Ammonia-oxidizing bacteria: a model for molecular microbial ecology

Phenol-driven ammonium recovery from coal chemical wastewater in a bioelectrochemical system (BES)

Bioelectrochemical systems (BES) have gained considerable attention in the past decade as a potentially sustainable and cost-effective method for coal chemical wastewater (CCW) treatment. However, a scarcity of studies focusing on the recovery NH4+-N in the recycling treatment of CCW via BES technology. In this study, a BES-ammonium recovery system (BES-ARS) was proposed to remove phenol and NH4+-N simultaneously, while NH4+-N was further recovered in a downstream recovery unit. Through systematic evaluation, we identified optimal condition for both phenol and NH4+-N removal. Specifically, an influent phenol-to-ammonium ratio of 2.0 was found to be ideal for maximizing simultaneous removal efficiency. Additionally, an evaluation of the nitrogen distribution showed that 97.9 % of NH4+-N migrated to the cathode chamber, with 82.5 % of NH4+-N being recovered in the absorbent under optimal condition. Furthermore, the solution not only reduces operational costs by up to 68 % compared to conventional treatments, but also conserves energy. This study presents an efficient and environmentally friendly treatment method for treating CCW, while recovering NH4+-N as a valuable resource.

Impact of environmental and process conditions on the microbial ecology and performance of full-scale slow sand filters in drinking water treatment

Slow sand filters (SSFs) are commonly used for treating drinking water, effectively removing contaminants such as particles, organic matter, and microorganisms. However, the ecological dynamics of prokaryotic communities within SSFs remain poorly understood. This study investigated the top sand layer, the Schmutzdecke (SCM), along with the influent and effluent water of full-scale SSFs at four drinking water treatment plants (DWTPs) in the Netherlands. These plants use SSFs as the final step in their treatment to produce unchlorinated drinking water. Two DWTPs treat surface water after dune infiltration and do not apply advanced oxidation processes prior the SSF. In contrast, the other two DWTPs treat reservoir-stored surface water and incorporate ozonation or UV and activated carbon filtration as part of their treatment train. All SSFs consistently reduced biomass in the effluent compared to the influent, confirming their role in biomass load reduction. Key biological and chemical parameters showed that pretreatment with dune infiltration produced more biologically stable drinking water compared to reservoir storage. Moreover, while SSFs act as polishing filters when treating dune-infiltrated surface water, they significantly alter the prokaryotic community and biological stability of the water when treating reservoir-stored surface water. Prokaryotic communities in the SCM and water samples showed distinct compositions rather than merely the accumulation of microorganisms in the SCM from the influent water, demonstrating that SSF are active ecosystems different from water. The SCM exhibited a higher relative abundance of the genera SWB02, Gemmata, Pedomicrobium, Nitrospira, and mle1-7, while in the water samples the genus Candidatus Omnitrophus was relatively more abundant. Moreover, each DWTP hosts a unique prokaryotic profiles in both the SCM and water samples. Source water, upstream treatment and/or the biological stability of the influent water are identified as potential causes affecting the prokaryotic communities in SSFs that affect the microbial water quality of the effluent water.

Soil nitrogen deficiency aggravated the aging of biodegradable microplastics in paddy soil under the input of organic substances with contrasting C/N ratios

The application of organic substances to the agricultural field has effectively enhanced soil nutrient levels and crop yields. Biodegradable microplastics (bio-MPs), a pervasive emerging contaminant, may potentially impact the soil ecosystem through their aging process. Here, a 150-day dark incubation experiment was conducted to elucidate the disparities in the aging process of polylactic acid bio-MPs (PLA-MPs) in soils with contrasting C/N ratios of organic substances, as the mechanisms underlying this process remain unclear. The study found that PLA-MPs resulted in an increase in soil pH, nutrient levels, and organic carbon content in soil-straw system. Additionally, PLA-MPs significantly influenced bacterial community composition and microbial metabolic activity in soil-straw system. Notably, more pronounced aging features of PLA-MPs was observed in soil-straw system (lower soil nitrogen environment) compared to soil-fertilizer system (higher soil nitrogen environment). Under lower soil nitrogen conditions, microorganisms may accelerate the aging process of PLA-MPs due to their preference for readily available energy sources; conversely, under higher soil nitrogen conditions, the aging of PLA-MPs may be decelerated as microorganisms preferentially utilize substances with easily accessible energy sources. Our findings provide valuable insights into the interaction between PLA-MPs and soil amended with the organic substances of contrasting C/N ratios.

Elucidation of the stress mechanisms on activated sludge stability induced by yttrium oxide nanoparticles with cytotoxicity: Performance deterioration, biointerface variation and microbial response

As technoscience advances, widespread use of nanoparticles (NPs) has resulted in environmental risks. This study focuses on the potential stress of 0-200 mg/L yttrium oxide (Y2O3) NPs on the activated sludge stability. Y2O3 NPs progressively suppressed nitrification, caused significant NO2- accumulation (200 mg/L) and diminished activities of key functional enzymes. Deteriorated flocculation corroborates the Y2O3 NPs' destruction. Extracellular polymeric substances were lessened, yet amplified microbial metabolites prove the microbial counteraction coping with Y2O3 NPs' cytotoxicity. Plausible blockage of different protein channels contributed to the wane in biological nitrogen-removal capacity. Plus, 50 mg/L Y2O3 NPs stimulated the β-glucan production. When exceeding 100 mg/L, plentiful Y2O3 NPs aggregate on sludge-surface, which inhibits nutrients transfer and metabolism. Furthermore, ammonia-oxidizing bacteria shifted from Nitrosomonas to Nitrosospira with Y2O3 NPs increase. Reduction in Nitrospira, Saccharimonada-genera, and Microlunatus further corroborates the impairment of pollutants removal. PICRUSt2 prediction demonstrates Y2O3 NPs impedes nitrogen and glycolytic metabolic pathway.

Response of Nitrogen Cycle Microorganisms to Multifactorial Global Changes in Soil Ecosystems

BACKGROUND

Climate change affects life on Earth. Meanwhile, microorganisms (unlike plants and animals) are usually not considered when studying climate change, particularly due to the impact of climatic fluctuation on them. A substantial variety of microbes and their responses to changing environmental conditions make determining their role in the ecosystem functioning very difficult. Nevertheless, microorganisms support the existence of all life forms on the planet. It is also important to know how microorganisms affect climate change and how this subsequently then affects microorganisms. Previous research demonstrates the leading role and importance of microorganisms in studying the biological aspects of climate change. Thus, this paper aimed to examine the correlation between nitrogen cycle microorganisms and climate change.

METHODS

The nitrogen cycle microorganism (NCM) soil formed the primary research object, which, simultaneously, is not associative microflora and belongs to the following groups: amino heterotrophs using organic forms of nitrogen, aminoautotrophs using mineral forms of nitrogen, and diazotrophs fixing nitrogen in the air. The response of NCMs in simultaneously increasing atmospheric CO2, precipitation, temperature, and nitrogen in an artificially created agricultural soil ecosystem was investigated.

RESULTS

The NCM number and their structure responded to these simulated changes. The increased volume of nitrogen significantly changed the NCM structure, which depends on temperature and precipitation. The dominance of NCMs was noted when the temperature and precipitation remained unchanged. However, the number of microorganisms consuming mineral forms of nitrogen increased following a rise in temperature and a reduction in precipitation. Further, the proportion of microorganisms consuming organic forms of nitrogen increased following a decrease in temperature and increased precipitation. Total NCMs reduced significantly when the CO2 increased; this decrease was most pronounced with increased precipitation. Changes in the group composition of the community are associated with an increase in the nitrification process, with no changes in total NCMs.

CONCLUSIONS

These results illustrate that the ever-increasing concentration of CO2 in the atmosphere has a direct impact on both Earth's climate and alters the composition and activity of microbial populations.

Impacts of Land Use on Soil Nitrogen-Cycling Microbial Communities: Insights from Community Structure, Functional Gene Abundance, and Network Complexity

This study investigates the effects of different land-use types (forest, arable land, and wetland) on key soil properties, microbial communities, and nitrogen cycling in the Lesser Khingan Mountains. The results revealed that forest (FL) and wetland (WL) soils had significantly higher soil organic matter (SOM) content compared with arable land (AL), with total phosphorus (TP) being highest in FL and available nitrogen (AN) significantly higher in WL. In terms of enzyme activity, AL and WL showed reduced activities of ammonia monooxygenase (AMO), β-D-glucosidase (β-G), and β-cellobiosidase (CBH), while exhibiting increased N-acetyl-β-D-glucosaminidase (NAG) activity, highlighting the impact of land use on nitrogen dynamics. WL also exhibited significantly higher microbial diversity and evenness compared with FL and AL. The dominant bacterial phyla included Actinobacteriota, Proteobacteria, and Acidobacteriota, with Acidobacteriota being most abundant in FL and Proteobacteria most abundant in WL. Network analysis showed that AL had the most complex and connected microbial network, while FL and WL had simpler but more stable networks, suggesting the influence of land use on microbial community interactions. Regarding nitrogen cycling genes, AOA-amoA was most abundant in AL, while AOB-amoA was significantly enriched in FL, reflecting the influence of land use on ammonia oxidation. These findings highlight how land-use types significantly affect soil properties, microbial community structures, and nitrogen cycling, offering valuable insights for sustainable land management.

Chromolaena odorata affects soil nitrogen transformations and competition in tropical coral islands by altering soil ammonia oxidizing microbes

Invasive plants can change the community structure of soil ammonia-oxidizing microbes, affect the process of soil nitrogen (N) transformation, and gain a competitive advantage. However, the current researches on competition mechanism of Chromolaena odorata have not involved soil nitrogen transformation. In this study, we compared the microbially mediated soil transformations of invasive C. odorata and natives (Pisonia grandis and Scaevola taccada) of tropical coral islands. We assessed how differences in plant biomass and tissue N contents, soil nutrients, N transformation rates, microbial biomass and activity, and diversity and abundance of ammonia oxidizing microbes associated with these species impact their competitiveness. The results showed that C. odorata outcompeted both native species by allocating more proportionally biomass to aboveground parts in response to interspecific competition (12.92 % and 22.72 % more than P. grandis and S. taccada, respectively). Additionally, when C. odorata was planted with native plants, the available N and net mineralization rates in C. odorata rhizosphere soil were higher than in native plants rhizosphere soils. Higher abundance of ammonia-oxidizing bacteria in C. odorata rhizosphere soil confirmed this, being positively correlated with soil N mineralization rates and available N. Our findings help to understand the soil N acquisition and competition strategies of C. odorata, and contribute to improving evaluations and predictions of invasive plant dynamics and their ecological effects in tropical coral islands.

Organic farming systems improve soil quality and shape microbial communities across a cotton-based crop rotation in an Indian Vertisol

The adverse effects of intensified cropland practices on soil quality and biodiversity become especially evident in India, where nearly 60% of land is dedicated to cultivation and almost 30% of soil is already degraded. Intensive agricultural practice significantly contributes to soil degradation, highlighting the crucial need for effective countermeasures to support sustainable development goals. A long-term experiment, established in the semi-arid Nimar Valley (India) in 2007, monitors the effect of organic and conventional management on the plant-soil system in a Vertisol. The focus of our study was to assess how organic and conventional farming systems affect biological and chemical soil quality indicators. Additionally, we followed the community structure of the soil microbiome throughout the vegetation phase under soya or cotton cultivation in the year 2019. We found that organic farming enhanced soil organic carbon and nitrogen content, increased microbial abundance and activity, and fostered distinct microbial communities associated with traits in nutrient mineralization. In contrast, conventional farming enhanced the abundance of bacteria involved in ammonium oxidation suggesting high nitrification and subsequent nitrogen losses with regular mineral fertilization. Our findings underscore the value of adopting organic farming approaches in semi-arid subtropical regions to rectify soil quality and minimize nitrogen losses.

Cenchrus spinifex Invasion Alters Soil Nitrogen Dynamics and Competition

Invasive plants often alter biological soil conditions to increase their own competitiveness. Through indoor simulated nitrogen deposition culture experiments, we investigated the differences in growth indicators and nutrient content levels between the invasive plant Cenchrus spinifex Cav. and the native symbiotic plant Agropyron cristatum (L.) Gaertn. under diverse nitrogen application modes and planting-competition ratios. Furthermore, we examined the alterations in key microbial communities involved in soil nitrogen cycling of C. spinifex. The results indicated that the invasion of C. spinifex could inhibit the growth of native plants, and in fact altered the accumulation and transformation processes related to soil nitrogen, resulting in reduced rates of soil nitrogen transformation. The overarching aim of this research was to construct a theoretical foundation for the scientific comprehension of the invasion mechanisms of C. spinifex, in order to better prevent the further spread of this invasive plant and mitigate its pernicious impact on the current environment.

Tipping the plant-microbe competition for nitrogen in agricultural soils

Nitrogen (N) is the most limiting nutrient in agroecosystems, and its indiscriminate application is at the center of the environmental challenges facing agriculture. To solve this dilemma, crops' nitrogen use efficiency (NUE) needs to increase - in other words, more of the applied nitrogen needs to reach humans. Microbes are the key to cracking this problem. Microbes use nitrogen as an energy source, an electron acceptor, or incorporate it in their biomass. These activities change the form and availability of nitrogen for crops' uptake, impacting its NUE, yields and produce quality. Plants (and microbes) have, however, evolved many mechanisms to compete for soil nitrogen. Understanding and harnessing these competitive mechanisms would enable us to tip the nitrogen balance to the advantage of crops. We will review these competitive mechanisms and highlight some approaches that were applied to reduce microbial competition for N in an agricultural context.

Comparative analysis of prokaryotic microbiomes in high-altitude active layer soils: insights from Ladakh and global analogues using In-Silico approaches

The active layer is the portion of soil overlaying the permafrost that freezes and thaws seasonally. It is a harsh habitat in which a varied and vigorous microbial population thrives. The high-altitude active layer soil in northern India is a unique and important cryo-ecosystem. However, its microbiology remains largely unexplored. It represents a unique reservoir for microbial communities with adaptability to harsh environmental conditions. In the Changthang region of Ladakh, the Tsokar area is a high-altitude permafrost-affected area situated in the southern part of Ladakh, at a height of 4530 m above sea level. Results of the comparison study with the QTP, Himalayan, Alaskan, Russian, Canadian and Polar active layers showed that the alpha diversity was significantly higher in the Ladakh and QTP active layers as the environmental condition of both the sites were similar. Moreover, the sampling site in the Ladakh region was in a thawing condition at the time of sampling which possibly provided nutrients and access to alternative nitrogen and carbon sources to the microorganisms thriving in it. Analysis of the samples suggested that the geochemical parameters and environmental conditions shape the microbial alpha diversity and community composition. Further analysis revealed that the cold-adapted methanogens were present in the Ladakh, Himalayan, Polar and Alaskan samples and absent in QTP, Russian and Canadian active layer samples. These methanogens could produce methane at slow rates in the active layer soils that could increase the atmospheric temperature owing to climate change.

Sealing solid agar in serum bottles for rapid isolation and long-term preservation of chemoautotrophic ammonia-oxidizing bacteria

Ammonia-oxidizing bacteria (AOB) are ubiquitous on the earth and have broad applications in bioremediation. However, the number of their species with standing in nomenclature and deposited in Microbial Culture Collections still remains low. Moreover, only a few novel species have been reported over the last decades. In this study, we sealed agar in serum bottles to develop a kind of solid agar plate with the oxygen concentration in the headspace maintained at low levels. By using these plates, eight AOB isolates including two novel species were obtained. When AOB cells were grown on the sealed solid agar plates, the time to form visible colonies was largely reduced and the maximum diameter of colonies reached 2 mm, which makes the process of AOB isolation rapid and efficient. Based on five AOB isolates, the headspace oxygen concentration had a significant influence on AOB growth either on solid plate or in liquid culture. Especially, when grown under 21 % O2, the number of colonies formed on solid agar plates was very low and sometimes no visible colony formed. Besides the application on AOB isolation, the sealed solid agar plate was also effective for the enumeration and preservation of AOB cells. When preserved under room temperature for more than ten months, the AOB colonies on the plate could still be recovered. This method provides a feasible way to isolate more novel AOB species from the environment and deposit more species in Microbial Culture Collections.

Interference of microplastics on autotrophic microbiome in paddy soils: Shifts in carbon fixation rate, structure, abundance, co-occurrence, and assembly process

Autotrophic microorganisms play a crucial role in soil CO2 assimilation. Although microplastic pollution is recognized as a significant global concern, its precise impact on carbon sequestration by autotrophic microorganisms in agroecosystem soil remains poorly understood. This study conducted microcosm experiments to explore how conventional polystyrene (PS) and biodegradable poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) microplastics affect carbon fixation rates (CFRs) and the community characteristics of soil autotrophic microorganisms in paddy agroecosystems. The results showed that compared with the control groups, 0.5 % and 1 % microplastic treatments significantly reduced soil CFRs by 11.8 - 24.5 % and 18.7 - 32.3 %, respectively. PS microplastics exerted a stronger inhibition effect on CFRs than PHBV microplastics in bulk soil. However, no significant difference was observed in the inhibition of CFRs by both types of microplastics in rhizosphere soils. Additionally, PS and PHBV microplastics altered the structure of autotrophic microbial communities, resulting in more stochastically dominated assembly and looser, more fragile coexistence networks compared to control groups. Moreover, microplastics drove the changes in autotrophic microbial carbon fixation primarily through their direct interference and the indirect effect by increasing soil organic carbon levels. Our findings enhance the understanding and predictive capabilities regarding the impacts of microplastic pollution on carbon sinks in agricultural soils.

Changes in microbial community structure related to biodegradation of eelgrass (Zostera marina)

Seagrass meadows produce organic carbon and deposit it on the seabed through the decaying process. Microbial activity is closely related to the process of eelgrass death and collapse. We investigated the microbial community structure of eelgrass during the eelgrass decomposition process by using a microcosm containing raw seawater and excised eelgrass leaves collected from a Zostera marina bed in Futtsu, Chiba Prefecture, Japan. The fast-growing microbes (i.e., Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia) rapidly adhered to the eelgrass leaf surface and proliferated in the first two weeks but gradually decreased the relative abundance as the months moved on. On the other hand, the slow-growing microbes (i.e., Cytophagia, Anaerolineae, Thaumarchaeota, and Actinobacteria) became predominant over the eelgrass surface late in the culture experiment (120, 180 days). The fast-growing groups of Gammaproteobacteria and Flavobacteriia appear to be closely related to the initial decomposition of eelgrass, especially the rapid decomposition of leaf-derived biopolymers. Changes in nitrogen content due to the bacterial rapid consumption of readily degradable organic carbon induced changes in the community structure at the early stage of eelgrass decomposition. In addition, shifts in the C/N ratio were driven by microbial community changes during later decomposition phases.

Microelectrode investigation of iron and copper surfaces aged in presence of monochloramine

Ductile iron and copper coupons were aged 137-189 days and 2 days, respectively, with 2 mg Cl2 L-1 monochloramine under four water chemistries (pH 7 or 9 and 0 or 3 mg L-1 orthophosphate). Subsequently, microelectrode profiles of monochloramine concentration, oxygen concentration, and pH were measured from the bulk water to near the coupon reactive surface, allowing estimation of flux and apparent surface reaction rate constants for monochloramine and oxygen. Both metals showed similar trends with orthophosphate where orthophosphate decreased metal reactivity with monochloramine (pH 9) and oxygen (pH 7). Comparing iron and copper coupons, apparent surface reaction rate constants for monochloramine and oxygen were one and two orders of magnitude greater, respectively, for iron coupons under all conditions. Overall, this research provides the first insights into monochloramine concentration, oxygen concentration, and pH by direct measurement near ductile iron and copper reactive surfaces aged in the presence of monochloramine.

Inhibitory effect of marine Bacillus sp. and its biomineralization on the corrosion of X65 steel in offshore oilfield produced water

The issue of material failure attributed to microbiologically influenced corrosion (MIC) is escalating in seriousness. Microorganisms not only facilitate corrosion but certain beneficial microorganisms also impede its occurrence. This study explored the impact of marine B. velezensis on the corrosion behavior of X65 steel in simulated offshore oilfield produced water. B. velezensis exhibited rapid growth in the initial stages, and the organic acid metabolites were found to promote corrosion. Subsequently, there was an increase in cross-linked "networked" biofilms products, a significant rise in the prismatic shape of corrosion products, and a tendency for continuous development in the middle and late stages. The organic/inorganic mineralized film layer formed on the surface remained consistently complete. Metabolic products of amino acid corrosion inhibitors were also observed to be adsorbed into the film. B. velezensis altered the kinetics of the X65 steel cathodic reaction, resulting in a deceleration of the electrochemical reaction rate. The mineralization induced by B. velezensis effectively slowed down the corrosion rate of X65 steel.

Ammonium-derived nitrous oxide is a global source in streams

Global riverine nitrous oxide (N2O) emissions have increased more than 4-fold in the last century. It has been estimated that the hyporheic zones in small streams alone may contribute approximately 85% of these N2O emissions. However, the mechanisms and pathways controlling hyporheic N2O production in stream ecosystems remain unknown. Here, we report that ammonia-derived pathways, rather than the nitrate-derived pathways, are the dominant hyporheic N2O sources (69.6 ± 2.1%) in agricultural streams around the world. The N2O fluxes are mainly in positive correlation with ammonia. The potential N2O metabolic pathways of metagenome-assembled genomes (MAGs) provides evidence that nitrifying bacteria contain greater abundances of N2O production-related genes than denitrifying bacteria. Taken together, this study highlights the importance of mitigating agriculturally derived ammonium in low-order agricultural streams in controlling N2O emissions. Global models of riverine ecosystems need to better represent ammonia-derived pathways for accurately estimating and predicting riverine N2O emissions.

Fast Bacterial Succession Associated with the Decomposition of Larix gmelinii Litter in Wudalianchi Volcano

In order to understand the role of microorganisms in litter decomposition and the nutrient cycle in volcanic forest ecosystems, the dominant forest species Larix gmelinii in the volcanic lava plateau of the Wudalianchi volcano was considered as the research object. We analyzed the response of bacterial community structure and diversity to litter decomposition for 1 year, with an in situ decomposition experimental design using litter bags and Illumina MiSeq high-throughput sequencing. The results showed that after 365 days, the litter quality residual rate of Larix gmelinii was 77.57%, and the litter N, P, C:N, C:P, and N:P showed significant differences during the decomposition period (p < 0.05). The phyla Cyanobacteria and the genus unclassified_o_Chloroplast were the most dominant groups in early decomposition (January and April). The phyla Proteobacteria, Actinobacteriota, and Acidobacteriota and the genera Massilia, Pseudomonas, and Sphingomona were higher in July and October. The microbial communities showed extremely significant differences during the decomposition period (p < 0.05), with PCoa, RDA, and litter QRR, C:P, and N as the main factors driving litter bacteria succession. Microbial functional prediction analysis showed that Chloroplasts were the major functional group in January and April. Achemoheterotrophy and aerobic chemoheterotrophy showed a significant decrease as litter decomposition progressed.

The significant contribution of comammox bacteria to nitrification in a constructed wetland revealed by DNA-based stable isotope probing

The discovery of Comammox bacteria (CMX) has changed our traditional concept towards nitrification, yet its role in constructed wetlands (CWs) remains unclear. This study investigated the contributions of CMX and two canonical ammonia-oxidizing microorganisms, ammonia-oxidizing bacteria (AOB) and archaea to nitrification in four regions (sediment, shoreside, adjacent soil, and water) of a typical CW using DNA-based stable isotope probing. The results revealed that CMX not only widely occurred in sediment and shoreside zones with high abundance (5.08 × 104 and 6.57 × 104 copies g-1 soil, respectively), but also actively participated in ammonia oxidation, achieving ammonia oxidation rates of 1.43 and 2.00 times that of AOB in sediment and shoreside, respectively. Phylogenetic analysis indicated that N. nitrosa was the dominant and active CMX species. These findings uncovered the crucial role of CMX in nitrification of sediment and shoreside, providing a new insight into nitrogen cycle of constructed wetlands.

Microbial Sources and Sinks of Nitrous Oxide during Organic Waste Composting

Composting is widely used for organic waste management and is also a major source of nitrous oxide (N2O) emission. New insight into microbial sources and sinks is essential for process regulation to reduce N2O emission from composting. This study used genome-resolved metagenomics to decipher the genomic structures and physiological behaviors of individual bacteria for N2O sources and sinks during composting. Results showed that several nosZ-lacking denitrifiers in feedstocks drove N2O emission at the beginning of the composting. Such emission became negligible at the thermophilic stage, as high temperatures inhibited all denitrifiers for N2O production except for those containing nirK. The nosZ-lacking denitrifiers were notably enriched to increase N2O production at the cooling stage. Nevertheless, organic biodegradation limited energy availability for chemotaxis and flagellar assembly to restrain nirKS-containing denitrifiers for nitrate reduction toward N2O sources but insignificantly interrupt norBC- and nosZ-containing bacteria (particularly nosZ-containing nondenitrifiers) for N2O sinks by capturing N2O and nitric oxide (NO) for energy production, thereby reducing N2O emission at the mature stage. Furthermore, nosZII-type bacteria included all nosZ-containing nondenitrifiers and dominated N2O sinks. Thus, targeted strategies can be developed to restrict the physiological behaviors of nirKS-containing denitrifiers and expand the taxonomic distribution of nosZ for effective N2O mitigation in composting.

Effective chloramine management without "burn" in biofilm affected nitrifying tanks using a low dose of copper

This paper highlights the potential to effectively inhibit nitrification and restore chloramine levels using a low copper concentration in a biofilm-affected (surface-to-volume ratio 16 m-1) continuous-flow laboratory-scale chloraminated system. High nitrite and low chloramine containing tanks are always recovered with chlorine "burn" by water utilities. The "burn" is not only costly and operationally complex, but also compromises the water quality, public health, and customer relations. A laboratory system comprising five reactors connected in series was operated. Each reactor simulated conditions typically encountered in full-scale systems. Low amount of copper (0.1-0.2 mg-Cu L-1) was dosed once per day into nitrified reactors. At any given time, only one reactor was dosed with copper. Not only inhibition of nitrification, chloramine decay associated with bulk water, biofilm and sediments also improved. However, the improvement was quicker and more significant when the influent to the reactor contained a high chloramine and a low nitrite concentration. Ammonia oxidising microbes exhibited resilience when exposed to low copper and chloramine concentrations for an extended period. Chloramine decay due to planktonic microbes and chemical reactions in bulk water decreased more rapidly than decay attributed to biofilm and sediments. The concept "biostable residual chlorine" explained how copper and chloramine can inhibit nitrification. Once nitrification was inhibited, the chloramine supplied from upstream effectively continued to suppress downstream nitrification, and this effect lasted more than 50 days even at 22 °C. The findings could be used to develop short-term copper dosing strategies and prevent negative impacts of nitrification and breakpoint chlorination.

Shallow wet irrigation reduces nitrogen leaching loss rate in paddy fields by microbial regulation and lowers rate of downward migration of leaching water: a 15N-tracer study

China consumes 35% of the world's fertilizer every year; however, most of the nitrogen fertilizers, which are essential for rice cultivation, are not used effectively. In this study, factors affecting the nitrogen leaching loss rate were studied in typical soil and rice varieties in South China. The effects of various irrigation measures on rice growth and nitrogen leaching loss were investigated by conducting experiments with eight groups. These groups included traditional irrigation (TI) and shallow wet irrigation (SWI). The TI is a common irrigation method for farmers in South China, maintaining a water layer of 5-8 cm depth. For SWI, after establishing a shallow water layer usually maintaining at 1-2 cm, paddy is irrigated when the field water level falls to a certain depth, then this process is then repeat as necessary. The nitrogen distribution characteristics were determined using 15N isotope tracing. In addition, the effects of nitrification, denitrification, and microbial composition on soil nitrogen transformation at different depths were studied by microbial functional gene quantification and high-throughput sequencing. The results revealed that in the SWI groups, the total nitrogen leaching loss rate reduced by 0.3-0.8% and the nitrogen use efficiency (NUE) increased by 2.18-4.43% compared with those in the TI groups. After the 15N-labeled nitrogen fertilizer was applied, the main pathways of nitrogen were found to be related to plant absorption and nitrogen residues. Furthermore, paddy soil ammonia-oxidizing archaea were more effective than ammonia-oxidizing bacteria for soil ammonia oxidation by SWI groups. The SWI measures increased the relative abundance of Firmicutes in paddy soil, enhancing the ability of rice to fix nitrogen to produce ammonium nitrogen, thus reducing the dependence of rice on chemical fertilizers. Moreover, SWI enhanced the relative abundance of nirS and nosZ genes within surface soil bacteria, thereby promoting denitrification in the surface soil of paddy fields. SWI also promoted ammonia oxidation and denitrification by increasing the abundance and activity of Proteobacteria, Nitrospirae, and Bacteroidetes. Collectively, SWI effectively reduced the nitrogen leaching loss rate and increase NUE.

Root Reduction Caused Directly or Indirectly by High Application of Nitrogen Fertilizer Was the Main Cause of the Decline in Biomass and Nitrogen Accumulation in Citrus Seedlings

Citrus is the largest fruit crop around the world, while high nitrogen (N) application in citrus orchards is widespread in many countries, which results not only in yield, quality and environmental issues but also slows down the establishment of citrus canopies in newly cultivated orchards. Thus, the objective of this study was to investigate the physiological inhibitory mechanism of excessive N application on the growth of citrus seedlings. A pot experiment with the citrus variety Orah (Orah/Citrus junos) at four N fertilization rates (0, 50, 100, and 400 mg N/kg dry soil, denoted as N0, N50, N100, and N400, respectively) was performed to evaluate the changes of root morphology, biomass, N accumulation, enzyme activities, and so on. The results showed that the N400 application significantly reduced the total biomass (from 14.24 to 6.95 g/Plant), N accumulation (from 0.65 to 0.33 g/Plant) and N use efficiency (92.69%) in citrus seedlings when compared to the N100 treatment. The partial least squares pathway model further showed that the decline of biomass and N accumulation by high N application were largely attributed to the reduction of root growth through direct and indirect effects (the goodness of fit under the model was 0.733.) rather than just soil N transformation and activity of root N uptake. These results are useful to optimize N management through a synergistic N absorption and utilization by citrus seedlings.

Effects of microplastics on carbon release and microbial community in mangrove soil systems

Mangrove ecosystems are major carbon sink biomes and also a sink of microplastics (MPs). The final enrichment of MPs in sediments may have a significant impact on the microbial community and carbon turnover in the soil. However, the effects of MP pollution on the mangrove soil microbial communities and carbon release remain unknown. Here, we conducted a manipulative incubation experiment by adding MPs to soil at different soil depths to examine the effect of enriched MPs on soil microorganisms and its function (i.e., decomposition of soil carbon). The results showed that the addition of MPs had no significant effect on the microbial diversity and CO2 cumulative emission in the topsoil but significantly increased CO2 release from the subsoil. The promoting effect of polylactide (PLA) on the release of CO2 from the subsoil was stronger than that of polyethylene (PE) and aging PE. In the subsoil, the activity of soil extracellular enzymes related to N acquisition increased with the MP addition, indicating an increase in microbial N deficiency. The subsoil was more sensitive to MPs because of the exacerbated nitrogen limitation. MP addition reduced the microbial diversity of the subsoil and altered soil microbial interactions. The increasing abundance of some microbial taxa, especially bacteria related to the sulfur cycle, indicated more active electron transfer and organic carbon mineralization in the subsoil. Our findings suggest that MP contamination has potential effects on microbial communities, nutrient cycling, and carbon release in mangrove soils that vary depending on soil depth.

Out of sight, but not out of season: Nitrifier distributions and population dynamics in a large oligotrophic lake

Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia-oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite-oxidizing bacteria (NOB) Nitrotoga dominate at depth in the summer, the ammonia-oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.

High throughput amplicon analysis reveals potential novel ammonia oxidizing prokaryotes in the eutrophic Jiaozhou Bay

Ammonia-oxidizing prokaryotes (AOPs) are the major contributors of ammonia oxidization with widely distribution. Here we investigated the phylogenetic diversity, community composition, and regulating factors of AOPs in Jiaozhou Bay (JZB) with high-throughput sequencing of amoA gene. Phylogenetic analysis showed most of the OTUs could not be clustered with any known AOPs, indicating there might exist putative novel AOPs. With new developed protocols for AOP community analysis, we confirmed that only 3 OTUs of ammonia-oxidizing archaea (AOA) could be affiliated to known Nitrosopumilaceae and Nitrososphaera, and the other OTUs were identified as novel AOA based on the threshold. All abstained OTUs of ammonia-oxidizing bacteria (AOB) were identified as novel clusters based on the threshold. Further analysis showed the novel AOPs had different distribution characteristics related to environmental factors. The high abundance and widespread distribution of these novel AOPs indicated that they played an important role in ammonia conversion in eutrophic JZB.

Competitive enrichment of comammox Nitrospira in floccular sludge

The discovery of complete ammonium oxidation (comammox) has subverted the traditional perception of two-step nitrification, which plays a key role in achieving biological nitrogen removal from wastewater. Floccular sludge-based treatment technologies are being applied at the majority of wastewater treatment plants in service where detection of various abundances and activities of comammox bacteria have been reported. However, limited efforts have been made to enrich and subsequently characterize comammox bacteria in floccular sludge. To this end, a lab-scale sequencing batch reactor (SBR) in the step-feeding mode was applied in this work to enrich comammox bacteria through controlling appropriate operational conditions (dissolved oxygen of 0.5 ± 0.1 g-O2/m3, influent ammonium of 40 g-N/m3 and uncontrolled longer sludge retention time). After 215-d operation, comammox bacteria gradually gained competitive advantages over counterparts in the SBR with a stable nitrification efficiency of 92.2 ± 2.2 %: the relative abundance of Nitrospira reached 42.9 ± 1.3 %, which was 13 times higher than that of Nitrosomonas, and the amoA gene level of comammox bacteria increased to 7.7 ± 2.1 × 106 copies/g-biomass, nearly 50 times higher than that of conventional ammonium-oxidizing bacteria. The enrichment of comammox bacteria, especially Clade A Candidatus Nitrospira nitrosa, in the floccular sludge led to (i) apparent affinity constants for ammonium and oxygen of 3.296 ± 0.989 g-N/m3 and 0.110 ± 0.004 g-O2/m3, respectively, and (ii) significantly low N2O and NO production, with emission factors being 0.136 ± 0.026 % and 0.023 ± 0.013 %, respectively.

Effect of nitrogen reduction by chemical fertilization with green manure (Vicia sativa L.) on soil microbial community, nitrogen metabolism and and yield of Uncaria rhynchophylla by metagenomics

Uncaria rhynchophylla is an important herbal medicine, and the predominant issues affecting its cultivation include a single method of fertilizer application and inappropriate chemical fertilizer application. To reduce the use of inorganic nitrogen fertilization and increase the yield of Uncaria rhynchophylla, field experiments in 2020-2021 were conducted. The experimental treatments included the following categories: S1, no fertilization; S2, application of chemical NPK fertilizer; and S3-S6, application of chemical fertilizers and green manures, featuring nitrogen fertilizers reductions of 0%, 15%, 30%, and 45%, respectively. The results showed that a moderate application of nitrogen fertilizer when combined with green manure, can help alleviate soil acidification and increase urease activity. Specifically, the treatment with green manure provided in a 14.71-66.67% increase in urease activity compared to S2. Metagenomics sequencing results showed a decrease in diversity in S3, S4, S5, and S6 compared to S2, but the application of chemical fertilizer with green manure promoted an increase in the relative abundance of Acidobacteria and Chloroflexi. In addition, the nitrification pathway displayed a progressive augmentation in tandem with the reduction in nitrogen fertilizer and application of green manure, reaching its zenith at S5. Conversely, other nitrogen metabolism pathways showed a decline in correlation with diminishing nitrogen fertilizer dosages. The rest of the treatments showed an increase in yield in comparison to S1, S5 showing significant differences (p < 0.05). In summary, although S2 demonstrate the ability to enhance soil microbial diversity, it is important to consider the long-term ecological impacts, and S5 may be a better choice.

Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean

Urea is hypothesized to be an important source of nitrogen and chemical energy to microorganisms in the deep sea; however, direct evidence for urea use below the epipelagic ocean is lacking. Here, we explore urea utilization from 50 to 4000 meters depth in the northeastern Pacific Ocean using metagenomics, nitrification rates, and single-cell stable-isotope-uptake measurements with nanoscale secondary ion mass spectrometry. We find that on average 25% of deep-sea cells assimilated urea-derived N (60% of detectably active cells), and that cell-specific nitrogen-incorporation rates from urea were higher than that from ammonium. Both urea concentrations and assimilation rates relative to ammonium generally increased below the euphotic zone. We detected ammonia- and urea-based nitrification at all depths at one of two sites analyzed, demonstrating their potential to support chemoautotrophy in the mesopelagic and bathypelagic regions. Using newly generated metagenomes we find that the ureC gene, encoding the catalytic subunit of urease, is found within 39% of deep-sea cells in this region, including the Nitrososphaeria (syn., Thaumarchaeota; likely for nitrification) as well as members of thirteen other phyla such as Proteobacteria, Verrucomicrobia, Plantomycetota, Nitrospinota, and Chloroflexota (likely for assimilation). Analysis of public metagenomes estimated ureC within 10-46% of deep-sea cells around the world, with higher prevalence below the photic zone, suggesting urea is widely available to the deep-sea microbiome globally. Our results demonstrate that urea is a nitrogen source to abundant and diverse microorganisms in the dark ocean, as well as a significant contributor to deep-sea nitrification and therefore fuel for chemoautotrophy.

Effects of sludge retention time (SRT) on nitrogen and phosphorus removal and the microbial community in an ultrashort-SRT activated sludge system

The ultrashort-sludge retention time activate sludge (USAS) process is considered promising for the recovery of energy and resource from wastewater. In this study, we developed five USAS systems (with sludge retention time (SRT) of 0.5, 1, 2, 3, and 4 d), and investigated the nitrogen and phosphorus removal, as well as the microbial community, in the USAS systems. The results revealed that the activated sludge in the USAS system with a shorter SRT can capture more organic matter from wastewater, with organic matter mineralization, capture, and loss rates of 12.9-45.9, 42.4-62.3, and 18.2-24.8%, respectively. In addition, ammonia oxidization only occurred in the USAS systems with SRTs of 3 and 4 d, and all the USAS systems with different SRTs exhibited phosphorus-removal ability. The microbial community analysis results revealed that the relative abundance of nitrifying and denitrifying bacteria (such as Thauera) increased with an increase in the SRT.

Growth of soil ammonia-oxidizing archaea on air-exposed solid surface

Soil microorganisms often thrive as microcolonies or biofilms within pores of soil aggregates exposed to the soil atmosphere. However, previous studies on the physiology of soil ammonia-oxidizing microorganisms (AOMs), which play a critical role in the nitrogen cycle, were primarily conducted using freely suspended AOM cells (planktonic cells) in liquid media. In this study, we examined the growth of two representative soil ammonia-oxidizing archaea (AOA), Nitrososphaera viennensis EN76 and "Nitrosotenuis chungbukensis" MY2, and a soil ammonia-oxidizing bacterium, Nitrosomonas europaea ATCC 19718 on polycarbonate membrane filters floated on liquid media to observe their adaptation to air-exposed solid surfaces. Interestingly, ammonia oxidation activities of N. viennensis EN76 and "N. chungbukensis" MY2 were significantly repressed on floating filters compared to the freely suspended cells in liquid media. Conversely, the ammonia oxidation activity of N. europaea ATCC 19718 was comparable on floating filters and liquid media. N. viennensis EN76 and N. europaea ATCC 19718 developed microcolonies on floating filters. Transcriptome analysis of N. viennensis EN76 floating filter-grown cells revealed upregulation of unique sets of genes for cell wall and extracellular polymeric substance biosynthesis, ammonia oxidation (including ammonia monooxygenase subunit C (amoC3) and multicopper oxidases), and defense against H2O2-induced oxidative stress. These genes may play a pivotal role in adapting AOA to air-exposed solid surfaces. Furthermore, the floating filter technique resulted in the enrichment of distinct soil AOA communities dominated by the "Ca. Nitrosocosmicus" clade. Overall, this study sheds light on distinct adaptive mechanisms governing AOA growth on air-exposed solid surfaces.

Juglone, a plant-derived 1,4-naphthoquinone, binds to hydroxylamine oxidoreductase and inhibits the electron transfer to cytochrome c554

IMPORTANCE

Nitrification, the microbial conversion of ammonia to nitrate via nitrite, plays a pivotal role in the global nitrogen cycle. However, the excessive use of ammonium-based fertilizers in agriculture has disrupted this cycle, leading to groundwater pollution and greenhouse gas emissions. In this study, we have demonstrated the inhibitory effects of plant-derived juglone and related 1,4-naphthoquinones on the nitrification process in Nitrosomonas europaea. Notably, the inhibition mechanism is elucidated in which 1,4-naphthoquinones interact with hydroxylamine oxidoreductase, disrupting the electron transfer to cytochrome c554, a physiological electron acceptor. These findings support the notion that phytochemicals can impede nitrification by interfering with the essential electron transfer process in ammonia oxidation. The findings presented in this article offer valuable insights for the development of strategies aimed at the management of nitrification, reduction of fertilizer utilization, and mitigation of greenhouse gas emissions.

Biogeographic distribution of autotrophic bacteria was more affected by precipitation than by soil properties in an arid area

Introduction

Autotrophic bacteria play an important role in carbon dioxide fixation and are widespread in terrestrial ecosystems. However, the biogeographic patterns of autotrophic bacteria and the driving factors still remain poorly understood.

Methods

Herein, we conducted a 391-km north to south transect (mean annual precipitation <600 mm) survey in the Loess Plateau of China, to investigate the biogeographic distributions of autotrophic bacteria (RubisCO cbbL and cbbM genes) and the environmental drivers across different latitude sites with clear vegetational and climatic gradients.

Results and discussion

The soils in northern region with lower precipitation are dominated by grassland/forest, which is typically separated from the soils in southern region with higher precipitation. The community structure of autotrophic bacterial cbbL and cbbM genes generally differed between the soils in the southern and northern Loess Plateau, suggesting that precipitation and its related land use practices/ecosystem types, rather than local soil properties, are more important in shaping the soil autotrophic microorganisms. The cbbL-containing generalist OTUs were almost equally abundant across the northern and southern Loess Plateau, while the cbbM-containing bacterial taxa were more prevalent in the low precipitation northern region. Such differences indicate differentiate distribution patterns of cbbM- and cbbL-containing bacteria across the north to south transect. Our results suggest that the community composition and the differentiate distributions of soil cbbL- and cbbM-containing bacterial communities depend on precipitation and the related ecosystem types in the north to south transect in the Loess Plateau of China.

Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite-oxidizing strains

IMPORTANCE

Synthetic nitrification inhibitors are routinely used with nitrogen fertilizers to reduce nitrogen losses from agroecosystems, despite having drawbacks like poor efficiency, cost, and entry into the food chain. Plant-derived BNIs constitute a more environmentally conducive alternative. Knowledge on the activity of BNIs to soil nitrifiers is largely based on bioassays with a single Nitrosomonas europaea strain which does not constitute a dominant member of the community of ammonia-oxidizing microorganisms (AOM) in soil. We determined the activity of several plant-derived molecules reported as having activity, including the recently discovered maize-isolated BNI, zeanone, and its natural analog, 2-methoxy-1,4-naphthoquinone, on a range of ecologically relevant AOM and one nitrite-oxidizing bacterial culture, expanding our knowledge on the intrinsic inhibition potential of BNIs toward AOM and highlighting the necessity for a deeper understanding of the effect of BNIs on the overall soil microbiome integrity before their further use in agricultural settings.

Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments

The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3--N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil.

The driving effects of nitrogen deposition on nitrous oxide and associated gene abundances at two water table levels in an alpine peatland

Alpine peatlands are recognized as a weak or negligible source of nitrous oxide (N2O). Anthropogenic activities and climate change resulted in the altered water table (WT) levels and increased nitrogen (N) deposition, which could potentially transition this habitat into a N2O emission hotspot. However, the underlying mechanism related with the effects is still uncertain. Hence, we conducted a mesocosm experiment to address the response of growing-season N2O emissions and the gene abundances of nitrification (bacterial amoA) and denitrification (narG, nirS, norB and nosZ) to the increased N deposition (20 kg N ha-1 yr-1) at two WT levels (WT-30, 30 cm below soil surface; WT10, 10 cm above soil surface) in the Zoige alpine peatland, Qinghai-Tibetan Plateau. The results showed that the WT did not affect N2O emissions, and this was attributed with the limitation of soil NO3-. The higher WT level increased denitrification (narG and nirS gene abundance) resulting in the depletion of soil NO3-, but the consequent NO3- deficiency further limited denitrification, while the WT did not affect nitrification (bacterial amoA gene abundance). Meanwhile, the N deposition increased N2O emissions, regardless of WT levels. This was associated with the N-deposition induced increase in denitrification-related gene abundances of narG, nirS, norB and nosZ at WT-30 and narG at WT10. Additionally, the N2O emission factor assigned to N deposition was 1.3 % at WT-30 and 0.9 % at WT10, respectively. Our study provided comprehensive understanding of the mechanisms referring N2O emissions in response to the interactions between climate change and human disturbance from this high-altitude peatland.

Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China

Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.

Metagenomics reveals taxon-specific responses of soil nitrogen cycling under different fertilization regimes in heavy metal contaminated soil

Soil deficiency, cyclic erosion, and heavy metal pollution have led to fertility loss and ecological function decline in mining areas. Fertilization is an important way to rapidly replenish soil nutrients, which have a major influence on the soil nitrogen cycling process, but different fertilization regimes have different impacts on soil properties and microbial functional potentials. Here, metagenomic sequencing was used to investigate the different responses of key functional genes of microbial nitrogen cycling to fertilization regimes and explore the potential effects of soil physicochemical properties on the key functional genes. The results indicated that AC-HH (ammonium chloride-high frequency and concentration) treatment significantly increased the gene abundance of norC (13.40-fold), nirK (5.46-fold), and napA (5.37-fold). U-HH (urea-high frequency and concentration) treatment significantly increased the gene abundance of hao (6.24-fold), pmoA-amoA (4.32-fold) norC (7.00-fold), nosZ (3.69-fold), and nirK (6.88-fold). Functional genes were distributed differently among the 10 dominant phyla. The nifH and nifK genes were distributed only in Proteobacteria. The hao gene was distributed in Gemmatimonadetes, Nitrospirae and Proteobacteria. Fertilization regimes caused changes in functional redundancy in soil, and nirK and nirB, which are involved in denitrification, were present in different genera. Fertilization regimes with high frequency and high concentration were more likely to increase the gene abundance at the genus level. In summary, this study provides insights into the taxon-specific response of soil nitrogen cycling under different fertilization regimes, where changes in fertilization regimes affect microbial nitrogen cycling by altering soil physicochemical properties in a complex dynamic environment.

Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer

Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia-oxidising bacteria (AOB). The apparent half-saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH3  + NH4 + and 18.5 ± 1.8 μmol N (mg protein)-1  h-1 , respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1-like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia-oxidising Nitrosomonas.

Multidrug-resistant plasmid RP4 increases NO and N2O yields via the electron transport system in Nitrosomonas europaea ammonia oxidation

Antibiotic resistance genes (ARGs) have recently become an important public health problem and therefore several studies have characterized ARG composition and distribution. However, few studies have assessed their impact on important functional microorganisms in the environment. Therefore, our study sought to investigate the mechanisms through which multidrug-resistant plasmid RP4 affected the ammonia oxidation capacity of ammonia-oxidizing bacteria, which play a key role in the nitrogen cycle. The ammonia oxidation capacity of N. europaea ATCC25978 (RP4) was significantly inhibited, and NO and N2O were produced instead of nitrite. Our findings demonstrated that the decrease in electrons from NH2OH decreased the ammonia monooxygenase (AMO) activity, leading to a decrease in ammonia consumption. In the ammonia oxidation process, N. europaea ATCC25978 (RP4) exhibited ATP and NADH accumulation. The corresponding mechanism was the overactivation of Complex Ⅰ, ATPase, and the TCA cycle by the RP4 plasmid. The genes encoding TCA cycle enzymes related to energy generation, including gltA, icd, sucD, and NE0773, were upregulated in N. europaea ATCC25978 (RP4). These results demonstrate the ecological risks of ARGs, including the inhibition of the ammonia oxidation process and an increased production of greenhouse gases such as NO and N2O.

Proterozoic Acquisition of Archaeal Genes for Extracellular Electron Transfer: A Metabolic Adaptation of Aerobic Ammonia-Oxidizing Bacteria to Oxygen Limitation

Many aerobic microbes can utilize alternative electron acceptors under oxygen-limited conditions. In some cases, this is mediated by extracellular electron transfer (or EET), wherein electrons are transferred to extracellular oxidants such as iron oxide and manganese oxide minerals. Here, we show that an ammonia-oxidizer previously known to be strictly aerobic, Nitrosomonas communis, may have been able to utilize a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multiheme cytochromes in N. communis further suggest a capacity for EET. Molecular clock analysis shows that the ancestors of β-proteobacterial ammonia oxidizers appeared after Earth's atmospheric oxygenation when the oxygen levels were >10-4pO2 (present atmospheric level [PAL]), consistent with aerobic origins. Equally important, phylogenetic reconciliations of gene and species trees show that the multiheme c-type EET proteins in Nitrosomonas and Nitrosospira lineages were likely acquired by gene transfer from γ-proteobacteria when the oxygen levels were between 0.1 and 1 pO2 (PAL). These results suggest that β-proteobacterial EET evolved during the Proterozoic when oxygen limitation was widespread, but oxidized minerals were abundant.

Anthropogenic land-use activities within watersheds reduce comammox activity and diversity in rivers

Nitrogen cycling plays a key role in maintaining river ecological functions which are threatened by anthropogenic activities. The newly discovered complete ammonia oxidation, comammox, provides novel insights into the ecological effects of nitrogen on that it oxidizes ammonia directly to nitrate without releasing nitrite as canonical ammonia oxidization conducted by AOA or AOB which is believed to play an important role in greenhouse gas generation. Theoretically, contribution of commamox, AOA and AOB to ammonia oxidization in rivers might be impacted by anthropogenic land-use activities through alterations in flow regime and nutrient input. While how land use pattern affects comammox and other canonical ammonia oxidizers remains elusive. In this study, we examined the ecological effects of land use practices on the activity and contribution of three distinctive groups of ammonia oxidizers (AOA, AOB, comammox) as well as the composition of comammox bacterial communities from 15 subbasins covering an area of 6166 km² in North China. The results showed that comammox dominated nitrification (55.71%-81.21%) in less disturbed basins characterized by extensive forests and grassland, while AOB became the major player (53.83%-76.43%) in highly developed basins with drastic urban and agricultural development. In addition, increasing anthropogenic land use activities within the watershed lowered the alpha diversity of comammox communities and simplified the comammox network. Additionally, the alterations of NH₄⁺-N, pH and C/N induced by land use change were found to be crucial drivers in determining the distribution and activity of AOB and comammox. Together, our findings cast a new light on aquatic-terrestrial linkages from the view of microorganism-mediated nitrogen cycling and can further be applied to target watershed land use management.

Polyethylene and polyvinyl chloride microplastics promote soil nitrification and alter the composition of key nitrogen functional bacterial groups

Microplastics (MPs) contamination in soils seriously threatens agroecosystems globally. However, very few studies have been done on the effects of MPs on the soil nitrogen cycle and related functional microorganisms. To assess MP's impact on the soil nitrogen cycle and related functional bacteria, we carried out a one-month soil incubation experiment using typical acidic soil. The soil was amended with alfalfa meal and was spiked with 1% and 5% (mass percentage) of low-density polyethylene (LDPE) and polyvinyl chloride (PVC) MPs. Our results showed that both LDPE and PVC addition significantly increased soil nitrification rate and nitrate reductase activity, which could further promote soil denitrification. The relative abundance of diazotrophs, ammonium oxidizing, and denitrifying bacterial groups were significantly altered with MPs addition. Moreover, the MPs treatments greatly enhanced denitrifying bacteria richness. Redundancy analysis showed that nitrate reductase activity was the most significant factor affecting the soil functional bacterial community. Correlation analysis shows that Nitrosospira genus might be for the improvement of soil nitrification rate. Our results implied that MPs exposure could significantly affect the soil nitrogen cycling in farmland ecosystems by influencing essential nitrogen functional microorganisms and related enzymatic activities.

Temperature and phosphorus: the main environmental factors affecting the seasonal variation of soil bacterial diversity in Nansi Lake Wetland

Introduction

The soil bacteria promote the circulation conversion of lake nutrients and play an important role in maintaining the balance of the lake ecosystem. Few studies have investigated the association of seasonal variation in bacteria and environmental factors in inland freshwater lake wetlands. Nansi Lake is a large shallow freshwater lake in northern China. It is an important hub of the eastern route of the South-to-North Water Diversion Project.

Methods

In this study, bacterial 16S rRNA genes were used to analyze the variation of soil bacterial community diversity in Nansi Lake Wetland and its influencing factors in different seasons.

Results

It is showed that the phylum, family, and genus with the largest relative abundance in the soil of Nansi Lake Wetland are Proteobacteria, Nitrosomonadaceae, and MND1, respectively. There were significant seasonal differences in soil bacterial diversity in Nansi Lake Wetland, which was significantly higher in summer than in winter. Seasonal variation in environmental factors was significantly correlated with the variation in bacterial communities. Temperature and the content of available phosphorus may be the key factors influencing seasonal variation in bacterial diversity.

Discussion

The results of this study further enhance our understanding of the relationship between bacterial community diversity and environmental factors in the lake wetland ecosystem, which can provide scientific data for the conservation of Nansi Lake Wetland.

Microbiological risks increased by ammonia-oxidizing bacteria under global warming: The neglected issue in chloraminated drinking water distribution system

A rising outbreak of waterborne diseases caused by global warming requires higher microbial stability in the drinking water distribution system (DWDS). Chloramine disinfection is gaining popularity in this context due to its good persistent stability and fewer disinfection byproducts. However, the microbiological risks may be significantly magnified by ammonia-oxidizing bacteria (AOB) in distribution systems during global warming, which is rarely noticed. Hence, this work mainly focuses on AOB to explore its impact on water quality biosafety in the context of global warming. Research indicates that global warming-induced high temperatures can directly or indirectly promote the growth of AOB, thus leading to nitrification. Further, its metabolites or cellular residues can be used as substrates for the growth of heterotrophic bacteria (e.g., waterborne pathogens). Thus, biofilm may be more persistent in the pipelines due to the presence of AOB. Breakpoint chlorination is usually applied to control such situations. However, switching between this strategy and chloramine disinfection would result in even more severe nitrification and other adverse effects. Based on the elevated microbiological risks in DWDS, the following aspects should be paid attention to in future research: (1) to understand the response of nitrifying bacteria to high temperatures and the possible association between AOB and pathogenic growth, (2) to reveal the mechanisms of AOB-mediated biofilm formation under high-temperature stress, and (3) to develop new technologies to prevent and control the occurrence of nitrification in drinking water distribution system.

Ecological distribution and function of comammox Nitrospira in the environment

Complete ammonia oxidizers (Comammox) are of great significance for studying nitrification and expanding the understanding of the nitrogen cycle. Moreover, Comammox bacteria are also crucial in natural and engineered environments due to their role in wastewater treatment and maintaining the flux of greenhouse gases to the atmosphere. However, only few studies are there regarding the Comammox bacteria and their role in ammonia and nitrite oxidation in the environment. This review mainly focuses on summarizing the genomes of Nitrospira in the NCBI database. Ecological distribution of Nitrospira was also reviewed and the influence of environmental parameters on genus Nitrospira in different environments has been summarized. Furthermore, the role of Nitrospira in carbon cycle, nitrogen cycle, and sulfur cycle were discussed, especially the comammox Nitrospira. In addition, the overviews of current research and development regarding comammox Nitrospira, were summarized along with the scope of future research. KEY POINTS: • Most of Comammox Nitrospira are widely distributed in both aquatic and terrestrial ecosystems, but it has been studied less frequently in the extreme environments. • Comammox Nitrospira can be involved in different nitrogen transformation process, but rarely involved in nitrogen fixation. • The stable isotope and transcriptome techniques are important methods to study the metabolic function of comammox Nitrospira.

Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations

Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.

Research advances of ammonia oxidation microorganisms in wastewater: metabolic characteristics, microbial community, influencing factors and process applications

Ammonia oxidation carried out by ammonia-oxidizing microorganisms (AOMs) is a central step in the global nitrogen cycle. Aerobic AOMs comprise conventional ammonia-oxidizing bacteria (AOB), novel ammonia-oxidizing archaea (AOA), which could exist in complex and extreme conditions, and complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate within a single cell. Anaerobic AOMs mainly comprise anaerobic ammonia-oxidizing bacteria (AnAOB), which can transform NH₄⁺-N and NO₂^--N into N₂ under anaerobic conditions. In this review, the unique metabolic characteristics, microbial community of AOMs and the influencing factors are discussed. Process applications of nitrification/denitrification, nitritation/denitrification, nitritation/anammox and partial denitrification/anammox in wastewater treatment systems are emphasized. The future development of nitrogen removal processes using AOMs is expected, enrichment of comammox facilitates the complete nitrification performance, inhibiting the activity of comammox and NOB could achieve stable nitritation, and additionally, AnAOB conducting the anammox process in municipal wastewater is a promising development direction.

Reactive and microbial inhibitory mechanisms depicting the panoramic view of pH stress effect on common biological nitrification

pH is a crucial factor of microbial nitrification, which often combines with high-strength ammonium to influence nitrogen removal pathway in wastewater treatment. However, the detailed inhibitory mechanisms of pH stress are not sufficiently disclosed yet. In this study, the pH stress effect on nitrification was comprehensively studied by a set of experiments which identified the reactivity of nitrification processes and activity of nitrifiers, the time dependence of inhibition effect and the hybrid pH stress effect with ammonium. The results revealed two distinct inhibitory mechanisms dominating in alkaline and acid ranges. In alkaline range (pH > 8), pH stress causes physiological damages on microorganisms which is named as microbial inhibition. It has the features of less recoverability of nitrifiers, time-dependent inhibition effect and low pH-tolerance of nitrite oxidation bacteria. Free ammonia enhanced microbial inhibition and greatly promoted nitrite accumulation. A novel reactive inhibition mechanism dominated in acid range (pH < 7) was disclosed. It only impedes ammonia oxidation process (AOP) but not impair microbial activity obviously and the effect is time-independent. The mechanism was clarified from H⁺ transport because AOP involved H⁺ production. The H⁺ transport was impeded under acid stress owing to the decrease of pH gradient across cell membrane. The two mechanisms formed a panoramic view of pH stress effect on nitrification advancing the understanding of nitrifier adaptability and nitritation regulation in wastewater treatment processes.

Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot

The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.