Potential relevance between soybean nitrogen uptake and rhizosphere prokaryotic communities under waterlogging stress

Diversified crop rotations exert a profound influence on the nosZI denitrifier community

Agricultural soils are a significant contributor to global nitrous oxide (N2O) emissions, which is primarily driven by microbial nitrification and denitrification processes. Diversifying crop rotations can enhance soil nitrogen (N) utilization and influence N-cycling microbes, particularly the denitrifiers. Here, we evaluated the abundance, diversity, and community structure of soil denitrifiers by analyzing the denitrification genes (nirS, nirK, and nosZI) with a 14-year experiment of continuous and rotated crop systems. Compared to continuous cotton (C), crop rotations altered abundance of the nirS, nirK, and nosZI genes, but the responses varied among different rotation patterns (p < 0.05). Diversified crop rotations decreased Shannon index of the nirS and nirK gene communities, while increased that of the nosZI gene communities. Diversified crop rotations greatly changed community structure of the nirS, nirK and nosZI gene communities (p < 0.05). Among the responsive operational taxonomic units (OTUs), 2.62 %, 2.52 %, and 4.31 % of the nirS, nirK, and nosZI genes were involved in the responses, respectively. Notably, a significant increase in OTUs belonged to N-fixing groups (i.e., Herbaspirillum and Rhodanobacter), while a decrease in OTUs affiliated to Achromobacter and Bosea was observed in diversified crop rotations. Furthermore, soil pH and C/N ratio correlated significantly with the nirS gene community structure (p < 0.05), SOC and C/N ratio correlated with the nirK gene community (p < 0.05), and soil pH, TN, NO3--N, and C/N ratio correlated with the nosZI gene community (p < 0.05), respectively. In conclusion, our study demonstrates that long-term diversified crop rotations significantly altered the microbial communities related to denitrification, especially the nosZI gene community. These findings highlight the importance of diversified crop rotations in fostering soil denitrifiers communities that contribute to N₂O reduction, potentially supporting sustainable agricultural practices by reducing greenhouse gas emissions. However, future studies should be focus on both the nosZI and nosZII clades communities to offer a more complete picture of microbial contributions to soil N-cycling and N2O emission reduction.

Effect of coexisting nutrient divalent cations on cadmium transport in soil-herbal crop systems

Cadmium (Cd) pollution in Chinese herbal medicines poses a serious risk to medication safety. Regulating Cd uptake, transport, and accumulation in plants through ion-ion interactions offers a novel, environmentally sustainable, and practical approach to address this issue. However, the effects and underlying mechanisms of coexisting divalent cations zinc (Zn), magnesium (Mg), and manganese (Mn) on Cd uptake by Ligusticum sinense cv. Chuanxiong (L. chuanxiong) have not been comprehensively studied or well understood. In this study, the application of coexisting these cations (Zn, Mg, Mn) could significantly promote the growth of L. chuanxiong (21.11%-36.04%) and change the mobility of Cd in the soil-crop system. Specifically, adding Zn decreased Cd content in soil and plants by 18.23% and 20.62%, respectively, while Mg increased it by 10.99% and 62.27%. Mn addition, however, had no significant effect. Similar trends in soil enzyme activity were also observed with Zn, Mg, and Mn treatments. Simultaneously, the findings explore how coexisting divalent cations influence plant physiological responses, including photosynthesis and antioxidant capacities, enabling L. chuanxiong to better manage Cd stress. This study underscores the potential of ion-to-ion interactions as an effective approach to mitigate Cd accumulation, offering a practical and sustainable solution for enhancing the safety of Chinese herbal medicines. Additionally, the effects of mixed cation applications on Cd dynamics are complex, shaped by interactions between ion types, dosages, and their specific properties. These insights provide a foundation for developing more effective remediation strategies for Cd-contaminated soils, particularly in the cultivation of medicinal plants.

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.

Dissecting the role of soybean rhizosphere-enriched bacterial taxa in modulating nitrogen-cycling functions

Crop roots selectively recruit certain microbial taxa that are essential for supporting their growth. Within the recruited microbes, some taxa are consistently enriched in the rhizosphere across various locations and crop genotypes, while others are unique to specific planting sites or genotypes. Whether these differentially enriched taxa are different in community composition and how they interact with nutrient cycling need further investigation. Here, we sampled bulk soil and the rhizosphere soil of five soybean varieties grown in Shijiazhuang and Xuzhou, categorized the rhizosphere-enriched microbes into shared, site-specific, and variety-specific taxa, and analyzed their correlation with the diazotrophic communities and microbial genes involved in nitrogen (N) cycling. The shared taxa were dominated by Actinobacteria and Thaumarchaeota, the site-specific taxa were dominated by Actinobacteria in Shijiazhuang and by Nitrospirae in Xuzhou, while the variety-specific taxa were more evenly distributed in several phyla and contained many rare operational taxonomic units (OTUs). The rhizosphere-enriched taxa correlated with most diazotroph orders negatively but with eight orders including Rhizobiales positively. Each group within the shared, site-specific, and variety-specific taxa negatively correlated with bacterial amoA and narG in Shijiazhuang and positively correlated with archaeal amoA in Xuzhou. These results revealed that the shared, site-specific, and variety-specific taxa are distinct in community compositions but similar in associations with rhizosphere N-cycling functions. They exhibited potential in regulating the soybean roots' selection for high-efficiency diazotrophs and the ammonia-oxidizing and denitrification processes. This study provides new insights into soybean rhizosphere-enriched microbes and their association with N cycling. KEY POINTS: • Soybean rhizosphere affected diazotroph community and enriched nifH, amoA, and nosZ. • Shared and site- and variety-specific taxa were dominated by different phyla. • Rhizosphere-enriched taxa were similarly associated with N-cycle functions.

Responses of plant immune system and rhizosphere soil microbiome to the elicitor BAR11 in Arabidopsis thaliana

Microbial elicitors have been shown to boost plant immunity by inducing defense responses to reduce plant disease. However, little is known about the changes in plant microbiome and metabolism in the process of enhancing plant immunity with elicitors. The protein elicitor BAR11, from Saccharothrix yanglingensis Hhs.015, induces defense responses in Arabidopsis thaliana that enhances resistance to pathogens. In this study, bar11 was inserted into Col-0 A. thaliana to obtain BAR11-Trans plant by Agrobacterium-mediated immersion transformation. BAR11-Trans exhibited an elevated defense level against Pseudomonas syringae pv. tomato DC3000 while experiencing a decline in biomass production of above-ground parts. In the process, BAR11-Trans increased the activity of phenylalanine ammonia lyase (PAL) and catalase (CAT), and up-regulated genes related to plant defense pathways. Furthermore, BAR11-Trans decreased root tip reactive oxygen species (ROS) levels while increasing ROS burst in the leaves. Soil transplantation experiments showed that soil planted with BAR11-Trans could enhance the resistance of Col-0 A. thaliana to DC3000. Analysis of A. thaliana rhizosphere soil through 16S rRNA amplified sequencing revealed that BAR11-Trans increased the relative abundance and diversity of the rhizosphere microbial community, leading to the recruitment of more plant probiotics. Additionally, the accumulation of kaempferitrin and robinin in BAR11-Trans influenced the physicochemical properties of rhizosphere soil and the composition of the bacterial community. In summary, BAR11-Trans exhibited heightened defense levels compared to Col-0, leading to increased secretion of secondary metabolites and the recruitment of a greater number of microorganisms to adapt to the environment. These findings offer novel insights for the potential application of elicitors in agricultural disease control.

Microbiome structure variation and soybean's defense responses during flooding stress and elevated CO2

Introduction

With current trends in global climate change, both flooding episodes and higher levels of CO2 have been key factors to impact plant growth and stress tolerance. Very little is known about how both factors can influence the microbiome diversity and function, especially in tolerant soybean cultivars. This work aims to (i) elucidate the impact of flooding stress and increased levels of CO2 on the plant defenses and (ii) understand the microbiome diversity during flooding stress and elevated CO2 (eCO2).

Methods

We used next-generation sequencing and bioinformatic methods to show the impact of natural flooding and eCO2 on the microbiome architecture of soybean plants' below- (soil) and above-ground organs (root and shoot). We used high throughput rhizospheric extra-cellular enzymes and molecular analysis of plant defense-related genes to understand microbial diversity in plant responses during eCO2 and flooding.

Results

Results revealed that bacterial and fungal diversity was substantially higher in combined flooding and eCO2 treatments than in non-flooding control. Microbial diversity was soil>root>shoot in response to flooding and eCO2. We found that sole treatment of eCO2 and flooding had significant abundances of Chitinophaga, Clostridium, and Bacillus. Whereas the combination of flooding and eCO2 conditions showed a significant abundance of Trichoderma and Gibberella. Rhizospheric extra-cellular enzyme activities were significantly higher in eCO2 than flooding or its combination with eCO2. Plant defense responses were significantly regulated by the oxidative stress enzyme activities and gene expression of Elongation factor 1 and Alcohol dehydrogenase 2 in floodings and eCO2 treatments in soybean plant root or shoot parts.

Conclusion

This work suggests that climatic-induced changes in eCO2 and submergence can reshape microbiome structure and host defenses, essential in plant breeding and developing stress-tolerant crops. This work can help in identifying core-microbiome species that are unique to flooding stress environments and increasing eCO2.

Biochar Enhances the Resistance of Legumes and Soil Microbes to Extreme Short-Term Drought

Short-term drought events occur more frequently and more intensively under global climate change. Biochar amendment has been documented to ameliorate the negative effects of water deficits on plant performance. Moreover, biochar can alter the soil microbial community, soil properties and soil metabolome, resulting in changes in soil functioning. We aim to reveal the extent of biochar addition on soil nutrients and the soil microbial community structure and how this improves the tolerance of legume crops (peanuts) to short-term extreme drought. We measured plant performances under different contents of biochar, set as a gradient of 2%, 3% and 4%, after an extreme experimental drought. In addition, we investigated how soil bacteria and fungi respond to biochar additions and how the soil metabolome changes in response to biochar amendments, with combined growth experiments, high-throughput sequencing and soil omics. The results indicated that biochar increased nitrites and available phosphorus. Biochar was found to influence the soil bacterial community structure more intensively than the soil fungal community. Additionally, the fungal community showed a higher randomness under biochar addition when experiencing short-term extreme drought compared to the bacterial community. Soil bacteria may be more strongly related to soil nutrient cycling in peanut agricultural systems. Although the soil metabolome has been documented to be influenced by biochar addition independent of soil moisture, we found more differential metabolites with a higher biochar content. We suggest that biochar enhances the resistance of plants and soil microbes to short-term extreme drought by indirectly modifying soil functioning probably due to direct changes in soil moisture and soil pH.