Anteromedial knee osteoarthritis (AMOA) evaluated with magnetic resonance imaging (MRI): a cohort study of 100 patients.

INTRODUCTION: Magnetic resonance imaging (MRI) scans are increasingly used for knee osteoarthritis evaluation and preoperative planning before unicompartmental knee arthroplasty (UKA), and often patients already have MRI scans before their initial surgeon consultation. This highlights the need for surgeons to understand anteromedial osteoarthritis (AMOA) patterns on MRI. Hence, we aim to describe MRI findings in patients with AMOA meeting current indications for medial UKA. MATERIALS AND METHODS: We analysed MRI scans from 100 knees evaluated for UKA between 2006 and 2013. Inclusion criteria comprised full-thickness medial compartment loss and intact lateral compartment joint space on preoperative radiographs. Assessment included cartilage lesions, osteophytes, meniscal damage, and anterior-cruciate ligament (ACL) status on tibial and femoral surfaces. Final decision to proceed with UKA relied on intraoperative findings, independent of MRI. RESULTS: Complete anteromedial tibial and femoral cartilage loss preserved posterior cartilage rims was evident in all cases. Cartilage thinning occurred in the lateral compartment in 34% of cases. While 62% displayed lateral osteophytes, only 6 exhibited small areas of full-thickness cartilage loss. ACL abnormalities varied: 27% normal, 3% ruptured, and 70% had intrasubstance high signal. Larger osteophytes in the medial (p = 0.012) and lateral (p = 0.002) intercondylar notch correlated significantly with ACL damage. All underwent medial UKA, with no evidence of areas with full lateral compartment cartilage loss intraoperatively. CONCLUSIONS: The MRI findings confirmed the radiographic diagnosis of bone-on-bone medial disease but highlights a range of findings in the ACL, lateral compartment, and patellofemoral joint compartment for patients who met the current x-ray and intraoperative indication for UKA. Further research is required to understand if these MRI changes will affect long-term outcomes.

Nutrient leaching potential along a time series of forest water reclamation facilities in northern Idaho.

Forest water reclamation is a decades-old practice of repurposing municipal reclaimed water using land application on forests to filter nutrients and increase wood production. However, long-term application may lead to nutrient saturation, leaching, and potential impairment of ground and surface water quality. We studied long-term effects of reclaimed water application on nutrient leaching potential in a four-decade time series of forest water reclamation facilities in northern Idaho. Our approach compared reclaimed water treated plots with untreated control plots at each of the forest water reclamation facilities. We measured soil nitrifier abundance and net nitrification rates and used tension lysimeters to sample soil matrix water and drain gauges to sample from a combination of matrix and preferential flow paths. We determined nutrient leaching as the product of soil water nutrient concentrations and model-estimated drainage flux. There was more than 450-fold increase in nitrifier abundance and a 1000-fold increase in net nitrification rates in treated plots compared with control plots at long-established facilities, indicating greater nitrate production with increased cumulative inputs. There were no differences in soil water ammonium, phosphate, and dissolved organic nitrogen concentrations between control and effluent treatments in tension lysimeter samples. However, concurrent with increased nitrifier abundance and net nitrification, nitrate concentration below the rooting zone was 2 to 4-fold higher and nitrate leaching was 4 to 10-fold higher in effluent treated plots, particularly at facilities that have been in operation for over two decades. Thus, net nitrification and nitrifier abundance assays are likely indicators of nitrate leaching potential. Inorganic nutrient concentrations in drain gauge samples were 2 to 11-fold higher than lysimeter samples, suggesting nutrient losses occurred predominantly through preferential flow paths. Nitrate was vulnerable to leaching during the wet season under saturated flow conditions. Although nitrogen saturation is a concern that should be mitigated at long-established facilities, these forest water reclamation facilities were able to maintain average soil water nitrate concentrations to less than 2 mg L-1, so that nitrogen and phosphorous are effectively filtered to below safe water standards.

Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France.

Exploring differences in nitrification within adjacent sedimentary structures of ridges and runnels on the Brouage mudflat, France, we quantified Potential Nitrification Rates (PNR) alongside amoA genes and transcripts. PNR was lower in ridges (≈1.7 fold-lower) than runnels, despite higher (≈1.8 fold-higher) ammonia-oxidizing bacteria (AOB) abundance. However, AOB were more transcriptionally active in runnels (≈1.9 fold-higher). Sequencing of amoA genes and transcripts revealed starkly contrasting profiles with transcripts from ridges and runnels dominated (≈91 % in ridges and ≈98 % in runnels) by low abundant (≈4.6 % of the DNA community in runnels and ≈0.8 % in ridges) but highly active phylotypes. The higher PNR in runnels was explained by higher abundance of this group, an uncharacterised Nitrosomonas sp. cluster. This cluster is phylogenetically similar to other active ammonia-oxidizers with worldwide distribution in coastal environments indicating its potential, but previously overlooked, contribution to ammonia oxidation globally. In contrast DNA profiles were dominated by highly abundant but low-activity clusters phylogenetically distinct from known Nitrosomonas (Nm) and Nitrosospira (Ns). This cluster is also globally distributed in coastal sediments, primarily detected as DNA, and often classified as Nitrosospira or Nitrosomonas. We therefore propose to classify this cluster as Ns/Nm. Our work indicates that low abundant but highly active AOB could be responsible for the nitrification globally, while the abundant AOB Ns/Nm may not be transcriptionally active, and as such account for the lack of correlation between rate processes and gene abundances often reported in the literature. It also raises the question as to what this seemingly inactive group is doing?

Finite Element Analysis of the Effect of Femoral Prosthesis Varus and Valgus Angle Installation on the Lateral Compartment in Unicompartmental Knee Arthroplasty.

BACKGROUND: This study used finite element analysis (FEA) to investigate the effect of varus and valgus angle on the lateral compartment in unicompartmental knee arthroplasty (UKA). METHODS: One patient who underwent UKA was enrolled as the subject. Thirteen working conditions of the femoral prosthesis were simulated at varus and valgus angles of 0°, 2°, 4°, 6°, 8°, 10°, and 12°. A load of 1,000 N was applied downward along the mechanical axis of the femur, and the highest stress values on the surface of the polyethylene liner, cancellous bone under the tibial prosthesis, cartilage of femur lateral condyle, lateral meniscus, and tibial lateral plateau cartilage in each model were recorded. The six highest points were used to calculate the mean value. RESULTS: The highest stress values on the surface of the polyethylene liner, cancellous bone under the tibial prosthesis, cartilage of femur lateral condyle, lateral meniscus, and tibial lateral plateau cartilage increased with an increase in the femoral prosthesis varus/valgus angle. As compared with the standard position of the femoral prosthesis, there was no significant difference in the surface stress values of the polyethylene liner, cancellous bone under the tibial prosthesis, cartilage of femur lateral condyle, lateral meniscus and tibial lateral plateau cartilage when the femoral prosthesis varus/valgus angle was less than 4° (p > 0.05). In addition, the stress magnitude on the polyethylene liner, cancellous bone under the tibial prosthesis, cartilage of femur lateral condyle, lateral meniscus, and tibial lateral plateau cartilage significantly increased when the femoral prosthesis varus/valgus angle was greater than 4° (p < 0.001). CONCLUSIONS: The optimal femoral prosthesis varus/valgus angle in UKA was less than 4°.

Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while NH4+ concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.

Relative contribution of ammonia-oxidizing bacteria and denitrifying fungi to N2O production during rice straw composting with biochar and biogas residue amendments.

Nitrous oxide (N2O) production is associated with ammonia-oxidizing bacteria (amoA-AOB) and denitrifying fungi (nirK-fungi) during the incorporation of biochar and biogas residue composting. This research examined the relative contribution of alterations in the abundance, diversity and structure of amoA-AOB and nirK-fungi communities on N2O emission by real-time PCR and sequence processing. Results showed that N2O emissions showed an extreme relation with the abundance of amoA-AOB (rs = 0.584) while giving credit to nirK-fungi (rs = 0.500). Nitrosomonas and Nitrosospira emerged as the dominant genera driving ammoxidation process. Biogas residue changed the community structure of AOB by altering Nitrosomonadaceae proportion and physiological capacity. The denitrification process, primarily governed by nirK-fungi, served as a crucial pathway for N2O production, unveiling the pivotal mechanism of biochar to suppress N2O emissions. C/N and NH4+-N were identified as significant parameters influencing the distribution of nirK-fungi, especially Micromonospora, Halomonas and Mesorhizobium.

DLTN-LOSP: A Novel Deep-Linear-Transition-Network-Based Resource Allocation Model with the Logic Overhead Security Protocol for Cloud Systems.

Cloud organizations now face a challenge in managing the enormous volume of data and various resources in the cloud due to the rapid growth of the virtualized environment with many service users, ranging from small business owners to large corporations. The performance of cloud computing may suffer from ineffective resource management. As a result, resources must be distributed fairly among various stakeholders without sacrificing the organization's profitability or the satisfaction of its customers. A customer's request cannot be put on hold indefinitely just because the necessary resources are not available on the board. Therefore, a novel cloud resource allocation model incorporating security management is developed in this paper. Here, the Deep Linear Transition Network (DLTN) mechanism is developed for effectively allocating resources to cloud systems. Then, an Adaptive Mongoose Optimization Algorithm (AMOA) is deployed to compute the beamforming solution for reward prediction, which supports the process of resource allocation. Moreover, the Logic Overhead Security Protocol (LOSP) is implemented to ensure secured resource management in the cloud system, where Burrows-Abadi-Needham (BAN) logic is used to predict the agreement logic. During the results analysis, the performance of the proposed DLTN-LOSP model is validated and compared using different metrics such as makespan, processing time, and utilization rate. For system validation and testing, 100 to 500 resources are used in this study, and the results achieved a make-up of 2.3% and a utilization rate of 13 percent. Moreover, the obtained results confirm the superiority of the proposed framework, with better performance outcomes.

Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean.

Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.

Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil.

AIMS: One of the main challenges of culture-independent soil microbiology is distinguishing the microbial community's viable fraction from dead matter. Propidium monoazide (PMA) binds the DNA of dead cells, preventing its amplification. This dye could represent a robust means to overcome the drawbacks of other selective methods, such as ribonucleic acid-based analyses. METHODS AND RESULTS: We quantified functional genes from viable archaea and bacteria in soil by combining the use of PMA and quantitative polymerase chain reaction. Four N-cycle-related functional genes (bacterial and archaeal ammonia monooxygenase, nitrate reductase, and nitrite reductase) were successfully quantified from the living fraction of bacteria and archaea of a paddy soil. The protocol was also tested with pure bacterial cultures and soils with different physical and chemical properties. CONCLUSIONS: The experiment results revealed a contrasting impact of mineral and organic fertilizers on the abundance of microbial genes related to the N-cycle in paddy soil.

Partial versus total knee arthroplasty for isolated antero-medial osteoarthritis - An analysis of PROMs and satisfaction.

AIM: This study aimed to compare the patient-reported functional outcomes and patient satisfaction after medial Unicompartmental Knee Arthroplasty (UKA) versus Total Knee Arthroplasty (TKA), performed for anteromedial osteoarthritis (AMOA) of the knee in patients from an Indian population, at a minimum 3-year follow-up. METHODS: This is a prospective matched cohort study (1:2 ratio). One hundred and one UKA cases were matched to 206 TKA cases by propensity score matching for age, body mass index (BMI), gender distribution, and the Charlson Comorbidity Index (CCI). The primary outcome (Oxford knee score, OKS) was assessed at a 3-year follow-up, along with secondary outcomes (Western Ontario and McMaster Universities Osteoarthritis Index [WOMAC] Score, Forgotten Joint Score (FJS), Anterior Knee Pain (Kujala) score, patient satisfaction, and revision rate at the final follow-up). RESULTS: The UKA group was superior to the TKA group in patient-reported functional outcomes based on the OKS (p = 0.004). Using the FJS score, UKA was more likely to be a forgotten joint compared to TKA (p < 0.001). However, differences in the OKS and FJS did not meet the reported minimal clinically important difference (MCID) thresholds. Quality of life (EuroQol-5D VAS scale) was found to be significantly higher in the UKA group (p < 0.001). Patients in the UKA group were more likely to be very satisfied (75.2%) versus the TKA group (62.1%, p = 0.023). CONCLUSION: For AMOA, UKA was associated with improved patient satisfaction compared to TKA. Although patient-reported outcome measures were statistically in favour of UKA over TKA, the differences were not clinically significant. Multicenter and randomized studies comparing the two procedures are warranted. EVIDENCE: Level-II Therapeutic.

Soil nitrogen functional transformation microbial genes response to biochar application in different irrigation paddy field in southern China.

Growing evidence points to the controlled irrigation (CI) and biochar application (BA) having agricultural economic value and ecological benefits, but their synergistic effect and microbial mechanism of nitrogen conversion remain unknown in paddy fields. The effects of different BA (0, 20, 40 t/hm2) on the soil nitrogen functional transformation microbial genes (nifH, AOA-amoA, AOB-amoA) in different irrigation (CI, flooding irrigation) were clarified. After one seasonal growth of paddy, the correlation between the abundance of functional genes OUT and soil nitrogen transformation environment factors during the typical growth period was analyzed. High-throughput sequencing results illustrated that the application of CC (40 t/hm2 biochar) increased the nifH genes bacterial community abundance; the abundance of dominant microorganism increased by 79.68~86.19%. Because biochar can potentially control the rates of N cycling in soil systems by adsorbing ammonia and increasing NH4+ storage, it increased soil NH4+-N and NO3--N content by 60.77% and 26.14%, improving microbial nitrogen fixation. Rare species Nitrosopumilus, Nitrosococcus, and Methylocystis appeared in biochar treatments group, which increased the diversity of microbial in paddy. The combined use of CI and BA affected soil inorganic nitrogen content, temperature (T), pH, Eh, etc., which affected urease, urea hydrolysis, and nitrogen functional transformation microorganism genes. Correlation analysis shows that soil NH4+-N, T, and Eh, respectively, are significant factors for the formation of nifH, AOA-amoA, and AOB-amoA soil bacterial communities, respectively. This study suggests that to maintain the biodiversity of soil and realize the sustainable development of rice cultivation, CI is of great importance in combination with BA.

Black Plastic Film Mulching Increases Soil Nitrous Oxide Emissions in Arid Potato Fields.

Black plastic film mulching is a common practice for potato production in the arid area of Northwest China. Many studies have reported the significant positive effect of black plastic film mulch on potato harvest, while the effect of black plastic film mulch treatment on soil nitrous oxide (N2O) emissions is still unclear. As a consequence, this study aimed to examine the effect of black plastic film mulch treatment on N2O emission from arid upland potato fields. With the static chamber-gas chromatography method, soil N2O emissions were measured. The results showed that black plastic film mulching treatment significantly increased cumulative soil N2O emissions by 21-26% compared with non-mulched treatment. Cumulative N2O emission positively correlated with soil temperature, soil moisture, soil CO2 concentration, and amoA-AOB abundance. This study indicated that black plastic film mulching, mainly through increasing soil temperature and soil moisture, increasing soil carbon dioxide (CO2) concentration, and promoting the abundance of nitrification-related functional gene of amoA-AOB, regulated N2O emissions. This study also highlighted that the specific soil environment under black plastic film mulch is conducive to N2O emissions and lay the foundation for settling the contradiction between food production and greenhouse gas mitigation in upland soils. The negative effects of black plastic film mulching on the environment should be considered in future applications in food production.

Novel database and cut-off value for bacterial amoA gene revealed a spatial variability pattern of the ammonia-oxidizing bacteria community from river to sea.

Ammonia-oxidizing bacteria (AOB) catalyze the first step of nitrification, oxidizing ammonia to nitrite, and are characterized by amoA gene encoding ammonia monooxygenase. To analyze the AOB community effectively, an integral taxonomy database containing 14,058 amoA sequences and the optimal cut-off value at 95 % for OTU clustering were determined. This method was evaluated to be efficient by the analysis of environmental samples from the river, estuary, and sea. Using this method, a significant spatial variance of the AOB community was found. The diversity of AOB was highest in the estuary and lowest in the ocean. Nitrosomonas were the predominant AOB in the sediments of the freshwater river and estuary. Nearly all the AOB-amoA sequences belonged to uncultured bacterium in the sediments of deep sea. In general, an integral AOB taxonomic database and a suitable cut-off value were constructed for the comprehensive exploration of the diversity of AOB from river to sea.

Stochastic factors drive dynamics of ammonia-oxidizing archaeal and bacterial communities in aquaculture pond sediment.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in nitrification, which is essential in the global nitrogen cycle. However, their dynamics and the underlying community processes in agricultural ecosystems under disturbance remain largely unknown. In this study we examined the spatiotemporal dynamics of AOA and AOB communities and analyzed their community processes in the sediment of aquaculture ponds across three different areas in China. We found some significant temporal changes in AOA and AOB community diversity and abundances, but no temporal changes in community composition, despite the significant variations in sediment properties between different sampling times. Nevertheless, significant differences were found for AOA and AOB communities between different areas. Distinct area-specific taxa were detected, and they were found to be important in determining the response of AOA and AOB communities to environmental factors. In addition, geographic distance was found to be significantly correlated with AOA and AOB community composition, which demonstrates that dispersal limitation could significantly contribute to the variations in AOA and AOB communities, and stochastic processes were found to be important in structuring AOA/AOB communities in aquaculture ponds. Taken together, our study indicates that the dynamics of AOA and AOB are based on their community characteristics in aquaculture pond sediment. Our results, for the first time, provide evidence for the dynamics of AOA and AOB communities being driven by stochastic factors in a disturbed environment, and might also be of use in the management of the aquaculture environment.

Effect of steel slag on ammonia removal and ammonia-oxidizing microorganisms in zeolite-based tidal flow constructed wetlands.

The ammonia removal performance of tidal flow constructed wetlands (TFCWs) requires to be improved under high hydraulic loading rates (HLRs). The pH decrease caused by nitrification may adversely affect the NH4+-N removal and ammonia-oxidizing microorganisms (AOMs) of TFCWs. Herein, TFCWs with zeolite (TFCW_Z) and a mixture of zeolite and steel slag (TFCW_S) were built to investigate the influence of steel slag on NH4+-N removal and AOMs. Both TFCWs were operated under short flooding/drying (F/D) cycles and high HLRs (3.13 and 4.69 m3/(m2 d)). The results revealed that a neutral effluent pH (6.98-7.82) was achieved in TFCW_S owing to the CaO dissolution of steel slag. The NH4+-N removal efficiencies in TFCW_S (91.2 ± 5.1%) were much higher than those in TFCW_Z (73.2 ± 7.1%). Total nitrogen (TN) removal was poor in both TFCWs mainly due to the low influent COD/TN. Phosphorus removal in TFCW_S was unsatisfactory because of the short hydraulic retention time. The addition of steel slag stimulated the flourishing AOMs, including Nitrosomonas (ammonia-oxidizing bacteria, AOB), Candidatus_Nitrocosmicus (ammonia-oxidizing archaea, AOA), and comammox Nitrospira, which may be responsible for the better ammonia removal performance in TFCW_S. PICRUSt2 showed that steel slag also enriched the relative abundance of functional genes involved in nitrification (amoCAB, hao, and nxrAB) but inhibited genes related to denitrification (nirK, norB, and nosZ). Quantitative polymerase chain reaction (qPCR) revealed that complete AOB (CAOB) and AOB contributed more to the amoA genes in TFCW_S and TFCW_Z, respectively. Therefore, this study revealed that the dominant AOMs could be significantly changed in zeolite-based TFCW by adding steel slag to regulate the pH in situ, resulting in a more efficient NH4+-N removal performance.

Evaluation of four primer sets for analysis of comammox communities in black soils.

Comammox, as a newly discovered ammonia oxidizer, urgently needs highly efficient and specific primers to detect its community structure and diversity. In this study, the performance of widely used primer set Ntsp-amoA 162F/359R and newly designed primer sets comamoA F/R, CA377f/C576r, and CB377f/C576r were evaluated, for high-throughput sequencing of comammox amoA genes in natural and arable soils sampled from two locations in the black soil region of northeast China. Results showed that, compared with the primer set comamoA F/R, primers Ntsp-amoA 162F/359R had more advantages in detecting comammox operational taxonomic unit (OTU) numbers, diversity, and community structure. The primer sets CA377f/C576r and CB377f/C576r had an advantage in detecting comammox sequences with low relative abundance. In addition, the results of the phylogenetic tree and the relative abundance of dominant OTUs showed that the comammox in the black soils of northeast China was dominated by Nitrospira Clade B. Furthermore, our study found that long-term land use reduced the alpha diversity of the comammox community, but lead to the convergent evolution of community structure. The Mantel test and canonical correspondence analysis indicated that soil NO3 --N content was the most important factor affecting the community structure of comammox. Our study provided experience accumulation for the selection of comammox primers for high-throughput sequencing in the black soil of northeast China.

Limited Impacts of Cover Cropping on Soil N-Cycling Microbial Communities of Long-Term Corn Monocultures.

Cover cropping (CC) is a promising in-field practice to mitigate soil health degradation and nitrogen (N) losses from excessive N fertilization. Soil N-cycling microbial communities are the fundamental drivers of these processes, but how they respond to CC under field conditions is poorly documented for typical agricultural systems. Our objective was to investigate this relationship for a long-term (36 years) corn [Zea mays L.] monocultures under three N fertilizer rates (N0, N202, and N269; kg N/ha), where a mixture of cereal rye [Secale cereale L.] and hairy vetch [Vicia villosa Roth.] was introduced for two consecutive years, using winter fallows as controls (BF). A 3 × 2 split-plot arrangement of N rates and CC treatments in a randomized complete block design with three replications was deployed. Soil chemical and physical properties and potential nitrification (PNR) and denitrification (PDR) rates were measured along with functional genes, including nifH, archaeal and bacterial amoA, nirK, nirS, and nosZ-I, sequenced in Illumina MiSeq system and quantified in high-throughput quantitative polymerase chain reaction (qPCR). The abundances of nifH, archaeal amoA, and nirS decreased with N fertilization (by 7.9, 4.8, and 38.9 times, respectively), and correlated positively with soil pH. Bacterial amoA increased by 2.4 times with CC within N269 and correlated positively with soil nitrate. CC increased the abundance of nirK by 1.5 times when fertilized. For both bacterial amoA and nirK, N202 and N269 did not differ from N0 within BF. Treatments had no significant effects on nosZ-I. The reported changes did not translate into differences in functionality as PNR and PDR did not respond to treatments. These results suggested that N fertilization disrupts the soil N-cycling communities of this system primarily through soil acidification and high nutrient availability. Two years of CC may not be enough to change the N-cycling communities that adapted to decades of disruption from N fertilization in corn monoculture. This is valuable primary information to understand the potentials and limitations of CC when introduced into long-term agricultural systems.

Effect of pesticides on nitrification activity and its interaction with chemical fertilizer and manure in long-term paddy soils.

Effect of pesticides on nitrification activity and its interaction among heavy metal concentrations (HMCs), antibiotic resistance genes (ARGs), and ammonia monooxygenase (amoA) genes of long-term paddy soils is little known. The aim was to study the effect of pesticides on net nitrification rate (NR), potential nitrification rate (NP), HMCs, ARGs (sulI, sulII, tetO, and tetQ), and amoA (amoA-AOA, amoA-AOB, and amoA-NOB) genes in long-term treated paddy soils. NR and NP were significantly decreased (p < 0.05), whereas HMCs (Pb2+, Cu2+, Zn2+, and Fe3+) were a significantly increased (p < 0.05) in chemical fertilizer with pesticide treated paddy soils as compared with chemical fertilizer treated paddy soils. The scatter plot matrix indicated that total carbon (TC), soil organic carbon (SOC), total nitrogen (TN), and Fe were linearly correlated with NR and NP in long-term treated paddy soils. ARGs and amoA genes were significantly decreased (p < 0.05) in chemical fertilizer and manure with pesticide treated paddy soils. Overall, the result indicated the response of pesticide and their combination of manure with pesticide interaction present in long-term paddy soils, which will play a great role in the control uses of pesticides, manure, and chemical fertilizers in paddy soils and protect the nitrogen cycle as well as environment.

Distribution and Oxidation Rates of Ammonia-Oxidizing Archaea Influenced by the Coastal Upwelling off Eastern Hainan Island.

Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with 15N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance of distinct clades for AOA communities at the respective gene and transcript levels, and a large increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO rates were generally higher in the deeper water (~25 m), which was in significant positive correlation with the proportion of cluster Water Column A (WCA) at the transcript level, indicating the potential contribution of this cluster to in situ ammonia oxidization. Our study demonstrated that coastal upwelling had a significant impact on the AOA community and ammonia oxidization rate; therefore, this physical forcing should be considered in the future assessment of the global nitrogen budgets and biogeochemical nitrogen cycles.

Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems.

Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.