Fertilization regimes affect crop yields through changes of diazotrophic community and gene abundance in soil aggregation

Organic amendments enhance rhizosphere carbon stabilization in macroaggregates of saline-sodic soils by regulating keystone microbial clusters

Photosynthetic carbon plays a pivotal role in soil organic carbon (SOC) sequestration in agricultural soils. However, how organic amendments regulate photosynthetic carbon accumulation through multitrophic microbes at the aggregate scale, especially the core microbiota, remains unclear. Here, we conducted a13CO2-labeled rhizo-box experiment on a saline-sodic soil with five treatments: no fertilizer (Ctrl), chemical fertilizer, pig manure (PM), milk vetch straw (MV), and vermicompost. The 13C-SOC in the MV and PM treatments was 2.4 and 1.4 times greater than that in the Ctrl, respectively. Compared with the Ctrl, organic amendments significantly increased 13C-macroaggregate-associated OC (13C-Macro-OC) by 122.4-615.8 % and 13C-mineral-associated OC (13C-MAOC) by 123.6-564.5 % in macroaggregates (> 0.25 mm). The 13C-Macro-OC was significantly positively correlated with biodiversity, the relative abundances of bacteria (mainly Acidobacteriota and Firmicutes) and fungi (mainly Ascomycota and Mucoromycota) in the keystone microbial cluster, network complexity, and the proportion of negative cross-trophic associations. Structural equation modeling revealed that the root trait-induced core microbiota, following organic amendments, affected photosynthetic carbon accumulation via 13C-MAOC in macroaggregates. In summary, our findings highlight the positive effects of milk vetch straw on SOC accumulation and provide a theoretical basis for the targeted regulation of SOC accumulation in saline-sodic soils through organic amendments.

Effect of freeze-thaw cycle aging on biochar application in DEHP contaminated Mollisols: Insights from soil properties and microbial community

Biochar holds significant promise for remediation of organic pollutants. However, the impact of biochar on di-(2-ethylhexyl) phthalate (DEHP)-contaminated Mollisols after freeze-thaw cycles is largely unknown, according to the seasonal traits observed at high latitudes. In this study, fresh biochar (BC) was produced from corn straw, and freeze-thaw aging biochar (FBC) was prepared by simulating winter temperatures in the Mollisol region of Northeast China using BC as a precursor. Pot experiments were conducted to evaluate the effects of freeze-thaw aging on the detoxification efficiency of biochar, the improvement of soil physical and chemical properties, and the regulation of soil microbial community structure and functional genes. The results indicated that biochar after freeze-thaw cycling significantly improved the physical and chemical properties of Mollisols compared with the control, reducing DEHP content by 99.08 % after 28 days. Metagenomic sequencing further revealed the presence of microorganisms and genetic elements potentially involved in DEHP degradation in the soil. The treatment group with freeze-thaw aging biochar exhibited higher microbial diversity and abundance, particularly in Proteobacteria, Bacteroides, and Firmicutes. Analysis of the DEHP degradation pathway via benzoic acid route revealed an increase in the abundance of degraded functional genes/enzymes (benC-xylZ, pacL, catB, pcaG, mhpE, and mhpF). The up-regulation of nitrogen fixation genes and nitrification genes (amoB, hao, narG, nifD, and vnfH) along with a 49.19 % increase in soil microbial biomass nitrogen suggested that freeze-thaw aging biochar benefited nitrogen cycling. Furthermore, the feasibility of applying biochar to high-latitude agricultural settings was validated using pakchoi (Brassica rapa L. ssp. chinensis) as a test crop. These findings suggest that the freeze-thaw aging process enhances the effectiveness of biochar in remediating DEHP-contaminated Mollisols. This study offers a novel perspective on the restoration and improvement of Mollisol productivity in high-latitude regions through biochar application.

Metagenomic insights into nitrogen cycling functional gene responses to nitrogen fixation and transfer in maize-peanut intercropping

The fixation and transfer of biological nitrogen from peanuts to maize in maize-peanut intercropping systems play a pivotal role in maintaining the soil nutrient balance. However, the mechanisms through which root interactions regulate biological nitrogen fixation and transfer remain unclear. This study employed a 15N isotope labelling method to quantify nitrogen fixation and transfer from peanuts to maize, concurrently elucidating key microorganisms and genera in the nitrogen cycle through metagenomic sequencing. The results revealed that biological nitrogen fixation in peanut was 50 mg and transfer to maize was 230 mg when the roots interacted. Moreover, root interactions significantly increased nitrogen content and the activities of protease, dehydrogenase (DHO) and nitrate reductase in the rhizosphere soil. Metagenomic analyses and structural equation modelling indicated that nrfC and nirA genes played important roles in regulating nitrogen fixation and transfer. Bradyrhizobium was affected by soil nitrogen content and DHO, indirectly influencing the efficiency of nitrogen fixation and transfer. Overall, our study identified key bacterial genera and genes associated with nitrogen fixation and transfer, thus advancing our understanding of interspecific interactions and highlighting the pivotal role of soil microorganisms and functional genes in maintaining soil ecosystem stability from a molecular ecological perspective.

Influence of long-term ecological reclamation on carbon and nitrogen cycling in soil aggregates: The role of bacterial community structure and function

Understanding the influence of microbial taxa and functions on soil carbon (C) and nitrogen (N) cycling, particularly concerning soil aggregate sizes, is crucial for ecosystem management. This study examines the taxonomic and functional dynamics of soil bacterial communities within different aggregate sizes over time. Soil samples from a reclamation forest on the Loess Plateau in North China were collected across reclamation ages of 0, 3, 18, and 28 years. Soil aggregates were categorized into large macro-aggregates (>2000 μm), small macro-aggregates (250-2000 μm), and micro-aggregates (<250 μm) using a modified dry-sieving method. Soil aggregate stability, C and N concentrations, newly derived plant C, enzyme activities, bacterial communities, and functional genes in each aggregate fraction were systematically analyzed. There was a notable increase in soil aggregate stability and a higher proportion of large aggregates was found with increasing forest age. There were significant differences in bacterial community structures, particularly between micro-aggregates and large macro-aggregates and across different forest ages. Reclamation led to an increased abundance of copiotrophic bacterial taxa. Decreases in N-acquiring enzyme activity in micro-aggregates were contrasted by an increase in C, N, and phosphorus (P) acquisition activities in larger aggregates over time. Larger aggregates showed a faster recovery of C and N cycling genes accompanied by a significant enhancement in acetyl-CoA and ammonia oxidation processes, underscoring their importance in soil nutrient cycling. These results highlight the critical role of aggregate size in shaping microbial community structures and functions that influence soil C and N cycling during reclamation and provide new perspectives highlighting the significance of incorporating aggregate size considerations into soil management and reclamation strategies.

Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling

Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R2 = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R2 = 0.076 ~ R2 = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.

Organic fertilization reduces nitrous oxide emission by altering nitrogen cycling microbial guilds favouring complete denitrification at soil aggregate scale

Agricultural management practices can induce changes in soil aggregation structure that alter the microbial nitrous oxide (N2O) production and reduction processes occurring at the microscale, leading to large-scale consequences for N2O emissions. However, the mechanistic understanding of how organic fertilization affects these context-dependent small-scale N2O emissions and associated key nitrogen (N) cycling microbial communities is lacking. Here, denitrification gas (N2O, N2) and potential denitrification capacity N2O/(N2O + N2) were assessed by automated gas chromatography in different soil aggregates (>2 mm, 2-0.25 and <0.25 mm), while associated microbial communities were assessed by sequencing and qPCR of N2O-producing (nirK and nirS) and reducing (nosZ clade I and II) genes. The results indicated that organic fertilization reduced N2O emissions by enhancing the conversion of N2O to N2 in all aggregate sizes. Moreover, potential N2O production and reduction hotspots occurred in smaller soil aggregates, with the degree depending on organic fertilizer type and application rate. Further, significantly higher abundance and diversity of nosZ clades relative to nirK and nirS revealed complete denitrification promoted through selection of denitrifying communities at microscales favouring N2O reduction. Communities associated with high and low emission treatments form modules with specific sequence types which may be diagnostic of emission levels. Taken together, these findings suggest that organic fertilizers reduced N2O emissions through influencing soil factors and patterns of niche partitioning between N2O-producing and reducing communities within soil aggregates, and selection for communities that overall are more likely to consume than emit N2O. These findings are helpful in strengthening the ability to predict N2O emissions from agricultural soils under organic fertilization as well as contributing to the development of net-zero carbon strategies for sustainable agriculture.

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.

Fertilizing-induced alterations of microbial functional profiles in soil nitrogen cycling closely associate with crop yield

Fertilization and rhizosphere selection are key regulators for soil nitrogen (N) cycling and microbiome. Thus, clarifying how the overall N cycling processes and soil microbiome respond to these factors is a prerequisite for understanding the consequences of high inputs of fertilizers, enhancing crop yields, and formulating reasonable nitrogen management strategies under agricultural intensification scenarios. To do this, we applied shotgun metagenomics sequencing to reconstruct N cycling pathways on the basis of abundance and distribution of related gene families, as well as explored the microbial diversity and interaction via high throughput sequencing based on a two-decade fertilization experiment in Loess Plateau of China semiarid area. We found that bacteria and fungi respond divergent to fertilization regimes and rhizosphere selection, in terms of community diversity, niche breadth, and microbial co-occurrence networks. Moreover, organic fertilization decreased the complexity of bacterial networks but increased the complexity and stability of fungal networks. Most importantly, rhizosphere selection exerted more strongly influences on the soil overall nitrogen cycling than the application of fertilizers, accompanied by the increase in the abundance of nifH, NIT-6, and narI genes and the decrease in the abundance of amoC, norC, and gdhA genes in the rhizosphere soil. Furthermore, keystone families screening from soil microbiome (e.g., Sphingomonadaceae, Sporichthyaceae, and Mortierellaceae), which were affected by the edaphic variables, contributed greatly to crop yield. Collectively, our findings emphasize the pivotal roles of rhizosphere selection interacting with fertilization regimes in sustaining soil nitrogen cycling processes in response to decades-long fertilization, as well as the potential importance of keystone taxa in maintaining crop yield. These findings significantly facilitate our understanding of nitrogen cycling in diverse agricultural soils and lay a foundation for manipulating specific microorganisms to regulate N cycling and promote agroecosystem sustainability.

Significant difference in the efficacies of silicon application regimes on cadmium species and environmental risks in rice rhizosphere

Silicon (Si) is commonly applied as base-fertilizer or foliar-topdressing to palliate the uptake-translocation-accumulation of cadmium (Cd) in rice through Si-Cd antagonism. However, little is known about the fate of Cd in rice rhizosphere soil and its eco-environmental effects under different Si treatments. Here, systematic works had been carried out to elucidate the Cd species, soil properties, and environmental risks in rice rhizosphere driven by different Si soil-fertilization regimes including CK (without Si-addition), TSi (added before transplanting stage), JSi (added at jointing stage), and TJSi (split into two equal parts, added half before transplanting and another half at jointing stage). Results showed that TJSi outperformed the rest of fertilization regimes. The solid-phase-Cd concentrations treated with TSi, TJSi and JSi were increased by 4.18%, 5.73% and 3.41%, respectively, when compared to CK. The labile Cd (F1+F2) proportion of TJSi was reduced by 16.30%, 9.30% and 6.78%, respectively, when compared to CK, TSi, and JSi. Simultaneously, the liquid-phase-Cd concentration was appreciably suppressed by TJSi throughout the rice lifecycle, while TSi mainly abated Cd dissociation during the vegetative period, and JSi attenuated it during the grain-filling stage. The mobility factor of Cd treated with TJSi was the lowest, which was significantly lower than that of TSi (9.30%) and JSi (6.78%), respectively. Similarly, the oral exposure risk of TJSi was reduced by 4.43% and 32.53%; and the food-chain exposure risk of TJSi was decreased by 13.03% and 42.78%. Additionally, TJSi was the most effective in promoting enzyme activities and nutrient content in rhizosphere soil. Overall, TJSi is more positive and sustainable than TSi and JSi in reconstructing Cd-contaminated rhizosphere environments and abating the environmental risks of Cd. Agronomic practices in Cd-contaminated paddy soils can be informed by applying Si-fertilizer separately before transplanting and at jointing stage to achieve soil welfare and food security.