Lower soil nitrogen-oxide emissions associated with enhanced denitrification under replacing mineral fertilizer with manure in orchard soils.

Emerging evidence suggests that replacing mineral fertilizers with organic livestock manure can effectively suppress reactive gaseous nitrogen (N) emissions from soils. However, the extent of this mitigation potential and the underlying microbial mechanisms in orchards remain unclear. To address this knowledge gap, we measured nitrous and nitric oxide (N2O and NO) emissions, microbial N cycling gene abundance, and N2O isotopomer ratios in pear and citrus orchards under three different fertilization regimes: no fertilization, mineral fertilizer, and manure plus mineral fertilizer. The results showed that although manure application caused large transient peaks of N2O, it reduced cumulative emissions of N2O and NO by an average of 20 % and 17 %, respectively, compared to the mineral fertilizer treatment. Partial replacement of mineral fertilizers with manure enhanced the contribution of AOA to nitrification and reduced the contribution of AOB, thus reducing N2O emissions from nitrification. Isotope analysis suggested that the pathway for N2O production in the soils of both orchards was dominated by bacterial denitrification and nitrifier denitrification. The manure treatment reduced the ratio of denitrification products. Additionally, the dual isotope mixing model results indicated that partially replacing mineral fertilizers with manure could promote soil denitrification, resulting in more N2O being reduced. N-oxide emissions were on average 67 % higher in the pear orchard than in the citrus orchard, probably due to the differences in soil physicochemical properties and growth habits between the two orchards. These findings underscore the potential of partially replacing mineral fertilizers with organic manure in orchards to reduce gaseous N emissions, contributing to the transition towards environmentally sustainable and climate-smart agricultural practices.

Climate controls on nitrate dynamics and gross nitrogen cycling response to nitrogen deposition in global forest soils.

Understanding the patterns and controls regulating nitrogen (N) transformation and its response to N enrichment is critical to re-evaluating soil N limitation or availability and its environmental consequences. Nevertheless, how climatic conditions affect nitrate dynamics and the response of gross N cycling rates to N enrichment in forest soils is still only rudimentarily known. Through collecting and analyzing 4426-single and 769-paired observations from 231 15N labeling studies, we found that nitrification capacity [the ratio of gross autotrophic nitrification (GAN) to gross N mineralization (GNM)] was significantly lower in tropical/subtropical (19%) than in temperate (68%) forest soils, mainly due to the higher GNM and lower GAN in tropical/subtropical regions resulting from low C/N ratio and high precipitation, respectively. However, nitrate retention capacity [the ratio of dissimilatory nitrate reduction to ammonium (DNRA) plus gross nitrate immobilization (INO3) to gross nitrification] was significantly higher in tropical/subtropical (86%) than in temperate (54%) forest soils, mainly due to the higher precipitation and GNM of tropical/subtropical regions, which stimulated DNRA and INO3. As a result, the ratio of GAN to ammonium immobilization (INH4) was significantly higher in temperate than in tropical/subtropical soils. Climatic rather than edaphic factors control heterotrophic nitrification rate (GHN) in forest soils. GHN significantly increased with increasing temperature in temperate regions and with decreasing precipitation in tropical/subtropical regions. In temperate forest soils, gross N transformation rates were insensitive to N enrichment. In tropical/subtropical forests, however, N enrichment significantly stimulated GNM, GAN and GAN to INH4 ratio, but inhibited INH4 and INO3 due to reduced microbial biomass and pH. We propose that temperate forest soils have higher nitrification capacity and lower nitrate retention capacity, implying a higher potential risk of N losses. However, tropical/subtropical forest systems shift from a conservative to a leaky N-cycling system in response to N enrichment.

Dynamic carbon-nitrogen coupling under global change.

Carbon-nitrogen coupling is a fundamental principle in ecosystem ecology. However, how the coupling responds to global change has not yet been examined. Through a comprehensive and systematic literature review, we assessed how the dynamics of carbon processes change with increasing nitrogen input and how nitrogen processes change with increasing carbon input under global change. Our review shows that nitrogen input to the ecosystem mostly stimulates plant primary productivity but inconsistently decreases microbial activities or increases soil carbon sequestration, with nitrogen leaching and nitrogenous gas emission rapidly increasing. Nitrogen fixation increases and nitrogen leaching decreases to improve soil nitrogen availability and support plant growth and ecosystem carbon sequestration under elevated CO2 and temperature or along ecosystem succession. We conclude that soil nitrogen cycle processes continually adjust to change in response to either overload under nitrogen addition or deficiency under CO2 enrichment and ecosystem succession to couple with carbon cycling. Indeed, processes of both carbon and nitrogen cycles continually adjust under global change, leading to dynamic coupling in carbon and nitrogen cycles. The dynamic coupling framework reconciles previous debates on the "uncoupling" or "decoupling" of ecosystem carbon and nitrogen cycles under global change. Ecosystem models failing to simulate these dynamic adjustments cannot simulate carbon-nitrogen coupling nor predict ecosystem carbon sequestration well.

Insights into the shift of microbial community related to nitrogen cycle, especially N2O in vanadium-polluted soil.

Soil is a vital contributor to the production of nitrous oxide (N2O), a potent greenhouse gas, through the nitrogen cycle, which can be influenced by accumulated vanadium (V) in soil but it is less pronounced. This work investigated the response of soil N2O fluxes along with major nitrogen cycle products (ammonium, nitrate, and nitrite) to different vanadium contents (0, 200, 500, 800, and 1100 mg V/kg), and the underlying microbial mechanisms. N2O fluxes was significantly influenced at high V content (1100 mg V/kg) due to its corresponding high water-soluble V content. Microbial composition and their correlations with nitrogen cycle products showed that microbes in dominant phyla (Actinobacteriota and Proteobacteria) and genus (Nocardioides, Lysobacter, Sphingomonas, and Marmoricola) might be the important contributor to N2O fluxes regardless of the V content. Moreover, high V contents (800, and 1100 mg V/kg) could enrich microbes involved in nitrogen cycle, but weaken their correlations with nitrogen-related products, such as in genus Bacillus, and change microbial correlation with N2O from associated with nitrate and nitrite to ammonium. Meanwhile, functional gene predication results showed that denitrifying genes nirKS and nosZ were negatively and positively correlated with V contents, respectively. These all further suggested that the shift of possible N2O metabolic pathways induced mainly by water-soluble V might be the underlying reason for N2O fluxes. These findings promote an understanding of the potential effect of metal pollution on N2O fluxes in soil.

Invasion by Cenchrus spinifex changes the soil microbial community structure in a sandy grassland ecosystem.

Continuous nitrogen deposition increases the nitrogen content of terrestrial ecosystems and alters the soil nitrogen cycling process. Invasive plants have strong environmental adaptability, which can not only affect the composition and diversity of soil microbial community but also significantly affect the transformation process of soil nitrogen, leading to successful invasion. Currently, research on invasive plant soil ecosystems mainly focused on changes in soil nutrients and soil microorganisms. As an invasive annual grass weed with strong ecological adaptability, the impact of Cenchrus spinifex at different growth periods on soil environment and soil microbial structure composition and diversity in sandy grassland ecosystems is still unclear. In this study, soil samples were collected from four habitats with different degrees of invasion in situ during the vegetation and reproductive growth periods of Cenchrus spinifex. High-throughput sequencing and qPCR technology were used to analyze the changes in the composition, structure and diversity characteristics of the soil microbial communities during Cenchrus spinifex invasion. The results indicated that Cenchrus spinifex invasion had different effects on the soil environment at different growth periods, and Cenchrus spinifex had a preference for the utilization of ammonium nitrogen during vegetation growth period. Moreover, Cenchrus spinifex invasion significantly changed the composition and structure of soil bacterial communities, and the response of soil bacterial and fungal communities to the invasion was inconsistent. Additionally, the bacterial network was more stable than the fungal network. At different growth periods, Cenchrus spinifex had a significant impact on the key microbial communities of soil nitrogen cycling. The invasion increased the abundance of nifH and AOA-amoA, while decreased the abundance of AOA-amoB. Alkaline hydrolyzed nitrogen, total nitrogen and total phosphorus content were key factors that affect vegetation growth period and change the key microbial communities of nitrogen cycling. Alkaline hydrolyzed nitrogen, total phosphorus and organic carbon were key factors in reproductive growth period that alter the nitrogen cycling of key microbial communities.

Climate warming, but not Spartina alterniflora invasion, enhances wetland soil HONO and NOx emissions.

Climate warming and invasive plant growth (plant invasion) may aggravate air pollution by affecting soil nitrogen (N) cycling and the emissions of reactive N gases, such as nitrous acid (HONO) and nitrogen oxides (NOx). However, little is known about the response of soil NOy (HONO + NOx) emissions and microbial functional genes to the interaction of climate warming and plant invasion. Here, we found that experimental warming (approximately 1.5 °C), but not Spartina alterniflora invasion, increased NOy emissions (0-140 ng N m-2 s-1) of treated wetland soils by 4-10 fold. Warming also decreased soil archaeal and fungal richness and diversity, shifted their community structure (e.g., decreased the archaeal classes Thermoplasmata and Iainarchaeia, and increased the archaeal genus Candidatus Nitrosoarchaeum, and the fungal classes Saccharomycetes and Tritirachiomycetes), and decreased the overall abundance of soil N cycling genes. Structural equation modeling revealed that warming-associated changes in edaphic factors and the microbial N cycling potential are responsible for the observed increase in soil NOy emissions. Collectively, the results showed that climate warming accelerates soil N cycling by stimulating large soil HONO and NOx emissions, and influences air quality by contributing to atmospheric reactive N and ozone cycling.

[Effect of pH on the Abundance and Community Structure of Comammox Nitrospira in Paddy Soils].

Soil pH is recognized as an important environmental factor in determining the niche differentiation for ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities. Species of comammox, a single microorganism capable of the complete oxidation of ammonia to nitrate, have recently been discovered. Metagenomic analysis and quantitative PCR showed that Comammox Nitrospira were found in a wide range of environments, including soil. Comammox bacteria are differentiated into one of two clades (A and B) based on the phylogeny of genes encoding the α-subunit of ammonia monooxygenase genes (amoA). However, all discovered Comammox Nitrospira strains have been isolated and cultured in aquatic ecosystems, including N. inopinata, N. nitrosa, and N. nitrificans, all belonging to clade A. Currently, Comammox Nitrospira has not been obtained from soil environments, which limits our understanding of soil Comammox Nitrospira. Here we hypothesized that, as AOA and AOB, the ecological site of Comammox Nitrospira may also be affected by pH. Therefore, soil samples with differing pH were collected, and the abundances and community structures were studied to elucidate the mechanism of pH effect on the distributions and community compositions of Comammox Nitrospira in soil. Quantitative PCR of comammox clade A and clade B amoA genes in DNA extracts were performed using QuantStudio TM6 Flex Real-Time PCR Systems. The community compositions for Comammox Nitrospira were studied by the cloning libraries of amoA genes method. The results showed that the abundance of Comammox clade A amoA gene in acidic paddy soil was two orders of magnitude higher than that in neutral paddy soil (P<0.05), and the abundance of Comammox clade B in acidic paddy soil was significantly higher than that in neutral paddy soil (P<0.05); the abundance of Comammox clade A amoA gene in acidic paddy soil was 60 times higher than that of clade B, whereas the abundance ratio of Comammox clade A and clade B amoA genes in neutral paddy soil was about two times higher. These results indicated that soil pH significantly affected the abundance of Comammox Nitrospira. The results of cloning and sequencing showed that the Comammox in neutral paddy soil was mainly N. inopinata, which belonged to clade A; no strain belonging to clade B was annotated. Comammox clade A in acidic paddy soil was mainly Composed of N. inopinata and N. nitrosa, and clade B was mainly uncultured bacterium (FN395328). The results indicated that soil pH was an important factor in shaping Comammox Nitrospira community structure. Comammox Nitrospira were detected in all soil samples, and Comammox clade A had a preference for acidic environments. It seemed that species from N. nitrosa possessed the ecological niche of low pH environments, whereas species from N. inopinata preferred to live in neutral environments. In conclusion, pH had a significant effect on the abundance and community structure of Comammox Nitrospira, which was one of the important factors affecting the niche differentiation of Comammox Nitrospira.

Soil Health Management Enhances Microbial Nitrogen Cycling Capacity and Activity.

Soil microbial transformations of nitrogen (N) can be affected by soil health management practices. Here, we report in situ seasonal dynamics of the population size (gene copy abundances) and functional activity (transcript copy abundances) of five bacterial genes involved in soil N cycling (ammonia-oxidizing bacteria [AOB] amoA, nifH, nirK, nirS, and nosZ) in a long-term continuous cotton production system under different management practices (cover crops, tillage, and inorganic N fertilization). Hairy vetch (Vicia villosa Roth), a leguminous cover crop, most effectively promoted the expression of N cycle genes, which persisted after cover crop termination throughout the growing season. Moreover, we observed similarly high or even higher N cycle gene transcript abundances under vetch with no fertilizer as no cover crop with N fertilization throughout the cover crop peak and cotton growing seasons (April, May, and October). Further, both the gene and transcript abundances of amoA and nosZ were positively correlated to soil nitrous oxide (N2O) emissions. We also found that the abundances of amoA genes and transcripts both positively correlated to field and incubated net nitrification rates. Together, our results revealed relationships between microbial functional capacity and activity and in situ soil N transformations under different agricultural seasons and soil management practices.IMPORTANCE Conservation agriculture practices that promote soil health have distinct and lasting effects on microbial populations involved with soil nitrogen (N) cycling. In particular, using a leguminous winter cover crop (hairy vetch) promoted the expression of key functional genes involved in soil N cycling, equaling or exceeding the effects of inorganic N fertilizer. Hairy vetch also left a legacy on soil nutrient capacity by promoting the continued activity of N cycling microbes after cover crop termination and into the main growing season. By examining both genes and transcripts involved in soil N cycling, we showed different responses of functional capacity (i.e., gene abundances) and functional activity (i.e., transcript abundances) to agricultural seasons and management practices, adding to our understanding of the effects of soil health management practices on microbial ecology.

Microbial indicators are better predictors of wheat yield and quality than N fertilization.

In view of their key roles in many soil- and plant-related processes, we hypothesized that soil microorganisms could play a larger role in determining wheat baking quality than nitrogen fertilization. A field experiment was conducted under bread wheat production conditions, where different fertilization treatments, ranging from 0-120 kg/ha NH4NO3, were applied. Soil samples were taken in May, June and July. Functional genes in the nitrogen cycle were quantified and amplicons of the 16S rRNA gene and the ITS region were sequenced. Wheat yields were measured, and the grain baking quality was analysed for each plot. Fertilisation did not significantly influence the yields and the grain quality. Many bacterial and fungal Amplicon Sequence Variants showed significant positive or negative correlations with yield and grain baking quality parameters. Among the functional gene quantified, the archaeal amoA showed strong negative correlations with the wheat yields and many grain and flour quality parameters. Regression models were able to explain up to 81% of the variability in grain quality based on the microbial data from the May sampling. A better understanding of the microbiology of wheat fields could lead to an optimized management of the N fertilization to maximize yields and grain quality.

Management versus site effects on the abundance of nitrifiers and denitrifiers in European mountain grasslands.

It is well established that the abundances of nitrogen (N) transforming microbes are strongly influenced by land-use intensity in lowland grasslands. However, their responses to management change in less productive and less fertilized mountain grasslands are largely unknown. We studied eight mountain grasslands, positioned along gradients of management intensity in Austria, the UK, and France, which differed in their historical management trajectories. We measured the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as nitrite-reducing bacteria using specific marker genes. We found that management affected the abundance of these microbial groups along each transect, though the specific responses differed between sites, due to different management histories and resulting variations in environmental parameters. In Austria, cessation of management caused an increase in nirK and nirS gene abundances. In the UK, intensification of grassland management led to 10-fold increases in the abundances of AOA and AOB and doubling of nirK gene abundance. In France, ploughing of previously mown grassland caused a 20-fold increase in AOA abundance. Across sites the abundance of AOB was most strongly related to soil NO3--N availability, and AOA were favored by higher soil pH. Among the nitrite reducers, nirS abundance correlated most strongly with N parameters, such as soil NO3--N, microbial N, leachate NH4+-N, while the abundance of nirK-denitrifiers was affected by soil total N, organic matter (SOM) and water content. We conclude that alteration of soil environmental conditions is the dominant mechanism by which land management practices influence the abundance of each group of ammonia oxidizers and nitrite reducers.

[Responses of soil nitrogen transformation to long-term nitrogen fertilization and precipitation changes in a broad-leaved Korean pine forest in Changbai Mountains, China.] / 长白山阔叶红松林土壤氮转化过程对长期施氮和降水变化的响应.

Soil nitrogen (N) cycling, one of the most important biogeochemical processes in forest ecosystems, has significant environmental effects. However, little is known about how it responds to N deposition and precipitation changes. Here, we examined the main effects of N deposition (NF), rainfall reduction (RR) and their interactive effect (RF) on soil N cycling by N addition and transparent V-shaped board interception in a broad-leaved Korean pine forest in Changbai Mountains. The responses of soil nitrification, denitrification, nitrifying functional genes (ammonia-oxidizing archaea AOA and ammonia-oxidizing bacteria AOB), denitrifying functional genes (nirK, nirS and nosZ) and N fixing function genes (nifH) to NF, RR and RF treatments were analyzed. We found significant positive correlations between nitrification and soil NH4+-N, denitrification and and NO3--N, respectively. Soil nitrification and denitrification were not significantly influenced by the three treatments, while denitrification showed an obvious seasonal dynamics. Long-term RR treatment inhibited soil net nitrification, while NF and RF treatments promoted soil net nitrification; nifH and nosZ genes of bacteria were strong resistant to stress, and their diversity was not susceptible to the changes of N and rainfall. Under drought condition, nirK gene of soil bacteria was more susceptible to N deposition. AOA had a higher sensitivity to drought, while AOB had higher sensitivity to NF and RF treatments. The three treatments affected soil net nitrification and altered the diversity of AOB, AOA and nirK-harboring denitrifier in varying degrees, which might affect the release of N-containing gas and ecosystem services.

Soil microbial communities respond differently to three chemically defined polyphenols.

High molecular weight polyphenols (e.g. tannins) that enter the soil may affect microbial populations, by serving as substrates for microbial respiration or by selecting for certain microbes. In this study we examined how three phenolic compounds that represent some environmentally widespread tannins or their constituent functional groups were respired by soil microorganisms and how the compounds affected the abundance and diversity of soil bacteria and archaea, including ammonia oxidizers. An acidic, silt loam soil from a pine forest was incubated for two weeks with the monomeric phenol methyl gallate, the small polyphenol epigallocatechin gallate, or the large polyphenol oenothein B. Respiration of the polyphenols during the incubation was measured using the Microresp™ system. After incubation, metabolic diversity was determined by community level physiological profiling (CLPP), and genetic diversity was determined using denaturing gradient gel electrophoresis (DGGE) analysis on DNA extracted from the soil samples. Total microbial populations and ammonia-oxidizing populations were measured using real time quantitative polymerase chain reaction (qPCR). Methyl gallate was respired more efficiently than the higher molecular weight tannins but not as efficiently as glucose. Methyl gallate and epigallocatechin gallate selected for genetically or physiologically unique populations compared to glucose. None of the polyphenols supported microbial growth, and none of the polyphenols affected ammonia-oxidizing bacterial populations or ammonia-oxidizing archaea. Additional studies using both a wider range of polyphenols and a wider range of soils and environments are needed to elucidate the role of polyphenols in determining soil microbiological diversity.