Effects of synthetic nitrogen fertilizer and manure on fungal and bacterial contributions to N2O production along a soil acidity gradient

Experimental evidence for viral impact on microbial community, nitrification, and denitrification in an agriculture soil

Viruses are ubiquitous, and their potential impacts on biogeochemical cycles in soil have largely been inferred from correlation evidence and virome studies. Manure has been demonstrated to affect nitrogen cycle by altering soil nutrients and microbial communities. However, the direct impacts of viruses derived from manure on microbial community, nitrification, and denitrification remained exclusive. In this study, concentrated viral extracts obtained from manure were added into an agricultural soil in varying dosages: a one-time addition of 10-fold viruses or a weekly addition of 1-fold viruses for ten weeks. The results showed that both viral extracts and manure significantly changed the microbial community compositions and structures. The effect of manure on microbial diversity was concentration-dependent, differing from the viral impact on microbial diversity in soil. Deterministic processes predominated in the assembly of microbial communities in both viral and manure treatments, with an increased contribution of deterministic processes observed after these treatments. Additionally, a high concentration (10-fold) of viruses enhanced N2O production and reduction in soil. In the control treatment, N2O production was driven by bacterial denitrification, fungal denitrification, and chemo-denitrification. However, bacteria became the dominant driver of N2O production in both virus and manure treatments. Overall, experimental evidence for viral impacts on the composition and assembly of microbial community, as well as on nitrification and denitrification processes, was provided through a 70-day microcosm experiment. These findings highlight the importance of viruses in regulating the distribution and functioning of microbes in terrestrial ecosystems.

Partial substitution of manure increases N2O emissions in the alkaline soil but not acidic soils

The fertilization regimes of combining manure with synthetic fertilizer are benefits for crop yields and soil fertility in cropping systems as compared to sole synthetic fertilization, but the responses of nitrous oxide (N2O) emissions to these practices are inconsistent in the literatures. We hypothesized that it is caused by different proportions of nitrogen (N) applied as manure and various soil properties. Here, we conducted a microcosm experiment, and measured the N2O emissions from control (no N) and five manure substitution treatments (supplied 100 mg N kg-1 using the combination of urea with manure) with a range of proportions of N applied as manure (0, 25%, 50%, 75%, and 100%) in three different soil types (fluvo-aquic soil, black soil, and latosol) under aerobic condition. The stimulated effect on N2O emissions was more pronounced after manure application in an alkaline soil with high nitrification rate, due to relatively rapid soil DOC depletion and N mineralization of manure. N2O emissions from partial substitution of urea with manure were significantly higher than manure-only addition under high soil pH due to abundant labile C from manure. However, there was no difference between manure substitution treatments under acid soils. Nitrification inhibitor substantially decreased N2O emissions with increasing soil pH, but it was less effective in mitigating N2O emissions with larger proportion of manure. This is likely due to the slow nitrification under low soil pH, and denitrification derived N2O increased with increasing manure application rate. Collectively, our study shows that the application of manure substitution to alkaline soils requires careful consideration, which might have rapid nitrification potential and hence trigger significant N2O emissions. The knowledge gained in this work will help the decision-makers in optimizing a sound N fertilization regime interacted with soil properties for sustainable crop production and N2O mitigation.

Organic amendment in climate change mitigation: Challenges in an era of micro- and nanoplastics

As a global strategy for mitigating climate change, organic amendments play critical roles in restoring stocks in carbon (C) depleted soils, preserving existing stocks to prevent further soil organic carbon (SOC) loss, and enhancing C sequestration. However, recent emerging evidence of a significant proportion of micro- and nanoplastics (M/NPs) occurrence in most organic substrates (e.g., compost manure, farmyard manure, and sewage sludge) compromises its role in climate change mitigation. Given the predicted surge of soil M/NPs proliferation in the coming years, we argued whether organic amendment remains a reliable climate change mitigation strategy. Toxicity effects of M/NPs influx within the soil matrix disrupt plants and their associated key microbial taxa responsible for crucial biogeochemical processes and restructuring of SOC, leading to increasing emissions of potent greenhouse gases (GHGs, e.g., CO2, CH4, and N2O) that feedback to aggravate the rapidly changing climate. Here, we summarize evidence based on literature that the discovery of M/NPs in organic substrates compromises its role in the climate change mitigation strategy. We briefly discuss the overview of synthetic fertilizers and their impact on SOC and atmospheric emissions. We discuss the role of organic amends in climate change mitigation and the emergence of M/NPs in it. We discuss M/NPs-induced damages to SOC and subsequent emissions of GHGs. We briefly highlight management approaches to clean organic substrates of M/NPs to improve their use in agrosystems and provide recommendations for future research studies. We found that organic amendment plays pivotal role in modulating the biotic and abiotic drivers responsible for climate mitigation. However, M/NPs in organic amendments weaken the regulatory mechanisms of organic amendments in plant-soil systems. We conclude that organic amendments of soils are critical for restoring SOC and mitigating the rapidly changing climate; yet, the discovery of M/NPs in organic substrates put their usage in a dilemma.

nirS and nosZII bacterial denitrifiers as well as fungal denitrifiers are coupled with N2O emissions in long-term fertilized soils

Fertilizer application plays a critical role in soil fertility and crop yield and has been reported to significantly affect soil denitrification. However, the mechanisms by which denitrifying bacteria (nirK, nirS, nosZI, and nosZII) and fungi (nirK and p450nor) affect soil denitrification are poorly understood. Therefore, in this study, we investigated the effect of different fertilization treatments on the abundance, community structure, and function of soil denitrifying microorganisms in an agricultural ecosystem with long-term fertilization using mineral fertilizer or manure and their combination. The results showed that the application of organic fertilizer significantly increased the abundance of nirK-, nirS-, nosZI-, and nosZII-type denitrifying bacteria as the soil pH and phosphorus content increased. However, only the community structure of nirS- and nosZII-type denitrifying bacteria was influenced by the application of organic fertilizer, which led to a higher contribution of bacteria to nitrous oxide (N2O) emissions than that observed after inorganic fertilizer application. The increase in soil pH reduced the abundance of nirK-type denitrifying fungi, which may have presented a competitive disadvantage relative to bacteria, resulting in a lower contribution of fungi to N2O emissions than that observed after inorganic fertilizer application. The results demonstrated that organic fertilization had a significant impact on the community structure and activity of soil denitrifying bacteria and fungi. Our results also highlighted that after organic fertilizer application, nirS- and nosZII-denitrifying bacteria communities represent likely hot spots of bacterial soil N2O emissions while nirK-type denitrifying fungi represent hot spots for fungal soil N2O emissions.

Identification of Fungal and Bacterial Denitrification Inhibitors Targeting Copper Nitrite Reductase

The usage of nitrification inhibitors is one of the strategies that reduce or slow down the denitrification process to prevent nitrogen loss to the atmosphere in the form of N₂O. Directly targeting microbial denitrification could be one of the mitigation strategies; however, until now little efforts have been devoted toward the development of denitrification inhibitors. Here, we have identified small-molecule inhibitors of one of the proteins involved in the fungal denitrification pathway. Specifically, virtual screening was employed to identify the inhibitors of copper-containing nitrite reductase (FoNirK) of the filamentous fungus Fusarium oxysporum. Three series of chemical compounds were identified, out of which compounds belonging to two chemical scaffolds inhibited FoNirK enzymatic activity in low micromolar ranges. Several compounds also displayed moderate inhibition of fungal denitrification activity in vivo. Evaluation of in vitro activity against NirK from denitrifying bacterium Achromobacter xylosoxidans (AxNirK) and in vivo bacterial denitrification revealed a similar inhibitory profile.

Waste Cabbage-Integrated Nutritional Superabsorbent Polymers for Water Retention and Absorption Applications

To alleviate soil impoverishment and water shortage in desert areas, as well as to reduce the impact of waste cabbage on the environment and human health, we used waste cabbage as a substrate, 2-acrylamide-2-methyl-1-propane sulfonic acid (AMPS) and acrylic acid (AA) as polymerization units, and NH₄Cl and KNO₃ as nutriment to obtain two waste cabbage-superabsorbent polymers (CB-SAP_NH4Cl and CB-SAP_KNO3) by the one-pot method. The chemical structure, thermal stability, and morphology of the polymers were investigated by Fourier-transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA), and scanning electron microscope (SEM). Meanwhile, the water retention, water absorption, and salt resistance were compared with the purchased polymers. The results showed that the nutriment was successfully encapsulated inside the polymer, and CB-SAP_NH4Cl and CB-SAP_KNO3 at 1% nutrient concentration showed excellent water retention properties, salt resistance, and water absorption performance of 1546 and 1131 g/g (distilled water), 306 and 277 g/g (tap water), and 116 and 91 g/g (0.9% NaCl solution). Therefore, they are highly promising materials for the application.

Effects of Fermented Seaweed Fertilizer Treatment on Paddy Amino Acid Content and Rhizosphere Microbiome Community

Seaweed has often been reported on for it potential bioresources for fertilizers to improve crop productivity and reduce the use of chemical fertilizers (CF). However, little is known about the nutritional status of the crop grown with the implementation of seaweed fertilizers (SF). In this study, the amino acid content of rice produced by SF implementation was evaluated. Furthermore, the rhizosphere bacterial community was also investigated. The paddy seedlings were divided into five groups, control (C0), chemical fertilizer (CF), seaweed fertilizer (SF), chemical and seaweed fertilizer combination 25:75 (CFSF1), and chemical and fertilizer combination 50:50 (CFSF2). The CFSF2 group shown significantly better growth characteristics compared to other groups. Based on the concentration of macronutrients (N, P, K) in paddy leaf, CFSF2 also shown the best results. This also correlates with the abundant amino acid composition in CFSF2 in almost all tested amino acids, namely, serine, phenylalanine, isoleucine, valine, glycine, tyrosine, proline, threonine, histidine, and arginine. Interestingly, beneficial bacteria Rhizobiales were significantly higher in CFSF2-treated soil (58%) compared to CF (29%). Another important group, Vicinamibacterales, was also significantly higher in CFSF2 (58%) compared to CF (7%). Hence, these potentially contributed to the high rice amino acid content and yield in the CFSF2-treated paddy. However, further field-scale studies are needed to confirm the bioindustrial application of seaweed in agricultural systems.

Combined Application of Manure and Chemical Fertilizers Alters Soil Environmental Variables and Improves Soil Fungal Community Composition and Rice Grain Yield

Soil microorganisms play vital roles in energy flow and soil nutrient cycling and, thus, are important for crop production. A detailed understanding of the complex responses of microbial communities to diverse organic manure and chemical fertilizers (CFs) is crucial for agroecosystem sustainability. However, little is known about the response of soil fungal communities and soil nutrients to manure and CFs, especially under double-rice cropping systems. In this study, we investigated the effects of the application of combined manure and CFs to various fertilization strategies, such as no N fertilizer (Neg-CF); 100% chemical fertilizer (Pos-CF); 60% cattle manure (CM) + 40% CF (high-CM); 30% CM + 70% CF (low-CM); 60% poultry manure (PM) + 40% CF (high-PM), and 30% PM + 70% CF (low-PM) on soil fungal communities' structure and diversity, soil environmental variables, and rice yield. Results showed that synthetic fertilizer plus manure addition significantly increased the soil fertility and rice grain yield compared to sole CFs' application. Moreover, the addition of manure significantly changed the soil fungal community structure and increased the relative abundance of fungi such as phyla Ascomycota, Basidiomycota, Mortierellomycota, and Rozellomycota. The relative abundances dramatically differed at each taxonomic level, especially between manured and non-manured regimes. Principal coordinates analysis (PCoA) exhibited greater impacts of the addition of manure amendments than CFs on fungal community distributions. Redundancy analysis showed that the dominant fungal phyla were positively correlated with soil pH, soil organic C (SOC), total N, and microbial biomass C, and the fungal community structure was strongly affected by SOC. Network analysis explored positive relationships between microorganisms and could increase their adaptability in relevant environments. In addition, the structural equation model (SEM) shows the relationship between microbial biomass, soil nutrients, and rice grain yield. The SEM showed that soil nutrient contents and their availability directly affect rice grain yield, while soil fungi indirectly affect grain yield through microbial biomass production and nutrient levels. Our results suggest that manure application combined with CFs altered soil biochemical traits and soil fungal community structure and counteracted some of the adverse effects of the synthetic fertilizer. Overall, the findings of this research suggest that the integrated application of CF and manure is a better approach for improving soil health and rice yield.

Isotopic assessment of soil N2O emission from a sub-tropical agricultural soil under varying N-inputs

Nitrogen fertilizers result in high crop productivity but also enhance the emission of N₂O, an environmentally harmful greenhouse gas. Only approximately a half of the applied nitrogen is utilized by crops and the rest is either vaporized, leached, or lost as NO, N₂O and N₂ via soil microbial activity. Thus, improving the nitrogen use efficiency of cropping systems has become a global concern. Factors such as types and rates of fertilizer application, soil texture, moisture level, pH, and microbial activity/diversity play important roles in N₂O production. Here, we report the results of N₂O production from a set of chamber experiments on an acidic sandy-loam agricultural soil under varying levels of an inorganic N-fertilizer, urea. Stable isotope technique was employed to determine the effect of increasing N-fertilizer levels on N₂O emissions and identify the microbial processes involved in fertilizer N-transformation that give rise to N₂O. We monitored the isotopic changes in both substrate (ammonium and nitrate) and the product N₂O during the entire course of the incubation experiments. Peak N₂O emissions of 122 ± 98 μg N₂O-N m^-2 h^-1, 338 ± 49 μg N₂O-N m^-2 h^-1 and 739 ± 296 μg N₂O-N m^-2 h^-1 were observed for urea application rate of 40, 80, and 120 μg N g^-1. The duration of emissions also increased with urea levels. The concentration and isotopic compositions of the substrates and product showed time-bound variation. Combining the observations of isotopic effects in δ¹⁵N, δ¹⁸O, and ¹⁵N site preference, we inferred co-occurrence of several microbial N₂O production pathways with nitrification and/or fungal denitrification as the dominant processes responsible for N₂O emissions. Besides this, dominant signatures of bacterial denitrification were observed in a second N₂O emission pulse in intermediate urea-N levels. Signature of N₂O consumption by reduction could be traced during declining emissions in treatment with high urea level.

Insight into soil nitrogen and phosphorus availability and agricultural sustainability by plant growth-promoting rhizobacteria

Nitrogen and phosphorus are critical for the vegetation ecosystem and two of the most insufficient nutrients in the soil. In agriculture practice, many chemical fertilizers are being applied to soil to improve soil nutrients and yield. This farming procedure poses considerable environmental risks which affect agricultural sustainability. As robust soil microorganisms, plant growth-promoting rhizobacteria (PGPR) have emerged as an environmentally friendly way of maintaining and improving the soil's available nitrogen and phosphorus. As a special PGPR, rhizospheric diazotrophs can fix nitrogen in the rhizosphere and promote plant growth. However, the mechanisms and influences of rhizospheric nitrogen fixation (NF) are not well researched as symbiotic NF lacks summarizing. Phosphate-solubilizing bacteria (PSB) are important members of PGPR. They can dissolve both insoluble mineral and organic phosphate in soil and enhance the phosphorus uptake of plants. The application of PSB can significantly increase plant biomass and yield. Co-inoculating PSB with other PGPR shows better performance in plant growth promotion, and the mechanisms are more complicated. Here, we provide a comprehensive review of rhizospheric NF and phosphate solubilization by PGPR. Deeper genetic insights would provide a better understanding of the NF mechanisms of PGPR, and co-inoculation with rhizospheric diazotrophs and PSB strains would be a strategy in enhancing the sustainability of soil nutrients.

Soil acidification induced decline disease of Myrica rubra: aluminum toxicity and bacterial community response analyses

The decline disease of Myrica rubra tree is commonly induced by soil acidification, which affects the yield and the quality of fruits. It is hypothesized that aluminum toxicity and microbial community changes caused by soil acidification were the main causes of decline of Myrica rubra tree. In order to explore the decline mechanism of Myrica rubra tree, soils around healthy and decline trees of Myrica rubra were collected to compare the concentrations of different aluminum forms, enzyme activities, and bacterial community structure. In this study, soil samples were collected from the five main production areas of Myrica rubra, Eastern China. The results showed that diseased soils had higher exchangeable aluminum, lower enzyme activities, and lower microbial diversity than healthy soils at various sites. The toxic Al significantly decreased bacterial diversity and altered the bacterial community structure. The diseased soils had significantly lower α-diversity indices (ACE, Chao1, and Shannon) of bacterial community. The Al toxicity deceased the relative abundance of Acidobacteria and Planctomycetes, while enhanced the relative abundance of Cyanobacteria, Bacteroidetes, and Firmicutes in soils. Co-occurrence network analysis indicated that the Al toxicity simplified the bacterial network. The soil ExAl content was significantly and negatively correlated with the nodes (r = -0.69, p < 0.05) and edges (r = -0.77, p < 0.01) of the bacterial network. These results revealed that the Al toxicity altered soil bacterial community structure, resulting in the decline disease of Myrica rubra tree, while highlighted the role of Al forms in the plant growth. This finding is of considerable significance to the better management of acidification-induced soil degradation and the quality of fruits.

Stover return and nitrogen application affect soil organic carbon and nitrogen in a double-season maize field

Cultivation techniques have an important influence on grain yield of maize. This experiment investigated the effect of stover return (SR) and different nitrogen (N) application rate on soil organic carbon (SOC) composition, soil nutrient and maize yield. Different nitrogen application rate 100 (N100), 150 (N150), 200 (N200), 250 (N250) or 300 (N300) kg ha^-1 applied to the maize field with stover return and without stover return traditional planting (TP) method. Nitrogen application rate and stover return affected the SOC, labile organic carbon (LOC), microbial biomass (MBC), NO₃ ^- -N, NH₄ ⁺ -N and maize yield. Soil N, soil carbon content and maize yield of SR were all higher than TP. The SOC content of SR and TP were 9.67 and 9.19 g kg^-1 , respectively. Nitrogen application was significantly and positively correlated with soil MBC, LOC, SOC, NO₃ ^- -N, NH₄ ⁺ -N and yield. The maximum values of SOC composition, soil nutrients and maize yield were reached at SR with 250 kg ha^-1 . Stover return with application of N 250 kg ha^-1 significantly increased the growth attribute and maize yield in subtropical region compared with traditional planting.