Cluster 3a Research Articles

Reassembly of active ammonia oxidizing bacteria following invasion of exogenous microbiome in an acidic soil

Ammonia oxidation is the rate-limiting step of the global nitrogen cycle, and it is mainly catalyzed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). AOA can carry out nitrification even in acidic soils, whereas AOB activity was not consistently observed in acidic soils. In this study, we manipulated two environmental variables, i.e., the microbial composition and ammonium source (urea and ammonium sulphate), in an acidic forest soil and tested their impacts on AOB abundance, diversity and activity. Soil microcosms were established either using the native forest soil (FS) or after amending the forest soil with 5% (w/w) agricultural soil (AFS) to inoculate new, exogenous microbes. Under the same microcosm incubation condition for 28 days, AOB did not grow in FS but they grew in AFS, suggesting that exogenous microbial invasion could stimulate AOB activity in the acidic soil. Urea amendment led to higher growth of AOB than ammonium sulphate amended in AFS microcosms. DNA-based stable isotope probing revealed that the active AOB lineages were dominated by Nitrosospira cluster 3a.2 and Nitrosospira cluster 10 in the ammonium sulphate supplied soil, but shifted to co-dominance of Nitrosospira cluster 3a.2 and Nitrosospira cluster 1 after urea amendment, demonstrating differential preferences of ammonia sources of phylogenetically distinct AOB lineages. Additionally, AOB abundance showed lower stability than AOA in soils subjected to these two environmental changes, suggesting AOB are more important in determining the fate of soil nitrification following short-term environmental disturbances.

Comammox Nitrospira and AOB communities are more sensitive than AOA community to different fertilization strategies in a fluvo-aquic soil

Ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB) and the newly discovered complete ammonia oxidizers (comammox Nitrospira) are responsible for ammonia oxidation, which is the first and rate-limiting step of nitrification. A better understanding of the complex responses of AOA, AOB and comammox Nitrospira to inorganic and organic fertilization regimes is critical to get the whole picture of soil nitrification. Here, we investigated the abundances and community compositions of AOA, AOB and comammox Nitrospira in a fluvo-aquic soil under different fertilization strategies: nitrogen fertilizer reduction treatments (CK, PK, 50 % NPK and 75 % NPK), conventional fertilizer treatment (100 % NPK), N fertilizer reduction with organic manure substitution treatments (25 % OMNPK, 50 % OMNPK, 100 % OMPK and 200 % OMPK). The results indicated that 100 % NPK treatment significantly increased AOB abundance, while the abundances of AOA and comammox Nitrospira were enhanced significantly by 100 % and 200 % OMPK treatments. Principal coordinate analysis indicated different fertilization strategies had greater effect on the communities of AOB and comammox Nitrospira than those of AOA. Fertilizer application (other than CK) decreased the relative abundance of Nitrosospira cluster 3b of AOB while increased the relative abundance of Nitrosospira cluster 3a.2. Fertilizer, especially high manure application increased the relative abundance of comammox Nitrospira clade A.2 but decreased the relative abundance of clade B. Both redundancy analysis and mantel test showed AOB and comammox Nitrospira communities were regulated by more soil factors than AOA community. These results suggested the communities of AOB and comammox Nitrospira were more sensitive than AOA community to different fertilization strategies in a fluvo-aquic soil of northern China.

Cluster analysis of upper airway stimulation adherence patterns and implications on clinical care

Upper airway stimulation (UAS) therapy is effective for a subset of obstructive sleep apnea (OSA) patients with continuous positive airway pressure (CPAP) intolerance. While overall adherence is high, some patients have suboptimal adherence, which limits efficacy. Our goal was to identify therapy usage patterns during the first 3 months of therapy to enable targeted strategies for improved adherence. Therapy data was retrieved from 2098 patients for three months after device activation. Data included mean and standard deviation (SD) of hours of use, therapy pauses, hours from midnight the therapy was turned ON and OFF, percentage of missing days, and stimulation amplitude. Cluster analysis was performed using Gaussian mixture models that categorized patients into six main groups. The six groups and their prevalence can be summarized as Cluster 1A: Excellent Use (34%); Cluster 1B: Excellent Use with variable timing (23%); Cluster 2A: Good Use with missing days and late therapy ON (16%), Cluster 2B: Good Use with missing days, late therapy ON, and early therapy OFF (12%); Cluster 3A: Variable Use with frequent missing days (8%); Cluster 3B: Variable Use with frequent pauses (7%). Most patients (85%) are excellent or good users with mean therapy use >6 hours per night. Cluster analysis of early UAS usage patterns identified six distinct groups that may enable personalized interventions for improved long-term management. Differentiation of the patient clusters may have clinical implications with regard to sleep hygiene education, therapy discomfort, comorbid insomnia, and other conditions that impact adherence.

Responses of potential ammonia oxidation and ammonia oxidizers community to arsenic stress in seven types of soil

Soil arsenic contamination is of great concern because of its toxicity to human, crops, and soil microorganisms. However, the impacts of arsenic on soil ammonia oxidizers communities remain unclear. Seven types of soil spiked with 0 or 100 mg arsenic per kg soil were incubated for 180 days and sampled at days 1, 15, 30, 90 and 180. The changes in the community composition and abundance of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, clone library sequencing, and quantitative PCR (qPCR) targeting amoA gene. Results revealed considerable variations in the potential ammonia oxidation (PAO) rates in different soils, but soil PAO was not consistently significantly inhibited by arsenic, probably due to the low bioavailable arsenic contents or the existence of functional redundancy between AOB and AOA. The variations in AOB and AOA communities were closely associated with the changes in arsenic fractionations. The amoA gene abundances of AOA increased after arsenic addition, whereas AOB decreased, which corroborated the notion that AOA and AOB might occupy different niches in arsenic-contaminated soils. Phylogenetic analysis of amoA gene-encoded proteins revealed that all AOB clone sequences belonged to the genus Nitrosospira, among which those belonging to Nitrosospira cluster 3a were dominant. The main AOA sequence detected belonged to Thaumarchaeal Group 1.1b, which was considered to have a high ability to adapt to environmental changes. Our results provide new insights into the impacts of arsenic on the soil nitrogen cycling.

Synergistic effects of biological nitrification inhibitor, urease inhibitor, and biochar on NH3 volatilization, N leaching, and nitrogen use efficiency in a calcareous soil–wheat system

Urease inhibitors (UIs), chemical nitrification inhibitors (CNIs), and biochar (BC) are commonly applied nitrogen (N) management strategies in reducing soil N loss and increasing nitrogen use efficiency (NUE) in agriculture. Biological nitrification inhibitors (BNIs) are natural abilities of certain plant roots to suppress soil–nitrifier activity. They have some advantages over chemical nitrification inhibitors (CNIs), but their effects on N loss and NUE are not critically examined yet. In this study, the synergistic effects of BNI of methyl 3-(4-hydroxyphenyl) propionate (MHPP at dosage of 1000 mg kg−1), UI of N-(n-butyl), thiophosphoric triamide (NBPT, 2% of applied_urea_N), and BC (w heat straw biochar, 1% (w/w)) on NH3 volatilization, inorganic N leaching, plant N uptake (N_yield), and NUE are explored through a wheat growth pot experiment. MHPP and BC can increase NH3 volatilization, which increased by 18.5% in the BC treatment and 32.9% in the MHPP_BC treatment. Individual application or co-application of MHPP, NBPT, and BC significantly decreased N leaching by 25.4% to 42.6% (P < 0.05). The treatments of MHPP, BC, MHPP_NBPT, and MHPP_BC significantly increased the N_yield in the range of 7.41%–10.3% and the NUE in the range of 9.94%–13.7% compared with the CF treatment (P < 0.05). The partial mechanism of those strategies in regulating N pathways was by causing niche differentiation between ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA), and changing community structure mainly of AOB. NBPT, MHPP, and BC were found mainly in the targeted Nitrosospira cluster 3a.2 and Nitrosospira cluster 3b. In general, the application of MHPP_NBPT is a promising strategy for simultaneously reducing NH3 and increasing NUE.

Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil

Microbe-driven nitrification is a key process that affects nitrogen (N) utilization by plants and N loss to the environment in agro-ecosystems. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are important microorganisms that dominate the ammonia oxidation process (the first and rate-limiting step of nitrification). Calcareous soils are widely distributed, accounting for more than 30% of the Earth's land. However, the effects of long-term N fertilization on the potential nitrification rate (PNR) and on AOA and AOB in calcareous soils are poorly understood. In this study, we comprehensively assessed the effects of N application (applied at five rates as urea with 0, 73.5, 105, 136.5 and 250 kg N ha−1 for 12 years) on soil chemical characteristics, PNR, N use efficiency (NUE) and the community characteristics of AOB and AOA in a calcareous soil. N application rate affected AOB beta diversity more than that of AOA. Compared to no N control, N application significantly decreased the relative abundance of Group I.1b clade A of AOA and Nitrosospira cluster 3a.2 of AOB, but increased Nitrosomonas cluster 7 of AOB. The relative abundance of Nitrosospira cluster 3a.2 of AOB was negatively correlated with PNR. A structural equation model showed a direct effect of N application rate on the content of soil organic matter and nitrate, the alpha and beta diversity of AOA and AOB. Nitrate and AOB beta diversity were the key factors affecting PNR. Overall, the alpha, beta diversity and community composition of AOB contribute more to PNR than AOA in calcareous soils with high organic matter content. Understanding the relationship between the characteristics of AOA and AOB in calcareous soils and PNR will help to improve NUE.

Phenotypic Cluster Analysis of Acinetobacter Species Isolated From Ventilator Associated Pneumonia During the First Wave Of COVID 19 in Surabaya, Indonesia

Introduction: Coronavirus disease-2019 (COVID-19) has been reported as epidemic in December 2019 in Wuhan, Hubei Province, People Republic of China. Hospitalized COVID-19 patients, especially with worse clinical appearance and on ventilator, need thorough diagnostic tests as COVID-19 patients tend to mimic bacterial infections. Positive blood culture in COVID-19 patients is more likely to be contaminants and hospital associated infections than primary co-infections. This research aims to phenotypically group data of Acinetobacter isolates associated with Ventilator Associated Pneumonia (VAP) using hierarchical clustering. Method: This is a descriptive study presenting collection of Acinetobacter culture data performed by Microbiology laboratory of a COVID-19 referral hospital from 26 March 2020- 31 February 2021. Hierarchical clustering were performed using statistical software. Results: Hierarchical clustering were performed to 50 VAP associated Acinetobacter isolates. There are 4 cluster clades showed in biochemistry dendrogram. Two dominant clusters 1A and 3A were found and both similar MIC pattern. Conclusion: Acinetobacter phenotype cluster 1A and 3A dominates VAP associated isolates. This method can be applied to facilities with limited resource setting.

Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China.

Organic fertilizer application could have an impact on the nitrogen cycle mediated by microorganisms in arable soils. However, the dynamics of soil ammonia oxidizers and denitrifiers in response to compost addition are less understood. In this study, we examined the effect of four compost application rates (0, 11.25, 22.5 and 45 t/ha) on soil ammonia oxidizers and denitrifiers at soybean seedling, flowering and mature stage in a field experiment in Northeast China. As revealed by quantitative PCR, compost addition significantly enhanced the abundance of ammonia oxidizing bacteria (AOB) at seedling stage, while the abundance of ammonia oxidizing archaea was unaffected across the growing season. The abundance of genes involved in denitrification (nirS, nirK and nosZ) were generally increased along with compost rate at seedling and flowering stages, but not in mature stage. The non-metric multidimensional scaling analysis revealed that moderate and high level of compost addition consistently induced shift in AOB and nirS containing denitrifers community composition across the growing season. Among AOB lineages, Nitrosospira cluster 3a gradually decreased along with the compost rate across the growing season, while Nitrosomonas exhibited an opposite trend. Network analysis indicated that the complexity of AOB and nirS containing denitrifiers network gradually increased along with the compost rate. Our findings highlighted the positive effect of compost addition on the abundance of ammonia oxidizers and denitrifiers and emphasized that compost addition play crucial roles in shaping their community compositions and co-occurrence networks in black soil of Northeast China.

Long-term fertilization regimes change soil nitrification potential by impacting active autotrophic ammonia oxidizers and nitrite oxidizers as assessed by DNA stable isotope probing.

Chemoautotrophic ammonia-oxidizers and nitrite-oxidizers are responsible for a significant amount of soil nitrate production. The identity and composition of these active nitrifiers in soils under different long-term fertilization regimes remain largely under-investigated. Based on that soil nitrification potential significantly decreased in soils with chemical fertilization (CF) and increased in soils with organic fertilization (OF), a microcosm experiment with DNA stable isotope probing was further conducted to clarify the active nitrifiers. Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were found to actively respond to urea addition in soils with OF and no fertilizer (CK), whereas only AOB were detected in soils with CF. Around 98% of active AOB were Nitrosospira cluster 3a.1 in all tested soils, and more than 90% of active AOA were Nitrososphaera subcluster 1.1 in unfertilized and organically fertilized soils. Nitrite oxidation was performed only by Nitrospira-like bacteria in all soils. The relative abundances of Nitrospira lineage I and VI were 32% and 61%, respectively, in unfertilized soils, and that of Nitrospira lineage II was 97% in fertilized soils, indicating long-term fertilization shifted the composition of active Nitrospira-like bacteria in response to urea. This finding indicates that different fertilizer regimes impact the composition of active nitrifiers, thus, impacting soil nitrification potential.

Effects of the biological nitrification inhibitor 1,9-decanediol on nitrification and ammonia oxidizers in three agricultural soils

The application of biological nitrification inhibitors (BNIs) is considered an important new strategy to mitigate nitrogen losses from agricultural soils. 1,9-decanediol was recently identified as a new BNI in rice root exudates and was shown to inhibit nitrification in bioassays using Nitrosomonas. However, the effect of this compound on nitrification and ammonia oxidizers in soils remained unknown. In this study, three typical agriculture soils were collected to investigate the impact of 1,9-decanediol on nitrification and ammonia oxidizers in a 14-day microcosm incubation. High doses of 1,9-decanediol showed strong soil nitrification inhibition in all three agricultural soils, with the highest inhibition of 58.1% achieved in the acidic red soil, 37.0% in the alkaline fluvo-aquic soil, and 35.7% in the neutral paddy soil following 14 days of incubation. Moreover, the inhibition of 1,9-decanediol was superior to the widely used synthetic nitrification inhibitor, dicyandiamide (DCD) and two other BNIs, methyl 3-(4-hydroxyphenyl) propionate (MHPP) and α-linolenic acid (LN), in all three soils. The abundance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) was significantly inhibited by 1,9-decanediol addition across the three soils. All AOB sequences fell within the Nitrosospira group, and the dominant AOA sequences belonged to the Nitrososphaera cluster in all three soils. Changes in the community composition of AOB were more pronounced than AOA after the application of 1,9-decanediol. The AOB community structure shifted from Nitrosospira cluster 2 and cluster 3a toward Nitrosospira clusters 8a and 8b. As for AOA, no significant impact on the proportion of the dominant Nitrososphaera cluster was observed in the fluvo-aquic soil and paddy soil while only the Nitrosopumilus cluster decreased in the red soil. 1,9-decanediol could also significantly reduce soil N2O emissions, especially in acidic red soil. Our results provide evidence that 1,9-decanediol is capable of suppressing nitrification in agricultural soils through impeding both AOA and AOB rather than affecting soil NH4+ availability. 1,9-decanediol holds promise as an effective biological nitrification inhibitor for soil ammonia-oxidizing bacteria and archaea.

Neutrophilic bacteria are responsible for autotrophic ammonia oxidation in an acidic forest soil

Increasing evidence suggests that autotrophic ammonia oxidation in acidic soils is largely performed by archaea. However, ammonia oxidizing bacteria (AOB) are also found in acidic soils, and mechanisms have been demonstrated that enable the growth of AOB in low pH soils. This work used DNA stable isotope probing to examine the response of autotrophic ammonia oxidizers in an acidic forest soil (pH 5.0) following urea amendment. After application, increases in nitrate concentrations correlated only with increases in AOB and not ammonia oxidizing archaeal (AOA) amoA gene abundance, indicating that AOB may be responsible for urea-derived ammonia oxidation. To identify growing autotrophic populations associated with ammonia oxidation, qPCR and high throughput sequencing analysis of 16S rRNA gene amplicons demonstrated that 13CO2 was assimilated by Nitrosospira AOB rather than archaeal ammonia oxidizing populations, and Nitrospira-associated nitrite-oxidizing bacteria (NOB). Phylogenetic analysis of amoA genes demonstrated that the active ammonia oxidizers were closely related to neutrophilic Nitrosospira multiformis within Nitrosospira cluster 3a.2. These results demonstrate that AOB can dominate ammonia oxidation in acidic soils under specific conditions.

Effects of combined application of nitrogen fertilizer and biochar on the nitrification and ammonia oxidizers in an intensive vegetable soil

Soil amended with single biochar or nitrogen (N) fertilizer has frequently been reported to alter soil nitrification process due to its impact on soil properties. However, little is known about the dynamic response of nitrification and ammonia-oxidizers to the combined application of biochar and N fertilizer in intensive vegetable soil. In this study, an incubation experiment was designed to evaluate the effects of biochar and N fertilizer application on soil nitrification, abundance and community shifts of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Hangzhou greenhouse vegetable soil. Results showed that single application of biochar had no significant effect on soil net nitrification rates and ammonia-oxidizers. Conversely, the application of only N fertilizer and N fertilizer + biochar significantly increased net nitrification rate and the abundance of AOB rather than AOA, and only AOB abundance was significantly correlated with soil net nitrification rate. Moreover, the combined application of N fertilizer and biochar had greater effect on AOB communities than that of the only N fertilizers, and the relative abundance of 156 bp T-RF (Nitrosospira cluster 3c) decreased but 60 bp T-RF (Nitrosospira cluster 3a and cluster 0) increased to become a single predominant group. Phylogenetic analysis indicated that all the AOB sequences were grouped into Nitrosospira cluster, and most of AOA sequences were clustered within group 1.1b. We concluded that soil nitrification was stimulated by the combined application of N fertilizer and biochar via enhancing the abundance and shifting the community composition of AOB rather than AOA in intensive vegetable soil.

Irrigation frequency alters the abundance and community structure of ammonia-oxidizing archaea and bacteria in a northern Chinese upland soil

Ammonia oxidation, the first and rate-limiting step in nitrification, is a key process in biogeochemical nitrogen cycling. However, little is known about how irrigation affects ammonia oxidizing microorganisms in agroecosystems. In this study, effects of irrigation frequency on soil potential nitrification activity (PNA), the abundance and composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated using real-time PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP), and clone libraries for characterizing the ammonium monooxygenase genes (amoA) in a northern Chinese soil. Results showed that irrigation significantly increased soil PNA and archaeal amoA gene abundance but decreased bacterial amoA gene abundance. Soil PNA was positively correlated with archaeal amoA gene abundance and negatively correlated with bacterial. T-RFLP and PCA results showed that irrigation greatly changed the AOA and AOB community structures by altering the relative abundances of four T-RFs of AOA and four other T-RFs of AOB, respectively. Phylogenetic analysis revealed that all archaeal sequences fell into Group 1.1b, and the bacterial clones were dominated by Nitrosospira-like sequences within Cluster 3a.2. Irrigation induced the appearance of two archaeal and two bacterial OTUs and increased the relative abundance of another two archaeal and four bacterial OTUs, respectively. Additionally, soil moisture, soil pH, NH4+-N, and NO3−-N correlated significantly with the AOA community, and soil pH, total nitrogen (TN), and NO3−-N were significantly correlated with the AOB community. Our results demonstrate that irrigation greatly affected the abundance and community structure of AOA and AOB and that AOA appeared to play a more important role in nitrification in the study soil.

Effects of different fertilizer application methods on the community of nitrifiers and denitrifiers in a paddy soil

Nitrifiers and denitrifiers are the key drivers of N cycling in paddy soil. Little is known about the effects of different fertilization methods, especially side bar fertilization, on the community of nitrifiers and denitrifiers in paddy soils. Here we assess the relationships between soil physicochemical properties, denitrification and nitrification activities, and the underlying microbial communities in a surface layer of paddy field soil treated with different fertilization methods. Soil was unfertilized (control), treated with conventional chemical fertilizer (CF), CF plus pig manure (MC), or slow-release fertilizer (SR), or by slow-release side bar fertilization (SB). Soil was sampled after one season of early and late rice growth. We determined soil physicochemical properties, potential nitrification rates (PNR), and denitrification enzyme activities (DEA). Ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities were assessed via their ammonia monooxygenase (amoA) genes, and denitrifiers via nitrite reductases (nirK and nirS) and nitrous oxide reductase (nosZ). Quantitative PCR was used to assess gene abundance, terminal restriction fragment polymorphism (T-RFLP) to investigate fertilization effects on microbial communities, and clone library sequencing and phylogenetic analysis to explore the taxonomic diversity of the nitrifiers and denitrifiers. Fertilization significantly increased the amount of NH4 +-N in the soil of SB and MC treatments, whereas MC lowered the NO3 −-N level. DEA was higher for MC and CF than the other treatments. The PNR in MC-treated soil was significantly lower than that in CF-treated soil. There were no significant differences in AOA and nirS copy numbers; however, nirK and nosZ copy numbers were higher for MC compared with CF. The number of AOA terminal restriction fragments (TRFs) increased significantly with N addition and reached the highest level for SB, whereas the number of AOB TRFs did not change significantly between treatments. Similarly, the number of nirK TRFs increased under fertilization, with the highest number obtained for SR; however, no significant change was observed for nirS and nosZ TRFs across different treatments, except for their relative abundance. All AOA amoA genotypes were in archaeal group 1.1b, whereas 95% AOB were in Nitrosospira cluster 3a. More than 40% of nirS OTUs were affiliated with Herbaspirillum, a key N-cycle player in this paddy soil. The SB and MC treatments had significant effects on soil N, DEA, and PNR levels, and affected the community of N-functional microbes. SB in combination with pig manure would contribute to the improvement of paddy soil fertility.

Molecular analysis of group A rotaviruses detected in hospitalized children from Rawalpindi, Pakistan during 2014

As a part of strategy to control diarrheal diseases, World Health Organization (WHO) recommends to include rotavirus vaccines in national immunization programs. Sentinel surveillance networks have been established to monitor rotavirus disease burden and genotype distribution in both pre and post vaccine era in many countries. Unfortunately, due to lack of proper surveillance programs, data on rotavirus disease burden and genotype distribution from Pakistan is scarce. We investigated 502 stool samples from children (<5years) hospitalized due to gastroenteritis in Rawalpindi, Pakistan during 2014 for the presence of group A rotavirus (RVA) and its genotypic diversity. Among 147 ELISA positive samples, 131 were successfully genotyped for RVA. Common G types detected were G1 (23.6%), followed by G3 (22.9%), G12 (19.8%), G2 (19.08%) and G9 (9.9%). The most common P-type was P[8] (41.2%), followed by P[6] (29%) and P[4] (28.24%). G3P[8] (17.55%) was the most prevalent genotype combination followed by G12P[6] (16.7%), G2P[4] (15.2%) and G1P[8] (14.5%). Mixed infection of rotavirus G-P types was also observed in 6% of samples. Phylogenetic analysis of VP7 and VP4 genes of Pakistani strains showed that G1, G2, G9 and P[4], P[6], P[8] were closely related to strains circulating worldwide as well as previously reported strains from Pakistan. Pakistani G12P[8] strains NIH-BBH-3981 and NIH-BBH-4003 belonged to lineage 3 cluster 3a along with strains from USA and Italy whereas G12P[6] strains NIH-BBH-3978, NIH-BBH-4052 and NIH-BBH-4444 were closely related to strains from Italy, Thailand, United Kingdom and with previously reported G12 strains from Pakistan within lineage 3 cluster 3b. This pre-vaccination data supports the need for RVA vaccine inclusion at our national level and will be helpful in assessing the effect of vaccination on RVA genotype diversity due to vaccine selection pressure once post-vaccination data becomes available.

Responses of ammonia-oxidizing bacterial communities to land-use and seasonal changes in Mollisols of Northeast China

In this study, AOB community was investigated over a 2-year period in cultivated Mollisols (0–20 cm) with three fertilizer treatments [no fertilizer (NoF), chemical fertilizer (CF) and chemical fertilizer plus manure (CFM)] and in an adjacent plot under natural restoration (NR). The crop rotation of maize, soybean and wheat was repeated every three years. The NR plot was abandoned agricultural land that was naturally revegetated with grasses. The AOB communities were characterized by clone sequencing of amoA gene targets, which encode ammonia monooxygenase subunit A. Phylogenetic analyses showed that the AOB communities in the Mollisols of Northeast China were related to defined groups, including clusters 1, 2, 3a, 3b, 9, and 10 in Nitrosospira and cluster 7 in Nitrosomonas. Nitrosospira cluster 3 was the most frequently recovered AOB in all treatments, and cluster 3a.2 and 3a.2-related sequences were common in cultivated soils. However, 12–27% of sequences were not related to any known AOB species, indicating a high diversity of AOB communities in Mollisols. There was a distinct AOB community in the NR plot and the cultivated plots, consistent with the hypothesis that land-use alters AOB community, and this appeared to be related to the soil pH. Cultivated soils with added N fertilizer had a greater frequency of clones in the Nitrosospira cluster 10 sequence type, but suppressed clones in the Nitrosospira cluster 3a.1 sequence type, whereas Nitrosomonas sequences were only recovered from the CFM treatment. The AOB clone frequency differed between the growing and non-growing seasons, possibly because the AOB communities were favoured by warm, moist soil conditions or the active plant rhizosphere during the growing season. The ecological implications of land-use change and seasonality on the contribution of these diverse AOB communities to primary production in Mollisols merits further attention.

Agricultural land usage transforms nitrifier population ecology

Application of nitrogen fertilizer has altered terrestrial ecosystems. Ammonia is nitrified by ammonia and nitrite-oxidizing microorganisms, converting ammonia to highly mobile nitrate, contributing to the loss of nitrogen, soil nutrients and production of detrimental nitrogen oxides. Mitigating these costs is of critical importance to a growing bioenergy industry. To resolve the impact of management on nitrifying populations, amplicon sequencing of markers associated with ammonia and nitrite-oxidizing taxa (ammonia monooxygenase-amoA, nitrite oxidoreductase-nxrB, respectively) was conducted from long-term managed and nearby native soils in Eastern Washington, USA. Native nitrifier population structure was altered profoundly by management. The native ammonia-oxidizing archaeal community (comprised primarily by Nitrososphaera sister subclusters 1.1 and 2) was displaced by populations of Nitrosopumilus, Nitrosotalea and different assemblages of Nitrososphaera (subcluster 1.1, and unassociated lineages of Nitrososphaera). A displacement of ammonia-oxidizing bacterial taxa was associated with management, with native groups of Nitrosospira (cluster 2 related, cluster 3A.2) displaced by Nitrosospira clusters 8B and 3A.1. A shift in nitrite-oxidizing bacteria (NOB) was correlated with management, but distribution patterns could not be linked exclusively to management. Dominant nxrB sequences displayed only distant relationships to other NOB isolates and environmental clones.

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.

Aggregate-related changes in network patterns of nematodes and ammonia oxidizers in an acidic soil

Nitrification plays a central role in global nitrogen cycle, which is affected by biological interaction between soil microfauna and microorganisms. However, the complexity of soil biotic communities made it difficult to reveal organizational principles of the community and the interactions among species. Here, we used the network analysis to decipher the interactions between nematodes and ammonia oxidizers within aggregate fractions under 10-year manure application, and examine their associations with soil variables and potential nitrification activity (PNA). Three aggregate fractions included large macroaggregates (>2000 μm, LA), small macroaggregates (250–2000 μm, SA), and inter-aggregate soil and space (<250 μm, IA). Aggregate factions showed a remarkable effect on association networks of nematodes and ammonia oxidizers. The average connectivity (avgK) and the number of edges in overall networks increased with increasing aggregate sizes, while the average geodesic distance (GD) followed the opposite trend. The LA network could be viewed as a better organized or a better operational soil food web with more functional interrelated members than the SA and IA networks. The modules related to PNA were significantly correlated and clustered together as meta-modules in networks of aggregate fractions. The role-shifts prevailed among the network members such as significant module memberships (MMs) and generalist/specialist operational taxonomic units (OTUs). A half of shared nodes were further identified as shared MMs, dominated by ammonia-oxidizing bacteria (AOB) especially for Nitrosospira cluster 3a and 10. Soil pH could explain partly the shift of module hubs in different networks, while grazing by bacterivores might account for three exclusively connecters related to Nitrososphaera clusters 1.1. The strongly coupled modules correlated positively to pH and total carbon (TC), regardless of aggregate fractions. The network analysis approach provided new insights into potential importance of network interactions between nematodes and ammonia oxidizers in soil nitrogen cycling.

Impact of long-term continuous soybean cropping on ammonia oxidizing bacteria communities in the rhizosphere of soybean in Northeast China

Continuous cropping can be a serious problem in Chinese soybean production. This can result in yield reduction, root diseases, and changes in microbial community structure. We studied community structure, clone libraries, and abundance of ammonia oxidizing bacteria (AOB) in soybean fields there were in continuous soybean production for up to 17 years (SC17). Results showed that the potential nitrification rate (PNR) and amoA gene abundance of soybean in continuous cultivation for seven years (SC7) was 0.34 µg NO3− g−1 and 4.71 × 10−5 amoA gene copies/g dry soil, respectively. These values were lower than other treatments. Phylogenetic affiliation analysis based on blast results of amoA gene clone sequencing showed that the sequences belonged to seven clusters: Cluster 1, Cluster 3b, Cluster 3a.1, Cluster 3a.2, Cluster 9, Cluster 10, and Cluster 4. Correlation of AOB community compositions with environmental factors was performed using canonical correspondence analysis (CCA). Results indicated that the composition of AOB communities in maize–soybean (MS) rotation and continuous cropping of soybean for two years (SC2) were positively related to the PNR of soil, soil moisture, and soil total nitrogen content. Soybean fields continuously cropped for 11 years (SC11) and SC7 fields had AOB community compositions that were negatively related to these factors. The AOB community composition of SC17 was positively correlated to the soil total carbon content of soil. The results in this study indicate that the potential activity and abundance of AOB community in soil significantly changed after seven years continuous cropping compared to other continuous cropping intervals. Cropping systems have important effect on the diversity of functional microorganisms and associated nitrogen cycles.