Diversity Of AOA) And Bacteria Research Articles

Distribution of ammonia oxidizers and their role in N2 O emissions in the reservoir riparian zone.

As a transitional boundary between terrestrial and aquatic ecosystems, the riparian zone is considered a hotspot for N2 O production because of the active nitrogen processes. Ammoxidation is an important microbial pathway for N2 O production, but the distribution of ammonia oxidizers under different land-use types in the reservoir riparian zone and what role they played in N2 O emissions are still not clear. We investigated spatiotemporal distributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their role in N2 O emissions in different land-use types along the riparian zone of Miyun Reservoir: grassland, sparse woods, and woodland. We found significant differences in both AOA abundance and AOB diversity indices among land-use types. AOA and AOB communities were significantly separated by different land-use types. The main drivers to determine the distribution of ammonia-oxidizing microbial community were soil water content, NH4 + , NO3 - , and total organic carbon (TOC). In situ N2 O flux was highest in woodland with a mean value of 12.28 μg/m2 ·h, and it was substantially decreased by 121% and 123% in sparse woods and grassland. TOC content was decreased by 20% and 40% in sparse woods and grassland compared with woodland, and it was significantly positively correlated with in situ N2 O flux. Meanwhile, AOB diversity indices were significantly correlated with in situ N2 O flux. These results showed that the heterogeneity of physicochemical properties among different land-use types affected the community of AOA and AOB in riparian zones. AOB not AOA, and community diversity rather than abundance, played a role in N2 O emissions.

Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization.

Ammonia oxidizing archaea (AOA) and bacteria (AOB) mediate a crucial step in nitrogen (N) metabolism. The effect of N fertilizer rates on AOA and AOB communities is less studied in the wheat-fallow system from semi-arid areas. Based on a 17-year wheat field experiment, we explored the effect of five N fertilizer rates (0, 52.5, 105, 157.5, and 210 kg ha−1 yr−1) on the AOA and AOB community composition. This study showed that the grain yield of wheat reached the maximum at 105 kg N ha−1 (49% higher than control), and no further significant increase was observed at higher N rates. With the increase of N, AOA abundance decreased in a regular trend from 4.88 × 107 to 1.05 × 107 copies g−1 dry soil, while AOB abundance increased from 3.63 × 107 up to a maximum of 8.24 × 107 copies g−1 dry soil with the N105 treatment (105 kg N ha−1 yr−1). Application rates of N fertilizer had a more significant impact on the AOB diversity than on AOA diversity, and the highest AOB diversity was found under the N105 treatment in this weak alkaline soil. The predominant phyla of AOA and AOB were Thaumarchaeota and Proteobacteria, respectively, and higher N treatment (N210) resulted in a significant decrease in the relative abundance of genus Nitrosospira. In addition, AOA and AOB communities were significantly associated with grain yield of wheat, soil potential nitrification activity (PNA), and some soil physicochemical parameters such as pH, NH4-N, and NO3-N. Among them, soil moisture was the most influential edaphic factor for structuring the AOA community and NH4-N for the AOB community. Overall, 105 kg N ha−1 yr−1 was optimum for the AOB community and wheat yield in the semi-arid area.

Distribution of ammonia-oxidizing archaea and bacteria along an engineered coastal ecosystem in subtropical China.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the crucial players in nitrogen cycle. Both AOA and AOB were examined along a gradient of human activity in a coastal ecosystem from intertidal zone, grassland, and Casuarina equisetifolia forest to farmland. Results showed that the farmland soils had noticeably higher nitrate-N, available P than soils in the other three sites. Generally, AOA and AOB community structures varied across sites. The farmland mainly had Nitrosotalea-like AOA, intertidal zone was dominated by Nitrosopumilus AOA, while grassland and C. equisetifolia forest primarily harbored Nitrososphaera-like AOA. The farmland and C. equisetifolia forest owned Nitrosospira-like AOB, intertidal zone possessed Nitrosomonas-like AOB, and no AOB was detected in the grassland. AOA abundance was significantly greater than AOB in this coastal ecosystem (p < 0.05, n = 8). AOB diversity and abundance in the farmland were significantly higher than those in the other three sites (p < 0.05, n = 2). The biodiversity and abundance of AOA were not significantly correlated with any soil property (p < 0.05, n = 8). However, the diversity of AOB was significantly correlated with pH, available P and total P (p < 0.05, n = 6). The abundance of AOB was significantly correlated with pH, nitrite, available N, available P and total P (p < 0.05, n = 6). This study suggested that the community structures of AOA and AOB vary in the different parts in the bio-engineered coastal ecosystem and agricultural activity appears to influence these nitrifiers.

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

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

Ammonia-oxidizing bacteria are sensitive and not resilient to organic amendment and nitrapyrin disturbances, but ammonia-oxidizing archaea are resistant

Understanding the response of soil microorganisms to environmental disturbance is critical to predicting rates of ecosystem processes. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) drive the rate-limiting step of nitrification. However, the effect of fertilization disturbances (organic amendments and biochemical inhibitors) on the resistance and resilience of communities of AOB and AOA is unknown. Here, we explored the responses of the AOA and AOB communities (based on abundance, diversity, richness and composition) after disturbances caused by the application of inorganic N (urea alone, IN), an organic amendment (cattle manure, OA), a urease inhibitor (NBPT) and a nitrification inhibitor (nitrapyrin) or their combination in a calcareous soil after 85 days. A relative quantitative index of both the resistance (RS) and resilience (RL) was used to assess the variation of gene communities. The AOB community α-diversity, richness and abundance rapidly increased at 7 days after IN and OA (P < 0.05) compared to CK (without any disturbances), whereas those factors decreased after OA + nitrapyrin or OA + nitrapyrin + NBPT application. The RS indices of AOA abundance and diversity were higher than those of AOB after the IN, OA and nitrapyrin disturbances, indicating AOA were more resistant. NMDS analysis showed that the changes in the composition of the AOB community were observed both at 7 and 85 days after OA + nitrapyrin disturbance. In contrast, the AOA community composition did not change within 85 days after these disturbances. Moreover, the RL indices of AOB community were much lower than those of AOA. Soil pH and ammonium (NH4+) played major roles in the changes in the AOB community in response to disturbance. Taken together, our results highlight that AOB are sensitive and not resilient to organic amendment or nitrapyrin disturbance, while AOA are resistant to these disturbances in calcareous soil.

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.

Responses of ammonia‐oxidizing archaea and bacteria to nitrogen and phosphorus amendments in an alpine steppe

AbstractWith the increasing demands of livestock production, grasslands are under pressure from over‐intensified grazing. Phosphorus (P) and nitrogen (N) fertilization is widely employed to meet the nutrient demands of heavy grazing. Although soil ammonia‐oxidizers play a critical role in determining N dynamics after fertilizer application, their responses to fertilization are still not well understood in steppe grassland systems. Here, the individual and combined effects of N (0, 7.5 and 15 g N m−2 year−1) and P (0, 3.27, 6.55 and 13.09 g P m−2 year−1) applications on soil ammonia‐oxidizers were explored in the Tibetan alpine steppe. Ammonia‐oxidizing archaea (AOA) and bacteria (AOB) abundance and community composition were examined using qPCR, terminal restriction fragment length polymorphism and clone libraries. Results showed that AOB diversity was significantly increased by N fertilization and decreased by P fertilization. The abundance of AOB was significantly increased by N fertilization and its interactive effects with P application. In contrast, AOA community diversity and abundance remained unaffected by either N or P application. The AOB abundance and diversity were affected by the direct effects of N fertilization, as well as its indirect effects of N application through available N and ammonium (NH4+), and further analysis showed that NH4+ and pH were the main factors. The changes to the ammonia‐oxidizing community altered the total N content of plants and the N:P ratio of Gramineae. Plant P properties were influenced by P addition, which also interacted with soil pH and available N to indirectly affect AOB. Overall, AOB exhibited stronger responses to N and P fertilization of alpine steppe grassland than AOA, and appear to play a critical role in plant nutrient absorption under fertilization management.Highlights Effects of N and P application on AOA and AOB communities were evaluated. AOB, not AOA, responded to N or P, and their interaction, and NH4+ and pH were regulators of AOB. N application affected AOB community, resulting in changes to plant nutrient absorption. P addition affected plant tissue stoichiometry, and thus affected AOB community.

Influence of local and regional drivers on spatial and temporal variation of ammonia-oxidizing communities in Gulf of Mexico salt marshes.

We characterized ammonia-oxidizing archaea (AOA) and bacteria (AOB) from salt marsh sediments in the Gulf of Mexico over 5 years to identify environmental drivers of nitrifying community patterns following the Deepwater Horizon oil spill. Samples were collected from oiled and unoiled sites in July of 2012-2016 from 12 marshes spanning three regions on the Louisiana coast. No consistent oil effect was detected for either AOA or AOB abundance or community composition. At the local scale, abundance was correlated with changes in marsh elevation, suggesting that oxygen may be an important driver. Regional differences in abundance were best explained by salinity and soil moisture, while interannual variation may be more linked to changes in climate and Mississippi River discharge. Variation of AOA communities was correlated with organic sediment nutrients, while AOB communities were correlated with soil extractable nutrients. AOA and AOB diversity and AOB abundance decreased in 2014 in all regions, suggesting that broad-scale drivers, such as climate, may explain synchronous shifts throughout the coastal area. Our results provide insights about large-scale disturbances on nitrifying microbes in the Gulf of Mexico, and suggest that nitrogen cycling may be controlled primarily by local factors, but large-scale drivers might override these localized differences at times.

Effects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime Antarctica

Abstract. The colonization by a large number of sea animals, including penguins and seals, plays an important role in the nitrogen cycle of the tundra ecosystem in coastal Antarctica. However, little is known about the effects of sea animal colonization on ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities involved in nitrogen transformations. In this study, we chose active seal colony tundra soils (SSs), penguin colony soils (PSs), adjacent penguin-lacking tundra soils (PLs), tundra marsh soils (MSs), and background tundra soils (BSs) to investigate the effects of sea animal colonization on the abundance, activity, and diversity of AOA and AOB in maritime Antarctica. Results indicated that AOB dominated over AOA in PS, SS, and PL, whereas AOB and AOA abundances were similar in MS and BS. Penguin or seal activities increased the abundance of soil AOB amoA genes but reduced the abundance of AOA amoA genes, leading to very large ratios (1.5×102 to 3.2×104) of AOB to AOA amoA copy numbers. Potential ammonia oxidation rates (PAORs) were significantly higher (P=0.02) in SS and PS than in PL, MS, and BS and were significantly positively correlated (P&lt;0.001) with AOB amoA gene abundance. The predominance of AOB over AOA and their correlation with PAOR suggested that AOB play a more important role in the nitrification in animal colony soils. Sequence analysis for gene clones showed that AOA and AOB in tundra soils were from the Nitrososphaera and Nitrosospira lineages, respectively. Penguin or seal activities led to a predominance of AOA phylotypes related to Nitrososphaera cluster I and AOB phylotypes related to Nitrosospira clusters I and II but very low relative abundances in AOA phylotypes related to cluster II, and AOB phylotypes related to clusters III and IV. The differences in AOB and AOA community structures were closely related to soil biogeochemical processes under the disturbance of penguin or seal activities: soil C : N alteration and sufficient input of NH4+–N and phosphorus from animal excrements. The results significantly enhanced the understanding of ammonia-oxidizing microbial communities in the tundra environment of maritime Antarctica.

AOA and AOB communities respond differently to changes of soil pH under long-term fertilization

Archaeal and bacterial ammonia-oxidizers drive the first step of nitrification, ammonia oxidation. Despite their importance, the relative contribution of soil factors influencing the abundance, diversity and community composition of ammonia oxidizing archaea (AOA) and bacteria (AOB) are seldom compared. In this study, the AOA and AOB communities in soils from a long-term fertilization experiment (which formed gradients of pH and nutrients) were measured using 454 pyrosequencing of the amoA gene. Results showed that both AOA and AOB communities were influenced by fertilization practice. Changes of AOA abundance, diversity and community structure were closely correlated with a single factor, soil pH, and the abundance and diversity of AOA were lower under the acidified treatments. By contrast, AOB abundance was higher in the acidified soil than in the control soil while AOB diversity was little impacted by soil acidification, and both the abundance and diversity of AOB were most highly correlated with soil carbon and available phosphorus. These results indicated that AOB diversity seemed more resistant to soil acidification than that of AOA, and also suggested that AOB have greater ecophysiological diversity and broader range of habitats than AOA in this lime concretion black soil, and the potential contribution of AOB to ammonia oxidation in acid environments should not be overlooked.

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.

Response of ammonia-oxidizing archaea to heavy metal contamination in freshwater sediment

It has been well-documented that the distribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soils can be affected by heavy metal contamination, whereas information about the impact of heavy metal on these ammonia-oxidizing microorganisms in freshwater sediment is still lacking. The present study explored the change of sediment ammonia-oxidizing microorganisms in a freshwater reservoir after being accidentally contaminated by industrial discharge containing high levels of metals. Bacterial amoA gene was found to be below the quantitative PCR detection and was not successfully amplified by conventional PCR. The number of archaeal amoA gene in reservoir sediments were 9.62 × 102–1.35 × 107 copies per gram dry sediment. AOA abundance continuously decreased, and AOA richness, diversity and community structure also considerably varied with time. Therefore, heavy metal pollution could have a profound impact on freshwater sediment AOA community. This work could expand our knowledge of the effect of heavy metal contamination on nitrification in natural ecosystems.

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.

Vertical distribution of ammonia-oxidizing microorganisms across a soil profile of the Chinese Loess Plateau and their responses to nitrogen inputs

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) oxidize ammonia into nitrite, the first and rate-limiting step of microbial nitrification, and exert major controls over soil nitrogen transformations. The Loess Plateau in northwest China is characterized with deep soils that are often exposed to the surface and reactive nitrogen (N) inputs due to erosion and human removal of the surface soil. However, few have examined the distribution of AOA and AOB along the profile of Loess Plateau soils and their responses to N inputs. We examined the abundance and diversity of AOA and AOB along the soil profile (0–100cm) and their responses to two levels of N inputs (low at 10, and high at 100μgNg−1 soil) in a 55-d incubation experiment. While AOB were most numerous in the surface soil (0–20cm), AOA were most abundant in the subsoils (20–40 and 40–60cm), suggesting a niche differentiation between AOA and AOB along the soil profile. High N input increased AOB nearly ten-fold in the upper two layers of soils (0–20 and 20–40cm) and sixteen to twenty-five fold in the deeper soil layers (40–60, 60–80 and 80–100cm). However, it only increased AOA by 7% (40–60cm) to 48% (20–40cm). In addition, potential nitrification rate and N2O emissions correlated only with AOB. Finally, high N input significantly increased AOB diversity and led to nitrite accumulation in deep soil layers (60–80 and 80–100cm). Together, our results showed that high N input can significantly alter the diversity and function of ammonia-oxidizing microbes in the deep soil of Loess Plateau, suggesting the need to examine the generality of the observed changes and their potential environmental impacts.

Nitrifying activity and ammonia-oxidizing microorganisms in a constructed wetland treating polluted surface water

Ammonia oxidation, performed by both ammonia oxidizing bacteria (AOB) and archaea (AOA), is an important step for nitrogen removal in constructed wetlands (CWs). However, little is known about the distribution of these ammonia oxidizing organisms in CWs and the associated wetland environmental variables. Their relative importance to nitrification in CWs remains still controversial. The present study investigated the seasonal dynamics of AOA and AOB communities in a free water surface flow CW (FWSF-CW) used to ameliorate the quality of polluted river water. Strong seasonality effects on potential nitrification rate (PNR) and the abundance, richness, diversity and structure of AOA and AOB communities were observed in the river water treatment FWSF-CW. PNR was positively correlated to AOB abundance. AOB (6.76×105–6.01×107 bacterial amoA gene copies per gram dry sediment/soil) tended to be much more abundant than AOA (from below quantitative PCR detection limit to 9.62×106 archaeal amoA gene copies per gram dry sediment/soil). Both AOA and AOB abundance were regulated by the levels of nitrogen, phosphorus and organic carbon. Different wetland environmental variables determined the diversity and structure of AOA and AOB communities. Wetland AOA communities were mainly composed of unknown species and Nitrosopumilus-like organisms, while AOB communities were mainly represented by both Nitrosospira and Nitrosomonas.

Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems.

Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA) and bacteria (AOB), yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA) were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR) assays, targeting the ammonia monooxygenase-subunit (amoA) genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root) at the DNA level (P < 0.05). Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle, particularly nitrification of seagrass meadows in coral reef ecosystems.

Ammonia-oxidizing archaea and bacteria responding differently to fertilizer type and irrigation frequency as revealed by Illumina Miseq sequencing

Ammonia oxidation, the first and rate-limiting step of nitrification, can be strongly influenced by agricultural practices, but little is known about the effects of fertilization and irrigation combination on ammonia oxidizers in agricultural soils. This study was designed to reveal how fertilizer type and irrigation frequency affect the ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities in a northern Chinese wheat-maize rotation soil. Soil samples were collected from a long-term field experiment under different fertilization and irrigation regimes located in Wuqiao Experimental Station of China Agricultural University in June 2016. The abundance, diversity, and composition of AOA and AOB in the soils were investigated by using real-time PCR and Illumina Miseq sequencing approaches. The abundance of AOA was higher in the irrigated treatments, but lower in the treatments without irrigation, than that of AOB. The AOA abundance was positively correlated with soil moisture, pH, and NO3 −-N, while the AOB abundance was positively correlated with TN and NO3 −-N. Soil potential nitrification activity (PNA) was significantly positively correlated with the AOB abundance. Both fertilizer type and irrigation frequency significantly affected Shannon, ACE, and Chao1 indices of the AOB community, while only irrigation frequency had a significant impact on Shannon index of the AOA community. PCoA analysis results indicated that irrigation frequency greatly affected the AOA community structure, while fertilizer type played a more important role in affecting the AOB community structure. Mantel test and correlation heatmap analysis results indicated that soil moisture, pH, and NH4 +-N were significantly correlated to the AOA community structure, and TN and SOC were significantly correlated to the AOB community structure. This study demonstrated that irrigation frequency greatly influenced the AOA community, while fertilizer type had a stronger effect on the AOB community. It was AOB but not AOA played a more important role in soil nitrification. Moreover, soil moisture, pH, and TN were the main determinants in driving the AOA community and TN and SOC were the main factors in influencing the AOB community.

Prevalence of ammonia-oxidizing bacteria over ammonia-oxidizing archaea in sediments as related to nutrient loading in Chinese aquaculture ponds

Nitrogen (N) application in excess of assimilatory capacity for aquaculture ponds can lead to water-quality deterioration through ammonia accumulation with toxicity to fish. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) potentially process extra ammonium, so their abundance and diversity are of great ecological significance. This study aimed to reveal variations in communities of AOA and AOB as affected by aquaculture activities. From June to September 2012, water and sediments were sampled monthly in three ponds feeding Mandarin fish in a suburb of Wuhan City, China. Molecular methods based on ammonia monooxygenase (amoA) gene were used to determine abundance and diversity of AOA and AOB in the sediments. The pond with the highest fish stock had the highest nutrient loadings in terms of different forms of N and carbon (C) in both sediment and water. The abundance and diversity of AOB were significantly higher than those of AOA in the sediment. The AOB abundance showed a significantly positive relationship to concentration of soluble reactive phosphorus (SRP) in interstitial water, and both abundance and diversity of AOA were significantly negative to concentration of ammonium in interstitial water. Furthermore, AOA species affiliated to Nitrososphaera-like and Nitrosophaera Cluster was distinguishable from those observed in other aquaculture environments. Nutrients in sediment were enriched by intensive aquaculture activity, among which organic N and C, together with ammonium and SRP, shaped the communities of ammonia oxidizers, with AOB dominating over AOA in terms of abundance and diversity.

Diversity of ammonia-oxidizing bacteria and archaea in response to different aeration rates during cattle manure composting

Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) coexisted in the process of cattle manure composting under different rates of aeration in this study. The effect of aeration rates (12, 3 and 0L/min) on the communities of AOB and AOA in the cattle manure composting was evaluated using the molecular marker amoA gene for phylogenetic comparisons. Nitrosomonas and Nitrosospira affiliated with AOB were detected and the relative abundance of Nitrosomonas ranged from 69.1% to 100% showing its dominance in cattle manure composting. The diversity of AOA showed no significant change with the increase of aeration rates, only 2.0% of the sequences of marine cluster appeared under treatment with aeration rate of 12L/min. Relationships between diversity of AOB and AOA and physicochemical parameters were also explored. Canonical correspondence analysis (CCA) indicated that oxygen was significantly (p<0.05) correlated with diversity of AOB, but not with AOA. These results revealed that AOB were more important than AOA in nitrogen transformation, including nitrification during cattle manure composting under different aeration rates.

Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake.

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure.