds except one, but sediment AOB and AOA numbers varied greatly between ponds. Correlation analyses indicated a significant correlation between the abundance of AOB and arylsulfatase, as well as the abundance of AOA and total nitrogen (TN) and arylsulfatase. In addition, AOB/AOA ratio was found to be significantly correlated with the microbial biomass carbon. AOB were grouped into seven clusters affiliated to Nitrosospira and Nitrosomonas, and AOA were grouped into six clusters affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosopumilus. AOB/AOA diversity in the surface sediments of aquaculture ponds varied according to the levels of total organic carbon (TOC), and AOB and AOA diversity was significantly correlated with arylsulfatase and β-glucosidase, respectively. The compositions of the AOB communities were also found to be significantly influenced by sediment eutrophic status (TOC and TN levels), and pH. In addition, concentrations of acid phosphatase and arylsulfatase in surface sediments were significantly correlated with the prominent bacterial amoA genotypes, and concentrations of TOC and urease were found to be significantly correlated with the prominent archaeal amoA genotype compositions. Taken together, our results indicated that AOB and AOA communities in the surface sediments of Ctenopharyngodon idellus aquaculture ponds are regulated by organic matter and its availability to the microorganisms.

Forest harvest intensity and soil depth alter inorganic nitrogen pool sizes and ammonia oxidizer community composition

Intensive forest harvest techniques have the potential to alter soil carbon and nutrient stocks and biogeochemical processes. We investigated how differing levels of organic matter removal (OMR) during timber harvest influenced the long-term stability of nitrification and the microbes regulating this process. Nitrification is limited by the activity of ammonia oxidizing bacteria (AOB) and archaea (AOA); however, reports on the relative contribution of each of these groups to forest soil nitrification have varied and have not been investigated in response to OMR. The influence of soil depth on the structure and function of the ammonia-oxidizing community has also been underreported and was included in this study. We quantified soil physicochemical properties including concentrations of ammonium (NH4+) and nitrite (NO2−) + nitrate (NO3−), and also coupled next generation sequencing and qPCR of the amoA gene to a whole-soil assay that stimulates nitrification and allows for the discrimination of AOA-from AOB-activity using 1-octyne, which inhibits bacterial ammonia monooxygenase activity. Soils were collected (1 m depth) from replicated loblolly pine (Pinus taeda L.) stands subjected to three different intensities of OMR (i.e., unharvested control, bole-only harvest, and whole-tree harvest + forest floor removal). Increasing intensity of OMR and increasing soil depth lead to significant reductions in concentrations of in situ NH4+ and NO2− + NO3−. Sequencing and subsequent annotation of the ammonia oxidizing community revealed that AOA were dominated by Crenarchaeota and AOB were dominated by Nitrosospira spp. The abundance of both bacterial and archaeal amoA were influenced by OMR and soil depth; furthermore, archaeal amoA was more abundant than bacterial amoA across all soil depths and the ratio of AOA to AOB increased with depth. Community structure of AOA and AOB were influenced by soil depth; however, only AOB were altered by OMR. Soil incubations revealed nitrification was N-limited in these forest soils. Furthermore, AOA- and AOB-contributions to total nitrification were nearly equivalent in surface soils; however, AOA contribution increased to 75% at 1 m. In general, the highest rates of nitrification occurred in the soils taken from unharvested control stands; however, OMR treatment differences were only significant when soils were amended with high levels of ammonia indicating that at ambient levels, intensive OMR may not lead to long-term alterations in nitrification potential.

Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen.

Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation.

Change in the abundance and community composition of ammonia-oxidizing bacteria and archaea at soil aggregate level as native pasture converted to cropland in a semiarid alpine steppe of central Asia

The study aimed to improve understanding of the transformation of N in the Ili River Valley by investigating the abundance and community composition of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under different land uses at bulk soil and aggregate levels. Soil samples were collected from plots of three types of land use, i.e., native pasture (NP), conventional farming (CF), and organic farming (OF). Soil aggregates were separated using wet-sieving method. The abundance and structure of AOB and AOA communities were assessed by qPCR and DGGE, respectively. Compared with CF, OF and NP both increased soil TN and SOC stock but via contrasting mechanisms. The abundance of AOB under cropland uses (CF and OF) was higher than those of NP. The AOB sequences, belonging to Nitrosospira cluster 1, which is adaptable to high mineral N content in cold region, increased in CF than in other land uses. Conversion of NP to cropland did not affect the abundance, but the community structure of AOA. The abundance of AOB and AOA in large macroaggregate and silt and clay aggregate were significantly lower than those in small macroaggregate under cropland uses. In cropland, the small macroaggregate provided the microenvironment for the growth of AOB and AOA, thereby serving as a potential hotspot for ammonia oxidation. Reclamation of grassland to cropland significantly increased the AOB abundance, and shifted the community structure and spatial distribution variation of AOB and AOA at the soil aggregates. The results indicated that soil N cycle could be substantially altered and this should be well integrated in the improvement of regional land utilization.

A comparative study of ammonia-oxidizing archaea and bacteria in acidic and alkaline purple soils

Soil pH has been suggested as one of the most important factors affecting the ecological characteristics of soil ammonia-oxidizers (AO), which mediate the conversion of ammonia to nitrate via nitrite and contribute significantly to the leaching of nitrate to groundwater and the production of atmospheric nitrous oxide (N2O). However, the dynamics of the AO community in acidic purple soils, which are widely distributed in Southwest China, remain largely unknown. In this study, two typical purple soils with different pH values (acidic: ACI; alkaline: ALK) were collected and studied. The abundance of amoA (gene encoding ammonia monooxygenase) of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and that of the cbbL gene (encoding ribulose-1,5-biphosphate carboxylase/oxygenase) were determined by real-time PCR, and the community structures of AOB and AOA were investigated by cloning and sequencing. The results revealed that abundances of AOB and AOA were significantly lower in the ACI purple soil sample than in the ALK sample, but a higher ratio of AOA to AOB was found in the ACI purple soil sample. No significant difference in the abundance of cbbL was found between the two soils, but the ratio of AOB and AOA amoA to cbbL genes in the ACI soil samples was higher than that in the ALK sample. Moreover, the ALK and ACI soils harbored contrasting community compositions of AO. AOB in the ALK were dominated by cluster 3a (87 %), while the percentage of cluster 3a decreased and clusters 9 and 10 accounted for almost 77 % of the AOB community in the ACI soil. Nitrososphaera and Nitrosotalea were the major AOA phylotypes in the ALK and ACI soils, respectively. In conclusion, our results revealed the potential relations among pH, AO, and total chemoautotrophic bacteria in soil and that pH might have an essential impact on the adaptation and selection of AO in purple 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.

Ammonia- and methane-oxidizing microorganisms in high-altitude wetland sediments and adjacent agricultural soils.

Ammonia oxidation is known to be carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA), while methanotrophs (methane-oxidizing bacteria (MOB)) play an important role in mitigating methane emissions from the environment. However, the difference of AOA, AOB, and MOB distribution in wetland sediment and adjacent upland soil remains unclear. The present study investigated the abundances and community structures of AOA, AOB, and MOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China) and adjacent agricultural soils. Variations of AOA, AOB, and MOB community sizes and structures were found in water lily-vegetated and Acorus calamus-vegetated sediments and agricultural soils (unflooded rice soil, cabbage soil, and garlic soil and flooded rice soil). AOB community size was higher than AOA in agricultural soils and lily-vegetated sediment, but lower in A. calamus-vegetated sediment. MOB showed a much higher abundance than AOA and AOB. Flooded rice soil had the largest AOA, AOB, and MOB community sizes. Principal coordinate analyses and Jackknife Environment Clusters analyses suggested that unflooded and flooded rice soils had relatively similar AOA, AOB, and MOB structures. Cabbage soil and A. calamus-vegetated sediment had relatively similar AOA and AOB structures, but their MOB structures showed a large difference. Nitrososphaera-like microorganisms were the predominant AOA species in garlic soil but were present with a low abundance in unflooded rice soil and cabbage soil. Nitrosospira-like AOB were dominant in wetland sediments and agricultural soils. Type I MOB Methylocaldum and type II MOB Methylocystis were dominant in wetland sediments and agricultural soils. Moreover, Pearson's correlation analysis indicated that AOA Shannon diversity was positively correlated with the ratio of organic carbon to nitrogen (p < 0.05). This work could provide some new insights toward ammonia and methane oxidation in soil and wetland sediment ecosystems.

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.

Abundance and community structure of ammonia-oxidizing bacteria and archaea in purple soil under long-term fertilization

Ammonia-oxidizing microorganisms, which drive the first and rate-limiting step in the process of nitrification, play an important role in soil N-cycling processes. However, little is known about the ammonia-oxidizing bacteria (AOB) and archaea (AOA) in purple soils, which are characterized as lithologic soils without distinct pedogenic horizons and are mainly distributed in the Sichuan basin of Southwestern China. Here, the abundance and community structure of AOB and AOA in a 21-year fertilization experiment were investigated by real-time PCR and terminal restriction fragment-length polymorphism (T-RFLP), respectively. In the present study, nine different fertilization treatments were examined: NPK fertilization plus pig manure (NPK + M), NPK fertilization (NPK), without fertilization (CK), pig manure fertilization (M), P with NH4Cl and KCl plus pig manure (Cl + M), PK fertilization (PK), NK fertilization (NK), NP fertilization (NP), and N fertilization (N). Our results indicate that N-fertilized treatments have higher AOB abundances than the control (CK) and treatments without N amendment. The lowest AOA abundance and AOA/AOB ratios were observed in the treatment (Cl + M) with long-term application of NH4Cl plus KCl. The AOB community structure under combined addition of N and P differed from that under other treatments. The Cl + M treatment had a distinct AOA community structure and higher diversity compared with other treatments. Moreover, higher potential nitrification rates (PNR) were found in the combined N and P addition treatment groups than that in the other treatment groups, and the lowest PNR and pH (<6) were detected in the Cl + M treatment. These results highlight that not only nitrogen but also phosphorus may be a crucial factor affecting soil ammonia-oxidizing activity and triggering changes of AOB community composition. Moreover, soil pH might have an essential role in controlling the AOA community structure and ammonia-oxidizing activity in purple soil.

Shifts in the abundance and community structure of soil ammonia oxidizers in a wet sclerophyll forest under long-term prescribed burning

Fire shapes global biome distribution and promotes the terrestrial biogeochemical cycles. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in the biogeochemical cycling of nitrogen (N). However, behaviors of AOB and AOA under long-term prescribed burning remain unclear. This study was to examine how fire affected the abundances and communities of soil AOB and AOA. A long-term repeated forest fire experiment with three burning treatments (never burnt, B0; biennially burnt, B2; and quadrennially burnt, B4) was used in this study. The abundances and community structure of soil AOB and AOA were determined using quantitative PCR, restriction fragment length polymorphism and clone library. More frequent fires (B2) increased the abundance of bacterium amoA gene, but tended to decrease archaeal amoA genes. Fire also modified the composition of AOA and AOB communities. Canonical correspondence analysis showed soil pH and dissolved organic C (DOC) strongly affected AOB genotypes, while nitrate-N and DOC shaped the AOA distribution. The increased abundance of bacterium amoA gene by fires may imply an important role of AOB in nitrification in fire-affected soils. The fire-induced shift in the community composition of AOB and AOA demonstrates that fire can disturb nutrient cycles.

Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils

Ammonia oxidation is an important process for global nitrogen cycling. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can be the important players in nitrification process. However, their relative contribution to nitrification remains controversial. This study investigated the abundance and community structure of AOA and AOB in sediment of Miyun Reservoir and adjacent soils. Quantitative PCR assays indicated that the highest AOA abundance occurred in unplanted riparian soil, followed by reservoir sediment, reed-planted riparian soil and agricultural soil. The AOB community size in agricultural soil was much larger than that in the other habitats. Large variations in the structures of AOA and AOB were also observed among the different habitats. The abundance of Nitrosospira-like AOB species were detected in the agricultural soil and reservoir sediment. Pearson's correlation analysis showed the AOB diversity had positive significant correlations with pH and total nitrogen, while the AOA diversity might be negatively affected by nitrate nitrogen and ammonia nitrogen. This work could add new insights towards nitrification in aquatic and terrestrial ecosystems.

Abundance and community structure of ammonia oxidizing bacteria and archaea in a Sweden boreal forest soil under 19-year fertilization and 12-year warming

Purpose Boreal forests are considered to be more sensitive to global climate change compared with other terrestrial ecosystems, but the long-term impact of climate change and forest management on soil microbial functional diversity is not well understood. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the most important players in nitrogen (N) cycling-associated processes in terrestrial ecosystems. This study investigated the separate and combined impacts of long-term soil warming and fertilization on soil AOB and AOA community structures and abundances in a Norway spruce stand in northern Sweden.

Abundance and community structure of ammonia-oxidizing bacteria and archaea in a temperate forest ecosystem under ten-years elevated CO 2

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are considered as the key drivers of global nitrogen (N) biogeochemical cycling. Responses of the associated microorganisms to global changes remain unclear. This study was to determine if there was a shift in soil AOB and AOA abundances and community structures under free-air carbon dioxide (CO 2) enrichment (FACE) and N fertilization in Duke Forest of North Carolina, by using DNA-based molecular techniques, i.e., quantitative PCR, restriction fragment length polymorphism (RFLP) and clone library. The N fertilization alone increased the abundance of bacterial amoA gene, but this effect was not observed under elevated CO 2 condition. There was no significant effect of the N fertilization on the thaumarchaeal amoA gene abundance in the ambient CO 2 treatments, while such effect increased significantly under elevated CO 2. A total of 690 positive clones for AOA and 607 for AOB were selected for RFLP analysis. Analysis of molecular variance (AMOVA) indicated that effects of CO 2 enrichment and N fertilization on the community structure of AOA and AOB were not significant. Canonical correspondence analysis also showed that soil pH rather than elevated CO 2 or N fertilization shaped the distribution of AOB and AOA genotypes. A negative linear relationship between the δ 13C and archaeal amoA gene abundance indicated a positive effect of elevated CO 2 on the growth ammonia oxidizing archaea. On the other hand, the community structures of AOB and AOA are determined by the soil niche properties rather than elevated CO 2 and N fertilization.

Microbial community structure and occurrence of diverse autotrophic ammonium oxidizing microorganisms in the anammox process

The enrichment of anaerobic ammonium oxidizing (anammox) bacteria using an upflow anaerobic sludge bioreactor was successfully conducted for 400 days of continuous operation. The bacterial community structure of anammox bioreactor included Proteobacteria (42%), Chloroflexi (22%), Planctomycetes (20%), Chlorobi (7%), Bacteroidetes (5%), Acidobacteria (2%), and Actinobacteria (2%). All clones of Planctomycetes were affiliated with the anammox bacteria, Planctomycete KSU-1 (AB057453). The presence and diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) were identified by terminal restriction fragment length polymorphism (T-RFLP) based on the amoA gene sequences. The AOB in anammox bioreactor were affiliated with the Nitrosomonas europaea cluster. The T-RFLP result of AOA showed the diverse microbial community structure of AOA with three terminal restriction fragments (T-RFs).