Long-term organic and inorganic fertilization alters the diazotrophic abundance, community structure, and co-occurrence patterns in a vertisol

Environmental tipping points for global soil nitrogen-fixing microorganisms

Nitrogen-fixing microorganisms (NFMs) are important components of soil N sinks and are influenced by multiple environmental factors. We established a random forest model optimized by the distributed delayed particle swarm optimization (RODDPSO) algorithm to analyze the global NFM data. Soil pH, organic carbon (OC), mean annual precipitation (MAP), altitude, and total phosphorus (TP) are factors with contributions greater than 10% to NFMs. pH, OC, and MAP are the top three factors at the global scale. The tipping points of pH and OC for the NFMs were 7.84 and 2.71%, respectively. The contribution of MAP first increased but then decreased with peak value at 1,265.65 mm. Under the scenario SSP 8.5, 12% of the NFMs increase occur in Africa in 2100; 16% and 36% of the NFMs decrease in North America and Oceania in 2100, respectively. Our work created a global NFMs map and identified the critical tipping points.

Split application of phosphorus fertilizer in Chinese milk vetch-rice rotation enhanced rice yield by reshaping soil diazotrophic community

Chinese milk vetch (CMV) is widely recognized as the leading leguminous green manure utilized in the rice-green manure rotation system throughout southern China. While bacteria that form symbiotic relationships with CMV are responsible for fixing a significant portion of nitrogen (N) within agroecosystems. diazotrophic organisms play an essential role in the N cycle and enhance the pool of N readily accessible to plants. The goals of the current study were to investigate the effects of shifting partial phosphorus (P) fertilizer application from the rice season to the CMV season within a CMV-rice rotation system on soil nutrient levels, activity of soil enzymes and stoichiometric ratios, as well as diazotrophic community structure. The treatments consisted of a control group, a winter fallow-rice rotation without fertilizer application, and the treatments P0, P1, P2, and P3, representing 0, 1/3, 2/3, and the full dose, respectively, of phosphorus fertilizer (60 kg ha-1 P2O5) added in a single rotation system during the CMV season, while combined with 60 % of regular N application rate during the rice season. In comparison to P0, the application of treatments P1, P2, and P3 resulted in higher CMV dry biomass and rice production across the seasons from 2018 to 2021 and the P2 treatment significantly increased the contents of total N (TN), soil organic matter (OM), and available P (AP) by 49 %, 48 %, and 110 %, respectively. The activities of alkaline phosphatase and L-leucine aminopeptidase showed a significant decrease when subjected to the P1 and P2 treatments. The P2 treatment enhanced the relative abundance of Frankia and Skermanella by 2.6 % and 1.6 %, respectively, comparing with P0 treatment. Furthermore, correlation analysis revealed a positive relationship between Skermanella and Mesorhizobium with the contents of TN, OM, AP, ammonium-N, and nitrate-N. In conclusion, the application of 1/3 to 2/3 of the full dose P fertilizer in CMV season reshaped soil diazotrophic community, improved soil N content, and thereby increased rice yield with 40 % N fertilizer reduction.

Nitrogen fertilization and soil nitrogen cycling: Unraveling the links among multiple environmental factors, functional genes, and transformation rates

Anthropogenic nitrogen (N) inputs substantially influence the N cycle in agricultural ecosystems. However, the potential links among various environmental factors, nitrogen functional genes, and transformation rates under N fertilization remain poorly understood. Here, we conducted a five-year field experiment and collected 54 soil samples from three 0-4 m boreholes across different treatments: control, N-addition (nitrogen fertilizer) and NPK-addition (combined application of nitrogen, phosphorus and potassium fertilizers) treatments. Our results revealed pronounced variations in soil physiochemical parameters, metal concentrations and antibiotic levels under both N and NPK treatments. These alternations induced significant shifts in bacterial and fungal communities, altered NFG abundance and composition, and greatly enhanced rates of nitrate reduction processes. Notably, nutrients, antibiotics and bacteria exerted a more pronounced influence on NFGs and nitrate reduction under N treatment, whereas nutrients, metals, bacteria and fungi had a significant impact under NPK treatment. Furthermore, we established multidimensional correlations between nitrate reduction gene profiles and the activity rates under N and NPK treatments, contrasting with the absence of significant relationships in the control treatment. These findings shed light on the intricate relationships between microbial genetics and ecosystem functions in agricultural ecosystem, which is of significance for predicting and managing metabolic processes effectively.

Trade-offs in soil microbial functions and soil health in agroecosystems

Soil microbial communities play pivotal roles in maintaining soil health in agroecosystems. However, how the delivery of multiple microbial functions in agroecosystems is maintained remains poorly understood. This may put us at risk of incurring unexpected trade-offs between soil functions. We elucidate how interactions between soil microbes can lead to trade-offs in the functioning of agricultural soils. Interactions within soil microbial communities can result in not only positive but also neutral and negative relationships among soil functions. Altering soil conditions through soil health-improving agricultural management can alleviate these functional trade-offs by promoting the diversity and interrelationships of soil microbes, which can help to achieve more productive and sustainable agroecosystems.

Responses of diazotrophic network structure and community diversity to alfalfa-maize intercropping are soil property-dependent

Introduction

Intercropping and soil properties both affect soil diazotrophic communities. However, the specific effects that alfalfa-maize intercropping has on diazotrophic networks and community diversity under different soil properties remain unclear.

Methods

In this study, we investigated the soil diazotrophic communities of two crop systems, alfalfa monoculture (AA) and alfalfa-maize intercropping (A/M), in two sites with similar climates but different soil properties (poor vs. average).

Results and discussion

The diazotrophic network complexity and community diversity were higher at the site with poor soil than at the site with average soil (p < 0.05). Community structure also varied significantly between the sites with poor and average soil (p < 0.05). This divergence was mainly due to the differences in soil nitrogen, phosphorus, and organic carbon contents between the two sites. At the site with poor soil, the A/M system had lower diazotrophic diversity, lower network complexity and greater competition between diazotrophs than the AA system (p < 0.05) because intercropping intensified the soil phosphorus limitation under poor soil conditions. However, in the average soil, it was the A/M system that had an altered diazotrophic structure, with an increased abundance of 11 bacterial genera and a decreased abundance of three bacterial genera (p < 0.05).

Conclusion

Our results indicated that the effects of alfalfa-maize intercropping on diazotrophic communities were soil property-dependent.

Fertilization regulates global thresholds in soil bacteria

Global patterns in soil microbiomes are driven by non-linear environmental thresholds. Fertilization is known to shape the soil microbiome of terrestrial ecosystems worldwide. Yet, whether fertilization influences global thresholds in soil microbiomes remains virtually unknown. Here, utilizing optimized machine learning models with Shapley additive explanations on a dataset of 10,907 soil samples from 24 countries, we discovered that the microbial community response to fertilization is highly dependent on environmental contexts. Furthermore, the interactions among nitrogen (N) addition, pH, and mean annual temperature contribute to non-linear patterns in soil bacterial diversity. Specifically, we observed positive responses within a soil pH range of 5.2-6.6, with the influence of higher temperature (>15°C) on bacterial diversity being positive within this pH range but reversed in more acidic or alkaline soils. Additionally, we revealed the threshold effect of soil organic carbon and total nitrogen, demonstrating how temperature and N addition amount interacted with microbial communities within specific edaphic concentration ranges. Our findings underscore how complex environmental interactions control soil bacterial diversity under fertilization.

Enhancing intercropping sustainability: Manipulating soybean rhizosphere microbiome through cropping patterns

Understanding the responses of soybean rhizosphere and functional microbiomes in intercropping scenarios holds promise for optimizing nitrogen utilization in legume-based intercropping systems. This study investigated three cropping layouts under film mulching: sole soybean (S), soybean-maize intercropping in one row (IS), and soybean-maize intercropping in two rows (IIS), each subjected to two nitrogen levels: 110 kg N ha-1 (N110) and 180 kg N ha-1 (N180). Our findings reveal that cropping patterns alter bacterial and nifh communities, with approximately 5 % of soybean rhizosphere bacterial amplicon sequence variants (ASVs) and 42 % of rhizosphere nifh ASVs exhibiting altered abundances (termed sensitive ASVs). Root traits and soil properties shape these communities, with root traits exerting greater influence. Sensitive ASVs drive microbial co-occurrence networks and deterministic processes, predicting 85 % of yield variance and 78 % of partial factor productivity of nitrogen, respectively. These alterations impact bacterial and nifh diversity, complexity, stability, and deterministic processes in legume-based intercropping systems, enhancing performance in terms of yield, nitrogen utilization efficiency, land equivalent ratio, root nodule count, and nodule dry weight under IIS patterns with N110 compared to other treatments. Our findings underscore the importance of field management practices in shaping rhizosphere-sensitive ASVs, thereby altering microbial functions and ultimately impacting the productivity of legume-based intercropping systems. This mechanistic understanding of soybean rhizosphere microbial responses to intercropping patterns offers insights for sustainable intercropping enhancements through microbial manipulation.

Degradation of Complex Carbon Sources in Organic Fertilizers Facilitates Nitrogen Fixation

Biological nitrogen fixation is crucial for agriculture and improving fertilizer efficiency, but organic fertilizers in enhancing this process remain debated. Here, we investigate the impact of organic fertilizers on biological nitrogen fixation through experiments and propose a new model where bacterial interactions with complex carbon sources enhance nitrogen fixation. Field experiments showed that adding organic fertilizers increased the nitrogenase activity by 57.85%. Subculture experiments revealed that organic fertilizer addition enriched genes corresponding to complex carbon and energy metabolism, as well as nifJ involved in electron transfer for nitrogenase. It also enhanced bacterial interactions and enhanced connectors associated with complex carbon degradation. Validation experiments demonstrated that combinations increased nitrogenase activity by 2.98 times compared to the single. Our findings suggest that organic fertilizers promoted nitrogen fixation by enhancing microbial cooperation, improved the degradation of complex carbon sources, and thereby provided utilizable carbon sources, energy, and electrons to N-fixers, thus increasing nitrogenase activity and nitrogen fixation.

Phytostabilization of Heavy Metals and Fungal Community Response in Manganese Slag under the Mediation of Soil Amendments and Plants

The addition of soil amendments and plants in heavy metal-contaminated soil can result in a significant impact on physicochemical properties, microbial communities and heavy metal distribution, but the specific mechanisms remain to be explored. In this study, Koelreuteria paniculata was used as a test plant, spent mushroom compost (SMC) and attapulgite (ATP) were used as amendments, and manganese slag was used as a substrate. CK (100% slag), M0 (90% slag + 5% SMC + 5% ATP) and M1 (90% slag + 5% SMC + 5% ATP, planting K. paniculata) groups were assessed in a pilot-scale experiment to explore their different impacts on phytoremediation. The results indicated that adding the amendments significantly improved the pH of the manganese slag, enhancing and maintaining its fertility and water retention. Adding the amendments and planting K. paniculata (M1) significantly reduced the bioavailability and migration of heavy metals (HMs). The loss of Mn, Pb and Zn via runoff decreased by 15.7%, 8.4% and 10.2%, respectively, compared to CK. K. paniculata recruited and enriched beneficial fungi, inhibited pathogenic fungi, and a more stable fungal community was built. This significantly improved the soil quality, promoted plant growth and mitigated heavy metal toxicity. In conclusion, this study demonstrated that the addition of SMC-ATP and planting K. paniculata showed a good phytostabilization effect in the manganese slag and further revealed the response process of the fungal community in phytoremediation.

Effects of tillage and biochar on soil physiochemical and microbial properties and its linkage with crop yield

Vertisols are clayey soils with a high potential for improving production. Therefore, understanding the impact of tillage and fertilization on soil physicochemical properties and microbial community is essential for improving the vertisols with a high montmorillonite and smectite clay content. A 3-year field experiment was conducted to compare the effects of different tillage and fertilization practices at three depths of the vertisol under the wheat–maize cropping system in the North China Plain. The experimental treatments included rotary tillage without fertilization (R-CK), rotary tillage with chemical nitrogen (N), phosphorus (P), and potassium (K) fertilization (R-NPK), R-NPK plus biochar (R-NPKB), deep tillage without fertilization (D-CK), deep tillage with chemical N, P, and K fertilization (D-NPK), and D-NPK plus biochar (D-NPKB). The results showed that D-NPKB significantly improved winter wheat and summer maize yields by 14.4 and 3.8%, respectively, compared with R-NPK. The nitrate (NO₃^––N) content of the deeper soil layer in D-NPKB was significantly higher than that in D-NPK. Meanwhile, biochar application increased the pH in the three layers. Compared with R-NPK, D-NPKB significantly increased the average content of available phosphorus (AP), soil organic carbon (SOC), and total nitrogen (TN) by 73.7, 18.5, and 19.0%, respectively. Meanwhile, Gaiellale, Sphingomonadaceae, and Nocardioidaceae were the predominant bacteria at the family level across all treatments, with a total relative proportion ranging from 14.1 to 23.6%. In addition, the abundance of Bacillaceae in deep tillage was 9.4% higher in the 20–30-cm soil layer than that in rotary tillage. Furthermore, the correlation analysis revealed a significant positive correlation between crop yield and chemical factors such as NO₃^––N and the abundances of Gaiellalea, Sphingomonadaceae, and Nocardioidaceae. The findings collectively indicated that deep tillage combined with biochar application could increase the soil nutrients and modify the bacterial structure in the deeper soil layer and therefore will be beneficial for improving the productivity of the vertisols.

Manure applications alter the abundance, community structure and assembly process of diazotrophs in an acidic Ultisol

The excessive usage of nitrogen (N) fertilizers can accelerate the tendency of global climate change. Biological N fixation by diazotrophs contributes substantially to N input and is a viable solution to sustainable agriculture via reducing inorganic N fertilization. However, how manure application influences the abundance, community structure and assembly process of diazotrophs in soil aggregates is not fully understood. Here, we investigated the effect of manure amendment on diazotrophic communities in soil aggregates of an arable soil. Manure application increased soil aggregation, crop yield and the abundance of nifH genes. The abundance of nifH genes increased with aggregate sizes, indicating that diazotrophs prefer to live in larger aggregates. The abundance of nifH genes in large macroaggregates, rather than in microaggregates and silt and clay, was positively associated with plant biomass and crop yield. Both manure application and aggregate size did not alter the Shannon diversity of diazotrophs but significantly changed the diazotrophic community structure. The variation of diazotrophic community structure explained by manure application was greater than that by aggregate size. Manure application promoted the relative abundance of Firmicutes but reduced that of α-Proteobacteria. Stochastic processes played a dominant role in the assembly of diazotrophs in the control treatment. Low-rate manure (9 Mg ha−1) application, rather than medium-rate (18 Mg ha−1) and high-rate (27 Mg ha−1) manure, significantly increased the relative importance of deterministic processes in diazotrophic community assembly. Taken together, our findings demonstrated that long-term manure application increased nifH gene abundance and altered the community structure and assembly process of diazotrophs in soil aggregates, which advanced our understanding of the ecophysiology and functionality of diazotrophs in acidic Ultisols.

Organic amendments enhance soil microbial diversity, microbial functionality and crop yields: A meta-analysis

Fertilization plays an important role in changing soil microbial diversity, which is essential for determining crop yields. Yet, the influence of organic amendments on microbial diversity remains uncertain, and few studies have addressed the relative importance of microbial diversity versus other drivers of crop yields. Here, we synthesize 219 studies worldwide and found that organic amendments significantly increased microbial diversity components (i.e., Shannon, richness, and phylogenetic diversity) and shifted microbial community structure compared to mineral-only fertilization. The performance of microbial alpha diversity varied substantially with organic amendment types, microbial groups and changes in soil pH. Both microbial diversity and community structure exhibited significantly positive relationships with microbial functionality and crop yields. In addition, soil abiotic properties and microbial functionality had a much stronger impact on crop yields than microbial diversity and climate factors. Partial least squares path modeling showed that soil microbial diversity was an important underlying factor driving crop yields via boosting soil microbial functionality. Overall, our findings provide robust evidence for the positive diversity-functions relationships, emphasizing that substituting mineral fertilizers with organic amendments is a promising way to conserve microbial diversity and promote soil microbial functions and crop yields.

Responses of environmental and soil enzyme stoichiometric characteristics of wheat cropping system to fertilizer management in rain-fed areas of China

The application of organic fertilizer can improve soil fertility and maintain soil biodiversity. Soil enzyme activity can reflect the relationship between microbial nutrient demand and environmental nutrient availability. The experiment was established with a split-plot design, which included two main plots and two subplots. The main plots were 3 nitrogen levels (0, 150, 300 kg N ha^-1). The two subplots were chemical fertilizer alone and combination of manure and inorganic application; the soil enzyme activity and chemical properties of each treatment were measured and analyzed. In the study, ecological enzyme stoichiometry was used to study the limitation of microbial resources in dryland wheat system. The results showed that the combined application of manure and chemical fertilizers did not significantly increase the activities of soil C, N and P cycling-related enzymes but decreased the activities of soil L-leucine aminopeptidase (LAP). Long-term application of organic fertilizer and mineral fertilizer significantly increased the accumulation of soil organic carbon (SOC) and nitrogen (TN) and increased soil microbial biomass (MBC, MBN). Organic fertilizer treatment significantly increased soil available phosphorus (AP) and soil NO₃^--N contents, and decreased SOC/AP and TN/AP, but had no significant changes under different nitrogen application levels (N0, N1, N2). GHG emissions were increaseed with the amount of nitrogen applied, the addition of manure did not significantly increase the CO₂ and N₂O emissions, and soil organic matter mineralization and gas emission fluxes decreased at ripen stage. The C-acquiring enzyme was negatively correlated with N-acquiring enzyme but positively correlated with P-acquiring enzyme. The microbial limiting effect of C and P on microbial metabolism becomes increasingly intense as the reproductive period progresses. Redundancy analysis of soil enzyme activities and chemical properties showed that soil TN and MBN could better explain the variation characteristics of soil enzyme activities. Therefore, the study of soil extracellular enzyme stoichiometry and microbial nutrient restriction can give us a more comprehensive understanding of the soil environment. There are more implications can be given under different nitrogen management modes and different growth stages. The results also provided an effective theoretical basis for regulating the changes of soil microbial environment.

Green Manure Amendment Can Reduce Nitrogen Fertilizer Application Rates for Oilseed Rape in Maize–Oilseed Rape Rotation

Excessive use of chemical fertilizers has led to a reduction in the quality of arable land and environmental pollution. Using green manure to replace chemical fertilizers is one of the most effective solutions. To study the effect of green manure on the requirement for nitrogen fertilizer in oilseed rape, a field experiment with maize–oilseed rape rotation was conducted. Green manure was intercropped between rows of maize and returned after the maize harvest, with no green manure intercropped as control. Different nitrogen fertilizer treatments (0, 65%, 75% and 100% N rates, respectively) were applied during the oilseed rape season. The results showed that with a 35% reduction in nitrogen application rate, the rapeseed grain yield was significantly higher with the maize intercropping with green manure returned to the field than with the maize monocropping treatment at the same nitrogen level. Under conditions of intercropping and return of green manure, compared with the full standard rate of nitrogen fertilizer treatment, a reduction in nitrogen application of 25–30% in the rape season had no significant effect on rape yield. The agronomic efficiency of nitrogen fertilizer on oilseed rape increased significantly, by 47.61–121%, with green manure incorporation. In addition, green manure incorporation significantly increased the soil organic matter content and the soil-available nitrogen content when chemical nitrogen fertilization was abandoned. Benefit analysis showed that a 25–35% reduction in chemical nitrogen fertilizer applied to oilseed rape crops could be achieved by intercropping green manure in the maize season before the sowing of rapeseed in the experimental area. In the long-term, this measure would increase nitrogen utility, reduce production costs, and have concomitant environmental benefits of improving the quality of cultivated land.

Sugar and organic acid availability modulate soil diazotroph community assembly and species co-occurrence patterns on the Tibetan Plateau

Metabolites can mediate species interactions and the assembly of microbial communities. However, how these chemicals relate to the assembly processes and co-occurrence patterns of diazotrophic assemblages in root-associated soils remains largely unknown. Here, we examined the diversity and assembly of diazotrophic communities and further deciphered their links with metabolites on Tibetan Plateau. We found that the distribution of sugars and organic acids in the root-associated soils was significantly correlated with the richness of diazotrophs. The presence of these two soil metabolites explains the variability in diazotrophic community compositions. The differential concentrations of these metabolites were significantly linked with the distinctive abundances of diazotrophic taxa in same land types dominated by different plants or dissimilar soils by same plants. The assembly of diazotrophic communities is subject to deterministic ecological processes, which are widely modulated by the variety and amount of sugars and organic acids. Organic acids, for instance, 3-(4-hydroxyphenyl)propionic acid and citric acid, were effective predictors of the characteristics of diazotrophic assemblages across desert habitats. Diazotrophic co-occurrence networks tended to be more complex and connected within different land types covered by the same plant species. The concentrations of multiple sugars and organic acids were coupled significantly with the distribution of keystone species, such as Azotobacter, Azospirillum, Bradyrhizobium, and Mesorhizobium, in the co-occurrence network. These findings provide new insights into the assembly mechanisms of root-associated diazotrophic communities across the desert ecosystems of the Tibetan Plateau.Key points• Soil metabolites were significantly linked to the diversity of diazotrophic community.• Soil metabolites determined the assembly of diazotrophic community.• Sugars and organic acids were coupled mainly with keystone species in networks.

Straw Mulching and Nitrogen Fertilization Affect Diazotroph Communities in Wheat Rhizosphere

Diazotrophs that carry out the biological fixation of atmospheric dinitrogen (N₂) replenish biologically available nitrogen (N) in soil and are influenced by the input of inorganic and organic substrates. To date, little is known about the effects of combined organic substrate addition and N fertilization on the diazotroph community composition and structure in purple soils. We investigated the effects of N fertilization and straw mulching on diazotroph communities by quantifying and sequencing the nifH gene in wheat rhizosphere. The abundance and richness of diazotrophs were greater the higher the fertilization level in the mulched treatments, whereas in the nonmulched treatments (NSMs), richness was lowest with the highest N fertilization level. The abundance and α-diversity of diazotrophs correlated with most of the soil properties but not with pH. At the genus level, the relative abundances of Azospirillum, Bacillus, and Geobacter were higher in the NSMs and those of Pseudacidovorax, Skermanella, Azospira, Paraburkholderia, Azotobacter, Desulfovibrio, Klebsiella, and Pelomonas in the mulched treatments. The differences in community composition between the mulched and the NSMs were associated with differences in soil temperature and soil organic carbon and available potassium contents and C:N ratio. Overall, straw mulching and N fertilization were associated with changes in diazotroph community composition and higher abundance of nifH gene in alkaline purple soils.