Search Results (17)

Nutrient additions including nitrogen (N) and phosphorus (P) are widely considered as an important strategy for enhancing grassland productivity. However, the effects of these nutrients additions on soil nitrous oxide (N₂O) emissions and the underlying mechanisms remain debated. We conducted a two-year field experiment in an alpine grassland on Kunlun Mountain in northwestern China to assess the effects of N and P additions on N₂O emissions, in relation with nitrifying enzyme activity (NEA), denitrifying enzyme activity (DEA), and key functional genes abundance responsible for nitrification (amoA and Nitrobacter-like nxrA) and denitrification (narG, nirS, nirK and nosZ). Compared to the Control without nutrient addition (CK), N addition alone substantially increased cumulative N₂O emission (ƩN₂O) by 2.0 times. In contrast, P addition or combined N and P (N+P) addition did not significantly affect ƩN₂O, though both treatments significantly increased plant aboveground biomass. Such results indicate that P addition may mitigate N-induced N₂O emission, likely by reducing soil N availability through enhanced plant and microbial N uptake. Compared to CK, N or N+P addition significantly elevated NEA but did not affect DEA. Structural equation modeling (SEM) indicated that NEA was directly influenced by the gene abundances of ammonia-oxidizing bacteria (AOB) and Nitrobacter-like nxrA but not by ammonia-oxidizing archaea (AOA). However, SEM also revealed that soil environmental variables including soil temperature, pH, and water-filled pore space (WFPS) had a stronger direct influence on N₂O emissions than the abundances of nitrifiers. These results demonstrate that soil environmental conditions play a more significant role than functional gene abundances in regulating N₂O emissions following N and P additions in semi-arid alpine grasslands. This study highlights that the N+P application can potentially decrease N₂O emissions than N addition alone, while increasing productivity in the alpine grassland ecosystems. Full article

While climate is known to regulate forest productivity, the mechanistic contribution of soil microbial communities—and whether it differs between natural and plantation forests—remains poorly quantified at broad scales. Here, we provide a synthesis-level, unified analysis that jointly evaluates climate, edaphic conditions, and soil microbes to compare mechanistic pathways underlying productivity divergence between forest types. We synthesized 237 observations across China and integrated productivity metrics—gross primary productivity (GPP) and net primary productivity (NPP)—with microbial diversity, dominant taxa, and soil drivers to compare natural and plantation forests within the current environmental coverage. Plantation productivity showed nonlinear responses to microbial diversity and appeared more sensitive than natural forests. Natural forests exhibited higher bacterial Shannon and Chao1 but lower fungal Chao1 and were characterized by taxa such as Nitrobacter, Bradyrhizobium, and Cortinarius. In contrast, plantations were characterized by taxa often associated with disturbance tolerance and opportunistic life-history strategies (e.g., Sphingomonas, Fusarium, Gemmatimonas), consistent with potential functional simplification. Structural equation models identified climate as the strongest correlate of productivity, while soil properties showed contrasting associations with microbial diversity across forest types. Random forest models further highlighted cation-exchange capacity and total nitrogen as key predictors of microbial diversity in plantations. Overall, our results indicate that soil microbial communities are differentially associated with forest productivity across forest types and environmental contexts and underscore the need for future climate-comparable designs and management-intensity information to more robustly isolate microbial contributions. Full article

Copper nanoparticles (CuNPs) are increasingly used in agriculture either alone or in combination with pesticides. Recognizing the potential hazards of CuNPs in soil environments, our study evaluated their effects on the metabolic activity of Nitrobacter winogradskyi ATCC 2539, a chemolithoautotrophic bacterium crucial for the nitrification process, which involves the oxidation of nitrite to nitrate in soil ecosystems. This study evaluated the effects of concentration ranges of CuNPs (2.5 to 162.7 mg L⁻¹), CuONPs (3.2 to 203.6 mg L⁻¹), and various pesticides (iprodione, carbendazim, and 2,4-D) and their derivatives (3,5-dichloroaniline, catechol, and 2,4-dichlorophenol) at concentrations ranging from 0.04 to 2.56 mM. CuSO₄ was also used as a control for comparative purposes. Our findings indicated that the CuNPs significantly inhibited the metabolic activity of N. winogradskyi, resulting in a reduction of up to 95% at concentrations of ≥2.5 mg L⁻¹. The CuONPs were less toxic, while the pesticides and their derivatives generally showed lower toxicity. Notably, combinations of CuNPs with pesticides or their derivatives maintained high toxicity levels comparable to those of the CuNPs alone. According to the Loewe additivity model, these effects were largely additive and primarily associated with CuNPs or CuONPs. Protein profiling using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF)/TOF mass spectrometry (MS) revealed that carbendazim induced noticeable changes in protein profiles. These findings underscore the detrimental impacts of CuNPs and CuONPs on the metabolic activity of N. winogradskyi, posing a considerable risk to the health of agricultural soils. Overall, this research provides crucial insights into the risks associated with using CuNPs in agriculture, particularly regarding their potential threat to nitrifying microorganisms in soils. Full article

To study the factors affecting Penaeus vannamei production in small-scale greenhouse ponds, four ponds in Jiangmen, Guangdong Province, China were selected. This study investigated the variation in the characteristics of bacterial communities and pathogens in pond water and shrimp intestines, as well as water quality factors during the culture stage. Multivariate linear regression equations were used to analyse the potential factors affecting production. The nitrite concentration reached its peak in the mid-culture stage, with a maximum of 16.3 mg·L⁻¹, whereas total nitrogen and salinity were highest in the late culture stage, reaching 48.4 mg·L⁻¹ and 26, respectively. The dominant bacteria in the pond water were Marivita and Rhodobacteraceae, whereas in the shrimp intestines, they were Bacillus and Candidatus Bacilloplasma. The nitrifying bacteria in the pond water were dominated by Nitrosomonas and Nitrobacter. Pathogens detected in the pond water included acute hepatopancreatic necrosis disease (AHPND), Enterocytozoon hepatopenaei (EHP), and white spot syndrome virus (WSSV). The counts of EHP and the relative abundance of Ardenticatenales_norank and Marivita in the pond were the main factors affecting the shrimp production (p < 0.01). This study indicates that establishing optimal bacterial communities, such as Marivita, Nitrobacter, and Rhodobacteraceae, and controlling the counts of EHP and AHPND pathogens is crucial for regulating the pond environment and enhancing production. Full article

Though different types of commercial probiotics are supplemented in biofloc technology (BFT), very little information is available on their effects on the farmed fish. Therefore, this study focused on evaluating the effects of three most commonly used commercial probiotics on the growth performance, intestinal histomorphology, and intestinal microbiota of Nile tilapia (Oreochromis niloticus) reared in BFT. Tilapia fry, with an average weight of 3.02 ± 0.50 g, were stocked at a density of 60 fry/0.2 m³, and cultured for 90 days. Three commercial probiotics were administered, with three replications for each: a single-genus multi-species probiotic (Bacillus spp.) (T1), a multi-genus multi-species probiotic (Bacillus sp., Lactobacillus sp., Nitrosomonas sp., Nitrobacter sp.) (T2), and a multi-species probiotic (Bacillus spp.) combined with enzymes including amylase, protease, cellulase, and xylanase (T3). The results showed significant variations in growth and feed utilization, with T3 outperforming other treatments in terms of weight gain, liver weight, and intestine weight. Adding Bacillus spp. with enzymes (T3) to water significantly increased the histomorphological parameters (villi length, villi depth, crypt depth, muscle thickness, intestinal thickness) as well as microbes (total viable count and total lactic acid bacteria) of intestine of fish compared to T1 and T2, leading to improved digestion and absorption responses. It is concluded that the supplementation of commercial probiotics has potential benefits on farmed fish species in BFT. Full article

In efforts to reduce the consumption of fossil fuels and promote recycling biowaste, there is an interest in the production of post-hydrothermal liquefaction wastewater (HTL-AP) from the hydrothermal liquefaction (HTL) process that converts wet biomass into biocrude oil. This study explores ways of transforming potentially toxic HTL-AP into a fertilizer source for hydroponic cropping systems. This study specifically investigates the integration of the white-rot fungus Trametes versicolor with nitrifying bacteria (Nitrosomonas and Nitrobacter) to convert the organic nitrogen compounds into inorganic nitrogen while also producing the enzyme laccase, which has been shown to remove toxic compounds. This study aims to increase the concentration of nitrate-N to valorize wastewater as a suitable fertilizer by measuring several parameters, including laccase activity, pH, nitrate-N, and ammonia/ammonium-N concentrations, and analyzes interactions to optimize the conversion process. The data support the claim that the simultaneous inoculation of T. versicolor and nitrifying bacteria significantly increases nitrate-N concentrations in HTL-AP, as it increased by 17 times, or an increase of 32.69 mg/L. In addition, HTL-AP treated with T. versicolor and nitrifying bacteria reduced the treatment time by 120 h, highlighting a reduction in personnel time and energy consumption. Therefore, this research accentuates sustainability through fungal and bacterial treatments to develop eco-friendly hydroponic fertilizers. Future research should explore the potential of utilizing the combination of T. versicolor and nitrifying bacteria for the treatment of other industrial wastewaters. Full article

In this study, we developed a rapid and effective method for enriching the culture of nitrifying bioflocs (NBF) from aquacultural brackish water. The self-designed mixotrophic mediums with a single or mixed addition of sodium acetate, sodium citrate, and sucrose were used to investigate the enrichment process and nitrification efficiency of NBF in small-scale reactors. The results showed that NBF with an MLVSSs from 1170.4 mg L⁻¹ to 2588.0 mg L⁻¹ were successfully enriched in a period of less than 16 days. The citrate group performed the fastest enrichment time of 10 days, while the sucrose group had the highest biomass of 2588.0 ± 384.7 mg L⁻¹. In situ testing showed that the highest nitrification efficiency was achieved in the citrate group, with an ammonia oxidation rate of 1.45 ± 0.34 mg N L⁻¹ h⁻¹, a net nitrification rate of 2.02 ± 0.20 mg N L⁻¹ h⁻¹, and a specific nitrification rate of 0.72 ± 0.14 mg N g⁻¹ h⁻¹. Metagenomic sequencing revealed that Nitrosomonas (0.0~1.0%) and Nitrobacter (10.1~26.5%) were dominant genera for AOB and NOB, respectively, both of which had the highest relative abundances in the citrate group. Linear regression analysis further demonstrated significantly positive linear relations between nitrification efficiencies and nitrifying bacterial genera and gene abundance in NBF. The results of this study provide an efficient enrichment culture method of NBF for the operation of biofloc technology aquaculture systems, which will further promote its wide application in modern intensive aquaculture. Full article

The application of urea in agricultural soil significantly boosts nitrous oxide (N₂O) emissions. However, the reason for nitrite accumulation, the period of nitrite-oxidizing bacteria (NOB) suppression, and the main NOB species for nitrite removal behind urea fertilization have not been thoroughly investigated. In this study, four laboratory microcosm experiments were conducted to simulate urea fertilization in agricultural soils. We found that within 36 h of urea application, nitrite oxidation lagged behind ammonia oxidation, leading to nitrite accumulation and increased N₂O emissions. However, after 36 h, NOB activity recovered and then removed nitrite, leading to reduced N₂O emissions. Urea use resulted in an N₂O emission rate tenfold higher than ammonium. During incubation, Nitrobacter-affiliated NOB growth decreased initially but increased later with urea use, while Nitrospira-affiliated NOB appeared unaffected. Chlorate suppression of NOB lasted longer, increasing N₂O emissions. Urease inhibitors effectively reduced N₂O emissions by slowing urea hydrolysis and limiting free ammonia production, preventing short-term NOB suppression. In summary, short-term NOB suppression during urea hydrolysis played a crucial role in increasing N₂O emissions from agricultural soils. These findings revealed the reasons behind the surge in N₂O emissions caused by extensive urea application and provided guidance for reducing N₂O emissions in agricultural production processes. Full article

The accumulation of nitrite is frequently overlooked, despite the fact that nitrification is the most essential phase of the entire nitrogen (N) cycle and that nitrifying bacteria play a significant role in nitrification. At present, the effects of different N application rates on soil nitrite-oxidizing bacteria (NOB) abundance, community composition, diversity, and its main influencing factors are still unclear. In this study, five N fertilizer application rates under film mulching and a drip irrigation system were studied in the semi-arid area of Northeast China. The treatments were 0 kg ha⁻¹ (N0), 90 kg ha⁻¹ (N1), 150 kg ha⁻¹ (N2), 210 kg ha⁻¹ (N3), and 270 kg ha⁻¹ (N4). Fluorescent quantitative PCR and Illumina Miseq sequencing were used to analyze the abundance and community structure of NOB under different amounts of N application. The results showed that the increase in amounts of N application was strongly accompanied by an increase in the content of soil organic matter (SOM), total nitrogen (TN), nitrate nitrogen (NO₃⁻-N), and ammonium nitrogen (NH₄⁺-N), while the pH significantly reduced with an increase in N fertilization. N fertilization significantly increased soil nitrite oxidoreductase (NXR) activity, soil nitrification potential (PNR), and soil nitrite oxidation potential (PNO). A high N application rate significantly heightened the abundance of Nitrospira- and Nitrobacter-like NOB. N fertilizer considerably raised the Shannon index of Nitrospira-like NOB. The N application amount was the key factor affecting the community structure of Nitrospira-like NOB, and available nitrogen (AN) had the dominant influence on the community structure of Nitrospira-like NOB. N fertilizer can cause soil acidification, which affects NOB abundance and diversity. Nitrospira-like NOB may promote nitrite oxidation in different N application rates under a mulched fertigation system. The findings offered a crucial scientific foundation for further investigation into how nitrite-oxidizing bacteria respond to N fertilizer management strategies in farmland soil under film mulching drip irrigation in Northeast China. Full article

Nitrifying bacteria and archaea are ubiquitous and can transform ammonia locked up in soil or manure into nitrate, a more soluble form of nitrogen. However, nitrifying bacteria and archaea inhabiting maize rhizosphere have not been fully explored. This study evaluates the diversity and abundance of nitrifying bacteria and archaea across different growth stages of maize using 16S amplicon sequencing. Moreover, the influence of environmental factors (soil physical and chemical properties) on the nitrifying communities was evaluated. Rhizosphere soil DNA was extracted using Nucleospin Soil DNA extraction kit and sequenced on Illumina Miseq platform. MG-RAST was used to analyze the raw sequences. The physical and chemical properties of the soil were measured using standard procedure. The results revealed 9 genera of nitrifying bacteria; Nitrospira, Nitrosospira, Nitrobacter, Nitrosovibrio, Nitrosomonas, Nitrosococcus, Nitrococcus, unclassified (derived from Nitrosomonadales), unclassified (derived from Nitrosomonadaceae) and 1 archaeon Candidatus Nitrososphaera. The Nitrospirae phyla group, which had the most nitrifying bacteria, was more abundant at the tasselling stage (67.94%). Alpha diversity showed no significant difference. However, the Beta diversity showed significant difference (p = 0.01, R = 0.58) across the growth stages. The growth stages had no significant effect on the diversity of nitrifying bacteria and archaea, but the tasselling stage had the most abundant nitrifying bacteria. A correlation was observed between some of the chemical properties and some nitrifying bacteria. The research outcome can be put into consideration while carrying out a biotechnological process that involves nitrifying bacteria and archaea. Full article

The plant microbiome is involved in enhancing nutrient acquisition, plant growth, stress tolerance, and reducing chemical inputs. The identification of microbial functional diversity offers the chance to evaluate and engineer them for various agricultural processes. Using a shotgun metagenomics technique, this study examined the functional diversity and metabolic potentials of microbial communities in the rhizosphere of soybean genotype link 678. The dominant genera are Geobacter, Nitrobacter, Burkholderia, Candidatus, Bradyrhizobium and Streptomyces. Twenty-one functional categories were present, with fourteen of the functions being dominant in all samples. The dominant functions include carbohydrates, fatty acids, lipids and isoprenoids, amino acids and derivatives, sulfur metabolism, and nitrogen metabolism. A Kruskal–Wallis test was used to test samples’ diversity differences. There was a significant difference in the alpha diversity. ANOSIM was used to analyze the similarities of the samples and there were significant differences between the samples. Phosphorus had the highest contribution of 64.3% and was more prominent among the soil properties that influence the functional diversity of the samples. Given the functional groups reported in this study, soil characteristics impact the functional role of the rhizospheric microbiome of soybean. Full article

Salinization is considered a threat to agricultural soil and decreases crop yield worldwide. Nitrification and denitrification are the core processes of soil N-cycle. However, the response of nitrifiers and denitrifiers to salinity in agricultural soils remains ambiguous. The study aimed to explore the effect of salinity on nitrifiers and denitrifiers communities in agricultural soils along a naturally occurring salinity gradient. The effects of salinity on the abundance, composition, and interactions of nitrifiers and denitrifiers in surface soils were investigated. The abundance of nitrifiers significantly decreased in response to the increase in salinity. Ammonia-oxidizing archaea (AOA) were more susceptible to salinity elevation than ammonia-oxidizing bacteria (AOB). Nitrospira and Nitrobacter showed a similar trend to the salinity gradient, but the relative abundance of Nitrobacter was increased in the saline soils. High salinity decreased the abundance of napA and nirK, but had no significant effect on other marker genes for denitrification. Besides electrical conductivity, total sulfur (TS)+available potassium (AK) and TN+TS+C/N+total phosphorus (TP)+AK significantly explained the variation in denitrifier and nitrifier communities. We also found that high salinity decreased the connections between different N functional genes. These results implied the alteration of the nitrogen cycling community by high salinity mainly through decreasing AOA, NOB, and some denitrifiers with nitrate or nitrite reduction potentials and weakening the connectivity between nitrogen cycling drivers. Full article

Highly electrosensitive platforms have been developed using different nanocomposite materials based on carbon allotropes and different metallic nanoparticles for determination of nitrite and biogenic amines (BAs). The nitrification process occurred in soil represents an important source of pollution. The nitrification consists in biological oxidation of the relatively immobile ammonium (NH₄⁺) to highly mobile nitrate, via nitrite. This process is carried out mainly by the ammonia–oxidizing bacteria (Nitrosomonas sp. and Nitrobacter sp.) present in the soil microbial population [1,²]. The nitrite contamination of ground and surface waters represents the major concern associated with the nitrification process. Additionally, the growing needs for food and environmental safety has led to an increase in research for the detection of biogenic amines (BAs) in recent years. Despite the fact that BAs are increasingly present in food and beverages, causing toxic effects in the body, legislation that limits their presence in food chains needs to be updated, thus requiring sensitive tools for their detection [³,⁴]. Miniaturized analytical tools have been developed based on nanocomposite materials obtained through combination of different carbon allotrope materials (nanoribbons, nanotubes—single and multiwalled—and nanofibers) with metallic nanoparticles (Ag, Au-Ag, Pt, Cu). Thus, carbon based screen-printed electrodes (SPE) were chemically modified with the obtained nanocomposite materials and further characterized using different electrochemical techniques. In order to allow a selective and sensitive determination of analytes, an electropolymerized film was deposed on the modified sensors. For BAs determination were realized with two configurations of biosensors, a bienzymatic one consisting in immobilization of diamine oxidase (DAO) and horseradish peroxidase (HRP) onto the modified sensors, and, respectively, a mono-enzymatic system based on immobilization of DAO onto the modified sensors. It was taken into account that the charge of carbon-based nanomaterials on the surface of the sensors should not exceed 5%, in order to ensure a low based current. Morpho-structural and electrochemical characterization studies of the modified SPEs have been performed in order to achieve a high sensitivity and selectivity of detection, applying a low overvoltage. The co-polymeric film ensured a better stability of the nanocomposite material layers at the electrode surface and an optimal matrix for enzymes immobilization. Optimization of the nanocomposite-based sensors were performed, and finally detection of biogenic amines was carried out using biosensors based on single-walled carbon nanotubes and Pt nanoparticles, while nitrite determination was performed using multi-walled carbon nanotubes and AgNP modified sensors at applied potentials between −0.45 and +0.6 V vs. Ag/AgCL. The developed sensors and biosensors showed good sensitivities of nitrite and BAs detection. Although the enzyme DAO has a low enough activity to catalyze the oxidation of amine of interest, the detection limits were lowered due to the electrocatalytic activity of nanocomposite materials and the HRP enzyme used. Full article

Bioregenerative life support systems (BLSS) are currently in development to tackle low recovery efficiencies, high energy demands, as well as food, water, and oxygen production challenges through the regeneration of nutrients from waste streams. The MELiSSA pilot plant has been developed as a testbed for regenerative life support system bioreactor operation and characterization. As nitrogen is a vital resource in such systems, we studied the functional composition of a new packed-bed nitrifying bioreactor inoculated with a co-culture of Nitrosomonas europaea (ATCC 25978) and Nitrobacter winogradskyi (ATCC 25391). After 840 days of autotrophic continuous cultivation, the packed-bed was sampled at five vertical positions, each with three horizontal positions, and the biomass at each position was characterized via qPCR, 16S amplicon sequencing, and liquid chromatography tandem mass spectrometry. The total number of cells within the different sections fluctuated around 8.95 ± 5.10 × 10⁷ cells/mL of beads. Based on 16S amplicons and protein content, N. europaea and N. winogradskyi constituted overall 44.07 ± 11.75% and 57.53 ± 12.04% of the nitrifying bioreactor, respectively, indicating the presence of a heterotrophic population that, even after such a long operation time, did not affect the nitrification function of the bioreactor. In addition, DNA-based abundance estimates showed that N. europaea was slightly more abundant than N. winogradskyi, whereas protein-based abundance estimates indicated a much higher abundance of N. europaea. This highlights that single-method approaches need to be carefully interpreted in terms of overall cell abundance and metabolic activity. Full article

At a low COD:TN ratio (≤5) in influent, maintaining a longer HRT (≥9 h) and longer SRT (≥30 d) are suggested to improve higher N removal efficiency in case of operation at low DO (Dissolved oxygen) level (0.9 ± 0.2 mg-O₂/L). However, in case of operation at high DO level (4.0 ± 0.5 mg-O₂/L), short HRT (1 h) and typical SRT (17 d) make it possible to achieve nitrogen removal. On the other hand, at a high COD:TN ratio (≥8.4), a typical HRT (9–15 h), SRT (12–19 d), and DO level (1.3–2.6 mg-O₂/L) would be applied. Microbial distribution analysis showed an abundance of AOA (Ammonia-oxidizing archaea) under conditions of low DO (≤0.9 mg-O₂/L). Nitrosomonas sp. are mostly found in the all investigated water resource recovery facilities (WRRFs). Nitrosospira sp. are only found under operating conditions of longer SRT for WRRFs with a low COD:TN ratio. In comparison between abundances of Nitrobacter sp. and Nitrospira sp., abundances of Nitrobacter sp. are proportional to low DO concentration rather than abundance of Nitrospira sp. A predominance of nosZ-type denitrifiers were found at low DO level. Abundance of denitrifiers by using nirS genes showed an over-abundance of denitrifiers by using nirK genes at low and high COD:TN ratios. Full article