Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean

Bacillus suppresses nitrogen efficiency of soybean-rhizobium symbiosis through regulation of nitrogen-related transcriptional and microbial patterns

The regulation of legume-rhizobia symbiosis by microorganisms has obtained considerable interest in recent research, particularly in the common rhizobacteria Bacillus. However, few studies have provided detailed explanations regarding the regulatory mechanisms involved. Here, we investigated the effects of Bacillus (Bac.B) on Bradyrhizobium-soybean (Glycine max) symbiosis and elucidated the underlying ecological mechanisms. We found that two Bradyrhizobium strains (i.e. Bra.Q2 and Bra.D) isolated from nodules significantly promoted nitrogen (N) efficiency of soybean via facilitating nodule formation, thereby enhanced plant growth and yield. However, the intrusion of Bac.B caused a reverse shift in the synergistic efficiency of N2 fixation in the soybean-Bradyrhizobium symbiosis. Biofilm formation and naringenin may be importantin suppression of Bra.Q2 growth regulated by Bac.B. In addition, transcriptome and microbiome analyses revealed that Bra.Q2 and Bac.B might interact to regulateN transport and assimilation, thus influence the bacterial composition related to plant N nutrition in nodules. Also, the metabolisms of secondary metabolites and hormones associated with plant-microbe interaction and growth regulation were modulated by Bra.Q2 and Bac.B coinoculation. Collectively, we demonstrate that Bacillus negatively affects Bradyrhizobium-soybean symbiosis and modulate microbial interactions in the nodule. Our findings highlight a novel Bacillus-based regulation to improve N efficiency and sustainable agricultural development.

Organic amendments increased Chinese milk vetch symbiotic nitrogen fixation by enriching Mesorhizobium in rhizosphere

Symbiotic nitrogen fixation of Chinese milk vetch (Astragalus sinicus L.) can fix nitrogen from the atmosphere and serve as an organic nitrogen source in agricultural ecosystems. Exogenous organic material application is a common practice of affecting symbiotic nitrogen fixation; however, the results of the regulation activities remain under discussion. Studies on the impact of organic amendments on symbiotic nitrogen fixation have focused on dissolved organic carbon content changes, whereas the impact on dissolved organic carbon composition and the underlying mechanism remain unclear. In situ pot experiments were carried out using soils from a 40-year-old field experiment platform to investigate symbiotic nitrogen fixation rate trends, dissolved organic carbon concentration and component, and diazotroph community structure in roots and in rhizosphere soils following long-term application of different exogenous organic substrates, i.e., green manure, green manure and pig manure, and green manure and rice straw. Remarkable increases in rate were observed in and when compared with that in green manure treatment, with the greatest enhancement observed in the treatment. Moreover, organic amendments, particularly pig manure application, altered diazotroph community composition in rhizosphere soils, therefore increasing the abundance of the host-specific genus Mesorhizobium. Furthermore, organic amendments influence the diazotroph communities through two primary mechanisms. Firstly, the components of dissolved organic carbon promote an increase in available iron, facilitated by the presence of humus substrates. Secondly, the elevated content of dissolved organic carbon and available iron expands the niche breadth of Mesorhizobium within the rhizosphere. Consequently, these alterations result in a modified diazotroph community within the rhizosphere, which in turn influences Mesorhizobium nodulation in the root and symbiotic nitrogen fixation rate. The results of the present study enhance our understanding of the impact of organic amendments on symbiotic nitrogen fixation and the underlying mechanism, highlighting the key role of dissolved organic carbon composition on diazotroph community composition in the rhizosphere.

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.

Effect of conventional and biodegradable microplastics on the soil-soybean system: A perspective on rhizosphere microbial community and soil element cycling

As an exogenous carbon input, microplastics (MPs), especially biodegradable MPs, may significantly disrupt soil microbial communities and soil element cycling (CNPS cycling), but few studies have focused on this. Here, we focused on assessing the effects of conventional low-density polyethylene (LDPE), biodegradable polybutylene adipate terephthalate (PBAT), and polylactic acid (PLA) MPs on rhizosphere microbial communities and CNPS cycling in a soil-soybean system. The results showed that PBAT-MPs and PLA-MPs were more detrimental to soybean growth than LDPE-MPs, resulting in a reduction in shoot nitrogen (14.05% and 11.84%) and shoot biomass (33.80% and 28.09%) at the podding stage. In addition, dissolved organic carbon (DOC) increased by 20.91% and 66.59%, while nitrate nitrogen (NO3--N) significantly decreased by 56.91% and 69.65% in soils treated with PBAT-MPs and PLA-MPs, respectively. PBAT-MPs and PLA-MPs mainly enhanced copiotrophic bacteria (Proteobacteria) and suppressed oligotrophic bacteria (Verrucomicrobiota, Gemmatimonadota, etc.), increasing the abundance of CNPS cycling-related functional genes. LDPE-MPs tended to enrich oligotrophic bacteria (Verrucomicrobiota, etc.) and decrease the abundance of CNPS cycling-related functional genes. Correlation analysis revealed that MPs with different degradation properties selectively affected the composition and function of the bacterial community, resulting in changes in the availability of soil nutrients (especially NO3--N). Redundancy analysis further indicated that NO3--N was the primary constraining factor for soybean growth. This study provides a new perspective for revealing the underlying ecological effects of MPs on soil-plant systems.

Effects of Fishery Utilization on the Physicochemical Index and Microbial Community Composition in Saline-Alkaline Water

Fishery utilization of idle saline-alkaline water resources offers various benefits including reducing surrounding soil salinity, improving the ecological environment, increasing arable land area, and providing economic advantages to the fishery industry. However, for decades, the characteristics and regulatory mechanisms of microbial communities that affect fishery utilization have not been clear, which restricts their application. In this study, high-throughput 16S rRNA amplicon sequencing was employed to analyze the bacterial community in these water resources. The sequencing yielded high-quality sequences (2,765,063), resulting in the identification of 18,761 bacterial operational taxonomic units (OTUs). Analysis revealed that the type of saline-alkaline water had a more significant influence on the bacterial community compared to seasonal variations within the aquaculture period. The Chao index for saline-alkaline ponds (ASW) was significantly lower (P < 0.05) than for still saline-alkaline water (SSW) and flowing saline-alkaline water (FSW), while the Shannon index for ASW was also significantly lower (P < 0.05) compared to FSW. When comparing ASW to nonaquaculture saline-alkaline water, a decrease in Proteobacteria to 26.87% was noted, particularly α-proteobacteria and γ-proteobacteria, accompanied by a rapid increase in Actinobacteria and Cyanobacteria to 28.60%. Networkx analysis further revealed that ASW significantly increased competition and amensalism from secondary saline-alkaline water microorganisms, resulting in a more solitary bacterial community composition as an adaptive strategy to cope with intense environmental pressures. Key bacterial species such as Pseudomonas, Hydrogenophaga, and Flavobacterium were found to be involved in hydrogen-cycling, nitrogen-cycling, and carbon-cycling, respectively, with all three exhibiting high abundance in FSW. Consequently, FSW demonstrates significant advantages in biogeochemical cycling, pollutant degradation, and the utilization of indigenous probiotic bacteria. Although the surface of abandoned secondary saline-alkaline land was covered with white salt particles, the fishery utilization of saline-alkaline water with low salinity levels (4.0-5.5), and the presence of nitrate and phosphate were identified as primary determinants of bacterial community composition. Nevertheless, a comparison of coastal high-salinity ponds indicated that salinity still selectively affects bacterial communities to some extent. Overall, our study provides valuable insights into the microbial regulation of nitrite during saline-alkaline water aquaculture, thereby aiding in the efficient utilization of secondary saline-alkaline water resources for fisheries.

Nitrogen and Nod factor signaling determine Lotus japonicus root exudate composition and bacterial assembly

Symbiosis with soil-dwelling bacteria that fix atmospheric nitrogen allows legume plants to grow in nitrogen-depleted soil. Symbiosis impacts the assembly of root microbiota, but it is unknown how the interaction between the legume host and rhizobia impacts the remaining microbiota and whether it depends on nitrogen nutrition. Here, we use plant and bacterial mutants to address the role of Nod factor signaling on Lotus japonicus root microbiota assembly. We find that Nod factors are produced by symbionts to activate Nod factor signaling in the host and that this modulates the root exudate profile and the assembly of a symbiotic root microbiota. Lotus plants with different symbiotic abilities, grown in unfertilized or nitrate-supplemented soils, display three nitrogen-dependent nutritional states: starved, symbiotic, or inorganic. We find that root and rhizosphere microbiomes associated with these states differ in composition and connectivity, demonstrating that symbiosis and inorganic nitrogen impact the legume root microbiota differently. Finally, we demonstrate that selected bacterial genera characterizing state-dependent microbiomes have a high level of accurate prediction.

The microbiome dynamics and interaction of endosymbiotic Symbiodiniaceae and fungi are associated with thermal bleaching susceptibility of coral holobionts

The thermal bleaching percentage of coral holobionts shows interspecific differences under heat-stress conditions, which are closely related to the coral-associated microbiome. However, the ecological effects of community dynamics and interactions between Symbiodiniaceae and fungi on coral thermal bleaching susceptibility remain unclear. In this study, we analyzed the diversity, community structure, functions, and potential interaction of Symbiodiniaceae and fungi among 18 coral species from a high thermal bleaching risk atoll using next-generation sequencing. The results showed that heat-tolerant C3u sub-clade and Durusdinium dominated the Symbiodiniaceae community of corals and that there were no core amplicon sequence variants in the coral-associated fungal community. Fungal richness and the abundance of confirmed functional animal-plant pathogens were significantly positively correlated with the coral thermal bleaching percentage. Fungal indicators, including Didymellaceae, Chaetomiaceae, Schizophyllum, and Colletotrichum, were identified in corals. Each coral species had a complex Symbiodiniaceae-fungi interaction network (SFIN), which was driven by the dominant Symbiodiniaceae sub-clades. The SFINs of coral holobionts with low thermal bleaching susceptibility exhibited low complexity and high betweenness centrality. These results indicate that the extra heat tolerance of coral in Huangyan Island may be linked to the high abundance of heat-tolerant Symbiodiniaceae. Fungal communities have high interspecific flexibility, and the increase of fungal diversity and pathogen abundance was correlated with higher thermal bleaching susceptibility of corals. Moreover, fungal indicators were associated with the degrees of coral thermal bleaching susceptibility, including both high and intermediate levels. The topological properties of SFINs suggest that heat-tolerant coral have limited fungal parasitism and strong microbial network resilience.IMPORTANCEGlobal warming and enhanced marine heatwaves have led to a rapid decline in coral reef ecosystems worldwide. Several studies have focused on the impact of coral-associated microbiomes on thermal bleaching susceptibility in corals; however, the ecological functions and interactions between Symbiodiniaceae and fungi remain unclear. We investigated the microbiome dynamics and potential interactions of Symbiodiniaceae and fungi among 18 coral species in Huangyan Island. Our study found that the Symbiodiniaceae community of corals was mainly composed of heat-tolerant C3u sub-clade and Durusdinium. The increase in fungal diversity and pathogen abundance has close associations with higher coral thermal bleaching susceptibility. We first constructed an interaction network between Symbiodiniaceae and fungi in corals, which indicated that restricting fungal parasitism and strong interaction network resilience would promote heat acclimatization of corals. Accordingly, this study provides insights into the role of microorganisms and their interaction as drivers of interspecific differences in coral thermal bleaching.

Seagrass-mediated rhizosphere redox gradients are linked with ammonium accumulation driven by diazotrophs

Seagrasses can enhance nutrient mobilization in their rhizosphere via complex interactions with sediment redox conditions and microbial populations. Yet, limited knowledge exists on how seagrass-derived rhizosphere dynamics affect nitrogen cycling. Using optode and gel-sampler-based chemical imaging, we show that radial O2 loss (ROL) from rhizomes and roots leads to the formation of redox gradients around below-ground tissues of seagrass (Zostera marina), which are co-localized with regions of high ammonium concentrations in the rhizosphere. Combining such chemical imaging with fine-scale sampling for microbial community and gene expression analyses indicated that multiple biogeochemical pathways and microbial players can lead to high ammonium concentration within the oxidized regions of the seagrass rhizosphere. Symbiotic N2-fixing bacteria (Bradyrhizobium) were particularly abundant and expressed the diazotroph functional marker gene nifH in Z. marina rhizosphere areas with high ammonium concentrations. Such an association between Z. marina and Bradyrhizobium can facilitate ammonium mobilization, the preferred nitrogen source for seagrasses, enhancing seagrass productivity within nitrogen-limited environments. ROL also caused strong gradients of sulfide at anoxic/oxic interfaces in rhizosphere areas, where we found enhanced nifH transcription by sulfate-reducing bacteria. Furthermore, we found a high abundance of methylotrophic and sulfide-oxidizing bacteria in rhizosphere areas, where O2 was released from seagrass rhizomes and roots. These bacteria could play a beneficial role for the plants in terms of their methane and sulfide oxidation, as well as their formation of growth factors and phytohormones. ROL from below-ground tissues of seagrass, thus, seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations.

IMPORTANCE

Seagrasses are important marine habitats providing several ecosystem services in coastal waters worldwide, such as enhancing marine biodiversity and mitigating climate change through efficient carbon sequestration. Notably, the fitness of seagrasses is affected by plant-microbe interactions. However, these microscale interactions are challenging to study and large knowledge gaps prevail. Our study shows that redox microgradients in the rhizosphere of seagrass select for a unique microbial community that can enhance the ammonium availability for seagrass. We provide first experimental evidence that Rhizobia, including the symbiotic N2-fixing bacteria Bradyrhizobium, can contribute to the bacterial ammonium production in the seagrass rhizosphere. The release of O2 from rhizomes and roots also caused gradients of sulfide in rhizosphere areas with enhanced nifH transcription by sulfate-reducing bacteria. O2 release from seagrass root systems thus seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations.

Nitrogen Fertilizers Affect Microbial Hitchhiking to the Plant Roots

The phenomenon of microbial hitchhiking, where nonmotile microbes utilize transspecies motility to navigate within their environment, has been observed. However, the underlying factors driving microbial hitchhiking remain unclear. Our study explored how nitrogen fertilizers affect microbial hitchhiking in soil through an in situ planting experiment. We established twelve treatments encompassing the presence and absence of plants, the presence and absence of a filter membrane that is used to prevent hitchhiking, and three nitrogen levels. Results showed that nitrogen influenced bacterial diversity in all soils, an effect thwarted by filter membranes. In the presence of plants, nitrogen significantly affected the bacterial mobility, Bacillus abundance, and plant biomass, but these effects vanished when filters were used. The correlation between motile Bacillus and rhizosphere bacteria was strong without filters at the proper nitrogen levels but weakened with membrane treatments. Thus, plants and nitrogen together, not nitrogen alone, alter the soil microbiome via hitchhiking.

Dynamic root microbiome sustains soybean productivity under unbalanced fertilization

Root-associated microbiomes contribute to plant growth and health, and are dynamically affected by plant development and changes in the soil environment. However, how different fertilizer regimes affect quantitative changes in microbial assembly to effect plant growth remains obscure. Here, we explore the temporal dynamics of the root-associated bacteria of soybean using quantitative microbiome profiling (QMP) to examine its response to unbalanced fertilizer treatments (i.e., lacking either N, P or K) and its role in sustaining plant growth after four decades of unbalanced fertilization. We show that the root-associated bacteria exhibit strong succession during plant development, and bacterial loads largely increase at later stages, particularly for Bacteroidetes. Unbalanced fertilization has a significant effect on the assembly of the soybean rhizosphere bacteria, and in the absence of N fertilizer the bacterial community diverges from that of fertilized plants, while lacking P fertilizer impedes the total load and turnover of rhizosphere bacteria. Importantly, a SynCom derived from the low-nitrogen-enriched cluster is capable of stimulating plant growth, corresponding with the stabilized soybean productivity in the absence of N fertilizer. These findings provide new insights in the quantitative dynamics of the root-associated microbiome and highlight a key ecological cluster with prospects for sustainable agricultural management.

High Frankia abundance and low diversity of microbial community are associated with nodulation specificity and stability of sea buckthorn root nodule

Introduction

Actinorhizal symbioses are gaining attention due to the importance of symbiotic nitrogen fixation in sustainable agriculture. Sea buckthorn (Hippophae L.) is an important actinorhizal plant, yet research on the microbial community and nitrogen cycling in its nodules is limited. In addition, the influence of environmental differences on the microbial community of sea buckthorn nodules and whether there is a single nitrogen-fixing actinomycete species in the nodules are still unknown.

Methods

We investigated the diversity, community composition, network associations and nitrogen cycling pathways of the microbial communities in the root nodule (RN), nodule surface soil (NS), and bulk soil (BS) of Mongolian sea buckthorn distributed under three distinct ecological conditions in northern China using 16S rRNA gene and metagenomic sequencing. Combined with the data of environmental factors, the effects of environmental differences on different sample types were analyzed.

Results

The results showed that plants exerted a clear selective filtering effect on microbiota, resulting in a significant reduction in microbial community diversity and network complexity from BS to NS to RN. Proteobacteria was the most abundant phylum in the microbiomes of BS and NS. While RN was primarily dominated by Actinobacteria, with Frankia sp. EAN1pec serving as the most dominant species. Correlation analysis indicated that the host determined the microbial community composition in RN, independent of the ecological and geographical environmental changes of the sea buckthorn plantations. Nitrogen cycle pathway analyses showed that RN microbial community primarily functions in nitrogen fixation, and Frankia sp. EAN1pec was a major contributor to nitrogen fixation genes in RN.

Discussion

This study provides valuable insights into the effects of eco-geographical environment on the microbial communities of sea buckthorn RN. These findings further prove that the nodulation specificity and stability of sea buckthorn root and Frankia sp. EAN1pec may be the result of their long-term co-evolution.

Characterization of soybean chitinase genes induced by rhizobacteria involved in the defense against Fusarium oxysporum

Rhizobacteria are capable of inducing defense responses via the expression of pathogenesis-related proteins (PR-proteins) such as chitinases, and many studies have validated the functions of plant chitinases in defense responses. Soybean (Glycine max) is an economically important crop worldwide, but the functional validation of soybean chitinase in defense responses remains limited. In this study, genome-wide characterization of soybean chitinases was conducted, and the defense contribution of three chitinases (GmChi01, GmChi02, or GmChi16) was validated in Arabidopsis transgenic lines against the soil-borne pathogen Fusarium oxysporum. Compared to the Arabidopsis Col-0 and empty vector controls, the transgenic lines with GmChi02 or GmChi16 exhibited fewer chlorosis symptoms and wilting. While GmChi02 and GmChi16 enhanced defense to F. oxysporum, GmChi02 was the only one significantly induced by Burkholderia ambifaria. The observation indicated that plant chitinases may be induced by different rhizobacteria for defense responses. The survey of 37 soybean chitinase gene expressions in response to six rhizobacteria observed diverse inducibility, where only 10 genes were significantly upregulated by at least one rhizobacterium and 9 genes did not respond to any of the rhizobacteria. Motif analysis on soybean promoters further identified not only consensus but also rhizobacterium-specific transcription factor-binding sites for the inducible chitinase genes. Collectively, these results confirmed the involvement of GmChi02 and GmChi16 in defense enhancement and highlighted the diverse inducibility of 37 soybean chitinases encountering F. oxysporum and six rhizobacteria.

Tetracycline inhibits the nitrogen fixation ability of soybean (Glycine max (L.) Merr.) nodules in black soil by altering the root and rhizosphere bacterial communities

Tetracycline is a widely used antibiotic and may thus also be an environmental contaminant with an influence on plant growth. The aim of this study was to investigate the inhibition mechanisms of tetracycline in relation to soybean growth and ecological networks in the roots and rhizosphere. To this end, we conducted a pot experiment in which soybean seedlings were grown in soil treated with 0, 10, or 25 mg/kg tetracycline. The effects of tetracycline pollution on growth, productivity, oxidative stress, and nitrogenase activity were evaluated. We further identified the changes in microbial taxa composition and structure at the genus and species levels by sequencing the 16S rRNA gene region. The results showed that tetracycline activates the antioxidant defense system in soybeans, which reduces the abundance of Bradyrhizobiaceae, inhibits the nitrogen-fixing ability, and decreases the nitrogen content in the root system. Tetracycline was also found to suppress the formation of the rhizospheric environment and decrease the complexity and stability of bacterial networks. Beta diversity analysis showed that the community structure of the root was markedly changed by the addition of tetracycline, which predominantly affected stochastic processes. These findings demonstrate that the influence of tetracycline on soybean roots could be attributed to the decreased stability of the bacterial community structure, which limits the number of rhizobium nodules and inhibits the nitrogen-fixing capacity. This exploration of the inhibitory mechanisms of tetracycline in relation to soybean root development emphasises the potential risks of tetracycline pollution to plant growth in an agricultural setting. Furthermore, this study provides a theoretical foundation from which to improve our understanding of the physiological toxicity of antibiotics in farmland.

Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron

Microorganisms living in soil maintain intricate interactions among themselves, forming the soil microbiota that influences the rhizosphere microbiome and plant growth. However, the mechanisms underlying the soil microbial interactions remain unclear. Streptomyces and Mesorhizobium are commonly found in soil and serve as plant growth-promoting rhizobacteria (PGPR). Here, we identified an unprecedented interaction between the colonies of red-soil-derived Streptomyces sp. FXJ1.4098 and Mesorhizobium sp. BAC0120 and referred to it as "proximity-based defensive mutualism (PBDM)." We found that metabolite-mediated iron competition and sharing between the two microorganisms were responsible for PBDM. Streptomyces sp. FXJ1.4098 produced a highly diffusible siderophore, desferrioxamine, which made iron unavailable to co-cultured Mesorhizobium sp. BAC0120, thereby inhibiting its growth. Streptomyces sp. FXJ1.4098 also released poorly diffusible iron-porphyrin complexes, which could be utilized by Mesorhizobium sp. BAC0120, thereby restoring the growth of nearby Mesorhizobium sp. BAC0120. Furthermore, in ternary interactions, the PBDM strategy contributed to the protection of Mesorhizobium sp. BAC0120 close to Streptomyces sp. FXJ1.4098 from other microbial competitors, resulting in the coexistence of these two PGPR. A scale-up pairwise interaction screening suggested that the PBDM strategy may be common between Mesorhizobium and red-soil-derived Streptomyces. These results demonstrate the key role of iron in complex microbial interactions and provide novel insights into the coexistence of PGPR in soil.

Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials

BACKGROUND

As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms.

RESULTS

WSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release.

CONCLUSION

All the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.

GmRj2/Rfg1 control of soybean-rhizobium-soil compatibility

Coordinated evolution and mutual adaptation of soybean-rhizobium-soil (SRS) are crucial for soybean distribution, but the genetic mechanism involved had remained unclear. In a recent study, Li et al. identified a natural variant of the GmRj2/Rfg1 gene that affected the ability of soybean to adapt to distinct soil types by controlling soybean-rhizobium interaction, thus unravelling the mystery of SRS compatibility.

Variety-Driven Effect of Rhizosphere Microbial-Specific Recruitment on Drought Tolerance of Medicago ruthenica (L.)

As one of the environmental factors that seriously affect plant growth and crop production, drought requires an efficient but environmentally neutral approach to mitigate its harm to plants. Soil microbiomes can interact with plants and soil to improve the adverse effects of drought. Medicago ruthenica (L.) is an excellent legume forage with strong drought tolerance, but the key role of microbes in fighting drought stress remains unclear. What kind of flora plays a key role? Is the recruitment of such flora related to its genotype? Therefore, we selected three varieties of M. ruthenica (L.) for drought treatment, analyzed their growth and development as well as their physiological and biochemical characteristics, and performed 16S rRNA high-throughput sequencing analysis on their rhizosphere soils to clarify the variety-mediated response of rhizosphere bacteria to drought stress. It was found that among the three varieties of M. ruthenica (L.), Mengnong No.2, Mengnong No.1 and Zhilixing were subjected to drought stress and showed a reduction in plant height increment of 24.86%, 34.37%, and 31.97% and in fresh weight of 39.19%, 50.22%, and 41.12%, respectively, whereas dry weight was reduced by 23.26%, 26.10%, and 24.49%, respectively. At the same time, we found that the rhizosphere microbial community of Mengnong No. 2 was also less affected by drought, and it was able to maintain the diversity of rhizosphere soil microflora stable after drought stress, while Mennong No. 1 and Zhilixing were affected by drought stress, resulting in a decrease in rhizosphere soil bacterial community diversity indices to 92.92% and 82.27%, respectively. Moreover, the rhizosphere of Mengnon No. 2 was enriched with more nitrogen-fixing bacteria Rhizobium than the other two varieties of M. ruthenica (L.), which made it still have a good ability to accumulate aboveground biomass after drought stress. In conclusion, this study proves that the enrichment process of bacteria is closely related to plant genotype, and different varieties enrich different types of bacteria in the rhizosphere to help them adapt to drought stress, and the respective effects are quite different. Our results provide new evidence for the study of bacteria to improve the tolerance of plants to drought stress and lay a foundation for the screening and study mechanism of drought-tolerant bacteria in the future.

Genomic and Metabolic Characterization of Plant Growth-Promoting Rhizobacteria Isolated from Nodules of Clovers Grown in Non-Farmed Soil

The rhizosphere microbiota, which includes plant growth-promoting rhizobacteria (PGPR), is essential for nutrient acquisition, protection against pathogens, and abiotic stress tolerance in plants. However, agricultural practices affect the composition and functions of microbiota, reducing their beneficial effects on plant growth and health. Among PGPR, rhizobia form mutually beneficial symbiosis with legumes. In this study, we characterized 16 clover nodule isolates from non-farmed soil to explore their plant growth-promoting (PGP) potential, hypothesizing that these bacteria may possess unique, unaltered PGP traits, compared to those affected by common agricultural practices. Biolog profiling revealed their versatile metabolic capabilities, enabling them to utilize a wide range of carbon and energy sources. All isolates were effective phosphate solubilizers, and individual strains exhibited 1-aminocyclopropane-1-carboxylate deaminase and metal ion chelation activities. Metabolically active strains showed improved performance in symbiotic interactions with plants. Comparative genomics revealed that the genomes of five nodule isolates contained a significantly enriched fraction of unique genes associated with quorum sensing and aromatic compound degradation. As the potential of PGPR in agriculture grows, we emphasize the importance of the molecular and metabolic characterization of PGP traits as a fundamental step towards their subsequent application in the field as an alternative to chemical fertilizers and supplements.

Enhancing Soybean Yield: The Synergy of Sulfur and Rhizobia Inoculation

Sulfur deficiency severely limits soybean growth, inhibiting the rhizobia nitrogenase and soybean protein synthesis. This study assessed the impact of sulfur fertilization and rhizobia inoculation on soybean growth and nitrogen fixation through bacterial culture and hydroponic experiments. We selected three rhizobia strains for bacterial cultures and used six sulfur levels. The test demonstrated severe inhibition of Rhizobium USDA110 growth without sulfur. In hydroponic experiment, we employed five sulfur levels with USDA110 as the inoculum strain. Soybean growth, nitrogen fixation, yield, and root morphology-related parameters, and root nodule growth, were significantly inhibited without sulfur. Following Rhizobium inoculation, low sulfur concentrations (0.15-0.60 mM) stimulated early-stage (V9) root growth and increased shoot nitrogen accumulation, but inhibited root growth at R5 stage. Furthermore, Rhizobium inoculation notably enhanced soybean growth, nitrogen fixation, and yield, especially within the recommended low sulfur concentration range (0.15-0.30 mM). The maximum nodule nitrogenase activity at R5 stage and highest yield was recorded at a 0.3 mM sulfur concentration with Rhizobium inoculation, which was 9.51-1222.07% higher than other treatments. These findings highlight that low sulfur concentration and rhizobia inoculation enhance soybean growth, nitrogen fixation, and yield but reduce soybean root efficacy, increasing reliance on root nodules.

Rhizosphere microbial ecological characteristics of strawberry root rot

Introduction

Strawberry (Fragaria × ananassa Duch.) holds a preeminent position among small fruits globally due to its delectable fruits and significant economic value. However, strawberry cultivation is hampered by various plant diseases, hindering the sustainable development of the strawberry industry. The occurrence of plant diseases is closely linked to imbalance in rhizosphere microbial community structure.

Methods

In the present study, a systematic analysis of the differences and correlations among non-culturable microorganisms, cultivable microbial communities, and soil nutrients in rhizosphere soil, root surface soil, and non-rhizosphere soil of healthy and diseased strawberry plants affected by root rot was conducted. The goal was to explore the relationship between strawberry root rot occurrence and rhizosphere microbial community structure.

Results

According to the results, strawberry root rot altered microbial community diversity, influenced fungal community composition in strawberry roots, reduced microbial interaction network stability, and enriched more endophytic-phytopathogenic bacteria and saprophytic bacteria. In addition, the number of bacteria isolated from the root surface soil of diseased plants was significantly higher than that of healthy plants.

Discussion

In summary, the diseased strawberry plants changed microbial community diversity, fungal species composition, and enriched functional microorganisms significantly, in addition to reshaping the microbial co-occurrence network. The results provide a theoretical basis for revealing the microecological mechanism of strawberry root rot and the ecological prevention and control of strawberry root rot from a microbial ecology perspective.

Plant growth promoting rhizobacteria induced metal and salt stress tolerance in Brassica juncea through ion homeostasis

Soil heavy metal contamination and salinity constitute a major environmental problem worldwide. The affected area and impact of these problems are increasing day by day; therefore, it is imperative to restore their potential using environmentally friendly technology. Plant growth-promoting rhizobacteria (PGPR) provides a better option in this context. Thirty-seven bacteria were isolated from the rhizosphere of maize cultivated in metal- and salt-affected soils. Some selected bacterial strains grew well under a wide range of pH (4-10), salt (5-50 g/L), and Cd (50-1000 mg/L) stress. Three bacterial strains, Exiguobacterium aestuarii (UM1), Bacillus cereus (UM8), and Bacillus megaterium (UM35), were selected because of their robust growth and high tolerance to both stress conditions. The bacterial strains UM1, UM8, and UM35 showed P-solubilization, whereas UM8 and UM35 exhibited 1-aminocyclopropane-1-carboxylate deaminase activity and indole acetic acid (IAA) production, respectively. The bacterial strains were inoculated on Brassica juncea plants cultivated in Cd and salt-affected soils due to the above PGP activities and stress tolerance. Plants inoculated with the bacterial strains B. cereus and B. megaterium significantly (p < 0.05) increased shoot fresh weight (17 ± 1.17-29 ± 0.88 g/plant), shoot dry weight (2.50 ± 0.03-4.40 ± 0.32 g/plant), root fresh weight (7.30 ± 0.58-13.30 ± 0.58 g/plant), root dry weight (0.80 ± 0.04-2.00 ± 0.01 g/plant), and shoot K contents (62.76 ± 1.80-105.40 ± 1.15 mg/kg dwt) in normal and stressful conditions. The bacterial strain B. megaterium significantly (p < 0.05) decreased shoot Na+ and Cd++ uptake in single and dual stress conditions. Both bacterial strains, E. aestuarii and B. cereus, efficiently reduced Cd++ translocation and bioaccumulation in the shoot. Bacterial inoculation improved the uptake of K+ and Ca++, while restricted Na+ and Cd++ in B. juncea shoots indicated their potential to mitigate the dual stresses of salt and Cd in B. juncea through ion homeostasis.

Peanut-based Rotation Stabilized Diazotrophic Communities and Increased Subsequent Wheat Yield

The introduction of legumes into rotations can improve nitrogen use efficiency and crop yield; however, its microbial mechanism involved remains unclear. This study aimed to explore the temporal impact of peanut introduction on microorganisms related to nitrogen metabolism in rotation systems. In this study, the dynamics of diazotrophic communities in two crop seasons and wheat yields of two rotation systems: winter wheat - summer maize (WM) and spring peanut → winter wheat - summer maize (PWM) in the North China Plain were investigated. Our results showed that peanut introduction increased wheat yield and biomass by 11.6% (p < 0.05) and 8.9%, respectively. Lower Chao1 and Shannon indexes of the diazotrophic communities were detected in soils that sampling in June compared with those sampling in September, although no difference was found between WM and PWM. Principal co-ordinates analysis (PCoA) showed that rotation system significantly changed the diazotrophic community structures (PERMANOVA; p < 0.05). Compared with WM, the genera of Azotobacter, Skermanella, Azohydromonas, Rhodomicrobium, Azospirillum, Unclassified_f_Opitutaceae, and Unclassified_f_Rhodospirillaceae were significantly enriched (p < 0.05) in PWM. Furthermore, rotation system and sampling time significantly influenced soil properties, which significantly correlated with the top 15 genera in relative abundance. Partial least squares path modeling (PLS-PM) analysis further showed that the diazotrophic community diversity (alpha- and beta-diversity) and soil properties (pH, SOC and TN) significantly affected wheat yield. In conclusion, legume inclusion has the potential to stabilize diazotrophic community structure at the temporal scales and increase subsequent crop yield.

Characterization of three new plant growth-promoting microbes and effects of the interkingdom interactions on plant growth and disease prevention

KEY MESSAGE

The novel interkingdom PGPM consortia enhanced the ability of plant growth promotion and disease resistance, which would be beneficial to improve plant growth in sustainable agriculture through engineering microbiome. Plant growth-promoting microbes (PGPMs) play important roles in promoting plant growth and bio-controlling of pathogens. Much information reveals that the plant growth-promoting ability of individual PGPM affects plant growth. However, the effects of the PGPM consortia properties on plant growth remain largely unexplored. Here, we characterized three new PGPM strains including Rhodotorula graminis JJ10.1 (termed as J), Pseudomonas psychrotolerans YY7 (termed as Y) and P. chlororaphis T8 (termed as T), and assessed their effects in combination with Bacillus amyloliquefaciens FZB42 (termed as F) on plant growth promotion and disease prevention in Arabidopsis thaliana and tomato (Solanum lycopersicum) plants by investigating morphological changes, whole-genome sequencing and plant growth promoting (PGP) characterization. Results revealed that the three new strains R. graminis JJ10.1, P. psychrotolerans YY7 and P. chlororaphis T8 had the potential for being combined with B. amyloliquefaciens FZB42 to form interkingdom PGPM consortia. The combinations of R. graminis JJ10.1, B. amyloliquefaciens FZB42, and P. psychrotolerans YY7, i. e. JF and JYF, exhibited the strongest ability of synergetic biofilm production. Furthermore, the growth-promotion abilities of the consortia were significantly enhanced compared with those of individual strains under both inoculation and volatile organic compounds (VOCs) treatment. Importantly, the consortia showed stronger abilities of in planta disease prevention than individual strains. Findings of our study may provide future guidance for engineering the minimal microbiome communities to improve plant growth and/or disease resistance in sustainable agriculture.

Synergistic N2-fixation and salt stress mitigation in soybean through dual inoculation of ACC deaminase-producing Pseudomonas and Bradyrhizobium

We investigated the potential dual application of two Bradyrhizobium strains (B. diazoefficiens USDA110 and B. ottawaense SG09) and plant growth-promoting bacteria, PGPB (Pseudomonas spp.: OFT2 and OFT5), to improve nodulation and N2-fixation in soybean plants. The growth-promoting effects of dual inoculation were observed on plant growth, physiology, and nodulation of soybean under normal conditions compared with plants individually inoculated with either USDA110 or SG09. Both OFT2 and OFT5 promoted N2-fixation by 11% and 56%, respectively, when dual inoculation with USDA110 and by 76% and 81%, respectively, when dual inoculation with SG09. Salinity stress significantly reduces soybean growth, physiology, nutrient uptake, nodulation, and N2-fixation. However, these adverse effects were attenuated by the dual inoculation of PGPB and rhizobia depending on the combination of inoculants. In particular, dual inoculation of PGPB with SG09 was more effective in enhancing the salt tolerance of soybean by reducing salt-induced ethylene production and improving nutrient uptake. However, no such effect was observed with the combined inoculation of USDA110 and OFT5. An effective symbiotic association between SG09 and two Pseudomonas bacteria can be considered a beneficial approach to improving the symbiotic efficiency of nodulation and mitigating salinity stress in soybeans.

The role of microbial interactions on rhizobial fitness

Rhizobia are soil bacteria that can establish a nitrogen-fixing symbiosis with legume plants. As horizontally transmitted symbionts, the life cycle of rhizobia includes a free-living phase in the soil and a plant-associated symbiotic phase. Throughout this life cycle, rhizobia are exposed to a myriad of other microorganisms that interact with them, modulating their fitness and symbiotic performance. In this review, we describe the diversity of interactions between rhizobia and other microorganisms that can occur in the rhizosphere, during the initiation of nodulation, and within nodules. Some of these rhizobia-microbe interactions are indirect, and occur when the presence of some microbes modifies plant physiology in a way that feeds back on rhizobial fitness. We further describe how these interactions can impose significant selective pressures on rhizobia and modify their evolutionary trajectories. More extensive investigations on the eco-evolutionary dynamics of rhizobia in complex biotic environments will likely reveal fascinating new aspects of this well-studied symbiotic interaction and provide critical knowledge for future agronomical applications.

The Effect of Different Rhizobial Symbionts on the Composition and Diversity of Rhizosphere Microorganisms of Chickpea in Different Soils

BACKGROUND

Chickpea (Cicer arietinum L.) is currently the third most important legume crop in the world. It could form root nodules with its symbiotic rhizobia in soils and perform bio-nitrogen fixation. Mesorhizobium ciceri is a prevalent species in the world, except China, where Mesorhizobium muleiense is the main species associated with chickpea. There were significant differences in the competitive ability between M. ciceri and M. muleiense in sterilized and unsterilized soils collected from Xinjiang, China, where chickpea has been grown long term. In unsterilized soils, M. muleiense was more competitive than M. ciceri, while in sterilized soils, the opposite was the case. In addition, the competitive ability of M. ciceri in soils of new areas of chickpea cultivation was significantly higher than that of M. muleiense. It was speculated that there might be some biological factors in Xinjiang soils of China that could differentially affect the competitive nodulation of these two chickpea rhizobia. To address this question, we compared the composition and diversity of microorganisms in the rhizosphere of chickpea inoculated separately with the above two rhizobial species in soils from old and new chickpea-producing regions.

RESULTS

Chickpea rhizosphere microbial diversity and composition varied in different areas and were affected significantly due to rhizobial inoculation. In general, eight dominant phyla with 34 dominant genera and 10 dominant phyla with 47 dominant genera were detected in the rhizosphere of chickpea grown in soils of Xinjiang and of the new zones, respectively, with the inoculated rhizobia. Proteobacteria and Actinobacteria were dominant at the phylum level in the rhizosphere of all soils. Pseudomonas appeared significantly enriched after inoculation with M. muleiense in soils from Xinjiang, a phenomenon not found in the new areas of chickpea cultivation, demonstrating that Pseudomonas might be the key biological factor affecting the competitive colonization of M. muleiense and M. ciceri there.

CONCLUSIONS

Different chickpea rhizobial inoculations of M. muleiense and M. ciceri affected the rhizosphere microbial composition in different sampling soils from different chickpea planting areas. Through high throughput sequencing and statistical analysis, it could be found that Pseudomonas might be the key microorganism influencing the competitive nodulation of different chickpea rhizobia in different soils, as it is the dominant non-rhizobia community in Xinjiang rhizosphere soils, but not in other areas.

Manipulating rhizosphere microorganisms to improve crop yield in saline-alkali soil: a study on soybean growth and development

Introduction

Rhizosphere microorganisms can effectively promote the stress resistance of plants, and some beneficial rhizosphere microorganisms can significantly promote the growth of crops under salt stress, which has the potential to develop special microbial fertilizers for increasing the yield of saline-alkali land and provides a low-cost and environmentally friendly new strategy for improving the crop yield of saline-alkali cultivated land by using agricultural microbial technology.

Methods

In May 2022, a field study in a completely randomized block design was conducted at the Heilongjiang Academy of Agricultural Sciences to explore the correlation between plant rhizosphere microorganisms and soybean growth in saline-alkali soil. Two soybean cultivars (Hening 531, a salt-tolerant variety, and 20_1846, a salt-sensitive variety) were planted at two experimental sites [Daqing (normal condition) and Harbin (saline-alkali conditions)], aiming to investigate the performance of soybean in saline-alkali environments.

Results

Soybeans grown in saline-alkali soil showed substantial reductions in key traits: plant height (25%), pod number (26.6%), seed yield (33%), and 100 seed weight (13%). This underscores the unsuitability of this soil type for soybean cultivation. Additionally, microbial analysis revealed 43 depleted and 56 enriched operational taxonomic units (OTUs) in the saline-alkali soil compared to normal soil. Furthermore, an analysis of ion-associated microbes identified 85 mOTUs with significant correlations with various ions. A co-occurrence network analysis revealed strong relationships between specific mOTUs and ions, such as Proteobacteria with multiple ions. In addition, the study investigated the differences in rhizosphere species between salt-tolerant and salt-sensitive soybean varieties under saline-alkali soil conditions. Redundancy analysis (RDA) indicated that mOTUs in saline-alkali soil were associated with pH and ions, while mOTUs in normal soil were correlated with Ca2+ and K+. Comparative analyses identified significant differences in mOTUs between salt-tolerant and salt-sensitive varieties under both saline-alkali and normal soil conditions. Planctomycetes, Proteobacteria, and Actinobacteria were dominant in the bacterial community of saline-alkali soil, with significant enrichment compared to normal soil. The study explored the functioning of the soybean rhizosphere key microbiome by comparing metagenomic data to four databases related to the carbon, nitrogen, phosphorus, and sulfur cycles. A total of 141 KOs (KEGG orthologues) were identified, with 66 KOs related to the carbon cycle, 16 KOs related to the nitrogen cycle, 48 KOs associated with the phosphorus cycle, and 11 KOs linked to the sulfur cycle. Significant correlations were found between specific mOTUs, functional genes, and phenotypic traits, including per mu yield (PMY), grain weight, and effective pod number per plant.

Conclusion

Overall, this study provides comprehensive insights into the structure, function, and salt-related species of soil microorganisms in saline-alkali soil and their associations with salt tolerance and soybean phenotype. The identification of key microbial species and functional categories offers valuable information for understanding the mechanisms underlying plant-microbe interactions in challenging soil conditions.

Enhanced production of select phytocannabinoids in medical Cannabis cultivars using microbial consortia

The root microbiome of medical cannabis plants has been largely unexplored due to past legal restrictions in many countries. Microbes that live on and within the tissue of Cannabis sativa L. similar to other plants, provide advantages such as stimulating plant growth, helping it absorb minerals, providing protection against pathogen attacks, and influencing the production of secondary metabolites. To gain insight into the microbial communities of C. sativa cultivars with different tetrahydrocannabinol (THC) and cannabidiol (CBD) profiles, a greenhouse trial was carried out with and without inoculants added to the growth substrate. Illumina MiSeq metabarcoding was used to analyze the root and rhizosphere microbiomes of the five cultivars. Plant biomass production showed higher levels in three of five cultivars inoculated with the arbuscular mycorrhizal fungus Rhizophagus irregularis and microbial suspension. The blossom dry weight of the cultivar THE was greater when inoculated with R. irregularis and microbial suspension than with no inoculation. Increasing plant biomass and blossom dry weight are two important parameters for producing cannabis for medical applications. In mature Cannabis, 12 phytocannabinoid compounds varied among cultivars and were affected by inoculants. Significant differences (p ≤ 0.01) in concentrations of cannabidivarinic acid (CBDVA), cannabidivarin (CBDV), cannabigerol (CBG), cannabidiol (CBD), and cannabigerolic acid (CBGA) were observed in all Cannabis cultivars when amended with F, K1, and K2 inoculants. We found microbes that were shared among cultivars. For example, Terrimicrobium sp., Actinoplanes sp., and Trichoderma reesei were shared by the cultivars ECC-EUS-THE, CCL-ECC, and EUS-THE, respectively. Actinoplanes sp. is a known species that produces phosphatase enzymes, while Trichoderma reesei is a fungal train that produces cellulase and contributes to organic matter mineralization. However, the role of Terrimicrobium sp. as an anaerobic bacterium remains unknown. This study demonstrated that the use of inoculants had an impact on the production of phytocannabinoids in five Cannabis cultivars. These inoculants could have useful applications for optimizing cannabis cultivation practices and increasing the production of phytocannabinoids.

Nodulation number tempers the relative importance of stochastic processes in the assembly of soybean root-associated communities

Identifying the ecological forces that structure root-associated microbial communities is an essential step toward more sustainable agriculture. Legumes are widely utilized as model plants to study selective forces and their functioning in plant-microbial interactions owing to their ability to establish mutualism with rhizobia. Root nodules act as symbiotic organs to optimize the cost-benefit balance in this mutualistic relationship by modulating the number of nodules. However, it is not known whether the number of nodules is related to the structure of root-associated bacterial communities. Here, the root-associated bacterial communities of soybean grown in native soil by means of soybean cultivars with super- or normal nodulation were investigated across four developmental stages. We compared ecological processes between communities and found decreased relative importance of neutral processes for super-nodulating soybean, although the overall structures resembled those of normal-nodulating soybean. We identified the generalist core bacterial populations in each root-associated compartment, that are shared across root-associated niches, and persist through developmental stages. Within core bacterial species, the relative abundances of bacterial species in the rhizosphere microbiome were linked to host-plant functional traits and can be used to predict these traits from microbes using machine learning algorithms. These findings broaden the comprehensive understanding of the ecological forces and associations of microbiotas in various root-associated compartments and provide novel insights to integrate beneficial plant microbiomes into agricultural production to enhance plant performance.

Genome Survey and Chromosome-Level Draft Genome Assembly of Glycine max var. Dongfudou 3: Insights into Genome Characteristics and Protein Deficiencies

Dongfudou 3 is a highly sought-after soybean variety due to its lack of beany flavor. To support molecular breeding efforts, we conducted a genomic survey using next-generation sequencing. We determined the genome size, complexity, and characteristics of Dongfudou 3. Furthermore, we constructed a chromosome-level draft genome and speculated on the molecular basis of protein deficiency in GmLOX1, GmLOX2, and GmLOX3. These findings set the stage for high-quality genome analysis using third-generation sequencing. The estimated genome size is approximately 1.07 Gb, with repetitive sequences accounting for 72.50%. The genome is homozygous and devoid of microbial contamination. The draft genome consists of 916.00 Mb anchored onto 20 chromosomes, with annotations of 46,446 genes and 77,391 transcripts, achieving Benchmarking Single-Copy Orthologue (BUSCO) completeness of 99.5% for genome completeness and 99.1% for annotation. Deletions and substitutions were identified in the three GmLox genes, and they also lack corresponding active proteins. Our proposed approach, involving k-mer analysis after filtering out organellar DNA sequences, is applicable to genome surveys of all plant species, allowing for accurate assessments of size and complexity. Moreover, the process of constructing chromosome-level draft genomes using closely related reference genomes offers cost-effective access to valuable information, maximizing data utilization.

Enhance of tomato production and induction of changes on the organic profile mediated by Rhizobium biofortification

Introduction

The extensive use of chemical fertilizers has served as a response to the increasing need for crop production in recent decades. While it addresses the demand for food, it has resulted in a decline in crop productivity and a heightened negative environmental impact. In contrast, plant probiotic bacteria (PPB) offer a promising alternative to mitigate the negative consequences of chemical fertilizers. PPB can enhance nutrient availability, promote plant growth, and improve nutrient uptake efficiency, thereby reducing the reliance on chemical fertilizers.

Methods

This study aimed to evaluate the impact of native Rhizobium strains, specifically Rhizobium calliandrae LBP2-1, Rhizobium mayense NSJP1-1, and Rhizobium jaguaris SJP1- 2, on the growth, quality, and rhizobacterial community of tomato crops. Various mechanisms promoting plant growth were investigated, including phosphate solubilization, siderophore production, indole acetic acid synthesis, and cellulose and cellulase production. Additionally, the study involved the assessment of biofilm formation and root colonization by GFP-tagged strains, conducted a microcosm experiment, and analyzed the microbial community using metagenomics of rhizospheric soil.

Results

The results showed that the rhizobial strains LBP2-1, NSJP1-1 and SJP1-2 had the ability to solubilize dicalcium phosphate, produce siderophores, synthesize indole acetic acid, cellulose production, biofilm production, and root colonization. Inoculation of tomato plants with native Rhizobium strains influenced growth, fruit quality, and plant microbiome composition. Metagenomic analysis showed increased Proteobacteria abundance and altered alpha diversity indices, indicating changes in rhizospheric bacterial community.

Discussion

Our findings demonstrate the potential that native Rhizobium strains have to be used as a plant probiotic in agricultural crops for the generation of safe food and high nutritional value.

From salty to thriving: plant growth promoting bacteria as nature's allies in overcoming salinity stress in plants

Soil salinity is one of the main problems that affects global crop yield. Researchers have attempted to alleviate the effects of salt stress on plant growth using a variety of approaches, including genetic modification of salt-tolerant plants, screening the higher salt-tolerant genotypes, and the inoculation of beneficial plant microbiome, such as plant growth-promoting bacteria (PGPB). PGPB mainly exists in the rhizosphere soil, plant tissues and on the surfaces of leaves or stems, and can promote plant growth and increase plant tolerance to abiotic stress. Many halophytes recruit salt-resistant microorganisms, and therefore endophytic bacteria isolated from halophytes can help enhance plant stress responses. Beneficial plant-microbe interactions are widespread in nature, and microbial communities provide an opportunity to understand these beneficial interactions. In this study, we provide a brief overview of the current state of plant microbiomes and give particular emphasis on its influence factors and discuss various mechanisms used by PGPB in alleviating salt stress for plants. Then, we also describe the relationship between bacterial Type VI secretion system and plant growth promotion.

Natural variation of GmRj2/Rfg1 determines symbiont differentiation in soybean

Symbiotic nitrogen fixation (SNF) provides much of the N utilized by leguminous plants throughout growth and development. Legumes may simultaneously establish symbiosis with different taxa of microbial symbionts. Yet, the mechanisms used to steer associations toward symbionts that are most propitious across variations in soil types remain mysterious. Here, we demonstrate that GmRj2/Rfg1 is responsible for regulating symbiosis with multiple taxa of soybean symbionts. In our experiments, the GmRj2/Rfg1SC haplotype favored association with Bradyrhizobia, which is mostly distributed in acid soils, whereas the GmRj2/Rfg1HH haplotype and knockout mutants of GmRj2/Rfg1SC associated equally with Bradyrhizobia and Sinorhizobium. Association between GmRj2/Rfg1 and NopP, furthermore, appeared to be involved in symbiont selection. Furthermore, geographic distribution analysis of 1,821 soybean accessions showed that GmRj2/Rfg1SC haplotypes were enriched in acidic soils where Bradyrhizobia were the dominant symbionts, whereas GmRj2/Rfg1HH haplotypes were most prevalent in alkaline soils dominated by Sinorhizobium, and neutral soils harbored no apparent predilections toward either haplotype. Taken together, our results suggest that GmRj2/Rfg1 regulates symbiosis with different symbionts and is a strong determinant of soybean adaptability across soil regions. As a consequence, the manipulation of the GmRj2/Rfg1 genotype or application of suitable symbionts according to the haplotype at the GmRj2/Rfg1 locus might be suitable strategies to explore for increasing soybean yield through the management of SNF.

Diversity and regulation of symbiotic nitrogen fixation in plants

Plants associate with nitrogen-fixing bacteria to secure nitrogen, which is generally the most limiting nutrient for plant growth. Endosymbiotic nitrogen-fixing associations are widespread among diverse plant lineages, ranging from microalgae to angiosperms, and are primarily one of three types: cyanobacterial, actinorhizal or rhizobial. The large overlap in the signaling pathways and infection components of arbuscular mycorrhizal, actinorhizal and rhizobial symbioses reflects their evolutionary relatedness. These beneficial associations are influenced by environmental factors and other microorganisms in the rhizosphere. In this review, we summarize the diversity of nitrogen-fixing symbioses, key signal transduction pathways and colonization mechanisms relevant to such interactions, and compare and contrast these interactions with arbuscular mycorrhizal associations from an evolutionary standpoint. Additionally, we highlight recent studies on environmental factors regulating nitrogen-fixing symbioses to provide insights into the adaptation of symbiotic plants to complex environments.

Prevalence, attachment ability and strength of the biological control agent Bacillus thuringiensis on tomato

Bacillus thuringiensis (Bt) is commonly used as a biological control agent (BCA) to control insect pests in edible plant production and can as such be introduced into the food chain of fresh produce. Using standard food diagnostics Bt will be detected and reported as presumptive B. cereus. Tomato plants are often sprayed with Bt biopesticides for insect control, thus these Bt BCAs can also reach the tomato fruits and persist until consumption. In this study, vine tomatoes from the retail in Belgium (Flanders) were investigated for the occurrence and residual numbers of presumptive B. cereus and Bt. Of 109 tomato samples, 61 (56%) were tested positive for presumptive B. cereus. Of the presumptive B. cereus isolates (n = 213) recovered from these samples, 98% were identified as Bt by the production of parasporal crystals. Further quantitative real-time PCR assays on a subselection of Bt isolates (n = 61) showed that 95% of Bt isolates were indistinguishable from Bt biopesticide strains that are approved to be used on crops in the EU. Furthermore, the attachment strength of tested Bt biopesticide strains showed easier wash-off properties if using the commercial Bt granule formulation than the unformulated lab-cultured Bt or B. cereus spore suspensions.

Evaluation of Legume-Rhizobial Symbiotic Interactions Beyond Nitrogen Fixation That Help the Host Survival and Diversification in Hostile Environments

Plants often experience unfavorable conditions during their life cycle that impact their growth and sometimes their survival. A temporary phase of such stress, which can result from heavy metals, drought, salinity, or extremes of temperature or pH, can cause mild to enormous damage to the plant depending on its duration and intensity. Besides environmental stress, plants are the target of many microbial pathogens, causing diseases of varying severity. In plants that harbor mutualistic bacteria, stress can affect the symbiotic interaction and its outcome. To achieve the full potential of a symbiotic relationship between the host and rhizobia, it is important that the host plant maintains good growth characteristics and stay healthy under challenging environmental conditions. The host plant cannot provide good accommodation for the symbiont if it is infested with diseases and prone to other predators. Because the bacterium relies on metabolites for survival and multiplication, it is in its best interests to keep the host plant as stress-free as possible and to keep the supply stable. Although plants have developed many mitigation strategies to cope with stress, the symbiotic bacterium has developed the capability to augment the plant's defense mechanisms against environmental stress. They also provide the host with protection against certain diseases. The protective features of rhizobial-host interaction along with nitrogen fixation appear to have played a significant role in legume diversification. When considering a legume-rhizobial symbiosis, extra benefits to the host are sometimes overlooked in favor of the symbionts' nitrogen fixation efficiency. This review examines all of those additional considerations of a symbiotic interaction that enable the host to withstand a wide range of stresses, enabling plant survival under hostile regimes. In addition, the review focuses on the rhizosphere microbiome, which has emerged as a strong pillar of evolutionary reserve to equip the symbiotic interaction in the interests of both the rhizobia and host. The evaluation would draw the researchers' attention to the symbiotic relationship as being advantageous to the host plant as a whole and the role it plays in the plant's adaptation to unfavorable environmental conditions.

The dynamics and transmission of antibiotic resistance associated with plant microbiomes

Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.

Long-term fertilization coupled with rhizobium inoculation promotes soybean yield and alters soil bacterial community composition

Microbial diversity is an important indicator of soil fertility and plays an indispensable role in farmland ecosystem sustainability. The short-term effects of fertilization and rhizobium inoculation on soil microbial diversity and community structure have been explored extensively; however, few studies have evaluated their long-term effects. Here, we applied quantitative polymerase chain reaction (qPCR) and amplicon sequencing to characterize the effect of 10-year fertilizer and rhizobium inoculation on bacterial communities in soybean bulk and rhizosphere soils at the flowering-podding and maturity stages. Four treatments were examined: non-fertilization control (CK), phosphorus and potassium fertilization (PK), nitrogen and PK fertilization (PK + N), and PK fertilization and Bradyrhizobium japonicum 5821 (PK + R). Long-term co-application of rhizobium and PK promoted soybean nodule dry weight by 33.94% compared with PK + N, and increased soybean yield by average of 32.25%, 5.90%, and 5.00% compared with CK, PK, and PK + N, respectively. The pH of PK + R was significantly higher than that of PK and PK + N at the flowering-podding stage. The bacterial abundance at the flowering-podding stage was positively correlated with soybean yield, but not at the maturity stage. The significant different class Gemmatimonadetes, and the genera Gemmatimonas, and Ellin6067 in soil at the flowering-podding stage were negatively correlated with soybean yield. However, the bacterial community at class and genus levels at maturity had no significant effect on soybean yield. The key bacterial communities that determine soybean yield were concentrated in the flowering-podding stage, not at maturity stage. Rhizosphere effect, growth period, and treatment synergies resulted in significant differences in soil bacterial community composition. Soil organic matter (OM), total nitrogen (TN), pH, and available phosphorus (AP) were the main variables affecting bacterial community structure. Overall, long-term co-application of rhizobium and fertilizer not only increased soybean yield, but also altered soil bacterial community structure through niche reconstruction and microbial interaction. Rhizobium inoculation plays key role in reducing nitrogen fertilizer application and promoting sustainable agriculture practices.

Rhizosphere Microbiota Promotes the Growth of Soybeans in a Saline-Alkali Environment under Plastic Film Mulching

The rhizosphere microbiota plays a critical and crucial role in plant health and growth, assisting plants in resisting adverse stresses, including soil salinity. Plastic film mulching is an important method to adjust soil properties and improve crop yield, especially in saline-alkali soil. However, it remains unclear whether and to what extent the association between these improvements and rhizosphere microbiota exists. Here, from a field survey and a greenhouse mesocosm experiment, we found that mulching plastic films on saline-alkali soil can promote the growth of soybeans in the field. Results of the greenhouse experiment showed that soybeans grew better in unsterilized saline-alkali soil than in sterilized saline-alkali soil under plastic film mulching. By detecting the variations in soil properties and analyzing the high-throughput sequencing data, we found that with the effect of film mulching, soil moisture content was effectively maintained, soil salinity was obviously reduced, and rhizosphere bacterial and fungal communities were significantly changed. Ulteriorly, correlation analysis methods were applied. The optimization of soil properties ameliorated the survival conditions of soil microbes and promoted the increase in relative abundance of potential beneficial microorganisms, contributing to the growth of soybeans. Furthermore, the classification of potential key rhizosphere microbial OTUs were identified. In summary, our study suggests the important influence of soil properties as drivers on the alteration of rhizosphere microbial communities and indicates the important role of rhizosphere microbiota in promoting plant performance in saline-alkali soil under plastic film mulching.

Linking plant functional genes to rhizosphere microbes: a review

The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.

The positive effects of mineral-solubilizing microbial inoculants on asymbiotic nitrogen fixation of abandoned mine soils are driven by keystone phylotype

Toward the restoration of the increasing numbers of abandoned mines across China, external-soil spray seeding technologies have become more extensively utilized. However, considerable challenges remain that seriously hamper the effectiveness of these technologies, such as inadequate nutrient availability for plants. Previous studies have shown that mineral-solubilizing microbial inoculants can increase the nodules of legumes. However, their effects on symbiotic nitrogen fixation (SNF), asymbiotic nitrogen fixation (ANF), and diazotrophic communities remain unknown. Further, research into the application of functional microorganisms for the restoration of abandoned mines has been conducted either in greenhouses, or their application in the field has been too brief. Thus, we established a four-year field experiment in an abandoned mine and quantified the SNF, ANF, and diazotrophic communities. To the best of our knowledge, this study is the first to describe the long-term application of specific functional microorganisms for the remediation of abandoned mine sites in the field. We revealed that mineral-solubilizing microbial inoculants significantly increased the soil ANF rate and SNF content. There was no significant correlation between the diazotrophic alpha diversity and soil ANF rate; however, there were strong positive associations between the relative abundance and biodiversity of keystone phylotype (module #5) within ecological clusters and the ANF rate. Molecular ecological networks indicated that microbial inoculants increased network complexity and stability. Moreover, the inoculants significantly enhanced the deterministic ratio of diazotrophic communities. Furthermore, homogeneous selection predominantly mediated the assembly of soil diazotrophic communities. It was concluded that mineral-solubilizing microorganisms played a critical role in maintaining and enhancing nitrogen, which offers a new solution with great potential for the restoration of ecosystems at abandoned mine sites.

Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage

BACKGROUND

Plants sustain intimate relationships with diverse microbes. It is well-recognized that these plant-associated microbiota shape individual performance and fitness of host plants, but much remains to be explored regarding how they exert their function and maintain their homeostasis.

RESULTS

Here, using pink lady (Heterotis rotundifolia) as a study plant, we investigated the phenomenon of microbiota-mediated nitrogen fixation and elucidated how this process is steadily maintained in the root mucilage microhabitat. Metabolite and microbiota profiling showed that the aerial root mucilage is enriched in carbohydrates and diazotrophic bacteria. Nitrogen isotope-labeling experiments, ¹⁵N natural abundance, and gene expression analysis indicated that the aerial root-mucilage microbiota could fix atmospheric nitrogen to support plant growth. While the aerial root mucilage is a hotspot of nutrients, we did not observe high abundance of other environmental and pathogenic microbes inside. We further identified a fungus isolate in mucilage that has shown broad-spectrum antimicrobial activities, but solely allows the growth of diazotrophic bacteria. This "friendly" fungus may be the key driver to maintain nitrogen fixation function in the mucilage microhabitat. Video Abstract CONCLUSION: The discovery of new biological function and mucilage-habitat friendly fungi provides insights into microbial homeostasis maintenance of microenvironmental function and rhizosphere ecology.

The evolutionary ecology of rhizobia: multiple facets of competition before, during, and after symbiosis with legumes

Rhizobial bacteria have complex lifestyles that involve growth and survival in bulk soil, plant rhizospheres and rhizoplanes, legume infection threads, and mature and senescing legume nodules. In nature, rhizobia coexist and compete with many other rhizobial strains and species to form host associations. We review recent work defining competitive interactions across these environments. We highlight the use of sophisticated measurement tools and sequencing technologies to examine competition mechanisms in planta, and highlight environments (e.g. soil and senescing nodules) where we still know exceedingly little. We argue that moving toward an explicitly ecological framework (types of competition, resources, and genetic differentiation) will clarify the evolutionary ecology of these foundational organisms and open doors for engineering sustainable, beneficial associations with hosts.

Microbial community dynamics responding to nutrient allocation associated with soybean cultivar 'Jake' ozone adaptation

Tropospheric ozone (O₃), a major air pollutant, leads to significant global yield loss in soybean [Glycine max (L.) Merr.]. Soybean cultivar 'Jake' shows O₃ resilient traits in above-ground organs, but the root system remains sensitive to elevated O₃ (eO₃). Changing carbon (C) and nitrogen (N) resource composition during eO₃ stress suggests that eO₃ presumably alters belowground soil microbial communities and their driven nutrient transformation. Yet, the responses of belowground microbes to eO₃ and their feedback on nutrient cycling in 'Jake' are unknown. In this study, we holistically investigated soil microbial communities associated with C and N dynamics and bacterial-fungal inter-kingdom networks in the rhizosphere and bulk soil at different developmental stages of 'Jake' grown under sub-ambient O₃ [charcoal-filtered (CF) air, 12 h mean: 20 ppb] or eO₃ (12 h mean: 87 ppb). The results demonstrated eO₃ significantly decreased fungal diversity and complexity of microbial networks at different 'Jake' developmental stages, whereas bacterial diversity was more tolerant to eO₃ in both bulk soil and rhizosphere. In the bulk soil, no O₃-responsive microbial biomarkers were found to be associated with C and N content, implying eO₃ may stimulate niche-based processes during 'Jake' growth. In contrast, this study identified O₃-responsive microbial biomarkers that may contribute to the N acquisition (Chloroflexales) and C dynamics (Caldilineales, Thermomicrobiales, and Hypocreales) in the rhizosphere, which may support the O₃ resilience of the 'Jake' cultivar. However, further investigation is required to confirm their specific contributions by determining changes in microbial gene expression. Overall, these findings conduce to an expanding knowledge base that O₃ induces temporal and spatial changes in the effects of microbial and nutrient networks in the O₃-tolerant agriculture ecosystems.

Plant and Native Microorganisms Amplify the Positive Effects of Microbial Inoculant

Microbial inoculants can be used to restore abandoned mines because of their positive effects on plant growth and soil nutrients. Currently, soils in greenhouse pot studies are routinely sterilized to eradicate microorganisms, allowing for better inoculant colonization. Large-scale field sterilization of abandoned mining site soils for restoration is difficult, though. In addition, microbial inoculants have an impact on plants. Plants also have an impact on local microbes. The interactions among microbial inoculants, native microorganisms, and plants, however, have not been studied. We created a pot experiment utilizing the soil and microbial inoculant from a previous experiment because it promoted plant growth in that experiment. To evaluate the effects of the plants, native microorganisms, and microbial inoculants, we assessed several indicators related to soil elemental cycling and integrated them into the soil multifunctionality index. The addition of the microbial inoculant and sterilizing treatment had a significant impact on alfalfa growth. When exposed to microbial inoculant treatments, the plant and sterilization treatments displayed radically different functional characteristics, where most of the unsterilized plant treatment indices were higher than those of the others. The addition of microbial inoculant significantly increased soil multifunctionality in plant treatments, particularly in the unsterilized plant treatment, where the increase in soil multifunctionality was 260%. The effect size result shows that the positive effect of microbial inoculant on soil multifunctionality and unsterilized plant treatment had the most significant promotion effect. Plant and native microorganisms amplify the positive effects of microbial inoculant.

Soybean rhizosphere microorganisms alleviate Mo nanomaterials induced stress by improving soil microbial community structure

With the wide application of nanomaterials (NMs) in agriculture, it is particularly important to assess the impact of these NMs on soil microorganisms. In this study, different varieties of soybean rhizosphere microorganisms (RM) were employed to simulate the alleviate effect of molybdenum nanoparticles (Mo NPs) induced stress in presence of soybean plants. Mo NPs caused serious toxic effects on soybean growth and nitrogen fixation at a concentration of 100 mg kg^-1: plant height and biomass were reduced by 56.4% and 82.8%, respectively, and the ability to fix nitrogen was almostly lost. However, after adding different varieties of soybean RM (RM-Williams 82, RM-Youchun 1204, and RM-Zhongdou 41), the stress caused by high concentrations of Mo NPs on soybean plants was significantly reduced. The plant height, root length, biomass, and nitrogen fixation ability were improved by 70.8%, 80.7%, 145.8%, and 349.8%, respectively, following the addition of soybean RM-Williams 82. High-throughput sequencing revealed that Mo NPs treatment affected the microbial community structure. Among them, Flavisolibacter and Caulobacter genera abundance increased significantly, which might be the key factor in relieving Mo NPs-induced stress on soybean growth. These findings suggest a novel mode of RM as a promising strategy to prevent deleterious effects of stress with NPs on plants in the future.

Impact of sterilization and chemical fertilizer on the microbiota of oil palm seedlings

Soil nutrients and microbiota are known as essential components for healthy plant growth and crop productivity. However, limited studies have been conducted on the importance of soil microbiota in the early growth of oil palm seedlings (Elaeis guineensis Jacq.) under the influence of nitrogen, phosphorus and potassium (NPK) compound fertilizer (nitrogen, phosphorus, and potassium). In this study, we analyzed the root microbial community associated with seedlings grown under normal and sterilized soil conditions to ascertain the microbial strains potentially associated with soil, plant health and chemical fertilizer efficiency. Oil palm seedlings were grown under four treatments: (i) fertilized normal soil (+FN), (ii) unfertilized normal soil (-FN), (iii) fertilized sterilized soil (+FS) and (iv) unfertilized sterilized soil (-FS). Our findings revealed that chemical fertilizer promoted the growth of the copiotrophs Pseudomonadota and Bacteroidota in the control +FN, which are known to degrade complex polysaccharides. After autoclaving, the soil macronutrient content did not change, but soil sterilization reduced microbial diversity in the +FS and -FS treatments and altered the soil microbiota composition. Sterilized soil with a depleted microbial population adversely affected crop growth, which was exacerbated by fertilizer use. In the rhizosphere and rhizoplane compartments, a total of 412 and 868 amplicon sequence variances (ASVs) were found depleted in the +FS and -FS treatments, respectively. Several genera were identified in the ASVs with diminished abundance, including Humibacter, Microbacterium, Mycobacterium, 1921-2, HSB OF53-F07, Mucilaginibacter, Bacillus, Paenibacillus, and several unclassified genera, suggesting their possible roles in promoting the plant growth of oil palm seedlings. Soil sterilization might remove these beneficial microbes from the bulk soil pool, affecting the colonization ability in the rhizocompartments as well as their role in nutrient transformation. Therefore, this study provides useful insights concerning the benefits of a soil microbiome survey before making fertilizer recommendations.

Comparative study of symbiotic activity of legumes when using Risotorphin and Epin-extra

In a vegetation experiment with soybean plants of the Svapa and Mageva varieties and in a field experiment with bean plants of the Geliada and Shokoladnitsa varieties, we studied the effect of pre-sowing treatment of the seeds of these plants with Rizotorfin and Epin-extra on the nitrogenase activity of the nodules of these plants and their ultrastructure. Analysis of the ultrastructure of the nodule tissue of beans and soybeans was carried out in the flowering phase. It was found that the highest indices of the mass and number of nodules and the activity of nitrogenase in them were found in bean plants of the Heliada cultivar when the seeds were treated with Epin-extra against the background of inoculation with Rizotorfin, where the largest area of symbiosomes, volutin and their number was noted in the nodules. Beans of the Shokoladnitsa variety showed the protective effect of Rizotorfin. In the nodules of soybean plants of the Svapa variety, the seeds of which were treated with Epin-extra against the background of inoculation with Rizotorfin, the presence of a large number of symbiosomes, bacteroids, volutin inclusions with a larger area and a minimum number of inclusions of poly-β-hydroxybutyric acid (PHB) was noted, and the highest indicators of symbiotic activity. Soybean plants of the Mageva variety showed the protective effect of Rizotorfin. The efficiency of the symbiotic system was determined by the number and weight of nodules and the activity of the nitrogenase enzyme.

Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions

Bio-organic fertilizers (BOF) containing both organic amendments and beneficial microorganisms have been consistently shown to improve soils fertility and yield. However, the exact mechanisms which link amendments and yields remain disputed, and the complexity of bio-organic fertilizers may work in parallel in several ways. BOF may directly improve yield by replenishing soil nutrients or introducing beneficial microbial genes or indirectly by altering the soil microbiome to enrich native beneficial microorganisms. In this work, we aim to disentangle the relative contributions of direct and indirect effects on pear yield. We treated pear trees with either chemical fertilizer or organic fertilizer with/without the plant-beneficial bacterium Bacillus velezensis SQR9. We then assessed, in detail, soil physicochemical and biological properties (metagenome sequencing) as well as pear yield. We then evaluated the relative importance of direct and indirect effects of soil amendments on pear yield. Both organic treatments increased plant yield by up to 20%, with the addition of bacteria tripling the increase driven by organic fertilizer alone. This increase could be linked to alterations in soil physicochemical properties, bacterial community function, and metabolism. Supplementation of organic fertilizer SQR9 increased rhizosphere microbiome richness and functional diversity. Fertilizer-sensitive microbes and functions responded as whole guilds. Pear yield was most positively associated with the Mitsuaria- and Actinoplanes-dominated ecological clusters and with gene clusters involved in ion transport and secondary metabolite biosynthesis. Together, these results suggested that bio-organic fertilizers mainly act indirectly on plant yield by creating soil chemical properties which promote a plant-beneficial microbiome. IMPORTANCE Bio-organic fertilization is a widely used, eco-friendly, sustainable approach to increasing plant productivity in the agriculture and fruit industries. However, it remains unclear whether the promotion of fruit productivity is related to specific changes in microbial inoculants, the resident microbiome, and/or the physicochemical properties of rhizosphere soils. We found that bio-organic fertilizers alter soil chemical properties, thus manipulating specific microbial taxa and functions within the rhizosphere microbiome of pear plants to promote yield. Our work unveils the ecological mechanisms which underlie the beneficial impacts of bio-organic fertilizers on yield promotion in fruit orchards, which may help in the design of more efficient biofertilizers to promote sustainable fruit production.