Fungal endophyte Phomopsis liquidambari affects nitrogen transformation processes and related microorganisms in the rice rhizosphere

The endophytic fungus Phomopsis liquidambari performs an important ecosystem service by assisting its host with acquiring soil nitrogen (N), but little is known regarding how this fungus influences soil N nutrient properties and microbial communities. In this study, we investigated the impact of P. liquidambari on N dynamics, the abundance and composition of N cycling genes in rhizosphere soil treated with three levels of N (urea). Ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and diazotrophs were assayed using quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis at four rice growing stages (S0: before planting, S1: tillering stage, S2: grain filling stage, and S3: ripening stage). A significant increase in the available nitrate and ammonium contents was found in the rhizosphere soil of endophyte-infected rice under low N conditions. Moreover, P. liquidambari significantly increased the potential nitrification rates, affected the abundance and community structure of AOA, AOB, and diazotrophs under low N conditions in the S1 and S2 stages. The root exudates were determined due to their important role in rhizosphere interactions. P. liquidambari colonization altered the exudation of organic compounds by rice roots and P. liquidambari increased the concentration of soluble saccharides, total free amino acids and organic acids in root exudates. Plant-soil feedback mechanisms may be mediated by the rice-endophyte interaction, especially in nutrient-limited soil.

Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria

Ammonia-oxidizing bacteria (AOB) are important members of terrestrial, marine, and industrial microbial communities and play a fundamental role in the Nitrogen cycle within these systems. They are responsible for the first step of nitrification, ammonia oxidation to nitrite. Although AOB are widespread and essential to environmental and industrial systems, where they regularly experience fluctuations in ammonia availability, no comparative studies of the physiological response of diverse AOB species at the protein level exist. In the present study, we used 1D-LC-MS/MS proteomics to compare the metabolism and physiology of three species of ammonia AOB, Nitrosomonas europaea, Nitrosospira multiformis, and Nitrosomonas ureae, under ammonia replete and ammonia starved conditions. Additionally, we compared the expression of orthologous genes to determine the major differences in the proteome composition of the three species. We found that approximately one-third of the predicted proteome was expressed in each species and that proteins for the key metabolic processes, ammonia oxidation and carbon fixation, were among the most abundant. The red copper protein, nitrosocyanin was highly abundant in all three species hinting toward its possible role as a central metabolic enzyme in AOB. The proteomic data also allowed us to identify pyrophosphate-dependent 6-phosphofructokinase as the potential enzyme replacing the Calvin-Benson-Bassham cycle enzyme Fructose-1,6-bisphosphatase missing in N. multiformis and N. ureae. Additionally, between species, there were statistically significant differences in the expression of many abundant proteins, including those related to nitrogen metabolism (nitrite reductase), motility (flagellin), cell growth and division (FtsH), and stress response (rubrerythrin). The three species did not exhibit a starvation response at the proteome level after 24 h of ammonia starvation, however, the levels of the RuBisCO enzyme were consistently reduced after the starvation period, suggesting a decrease in capacity for biomass accumulation. This study presents the first published proteomes of N. ureae and N. multiformis, and the first comparative proteomics study of ammonia-oxidizing bacteria, which gives new insights into consistent metabolic features and differences between members of this environmentally and industrially important group.

Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China

Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira.

Effects of biological nitrification inhibitor in regulating NH3 volatilization and fertilizer nitrogen recovery efficiency in soils under rice cropping

Biological nitrification inhibitors are exudates from plant roots that can inhibit nitrification, and have advantages over traditional synthetic nitrification inhibitors. However, our understanding of the effects of biological nitrification inhibitors on nitrogen (N) loss and fertilizer N recovery efficiency in staple food crops is limited. In this study, acidic and calcareous soils were selected, and rice growth pot experiments were conducted to investigate the effects of the biological nitrification inhibitor, methyl 3-(4-hydroxyphenyl) propionate (MHPP) and/or a urease inhibitor (N-[n-butyl], thiophosphoric triamide [NBPT]) on NH₃ volatilization, N leaching, fertilizer N recovery efficiency under a 20% reduction of the conventional N application rate. Our results show that rice yield and fertilizer N recovery efficiency were more sensitive to reduced N application in the calcareous soil than in the acidic soil. MHPP stimulated NH₃ volatilization by 13.2% in acidic soil and 9.06% in calcareous soil but these results were not significant. In the calcareous soil, fertilizer N recovery efficiency significantly increased by 19.3% and 44.4% in the MHPP and NBPT+MHPP groups, respectively, relative to the reduced N treatment, and the rice yield increased by 16.7% in the NBPT+MHPP treatment (P < 0.05). However, such effects were not significant in the acidic soil. MHPP exerted a significant effect on soil ammonia oxidizers, and the response of abundance and community structure of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and total bacteria to MHPP depended on the soil type. MHPP+NBPT reduced NH₃ volatilization, N leaching, and maintaining rice yield for a 20% reduction in conventional N fertilizer application rate. This could represent a viable strategy for more sustainable rice production, despite the inevitable increase in cost for famers.

Density-Based Separation of Microbial Functional Groups in Activated Sludge

Mechanistic understanding of how activated sludge (AS) solids density influences wastewater treatment processing is limited. Because microbial groups often generate and store intracellular inclusions during certain metabolic processes, it is hypothesized that some microorganisms, like polyphosphate-accumulating organisms (PAOs), would have higher biomass densities. The present study developed a density-based separation approach and applied it to suspended growth AS in two full-scale domestic water resource recovery facilities (WRRFs). Incorporating quantitative real-time PCR (qPCR) and fluorescence in situ hybridization (FISH) analyses, the research demonstrated the effectiveness of density-based separation in enriching key microbial functional groups, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB) and PAOs, by up to 90-fold in target biomass fractions. It was observed that WRRF process functionalities have significant influence on density-based enrichment, such that maximum enrichments were achieved in the sludge fraction denser than 1.036 g/cm³ for the enhanced biological phosphorus removal (EBPR) facility and in the sludge fraction lighter than 1.030 g/cm³ for the non-EBPR facility. Our results provide important information on the relationship between biomass density and enrichment of microbial functional groups in AS, contributing to future designs of enhanced biological treatment processes for improved AS settleability and performance.

Smaller Aerobic Granules Significantly Reduce N2O Production by Ammonia-Oxidizing Bacteria: Evidences from Biochemical and Isotopic Analyses

The mitigation of nitrous oxide (N2O) is of primary significance to offset carbon footprints in aerobic granular sludge (AGS) systems. However, a significant knowledge gap still exists regarding the N2O production mechanism and its pathway contribution. To address this issue, the impact of varying granule sizes, dissolved oxygen (DO), and nitrite (NO2-) levels on N2O production by ammonia-oxidizing bacteria (AOB) during nitrification in AGS systems was comprehensively investigated. Biochemical and isotopic experiments revealed that increasing DO or decreasing NO2- levels reduced N2O emission factors (by 13.8 or 19.5%) and production rates (by 0.08 or 0.35 mg/g VSS/h) via weakening the role of the AOB denitrification pathway since increasing DO competed for more electrons required for AOB denitrification. Smaller granules (0.5 mm) preferred to diminish N2O production via enhancing the role of NH2OH pathway (i.e., 59.4-100% in the absence of NO2-), while larger granules (2.0 mm) induced conspicuously higher N2O production via the AOB denitrification pathway (approximately 100% at higher NO2- levels). Nitrifying AGS systems with a unified size of 0.5 mm achieved 42% N2O footprint reduction compared with the system with mixed sizes (0.5-2.0 mm) under optimal conditions (DO = 3.0 mg-O2/L and NO2- = 0 mg-N/L).

Nitrification is a minor source of nitrous oxide (N2 O) in an agricultural landscape and declines with increasing management intensity

The long-term contribution of nitrification to nitrous oxide (N₂ O) emissions from terrestrial ecosystems is poorly known and thus poorly constrained in biogeochemical models. Here, using Bayesian inference to couple 25 years of in situ N₂ O flux measurements with site-specific Michaelis-Menten kinetics of nitrification-derived N₂ O, we test the relative importance of nitrification-derived N₂ O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest. We found that the maximum potential contribution from nitrification to in situ N₂ O fluxes was 13%-17% in a conventionally fertilized annual cropping system, 27%-42% in a low-input cover-cropped annual cropping system, and 52%-63% in perennial systems including a late successional deciduous forest. Actual values are likely to be <10% of these values because of low N₂ O yields in cultured nitrifiers (typically 0.04%-8% of NH₃ oxidized) and competing sinks for available NH4+ in situ. Most nitrification-derived N₂ O was produced by ammonia-oxidizing bacteria rather than archaea, who appeared responsible for no more than 30% of nitrification-derived N₂ O production in all but one ecosystem. Although the proportion of nitrification-derived N₂ O production was lowest in annual cropping systems, these ecosystems nevertheless produced more nitrification-derived N₂ O (higher V_max ) than perennial and successional ecosystems. We conclude that nitrification is minor relative to other sources of N₂ O in all ecosystems examined.

Long-Term Exposure and Effects of rGO-nZVI Nanohybrids and Their Parent Nanomaterials on Wastewater-Nitrifying Microbial Communities

Single nanomaterials and nanohybrids (NHs) can inhibit microbial processes in wastewater treatment, especially nitrification. While existing studies focus on short-term and acute exposures of single nanomaterials on wastewater microbial community growth and function, long-term, low-exposure, and emerging NHs need to be examined. These NHs have distinctly different physicochemical properties than their parent nanomaterials and, therefore, may exert previously unknown effects onto wastewater microbial communities. This study systematically investigated long-term [∼6 solid residence time [(SRT)] exposure effects of a widely used carbon-metal NH (rGO-nZVI = 1:2 and 1:0.2, mass ratio) and compared these effects to their single-parent nanomaterials (i.e., rGO and nZVI) in nitrifying sequencing batch reactors. nZVI and NH-dosed reactors showed relatively unaffected microbial communities compared to control, whereas rGO showed a significantly different (p = 0.022) and less diverse community. nZVI promoted a diverse community and significantly higher (p < 0.05) biomass growth under steady-state conditions. While long-term chronic exposure (10 mg·L^-1) of single nanomaterials and NHs had limited impact on long-term nutrient recovery, functionally, the reactors dosed with higher iron content, that is, nZVI and rGO-nZVI (1:2), promoted faster NH₄⁺-N removal due to higher biomass growth and upregulation of amoA genes at the transcript level, respectively. The transmission electron microscopy images and scanning electron microscopy─energy-dispersive X-ray spectroscopy analysis revealed high incorporation of iron in nZVI-dosed biomass, which promoted higher cellular growth and a diverse community. Overall, this study shows that NHs have unique effects on microbial community growth and function that cannot be predicted from parent materials alone.

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

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

[Type and key drivers of nitrification for an acidic peat soil in Xiaoxing'an Mountain, China]

Acidic forest peat soil in Xiaoxing'an Mountain was used to investigate the type and key drivers of nitrification by carrying out nitrification incubation after adding 10 mL·L^-1 C₂H₂ and different amounts of (NH₄)₂SO₄(0, 1.2, 6.0 mmol N·kg^-1). Results showed that strong mineralization (0.9-1.4 mg N·kg^-1·d^-1) and nitrification (0.4-0.6 mg N·kg^-1·d^-1) after 2 weeks of incubation were observed for both nitrogen and no nitrogen treatments, and no significant difference was observed for different (NH₄)₂SO₄ application treatments. For C₂H₂ treatment, there was relatively stronger mineralization (0.8 mg N·kg^-1·d^-1), but no obvious nitrification (0 mg N·kg^-1·d^-1). These results indicated that the nitrification in acidic peat soil was mainly autotrophic, and inorganic nitrogen application did not affect nitrification rate significantly. Results also implied that the substrate (NH₃) for nitrification was from the organic N mineralization, rather than the (NH₄)₂SO₄ application. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) abundances increased significantly during 0-14 d regardless of nitrogen application. However, no significant difference in AOB and AOA abundances for different (NH₄)₂SO₄ application treatments was observed, indicating that ammonia oxidizers did not respond positively to (NH₄)₂SO₄ application. Compared with the treatments without C₂H₂, AOB and AOA abundances did not change significantly during the incubation in C₂H₂ treatment, suggesting that both AOA and AOB were likely the key players in nitrification in the acidic peat soil.

Degradation of Chloroquine by Ammonia-Oxidizing Bacteria: Performance, Mechanisms, and Associated Impact on N2O Production

Since the mass production and extensive use of chloroquine (CLQ) would lead to its inevitable discharge, wastewater treatment plants (WWTPs) might play a key role in the management of CLQ. Despite the reported functional versatility of ammonia-oxidizing bacteria (AOB) that mediate the first step for biological nitrogen removal at WWTP (i.e., partial nitrification), their potential capability to degrade CLQ remains to be discovered. Therefore, with the enriched partial nitrification sludge, a series of dedicated batch tests were performed in this study to verify the performance and mechanisms of CLQ biodegradation under the ammonium conditions of mainstream wastewater. The results showed that AOB could degrade CLQ in the presence of ammonium oxidation activity, but the capability was limited by the amount of partial nitrification sludge (∼1.1 mg/L at a mixed liquor volatile suspended solids concentration of 200 mg/L). CLQ and its biodegradation products were found to have no significant effect on the ammonium oxidation activity of AOB while the latter would promote N2O production through the AOB denitrification pathway, especially at relatively low DO levels (≤0.5 mg-O2/L). This study provided valuable insights into a more comprehensive assessment of the fate of CLQ in the context of wastewater treatment.

Achieving stable anammox process and revealing shift of bacteria during the start-up in landfill leachate treatment

Partial nitrification-anammox (PN/A) is an energy-efficient technology for nitrogen removal in landfill leachate treatment. Numerous studies have reported successful implementation of the PN/A process and its stable operation under laboratory conditions. One of the primary challenges in PN/A engineering applications is the mass of the seed sludge required for start-up. This study examined the PN/A using a sequence batch reactor (SBR) inoculating a common mixture to treat landfill leachate. After 70 days of operation, the system successfully realized a one-stage PN/A process and maintained a stable ammonium NH 4 + $$ \left({NH}_4^{+}\right) $$ removal efficiency of 97.65% ± 1%, where the effluent of NH 4 + $$ {NH}_4^{+} $$ and nitrate ( NO 3 - $$ {NO}_3^{-} $$ ) were less than 4 ± 1.5 mg L^-1 and 10 mg L^-1 . In addition, the relative abundances of Ca. Kuenenia and Ca. Brocadia, which are typical anaerobic ammonia-oxidizing bacteria (AnAOB), increased from 0.08% to 3.99% (70 days) and 0.01% to 0.45%, respectively. The relative abundances of ammonia-oxidizing bacteria (AOB) Nitrosomonas and Nitrosospira increased from 0.9% to 2.89% and 0.007% to 0.1% (70 days), respectively. Both AnAOB and AOB are important niches of the system. PRACTITIONER POINTS: The research realized PN/A rapidly by inoculating common mixture sludge. The experiment successfully enriched AnAOB from 0.09% to 3.89% within 70 days. The article revealing the ecological roles of AOB and AnAOB in the landfill leachate treatment.