Global analysis of agricultural soil denitrification in response to fertilizer nitrogen

Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally

Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural land. We combine our continental survey results with a global meta-analysis of available sequencing data that cover more than 2400 samples across six continents. Our combined results demonstrate that land conversion to agricultural land results in taxonomic and functional homogenization of soil bacteria, mainly driven by the increase in the geographic ranges of taxa in croplands. We find that 20% of phylotypes are decreased and 23% are increased by land conversion, with croplands enriched in Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota and Latescibacterota. Although there is no significant difference in functional composition between natural ecosystems and agricultural land, functional genes involved in nitrogen fixation, phosphorus mineralization and transportation are depleted in cropland. Our results provide a global insight into the consequences of land-use change on soil microbial taxonomic and functional diversity.

Comprehensive multi-gas study by means of fiber-enhanced Raman spectroscopy for the investigation of nitrogen cycle processes

The extensive use of synthetic fertilizers has led to a considerable increase in reactive nitrogen input into agricultural and natural systems, resulting in negative effects in multiple ecosystems, the so-called nitrogen cascade. Since the global population relies on fertilization for food production, synthetic fertilizer use needs to be optimized by balancing crop yield and reactive nitrogen losses. Fiber-enhanced Raman spectroscopy (FERS) is introduced as a unique method for the simultaneous quantification of multiple gases to the study processes related to the nitrogen cycle. By monitoring changes in the headspace gas concentrations, processes such as denitrification, nitrification, respiration, and nitrogen fixation, as well as fertilizer addition were studied. The differences in concentration between the ambient and prepared process samples were evident in the Raman spectra, allowing for differentiation of process-specific spectra. Gas mixture concentrations were quantified within a range of low ppm to 100% for the gases N2, O2, CO2, N2O, and NH3. Compositional changes were attributed to processes of the nitrogen cycle. With help of multivariate curve resolution, it was possible to quantify N2O and CO2 simultaneously. The impact of fertilizers on N-cycle processes in soil was simulated and analyzed for identifying active processes. Thus, FERS was proven to be a suitable technique to optimize fertilizer composition and to quantify N2O and NH3 emissions, all with a single device and without further sample preparation.

Modeling denitrification nitrogen losses in China's rice fields based on multiscale field-experiment constraints

Denitrification plays a critical role in soil nitrogen (N) cycling, affecting N availability in agroecosystems. However, the challenges in direct measurement of denitrification products (NO, N2 O, and N2 ) hinder our understanding of denitrification N losses patterns across the spatial scale. To address this gap, we constructed a data-model fusion method to map the county-scale denitrification N losses from China's rice fields over the past decade. The estimated denitrification N losses as a percentage of N application from 2009 to 2018 were 11.8 ± 4.0% for single rice, 12.4 ± 3.7% for early rice, and 11.6 ± 3.1% for late rice. The model results showed that the spatial heterogeneity of denitrification N losses is primarily driven by edaphic and climatic factors rather than by management practices. In particular, diffusion and production rates emerged as key contributors to the variation of denitrification N losses. These findings humanize a 38.9 ± 4.8 kg N ha-1  N loss by denitrification and challenge the common hypothesis that substrate availability drives the pattern of N losses by denitrification in rice fields.

Anthropogenic effects on global soil nitrogen pools

The amount of nitrogen stored in terrestrial soils, its "nitrogen pool", moderates biogeochemical cycling affecting primary productivity, nitrogen pollution and even carbon budgets. The soil nitrogen pools and the transformation of nitrogen forms within them are heavily influenced by environmental factors including anthropogenic activities. However, our understanding of the global distribution of soil nitrogen with respect to anthropogenic activity and human land use remains unclear. We constructed a meta-analysis from a global sampling, in which we compare soil total nitrogen pools and the driving mechanisms affecting each pool across three major classifications of human land use: natural, agricultural, and urban. Although the size of the nitrogen pool can be similar across natural, agricultural and urban soils, the ecological and human associated drivers vary. Specifically, the drivers within agricultural and urban soils as opposed to natural soils are more complex and often decoupled from climatic and soil factors. This suggests that the nitrogen pools of those soils may be co-moderated by other factors not included in our analyses, like human activities. Our analysis supports the notion that agricultural soils act as a nitrogen source while urban soils as a nitrogen sink and informs a modern understanding of the fates and distributions of anthropogenic nitrogen in natural, agricultural, and urban soils.

Soil glomalin-related protein affects aggregate N2O fluxes by modulating denitrifier communities in a fertilized soil

Agricultural ecosystems contribute significantly to atmospheric emissions of soil nitrous oxide (N₂O), which exacerbate environmental pollution and contribute to global warming. Glomalin-related soil protein (GRSP) stabilizes soil aggregates and enhances soil carbon and nitrogen storage in agricultural ecosystems. However, the underlying mechanisms and relative importance of GRSP on N₂O fluxes within soil aggregate fraction remain largely unclear. We examined the GRSP content, denitrifying bacterial community composition, and potential N₂O fluxes across three aggregate-size fractions (2000-250 μm, 250-53 μm, and <53 μm) under a long-term fertilization agricultural ecosystem, subjected to mineral fertilizer or manure and their combination. Our findings indicated that various fertilization treatments have no discernible impact on the size distribution of soil aggregates, paving the way to further research into the impact of soil aggregates on GRSP content, the denitrifying bacterial community composition, and potential N₂O fluxes. GRSP content increased with the increase in soil aggregate size. Potential N₂O fluxes (including gross N₂O production and N₂O reduction and net N₂O production) among aggregates were highest in microaggregates (250-53 μm), followed by macroaggregates (2000-250 μm) and lowest in silt + clay (<53 μm) fractions. Potential N₂O fluxes had a positive response to soil aggregate GRSP fractions. The non-metric multidimensional scaling analysis revealed that soil aggregate size could drive the denitrifying functional microbial community composition, and deterministic processes play more critical roles than stochasticity processes in driving denitrifying functional composition under soil aggregate fractions. Procrustes analysis revealed a significant correlation between denitrifying microbial community, soil aggregate GRSP fractions, and potential N₂O fluxes. Our study suggests that soil aggregate GRSP fractions influence potential nitrous oxide fluxes by affecting denitrifying microbial functional composition within soil aggregate.

From Soil to River: Revealing the Mechanisms Underlying the High Riverine Nitrate Levels in a Forest Dominated Catchment

Elevated riverine nitrate (NO₃^-) levels have led to increased eutrophication and other ecological implications. While high riverine NO₃^- levels were generally ascribed to anthropogenic activities, high NO₃^- levels in some pristine or minimally disturbed rivers were reported. The drivers of these unexpectedly high NO₃^- levels remain unclear. This study combined natural abundance isotopes, ¹⁵N-labeling techniques, and molecular techniques to reveal the processes driving the high NO₃^- levels in a sparsely populated forest river. The natural abundance isotopes revealed that the NO₃^- was mainly from soil sources and that NO₃^- removal processes were insignificant. The ¹⁵N-labeling experiments also quantitatively showed that the biological NO₃^- removal processes, i.e., denitrification, dissimilatory NO₃^- reduction to ammonium (DNRA), and anaerobic ammonia oxidation (anammox), in the soils and sediments were weak relative to nitrification in summer. While nitrification was minor in winter, the NO₃^- removal was insignificant relative to the large NO₃^- stock in the catchment. Stepwise multiple regression analyses and structural equation models revealed that in summer, nitrification in the soils was regulated by the amoA-AOB gene abundances and NH₄⁺-N contents. Low temperature constrained nitrification in winter. Denitrification was largely controlled by moisture content in both seasons, and anammox and DNRA could be explained by the competition with nitrification and denitrification on their substrate (nitrite-NO₂^-). We also revealed the strong hydrological control on the transport of soil NO₃^- to the river. This study effectively revealed the mechanisms underlying the high NO₃^- levels in a nearly pristine river, which has implications for the understanding of riverine NO₃^- levels worldwide.

Deep decarbonization options for the agriculture, forestry, and other land use (AFOLU) sector in Africa: a systematic literature review

Greenhouse gases (GHG) emanating from agriculture, forestry, and other land use (AFOLU) sector are among top contributors to anthropogenic climate change in Africa and globally. Minimizing AFOLU sector GHG emissions in Africa is notoriously hard because of difficulties in emission estimation, the disperse nature of AFOLU emissions, and the complex links between AFOLU activities and poverty reduction. Yet, there are very few systematic reviews dealing with decarbonization pathways for the AFOLU sector in Africa. This article explores the options for achieving deep decarbonization of AFOLU sector in Africa, through a systematic review. Using the method of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA Statement), 46 studies of interest were selected from the databases of Scopus, Google Scholar, and Web of Science. Four sub-themes were identified from the critical review of the selected studies covering key decarbonization approaches used in AFOLU sector. The literature suggests that while forest management and reforestation reduction of GHG in animal production and climate-smart practices in agriculture hold great promises for AFOLU sector decarbonization in Africa, there appears to be very limited coherent policy in the continent addressing any of these AFOLU sub-sectors.

Analysis of the external signals driving the transcriptional regulation of the main genes involved in denitrification in Haloferax mediterranei

Haloferax mediterranei is the model microorganism for the study of the nitrogen cycle in haloarchaea. This archaeon not only assimilate N-species such as nitrate, nitrite, or ammonia, but also it can perform denitrification under low oxygen conditions, using nitrate or nitrite as alternative electron acceptors. However, the information currently available on the regulation of this alternative respiration in this kind of microorganism is scarce. Therefore, in this research, the study of haloarchaeal denitrification using H. mediterranei has been addressed by analyzing the promoter regions of the four main genes of denitrification (narGH, nirK, nor, and nosZ) through bioinformatics, reporter gene assays under oxic and anoxic conditions and by site-directed mutagenesis of the promoter regions. The results have shown that these four promoter regions share a common semi-palindromic motif that plays a role in the control of the expression levels of nor and nosZ (and probably nirK) genes. Regarding the regulation of the genes under study, it has been concluded that nirK, nor, and nosZ genes share some expression patterns, and therefore their transcription could be under the control of the same regulator whereas nar operon expression displays differences, such as the activation by dimethyl sulfoxide with respect to the expression in the absence of an electron acceptor, which is almost null under anoxic conditions. Finally, the study with different electron acceptors demonstrated that this haloarchaea does not need complete anoxia to perform denitrification. Oxygen concentrations around 100 μM trigger the activation of the four promoters. However, a low oxygen concentration per se is not a strong signal to activate the promoters of the main genes involved in this pathway; high activation also requires the presence of nitrate or nitrite as final electron acceptors.

Long-term nitrogen addition increases denitrification potential and functional gene abundance and changes denitrifying communities in acidic tea plantation soil

The response of soil denitrification to nitrogen (N) addition in the acidic and perennial agriculture systems and its underlying mechanisms remain poorly understood. Therefore, a long-term (12 years) field trial was conducted to explore the effects of different N application rates on the soil denitrification potential (DP), functional genes, and denitrifying microbial communities of a tea plantation. The study found that N application to the soil significantly increased the DP and the absolute abundance of denitrifying genes, such as narG, nirK, norB, and nosZ. The diversity of denitrifying communities (genus level) significantly decreased with increasing N rates. Moreover, the denitrifying communities composition significantly differed among the soils with different rates of N fertilization. Further variance partitioning analysis (VPA) revealed that the soil (39.04%) and pruned litter (32.53%) properties largely contributed to the variation in the denitrifying communities. Dissolved organic carbon (DOC) and soil pH, pruned litter's total crude fiber (TCF) content and total polyphenols to total N ratio (TP/TN), and narG and nirK abundance significantly (VIP >1.0) influenced the DP. Finally, partial least squares path modeling (PLS-PM) revealed that N addition indirectly affected the DP by changing specific soil and pruned litter properties and functional gene abundance. Thus, the findings suggest that tea plantation is a major source of N₂O emissions that significantly enhance under N application and provide theoretical support for N fertilizer management in an acidic tea plantation system.

Integrating major agricultural practices into the TRIPLEX-GHG model v2.0 for simulating global cropland nitrous oxide emissions: Development, sensitivity analysis and site evaluation

Nitrous oxide (N₂O) emissions from croplands are one of the most important greenhouse gas sources while the estimation of which remains large uncertainties globally. To simulate N₂O emissions from global croplands, the process-based TRIPLEX-GHG model v2.0 was improved by coupling the major agricultural activities. Sensitivity experiment was used to measure the impact of the integrated processes to modeled N₂O emission found chemical N fertilization have the highest relative effect sizes. While the coefficient of the NO₃^- consumption rate for denitrification (COE_dNO3), controlling the first step of the denitrification process was identified to be the most sensitive parameter based on sensitivity analysis of model parameters. The model performed well when simulating the magnitude of the daily N₂O emissions for 39 calibration sites and the continental mean of the parameters were used to producing reasonable estimations for the means of the measured daily N₂O fluxes (R² = 0.87, slope = 1.07) and emission factors (EFs, R² = 0.70, slope = 0.72) during the experiment periods. The model reliability was further confirmed by model validation. General trend of modeled daily N₂O emissions were reasonably consistent with the observations of selected validated sites. In addition, high correlations between the results of modeled and observed mean N₂O emissions (R² = 0.86, slope = 0.82) and EFs (R² = 0.66, slope = 0.83) from 68 validation sites were obtained. Further improvement on more detailed estimations for the variation of the environmental factors, management effects as well as accurate model input model driving data are required to reduce the uncertainties of model simulations. Consequently, our simulation results demonstrate that the TRIPLEX-GHG model v2.0 can reliably estimate N₂O emissions from various croplands at the global scale, which contributes to closing global N₂O budget and sustainable development of agriculture.

The active functional microbes contribute differently to soil nitrification and denitrification potential under long-term fertilizer regimes in North-East China

Nitrogen (N) cycling microorganisms mediate soil nitrogen transformation processes, thereby affecting agricultural production and environment quality. However, it is not fully understood how active N-cycling microbial community in soil respond to long-term fertilization, as well as which microorganisms regulate soil nitrogen cycling in agricultural ecosystem. Here, we collected the soils from different depths and seasons at a 29-year fertilization experimental field (organic/chemical fertilizer), and investigated the transcriptions of N-cycling functional genes and their contribution to potential nitrification and denitrification. We found that long-term fertilization exerted significant impacts on the transcript abundances of nitrifiers (AOA amoA, AOB amoA and hao) and denitrifiers (narG and nosZ), which was also notably influenced by season variation. The transcriptions of AOA amoA, hao, and narG genes were lowest in autumn, and AOB amoA and nosZ transcript abundances were highest in autumn. Compared to no fertilization, soil potential nitrification rate (PNR) was reduced in fertilization treatments, while soil potential denitrification rate (PDR) was significantly enhanced in organic combined chemical fertilizer treatment. Both PNR and PDR were highest in 0–20 cm among the tested soil depths. Path model indicated active nitrifiers and denitrifiers had significant impact on soil PNR and PDR, respectively. The transcriptions of AOA amoA and nxr genes were significantly correlated with soil PNR (Pearson correlation, r > 0.174, p < 0.05). Significant correlation of napA and nosZ transcriptions with soil PDR (Pearson correlation, r > 0.234, p < 0.05) was also revealed. Random forest analysis showed that SOC content and soil pH were the important factors explaining the total variance of active nitrifers and denitrifiers, respectively. Taken together, long-term fertilization regimes reduced soil PNR and enhanced PDR, which could be attributed to the different responses of active N-cycling microorganisms to soil environment variations. This work provides new insight into the nitrogen cycle, particularly microbial indicators in nitrification and denitrification of long-term fertilized agricultural ecosystems.

Urea fertilization and grass species alter microbial nitrogen cycling capacity and activity in a C4 native grassland

Soil microbial transformation of nitrogen (N) in nutrient-limited native C₄ grasslands can be affected by N fertilization rate and C₄ grass species. Here, we report in situ dynamics of the population size (gene copy abundances) and activity (transcript copy abundances) of five functional genes involved in soil N cycling (nifH, bacterial amoA, nirK, nirS, and nosZ) in a field experiment with two C₄ grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) under three N fertilization rates (0, 67, and 202 kg N ha^-1). Diazotroph (nifH) abundance and activity were not affected by N fertilization rate nor grass species. However, moderate and high N fertilization promoted population size and activity of ammonia oxidizing bacteria (AOB, quantified via amoA genes and transcripts) and nitrification potential. Moderate N fertilization increased abundances of nitrite-reducing bacterial genes (nirK and nirS) under switchgrass but decreased these genes under big bluestem. The activity of nitrous oxide reducing bacteria (nosZ transcripts) was also promoted by moderate N fertilization. In general, high N fertilization had a negative effect on N-cycling populations compared to moderate N addition. Compared to big bluestem, the soils planted with switchgrass had a greater population size of AOB and nitrite reducers. The significant interaction effects of sampling season, grass species, and N fertilization rate on N-cycling microbial community at genetic-level rather than transcriptional-level suggested the activity of N-cycling microbial communities may be driven by more complex environmental factors in native C₄ grass systems, such as climatic and edaphic factors.

Sulfonamide antibiotics alter gaseous nitrogen emissions in the soil-plant system: A mesocosm experiment and meta-analysis

Veterinary antibiotics are widely used in many countries worldwide to treat diseases and protect the health of animals. However, the effects of sulfonamide antibiotics introduced via manure and wastewater irrigation on nitrogen (N) loss in the soil-plant system remain poorly understood. Here, we conducted a pot experiment to assess the effects of sulfamethazine (SMZ) and its degradation product (2-amino-4,6-dimethylpyrimidine, ADPD) at four concentration gradients (i.e., 0, 1, 10, 100 mg kg^-1) on nitrous oxide (N₂O) and ammonia (NH₃) emissions, and the abundances of N-cycling functional genes and sulfonamide resistance genes. We also collated 350 observations from 62 published papers and performed a meta-analysis of antibiotic addition effects on N₂O emission and soil net nitrification and denitrification. Antibiotics additions showed an inhibitory effect on N₂O emissions, which accords with the trend of our meta-analysis showing a significant decrease of 32%. The decreased N₂O emissions were attributed to the significant reduction in the abundances of total bacterial communities, ammonia oxidizers, and nir-type denitrifiers and to the resultant changes in soil inorganic N. N₂O emissions did not differ between non-environmentally relevant concentrations for SMZ but lowered with increasing ADPD concentrations. This discrepancy can be explained by differential responses of the gene abundances of ammonia oxidizers and nirK-type denitrifiers and the development of antibiotic resistance genes in the highest concentration following antibiotic additions. Antibiotic additions increased soil NH₃ volatilization but did not affect vegetable yield. Therefore, these findings provide insight into how the prevalence of antibiotics in soils could alter the N-cycling process and associated gas emissions, with implications for understanding the ecological risks of antibiotics in agriculture.

NorA, HmpX, and NorB Cooperate to Reduce NO Toxicity during Denitrification and Plant Pathogenesis in Ralstonia solanacearum

Ralstonia solanacearum, which causes bacterial wilt disease of many crops, requires denitrifying respiration to survive in its plant host. In the hypoxic environment of plant xylem vessels, this pathogen confronts toxic oxidative radicals like nitric oxide (NO), which is generated by both bacterial denitrification and host defenses. R. solanacearum has multiple distinct mechanisms that could mitigate this stress, including putative NO-binding protein (NorA), nitric oxide reductase (NorB), and flavohaemoglobin (HmpX). During denitrification and tomato pathogenesis and in response to exogenous NO, R. solanacearum upregulated norA, norB, and hmpX. Single mutants lacking ΔnorB, ΔnorA, or ΔhmpX increased expression of many iron and sulfur metabolism genes, suggesting that the loss of even one NO detoxification system demands metabolic compensation. Single mutants suffered only moderate fitness reductions in host plants, possibly because they upregulated their remaining protective genes. However, ΔnorA/norB, ΔnorB/hmpX, and ΔnorA/hmpX double mutants grew poorly in denitrifying culture and in planta. It is likely that the loss of norA, norB, and hmpX is lethal, since the methods used to construct the double mutants could not generate a triple mutant. Functional aconitase activity assays showed that NorA, HmpX, and especially NorB are important for maintaining iron-sulfur cluster proteins. Additionally, plant defense genes were upregulated in tomatoes infected with the NO-overproducing ΔnorB mutant, suggesting that bacterial detoxification of NO reduces the ability of the plant host to perceive the presence of the pathogen. Thus, R. solanacearum's three NO detoxification systems each contribute to and are collectively essential for overcoming metabolic nitrosative stress during denitrification, for virulence and growth in the tomato, and for evading host plant defenses. IMPORTANCE The soilborne plant pathogen Ralstonia solanacearum (Rs) causes bacterial wilt, a serious and widespread threat to global food security. Rs is metabolically adapted to low-oxygen conditions, using denitrifying respiration to survive in the host and cause disease. However, bacterial denitrification and host defenses generate nitric oxide (NO), which is toxic and also alters signaling pathways in both the pathogen and its plant hosts. Rs mitigates NO with a trio of mechanistically distinct proteins: NO-reductase (NorB), predicted iron-binding (NorA), and oxidoreductase (HmpX). This redundancy, together with analysis of mutants and in-planta dual transcriptomes, indicates that maintaining low NO levels is integral to Rs fitness in tomatoes (because NO damages iron-cluster proteins) and to evading host recognition (because bacterially produced NO can trigger plant defenses).

Response of N2O emission and denitrification genes to different inorganic and organic amendments

Denitrification is a key biochemical process in nitrogen cycling and nitrous oxide (N₂O) production. In this study, the impacts of different inorganic and organic amendments (OAs) on the abundance of denitrifying genes (nirS, nirK and nosZ) and the level of N₂O emission were examined with incubation experiments. Six treatments included the indicated applications: (i) no fertilization (CK); (ii) urea application alone (U); (iii) wheat straw plus urea (U + WS); (iv) pig manure plus urea (U + PM); (v) compost product plus urea (U + CP); and (vi) improved compost product plus urea (U + IC). The results indicated that all fertilization treatments increased accumulative N₂O emissions compared with the CK treatment. The U + WS, U + PM and U + CP treatments increased N₂O emissions by 2.12–141.3%, and the U + IC treatment decreased N₂O emissions by 23.24% relative to the U treatment. nirK was the dominant denitrification gene rather than nirS and nosZ found in soil. Additionally, the highest abundance of nirK gene was that with the U + PM treatment, and the lowest was that with the U + IC treatment. Additionally, changes in the nirK gene were highly correlated with levels of dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and nitrate nitrogen (NO₃^–N). Automatic linear modeling revealed that N₂O emission was closely related to the nirK gene, DOC and NO₃^–N. Overall, the use of urea and improved compost as co-amendments retarded N₂O emission to a considerable degree compared with other OA additions.

Variations and controlling factors of soil denitrification rate

The denitrification process profoundly affects soil nitrogen (N) availability and generates its byproduct, nitrous oxide, as a potent greenhouse gas. There are large uncertainties in predicting global denitrification because its controlling factors remain elusive. In this study, we compiled 4301 observations of denitrification rates across a variety of terrestrial ecosystems from 214 papers published in the literature. The averaged denitrification rate was 3516.3 ± 91.1 µg N kg^-1  soil day^-1 . The highest denitrification rate was 4242.3 ± 152.3 µg N kg^-1  soil day^-1 under humid subtropical climates, and the lowest was 965.8 ± 150.4 µg N kg^-1 under dry climates. The denitrification rate increased with temperature, precipitation, soil carbon and N contents, as well as microbial biomass carbon and N, but decreased with soil clay contents. The variables related to soil N contents (e.g., nitrate, ammonium, and total N) explained the variation of denitrification more than climatic and edaphic variables (e.g., mean annual temperature (MAT), soil moisture, soil pH, and clay content) according to structural equation models. Soil microbial biomass carbon, which was influenced by soil nitrate, ammonium, and total N, also strongly influenced denitrification at a global scale. Collectively, soil N contents, microbial biomass, pH, texture, moisture, and MAT accounted for 60% of the variation in global denitrification rates. The findings suggest that soil N contents and microbial biomass are strong predictors of denitrification at the global scale.

Arthropod-Microbiota Integration: Its Importance for Ecosystem Conservation

Recent reports indicate that the health of our planet is getting worse and that genuine transformative changes are pressing. So far, efforts to ameliorate Earth's ecosystem crises have been insufficient, as these often depart from current knowledge of the underlying ecological processes. Nowadays, biodiversity loss and the alterations in biogeochemical cycles are reaching thresholds that put the survival of our species at risk. Biological interactions are fundamental for achieving biological conservation and restoration of ecological processes, especially those that contribute to nutrient cycles. Microorganism are recognized as key players in ecological interactions and nutrient cycling, both free-living and in symbiotic associations with multicellular organisms. This latter assemblage work as a functional ecological unit called "holobiont." Here, we review the emergent ecosystem properties derived from holobionts, with special emphasis on detritivorous terrestrial arthropods and their symbiotic microorganisms. We revisit their relevance in the cycling of recalcitrant organic compounds (e.g., lignin and cellulose). Finally, based on the interconnection between biodiversity and nutrient cycling, we propose that a multicellular organism and its associates constitute an Ecosystem Holobiont (EH). This EH is the functional unit characterized by carrying out key ecosystem processes. We emphasize that in order to meet the challenge to restore the health of our planet it is critical to reduce anthropic pressures that may threaten not only individual entities (known as "bionts") but also the stability of the associations that give rise to EH and their ecological functions.

K fertilizer alleviates N2O emissions by regulating the abundance of nitrifying and denitrifying microbial communities in the soil-plant system

Potassium (K) fertilizer additions can result in high crop yields of good quality and low nitrogen (N) loss; however, the interaction between K and N fertilizer and its effect on N₂O emissions and associated microbes remain unclear. We investigated this in a pot experiment with six fertilizer treatments involving K and two sources of N, using agricultural soil from the suburbs of Wuhan, central China. The aim was to determine the effects of the interaction between K and different forms of N on the N₂O flux and the abundance of nitrifying and denitrifying microbial communities, using static chamber-gas chromatography and high-throughput sequencing methods. Compared with no fertilizer control (CK), the addition of nitrate fertilizer (NN) or ammonia fertilizer (AN) or K fertilizer significantly increased N₂O emissions. However, the combined application (NNK) of K and NN significantly reduced the average N₂O emissions by 28.3%, while the combined application (ANK) of K and AN increased N₂O emissions by 22.7%. The abundance of nitrifying genes amoA in ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) changed in response to N and/or K fertilization, but the denitrifying genes narG, nirK and norl were strongly correlated with N₂O emissions. This suggests that N or K fertilizer and their interaction affect N₂O emissions mainly by altering the abundance of functional genes of denitrifying microbes in the soil-plant system. The genera Paracoccus, Rubrivivax and Geobacter as well as Streptomyces and Hyphomicrobium play an important role in N₂O emissions during denitrification with the combined application of N and K.

The inhibition effect of tea polyphenols on soil nitrification is greater than denitrification in tea garden soil

Tea polyphenols are the most widely distributed class of secondary metabolites (Camellia sinensis) and account for a considerable proportion of the pruning residues of tea. A large amount of tea polyphenols have fallen down over soil with prunning residues every year. However, the effect of tea polyphenols on soil nitrogen cycle, especially the denitrification process and its related microbial communities, remains unclear. Epigallocatechin gallate (EGCG), the most abundant component of tea polyphenols, was selected to simulate the effects of tea polyphenols on soil nitrification, denitrification, related functional genes and microbial community. The results indicated that addition of EGCG can significantly (p < 0.05) inhibit soil nitrification. Copy numbers of bacterial and archaeal ammonia monooxygenase genes (amoA) decreased as EGCG concentration increased. Further, the ammonia oxidisers exhibited a significantly (p < 0.05) greater niche differentiation under the effect of EGCG compared with the control treatment (no EGCG addition). However, the inhibition effect of EGCG over soil denitrification was most significant at 34 and 36 day of incubation period, and such inhibitory effect was more apparent on nitrification compared with denitrification. EGCG addition increased the diversity of bacterial community. The composition of bacterial community was significantly altered and community variation was primary explained by EGCG, NH₄⁺-N, NO₃^--N, soil organic carbon contents and potential denitrification rates. EGCG addition significantly increased relative abundance of Proteobacteria and Bacteroidetes phyla whereas decreased Actinobacteria. Overall, tea polyphenols can inhibit soil nitrification to a larger extent than denitrification by reducing the abundance of microorganisms carrying the related functional genes. Our results can serve as important basis of reducing the nitrogen pollution risk in tea orchards and could be considered as a powerful natural nitrification inhibitor to reduce the environmental risks caused by unreasonable nitrogen fertiliser adaptation.

High Nitrate Accumulation in the Vadose Zone after Land-Use Change from Croplands to Orchards

Additional evidence indicates that the nitrate stored in the deep soil profile has an important role in regulating the global nitrogen (N) cycle. This study assessed the effects of land-use changes from croplands to intensive orchards (LUCO) on N surplus, nitrate accumulation in deep soil, and groundwater quality in the kiwifruit belt of the northern slope region of the Qinling Mountains, China. LUCO resulted in comparatively high N surplus in orchards (282 vs 1206 kg ha^-1 yr^-1, respectively). The average nitrate accumulation within the 0-10 m profiles of orchards was 7113 kg N ha^-1, which was equal to approximately the total N surplus of 6 years of the orchards. The total nitrate stock within 0-10 m soil profiles of the kiwifruit belt was 266.5 Gg N, which was 3.5 times higher than the total annual N input. The nitrate concentrations of 97% of groundwater samples exceeded the WHO standard. The LUCO resulted in large nitrate storage in the vadose zone and caused serious contamination of groundwater. Our study highlights that nitrate accumulation in the vadose zone of an intensive land-use system is one of the main fates of surplus N and also a hotspot of nitrate accumulation.

Soil Health Management Enhances Microbial Nitrogen Cycling Capacity and Activity

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.

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.

Nitrogen sources, processes, and associated impacts of climate and land-use changes in a coastal China watershed: Insights from the INCA-N model

The Integrated Nitrogen CAtchments (INCA-N) model was applied to identify the sources and processes controlling riverine nitrogen (N) export in the Jiulong River watershed, coastal China. Future riverine N exports were simulated under various scenarios of climate and land-use changes. The modeling results showed good agreement between the observed and simulated values of streamflow, N concentrations, and loads. It was revealed that fertilizer application, atmospheric N deposition, and sewage discharges were the main N sources, while the primary N cycling processes included soil nitrification, soil denitrification, and N leaching. Nitrate-N exports were predominantly impacted by climate change, whereas ammonium-N exports were more affected by land-use change. The coupled effects of climate and land-use changes were projected to amplify nitrogen export by 30%, 36%, and 36% for nitrate-N and 32%, 48%, and 71% for ammonium-N during the years for 2030s, 2050s, and 2080s, respectively.

Blind spots in global soil biodiversity and ecosystem function research

Soils harbor a substantial fraction of the world's biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.

C:N ratio is not a reliable predictor of N2O production in acidic soils after a 30-day artificial manipulation

To test the effect of C:N ratio on soil N₂O production, N₂O production rates and pathways associated with nitrification (AOA-amoA, AOB-amoA, fungal ITS rDNA, bacterial 16S rRNA), and denitrification-related (nirK, nirS, nosZ) genes were investigated in subtropical forest (SF) and cropland (SC) soil in China in a 30-day C:N ratio manipulation. In addition, 24-hour C:N ratio manipulation, including the addition of acetic acid, were conducted to verify the results observed in the 30-day experiment. After 30 days of manipulation, the N₂O production rates (N₂O_t) increased from 2.46 in CN23 treatment to 4.71 μg N kg^-1 day^-1 in CN 10 treatment in SF, while it decreased from 4.17 in CN23 treatment to 3.83 μg N kg^-1 day^-1 in CN10 treatment in SC. The results in 24-hour experiment were consistent with those in 30-day experiment, and the addition of acetic acid increased N₂O_t in SC, but not in SF. Soil C:N ratios and inorganic N (NH₄⁺ + NO₃^-) concentrations influenced the contribution of denitrification to N₂O production and the N₂O production rate via denitrification. Soil AOA played a dominant role in autotrophic nitrification-derived N₂O production, resulting in a high contribution of autotrophic nitrification under low pH. Therefore, pH instead of C:N ratio, is a key parameter for evaluating autotrophic nitrification-derived N₂O via AOA and AOB. Soil C:N ratio was significantly and positively correlated with the contribution of heterotrophic nitrification to N₂O production, while there was no significant correlation with the N₂O production rate via heterotrophic nitrification. This is mainly because the responsible heterotrophs (i.e., fungi and bacteria) were negatively and positively correlated with C:N ratio in SF and SC, respectively. Therefore, C:N ratio is not a strong predictor of soil N₂O production, the initial C or N content and composition of functional genes could provide key information in acidic soils after a 30-day artificial C:N ratio manipulation.

Assessing the risk of bias in choice of search sources for environmental meta-analyses

Results of meta-analyses are potentially valuable for informing environmental policy and practice decisions. However, selective sampling of primary studies through searches exclusively using widely used bibliographic platform(s) could bias estimates of effect sizes. Such search strategies are common in environmental evidence reviews, and if risk of bias can be detected, this would provide the first empirical evidence that comprehensiveness of searches needs to be improved. We compare the impact of using single and multiple bibliographic platform(s) searches vs more comprehensive searches on estimates of mean effect sizes. We used 137 published meta-analyses, based on multiple source searches, analyzing 9388 studies: 8095 sourced from commercially published articles; and 1293 from grey literature and unpublished data. Single-platform and multiple-platform searches missed studies in 100 and 80 of the meta-analyses, respectively: 52 and 46 meta-analyses provided larger-effect estimates; 32 and 28 meta-analyses provided smaller-effect estimates; eight and four meta-analyses provided opposite direction of estimates; and two each were unable to estimate effects due to missing all studies. Further, we found significant positive log-linear relationships between proportions of studies missed and the deviations of mean effect sizes, suggesting that as the number of studies missed increases, deviation of mean effect size is likely to expand. We also found significant differences in mean effect sizes between indexed and non-indexed studies for 35% of meta-analyses, indicating high risk of bias when the searches were restricted. We conclude that the restricted searches are likely to lead to unrepresentative samples of studies and biased estimates of true effects.

Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China

Organic fertilizer application could have an impact on the nitrogen cycle mediated by microorganisms in arable soils. However, the dynamics of soil ammonia oxidizers and denitrifiers in response to compost addition are less understood. In this study, we examined the effect of four compost application rates (0, 11.25, 22.5 and 45 t/ha) on soil ammonia oxidizers and denitrifiers at soybean seedling, flowering and mature stage in a field experiment in Northeast China. As revealed by quantitative PCR, compost addition significantly enhanced the abundance of ammonia oxidizing bacteria (AOB) at seedling stage, while the abundance of ammonia oxidizing archaea was unaffected across the growing season. The abundance of genes involved in denitrification (nirS, nirK and nosZ) were generally increased along with compost rate at seedling and flowering stages, but not in mature stage. The non-metric multidimensional scaling analysis revealed that moderate and high level of compost addition consistently induced shift in AOB and nirS containing denitrifers community composition across the growing season. Among AOB lineages, Nitrosospira cluster 3a gradually decreased along with the compost rate across the growing season, while Nitrosomonas exhibited an opposite trend. Network analysis indicated that the complexity of AOB and nirS containing denitrifiers network gradually increased along with the compost rate. Our findings highlighted the positive effect of compost addition on the abundance of ammonia oxidizers and denitrifiers and emphasized that compost addition play crucial roles in shaping their community compositions and co-occurrence networks in black soil of Northeast China.

Effect of N dose, fertilisation duration and application of a nitrification inhibitor on GHG emissions from a peach orchard

Despite only occupying 5% of the worldwide arable area, fruit tree crops are of vital economic importance in many regions. Intensive cropping practices can lead to greenhouse gas (GHG) emissions. In order to reduce these emissions, numerous studies have been made on lowering N inputs or applying nitrification inhibitors (NIs) which tend to maintain or even increase yield while reducing N leaching and nitrogenous emissions to the atmosphere. However, very few studies have been conducted on potential GHG emissions from the peach crop. In this work, a three-year study was carried out in a commercial peach orchard with a split-plot design with three replicates, in which the main factor was N dose (25, 50 and 100 kg N ha^-1 year^-1, and 50 kg N ha^-1 year^-1 applied during a shorter period of time in 2015 and 2016; and only 70 kg N ha^-1 year^-1 in 2017). Subplots in the study were used to analyse the effect of the application of a NI (3,4-dimethylpyrazole phosphate; DMPP). The aim was to qualitatively compare the effect of these factors on N₂O, N₂O + N₂, CH₄ and CO₂ emissions from a peach orchard soil in order to recommend agricultural practices that minimise emissions without concurrent yield reductions. We show that N₂O and N₂O + N₂ emissions were linked to fertilisation and increased with N dose. The N₂O emissions were mitigated (up to 49%) by DMPP up to the 50 kg N ha^-1 dose (not significantly). It seems that between 70 and 100 kg N ha^-1 the application of DMPP loses effectiveness. Methane oxidation increased with N dose and decreased with DMPP application; CO₂ emissions increased with DMPP and were unaffected by N dose. The intermediate N dose (50 kg N ha^-1) applied during a shorter period of time increased yield (not significantly) and NUE without increasing GHG emissions.

Valorization of agricultural wastes could improve soil fertility and mitigate soil direct N2O emissions

The emerging need for sustainable management of the increasing quantities of urban and industrial organic wastes creates opportunities for the development of alternative strategies for the improvement of degraded soils. The current study was performed to examine the effects of agricultural wastes application on soil bacterial community as well as CO₂ and N₂O direct gas emissions. Untreated soils were compared with soils, which received the same amount of N (100 μg/g soil) in the form of ammonium nitrate and organic agricultural waste. In particular, soils were incubated with three different organic agricultural wastes, orange (OP), mandarin (MP) and banana peels (BP) and ammonium nitrate (F) after adjusting soil water at 70% of its holding capacity. In the current study, soil chemical characteristics, quantitative PCR of denitrifiers (nirK, nirS, nosZI and nosZII) and16s rRNA amplicon sequencing were assessed to examine the links between the soil microbial communities and short-term soil direct N₂O emissions when treated with agricultural wastes. The highest soil direct N₂O emissions were recorded in soils received ammonium nitrate while soils received agricultural wastes exhibited substantially lower soil direct N₂O emissions. On the contrary, agricultural wastes stimulated CO₂ accumulation as well as the growth of copiotrophic bacterial groups like Proteobacteria and Firmicutes. Interestingly, direct soil N₂O emissions were decoupled from the density of denitrifier community while agricultural wastes caused a substantial reduction of the relative abundance of bacterial taxa associated with N₂O emissions in the soil. This study proves evidence that agricultural wastes could be integrated in a waste management strategy, which inter alia includes their direct use in agricultural ecosystems resulting in reduced N₂O emissions.

HN2 O2 - as a Ligand in Mononuclear Hydrogenhyponitrite-κ2 -N,O Ruthenium Complexes with Bisphosphane Co-Ligands

The hyponitrite anion is a tentative intermediate in the reduction of nitric oxide (NO) to nitrous oxide (N₂ O) catalyzed by nitric-oxide reductase (NOR) in the process of bacterial denitrification. Owing to the considerable number of known coordination modes for the hyponitrito ligand, its actual bonding form in the enzymatic cycle is a point of current discussion. Here, we contribute to the hardly known ligand properties of a key intermediate, the monoprotonated hyponitrite anion. Three air- and water-stable ruthenium complexes with hydrogenhyponitrite as the ligand were synthesized by using commercially available bisphosphane co-ligands (1,2-bis(diphenylphosphino)ethane (dppe), 1,3-bis(diphenylphosphino)propane (dppp), 1,2-bis(diphenylphosphino)ethene (dppv)). The starting compounds [Ru(dppe)₂ (tos)]BF₄ (1) and [Ru(dppp)₂ (tos)]BF₄ (2) contained the bidentate coordinating tosylate anion (tos) as a particularly well-suited leaving group. To confirm the protonated and deprotonated species, X-ray diffraction, IR, UV/Vis spectroscopy (solution and solid state), solid-state NMR spectroscopy, and high-resolution mass spectroscopy were used. DFT calculations give insight into the bonding situation. We report on [Ru(dppe)₂ (HN₂ O₂ )]BF₄ (5), [Ru(dppp)₂ (HN₂ O₂ )]BF₄ (6), [Ru(dppv)₂ (HN₂ O₂ )]BF₄ (7), [Ru(dppp)₂ (HN₂ O₂ )]BF₄ ⋅Imi (9; Imi=imidazole) as the first mononuclear trans-hydrogenhyponitrite complexes. Isolated deprotonated analogs are [Ru(dppe)₂ (N₂ O₂ )]⋅HImi(BF₄ ) (8) and [Ru(dppv)₂ (N₂ O₂ )] ⋅HImi(BF₄ )⋅Imi (10).

How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities

Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.