Soil beneficial bacteria and their role in plant growth promotion: a review

Combining plant growth-promoting bacteria as a tool to improve the metabolism and productivity of sugarcane

Sugarcane (Saccharum spp.) is a globally important crop, and strategies to minimize the negative impacts of its cultivation and enhance its development are highly relevant. Plant growth-promoting bacteria (PGPB) can sustainably foster plant growth in agricultural systems and mitigate adverse effects of stress on plants. This is the first study to investigate the combined use of Azospirillum brasilense (Ab) and Nitrospirillum amazonense (Na), two microorganisms widely applied in agricultural systems, aiming to elucidate their effects on the nutritional status, biochemical responses, and productive parameters of sugarcane. Greenhouse experiments were conducted under controlled water and temperature conditions with four treatments: application of Ab, Na, or Ab + Na (Mix) or no PGPB application (control). Sugarcane was cultivated until the middle of the rapid growth stage. To validate the results, the greenhouse trials were replicated under field conditions at two sites (Maracaí-SP and Pradópolis-SP). The results showed that the inoculation of sugarcane with plant growth-promoting bacteria (PGPB), particularly Ab and Mix, enhanced nutritional aspects, especially N content. These increases were significant under greenhouse (p ≤ 0.05) and field conditions (p ≤ 0.10). Additionally, inoculation reduced oxidative stress and improved photosynthetic parameters, such as net photosynthetic rate, water use efficiency, and carboxylation efficiency. These cascading effects contributed to significant gains in crop productivity, with an average increase in stalk yield of 10.9 % for Ab and 12.2 % for Mix across both environments. Similarly, there was an increase in sugar yield per hectare, with gains of 13.3 % for Ab and 13.7 % for Mix compared to the control. These findings highlight the potential of PGPB as a sustainable strategy to enhance crop productivity and resilience, contributing to environmentally balanced agricultural systems. Although the benefits of PGPB were evident, differences between Ab and Mix were not pronounced. Therefore, additional studies are needed to explore the potential of these combinations under adverse conditions, when their effects could be more pronounced.

Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns

Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.

PGPB-driven bioenrichment and metabolic modulation of Salicornia europaea under marine Aquaponic conditions

This study analyzed the secondary metabolite profile of Salicornia europaea inoculated with Brevibacterium casei EB3 and Pseudomonas oryzihabitans RL18 in aquaponic systems, exploring the metabolic mechanisms responsible for the observed shifts. Experiments were conducted in both microcosm and pilot-scale aquaponic setups to evaluate how these metabolic shifts vary across different system scales and their potential contributions to the observed increased accumulation of bioactive compounds with antioxidant and antimicrobial properties, including some phenolic acids, such as caffeic acid (154-fold), flavonoids (2.85-fold), and some unsaturated fatty acids, such as oct-3-enoic acid (32-fold). Metabolic profiling revealed shifts in pathways associated with plant growth and stress resilience, such as amino acid and phenolic biosynthesis. Additionally, differences in metabolic responses observed between microcosm and pilot-scale systems underscored the importance of understanding scaling effects. These findings highlight the potential for optimizing aquaponic systems by leveraging microbial-plant interactions to enhance ecological and economic outcomes. This approach offers valuable applications in nutrient recycling, phytopharmaceutical development, and the advancement of saline agriculture within integrated aquaculture frameworks.

Unlocking the potential of ecofriendly guardians for biological control of plant diseases, crop protection and production in sustainable agriculture

Several beneficial microbial strains inhibit the growth of different phytopathogens and commercialized worldwide as biocontrol agents (BCAs) for plant disease management. These BCAs employ different strategies for growth inhibition of pathogens, which includes production of antibiotics, siderophores, lytic enzymes, bacteriocins, hydrogen cyanide, volatile organic compounds, biosurfactants and induction of systemic resistance. The efficacy of antagonistic strains could be further improved through genetic engineering for better disease suppression in sustainable farming practices. Some antagonistic microbial strains also possess plant-growth-promoting activities and their inoculation improved plant growth in addition to disease suppression. This review discusses the characterization of antagonistic microbes and their antimicrobial metabolites, and the application of these BCAs for disease control. The present review also provides a comprehensive summary of the genetic organization and regulation of the biosynthesis of different antimicrobial metabolites in antagonistic strains. Use of molecular engineering to improve production of metabolites in BCAs and their efficacy in disease control is also discussed. The application of these biopesticides will reduce use of conventional pesticides in disease control and help in achieving sustainable and eco-friendly agricultural systems.

Fluroxypyr Inhibits Maize Growth by Disturbing the Diversity of the Endophytic Bacterial Communities in Maize Roots

Fluroxypyr (4-amino-3,5-dichloro-6-fluoro-2-pyridyloxyacetic acid) is a widely used herbicide sprayed on crops worldwide. The effects of fluroxypyr on maize growth and the soil microbial community structure have not been reported. In this study, the impacts of fluroxypyr on maize growth and the bacterial community structure in endophytes and rhizospheric/non-rhizospheric soils were evaluated. We found that the community structures of the non-rhizospheric and rhizospheric soils were similar. The alpha diversity showed that the richness of the endophytic communities in the mature maize roots was reduced after herbicide application. No statistically significant differences were observed between the fluroxypyr-treated and control soils in either the non-rhizospheric or rhizospheric soils. However, the composition of the endophytic bacterial community structure suggested that fluroxypyr led to a 59.1% reduction in the abundance of Acinetobacter and a 75.6% reduction in Agrobacterium, both of which are considered growth-promoting bacteria. In addition, we observed a negative effect of fluroxypyr on maize growth, including a decreased ear length and root size and a reduction in the 100-grain weight. In summary, our study suggests that fluroxypyr may negatively impact the mature growth of maize by reducing the abundance of Bacillus kineticus and Agrobacterium tumefaciens in the endophytic community of the mature root system.

Exploring the structure and assembly of seagrass microbial communities in rhizosphere and phyllosphere

Microbial community assembly and interactions are pivotal research areas within microbial ecology, yet relevant studies in seagrass rhizospheres and phyllosphere remain relatively scarce. In this study, we utilized high-throughput sequencing technology to investigate the microbial communities in different periods and microhabitats (rhizosphere and phyllosphere) of two seagrass species (Zostera marina and Phyllospadix iwatensis). Our findings suggest that microhabitats have a more pronounced impact on the composition of seagrass-associated microbial communities compared to periods and species. Further investigations reveal that the phyllosphere microbial community exhibits a more intricate co-occurrence network and interactions than the rhizosphere microbial community. Keystone taxa show distinct functional roles in different microhabitats of seagrasses. Additionally, we observed that differences in seagrass microhabitats influence community assembly, with the rhizosphere microbial community being more influenced by deterministic processes (heterogeneous selection) compared to the phyllosphere. These findings contribute to our understanding of the intricate interactions between seagrasses and their associated microbial communities, providing valuable insights into their distribution patterns and microhabitat preferences.IMPORTANCEStudying the community structure and assembly of different microhabitats in seagrass beds contributes to revealing the complexity and dynamic processes of seagrass ecosystems. In the rhizosphere microhabitat of seagrasses, microbial communities may assist in disease resistance or enhance nutrient uptake efficiency in seagrasses. On the other hand, in the microhabitat on the surface of seagrass blades, microorganisms may be closely associated with the physiological functions and nutrient cycling of seagrass blades. Therefore, understanding the structure and assembly mechanisms of rhizosphere and phyllosphere microbial communities is crucial for exploring the interactions between seagrass and microbial communities, as well as for enhancing our comprehension of the stability and resilience of seagrass bed ecosystems.

Soil characteristics and bacterial community characteristics of shelterbelts of different tree species in black soil region of China

To understand how surface soil characteristics and bacterial communities are affected by the establishment of farmland shelterbelts. Five types of shelterbelts in the mid-west of Heilongjiang Province China were selected for the study. The physicochemical characteristics and bacterial diversity of Populus×xiaohei monoculture (X), Larix gmelinii monoculture (L), Pinus sylvestris monoculture (Z), Pinus sylvestris and Larix gmelinii mixed forest (ZL), and Fraxinus mandshurica and Larix gmelinii mixed forest (SL), as well as in fallow land (CK), were measured and analyzed, respectively. Soil physicochemical characteristics and bacterial diversity (via high-throughput sequencing) were analyzed across 0-20 cm depths. Results showed that shelterbelts significantly altered soil characteristics: X increased moisture, ammonium nitrogen, and microbial biomass nitrogen but reduced aeration. ZL exhibited the highest bacterial richness and enhanced water-holding capacity, aeration, and nutrient retention (total organic carbon, nitrogen, phosphorus). ZL outperformed monocultures in promoting soil health, with available potassium (0-10 cm) and pH (10-20 cm) identified as key drivers of bacterial community variation. Unique genera like Krasilnikovia and Rubrobacter dominated shelterbelt soils, reflecting species-specific effects. Shelterbelts induced surface accumulation of nitrate-nitrogen, potassium, and microbial biomass carbon. Overall, Pinus sylvestris and Larix gmelinii mixed forests optimized soil structure, microbial diversity, and nutrient cycling, underscoring their ecological benefits for sustainable agroforestry. This study highlights the critical role of mixed forest shelterbelts in enhancing soil health and microbial biodiversity, which are essential for sustainable land management practices in the black soil region of China.

Although invisible, fungi are recognized as the engines of a microbial powerhouse that drives soil ecosystem services

Soil ecosystem services (SES) are the benefits that humans derive from soil. These services emerge from the complex interactions between biotic and abiotic processes within soil systems. They are vital for maintaining ecosystem resilience and ensuring long-term sustainability. Soil hosts a diverse group of biota, among them fungi play a crucial role in supporting and enhancing SES due to their remarkable adaptability and ability to thrive under unfavorable conditions. This review explores the multifaceted roles of fungi in SES, emphasizing their growing importance in strengthening ecosystem resilience and climate change adaptation. Fungi significantly contribute to the key ecosystem processes such as soil aggregation, organic matter (OM) decomposition, nutrients cycling, plant productivity, and carbon (C) sequestration. However, potential threats to fungal abundance and diversity could undermine these critical functions, highlighting the need for proactive measures to preserve fungal communities. The pivotal role of fungi in SES, including agricultural production and climate regulation, tailor them as indispensable microbial engines that shape and maintain ecosystem resilience. Emerging evidence suggests that soil fungal communities may become increasingly prominent under the future climate scenarios. Thus, understanding how fungal functional roles evolve in response to climate change is emergent for safeguarding SES and ensuring environmental sustainability. Furthermore, the co-occurrance of fungi with other soil organisms in supporting SES highlights the need to integrate diverse soil biota alongside fungi to promote sustainable SES. Collaborative efforts to comprehend and manage soil microbial communities are imperative for maintaining the long-term ecological stability of ecosystems.

Early and high-throughput plant diagnostics: strategies for disease detection

The rising global occurrence of plant pathogens highlights the need for a thorough reassessment of current disease detection and management schemes. To that end, we review the utility and limitations of the available sensing platforms deployed for phytodiagnostics in the field. We also discuss recent advances in the use of broad-spectrum biomarkers such as phytohormones and volatile organic compounds (VOCs), and assess the feasibility of deploying these platforms on a large scale. Because these platforms are often complementary, we propose a compressed sensing approach that combines several sensing platforms to manage plant pathogens while minimizing additional costs. Finally, we provide an outlook for the potential benefits of integrating new sensing technologies into farming for timely interventions.

Flavobacterium plantiphilum sp. nov., Flavobacterium rhizophilum sp. nov., Flavobacterium rhizosphaerae sp. nov., Chryseobacterium terrae sp. nov., and Sphingomonas plantiphila sp. nov. isolated from salty soil showing plant growth promoting potential

Members of the genera Flavobacterium, Chryseobacterium and Sphingomonas constitute a group of microorganisms in the rhizosphere associated with plant growth promoting (PGP) features. A polyphasic approach was employed to ascertain the taxonomic status of five selected strains. Overall genome relatedness indices of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genera Flavobacterium, Chryseobacterium and Sphingomonas were found to be below the established thresholds, respectively. Morphological, physiological, and biochemical characteristics of the strains confirmed their status as five novel species. A large variety of genes involved in plant growth promotion and carbohydrate utilization were found in all strains suggesting a contribution of all strains to PGP. Based on the result of the polyphasic characterization, the following names are proposed: Chryseobacterium terrae sp. nov., with the strain ST-37T as the type strain (= CCM 9260T = LMG 32728T); Flavobacterium plantiphilum sp. nov., with the strain ST-87T as the type strain CIP 112180T = DSM 114790T = LMG 32757T); Flavobacterium rhizophilum sp. nov., with the strain ST-75T as the type strain (= CIP 112185T = DSM 114831T = LMG 32758T); Flavobacterium rhizosphaerae sp. nov., with the strain ST-119T as the type strain (CIP 112181T = DSM 114832T = LMG 32756T); and Sphingomonas plantiphila sp. nov. with the strain ST-64 T as the type strain (= CCM 9261T = CIP 112178T = DSM 114515T = LMG 32729T).

The effect of global change on the expression and evolution of floral traits

BACKGROUND

Pollinators impose strong selection on floral traits, but other abiotic and biotic agents also drive the evolution of floral traits and influence plant reproduction. Global change is expected to have widespread effects on biotic and abiotic systems, resulting in novel selection on floral traits in future conditions.

SCOPE

Global change has depressed pollinator abundance and altered abiotic conditions, thereby exposing flowering plant species to novel suites of selective pressures. Here, we consider how biotic and abiotic factors interact to shape the expression and evolution of floral characteristics (the targets of selection), including floral size, colour, physiology, reward quantity and quality, and longevity, amongst other traits. We examine cases in which selection imposed by climatic factors conflicts with pollinator-mediated selection. Additionally, we explore how floral traits respond to environmental changes through phenotypic plasticity and how that can alter plant fecundity. Throughout this review, we evaluate how global change might shift the expression and evolution of floral phenotypes.

CONCLUSIONS

Floral traits evolve in response to multiple interacting agents of selection. Different agents can sometimes exert conflicting selection. For example, pollinators often prefer large flowers, but drought stress can favour the evolution of smaller flowers, and the size of floral organs can evolve as a trade-off between selection mediated by these opposing actors. Nevertheless, few studies have manipulated abiotic and biotic agents of selection factorially to disentangle their relative strengths and directions of selection. The literature has more often evaluated plastic responses of floral traits to stressors than it has considered how abiotic factors alter selection on these traits. Global change will likely alter the selective landscape through changes in the abundance and community composition of mutualists and antagonists and novel abiotic conditions. We encourage future work to consider the effects of abiotic and biotic agents of selection on floral evolution, which will enable more robust predictions about floral evolution and plant reproduction as global change progresses.

Synthetic Microbial Communities Enhance Pepper Growth and Root Morphology by Regulating Rhizosphere Microbial Communities

Synthetic microbial community (SynCom) application is efficient in promoting crop yield and soil health. However, few studies have been conducted to enhance pepper growth via modulating rhizosphere microbial communities by SynCom application. This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper growth by modulating the rhizosphere microbiome using high-throughput sequencing technology. SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper by 20.9%, 36.33%, 68.84%, 64.34%, 29.65%, 27.78%, 117.42%, 35.4%, 21.52%, and 39.76%, respectively, relative to the control. The Chao index of the rhizosphere microbial community and Bray-Curtis dissimilarity of the fungal community significantly increased, while Bray-Curtis dissimilarity of the bacterial community significantly decreased by SynCom inoculation. The abundances of key taxa such as Scedosporium, Sordariomycetes, Pseudarthrobacter, norankSBR1031, and norankA4b significantly increased with SynCom inoculation, and positively correlated with indices of pepper growth. Our findings suggest that SynCom inoculation can effectively enhance pepper growth and regulate root morphology by regulating rhizosphere microbial communities and increasing key taxa abundance like Sordariomycetes and Pseudarthrobacter, thereby benefiting nutrient acquisition, resistance improvement, and pathogen resistance of crops to ensure sustainability.

Field Reduction of Ectomycorrhizal Fungi Has Cascading Effects on Soil Microbial Communities and Reduces the Abundance of Ectomycorrhizal Symbiotic Bacteria

Specific interactions between bacteria and ectomycorrhizal fungi (EcMF) can benefit plant health, and saprotrophic soil fungi represent a potentially antagonistic guild to these mutualisms. Yet there is little field-derived experimental evidence showing how the relationship among these three organismal groups manifests across time. To bridge this knowledge gap, we experimentally reduced EcMF in forest soils and monitored both bacterial and fungal soil communities over the course of a year. Our analyses demonstrate that soil trenching shifts the community composition of fungal communities towards a greater abundance of taxa with saprotrophic traits, and this shift is linked to a decrease in both EcMF and a common ectomycorrhizal helper bacterial genus, Burkholderia, in a time-dependent manner. These results not only reveal the temporal nature of a widespread tripartite symbiosis between bacteria, EcMF and a shared host tree, but they also refine our understanding of the commonly referenced 'Gadgil effect' by illustrating the cascading effects of EcMF suppression and implicating soil saprotrophic fungi as potential antagonists on bacterial-EcMF interactions.

Impact of microbial-based biopreparations on soil quality, plant health, and fruit chemistry in raspberry cultivation

Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.

Structural and functional analysis of rhizospheric bacterial diversity in the Pranmati basin, Himalayan critical zone observatory

The study explores the structural and functional dynamics of rhizospheric bacterial diversity in the Pranmati basin, focusing on their ecological significance, diversity, and functional roles across dominant vegetation types; Rhododendron arboreum, Myrica esculenta, and Quercus leucotrichophora. The research provides critical insights into soil health and ecosystem functioning by analysing rhizospheric soil properties among the selected vegetations. The research findings reveal that Myrica esculenta exhibits the highest root colonization (95.8%) and moisture content (92.6%), while Quercus leucotrichophora shows the lowest (76.2% and 83.2%), respectively. The microbial community is predominantly composed of Proteobacteria, with 62-65% abundance across different vegetation types. Key genera such as Bacillus, Acinetobacter, and Paenibacillus are notably enriched, highlighting their significant role in phosphate solubilization and nutrient cycling. Venn diagram analysis identified 136 common bacterial species among vegetation types reflecting ecological significance in forest ecosystem. The functional metabolism, diversity indices, and core microbiome analysis underscore the distinct microbial profiles associated with different vegetation types, which are crucial for overall forest soil health. The importance of this research lies in its contribution to environmental management by providing a comprehensive understanding of how microbial communities interact with various vegetation types and influence soil health in the Pranmati basin. These insights are essential for developing targeted strategies to enhance soil fertility and manage forest ecosystems in terms of conservation and restoration efforts in sensitive ecological regions. This study is pioneer as it establishes a functional analysis of rhizospheric bacterial diversity in the Pranmati basin, offering a baseline data for future research on bacterial community structure and their functional role in Himalayan Critical Zone Observatory to the best of our knowledge.

Opportunities and challenges of using human excreta-derived fertilizers in agriculture: A review of suitability, environmental impact and societal acceptance

Human excreta-derived fertilizers (HEDFs) are organic fertilizers made from human excreta sources such as urine and feces. HEDFs can contribute to a sustainable and circular agriculture by reuse of valuable nutrients that would otherwise be discarded. However, HEDFs may contain contaminants such as pharmaceuticals, persistent organic compounds, heavy metals and pathogens which can negatively affect plant, water and soil quality. Moreover, consumer prejudice, farmer hesitance and strict regulations can discourage utilization of HEDFs. Here, we conducted a thorough review of published literature to explore the opportunities and challenges of using HEDFs in agricultural systems by evaluating the suitability of human excreta as a nutrient source, their typical contaminant composition, how they affect the quality of crops, soils and water and their societal impact and acceptance. We found that HEDFs are suitable nutrient-rich fertilizers, but may contain contaminants. Processing treatments increase the fertilizer quality by reducing these contaminants, but they do not remove all contaminants completely. Regarding the environmental impacts of these fertilizers, we found overall positive effects on crop yield, soil nutrients, plant-soil-microbe interactions and plant pathogen suppression. The use of HEDFs reduces water contamination from sewage waste dumping, but nutrient leaching dependent on soil type may still affect water quality. We found no increased risks with human pathogens compared to inorganic fertilizers but identified processing treatment as well as crop and soil type significantly affect these risks. Lastly, we found that public acceptance is possible with clear regulations and outreach to inform consumers and farmers of their multi-faceted benefits and safe usage after processing treatments. In summary, this review emphasizes the great potential of HEDFs and its positive impacts on society, especially in regions where conventional fertilizers are scarce, while also stressing the need for adaptation to specific soils and crops.

Mechanisms and Impact of Rhizosphere Microbial Metabolites on Crop Health, Traits, Functional Components: A Comprehensive Review

Current agricultural practices face numerous challenges, including declining soil fertility and heavy reliance on chemical inputs. Rhizosphere microbial metabolites have emerged as promising agents for enhancing crop health and yield in a sustainable manner. These metabolites, including phytohormones, antibiotics, and volatile organic compounds, play critical roles in promoting plant growth, boosting resistance to pathogens, and improving resilience to environmental stresses. This review comprehensively outlines the mechanisms through which rhizosphere microbial metabolites influence crop health, traits, functional components, and yield. It also discusses the potential applications of microbial secondary metabolites in biofertilizers and highlights the challenges associated with their production and practical use. Measures to overcome these challenges are proposed, alongside an exploration of the future development of the functional fertilizer industry. The findings presented here provide a scientific basis for utilizing rhizosphere microbial metabolites to enhance agricultural sustainability, offering new strategies for future crop management. Integrating these microbial strategies could lead to increased crop productivity, improved quality, and reduced dependence on synthetic chemical inputs, thereby supporting a more environmentally friendly and resilient agricultural system.

Characterization and bioefficacy of grapevine bacterial endophytes against Colletotrichum gloeosporioides causing anthracnose disease

Introduction

Grapevine (Vitis vinifera L.), one of the economically important fruit crops cultivated worldwide, harbours diverse endophytic bacteria (EBs) responsible for managing various fungal diseases. Anthracnose (Colletotrichum gloeosporioides) (Penz.) is one of the major constraints in quality grape production and therefore its management is a major concern among the grape growers.

Materials and methods

Among the 50 EBs isolated from healthy leaf segments from the eight grapevine genotypes, biologically potential 20 EBs were purified and identified based on morphological, and biological characteristics and sequence analysis of 16S rRNA region. The antagonistic activities of EBs against Colletotrichum gloeosporioides were studied in vitro conditions.

Results

The colony morphologies of EBs are white and yellow-coloured colonies, circular to irregular in shape, and entire, and flat margins. Among the 20 purified EBs, 19 isolates were found to be Gram-positive except one i.e., MS2 isolate. The 12 isolates reduced nitrate and 14 isolates produced urease enzyme. The in vitro assay revealed that two isolates, SB4 and RF1, inhibited 56.1% and 55.6% mycelial growth of C. gloeosporioides, respectively. Further, the identity of EBs was confirmed through PCR amplification of the 16S rRNA region resulting in ~1400 bp size amplicons. The sequence analysis of representative 15 isolates revealed that 5 EB isolates viz., SB5, CS2, RG1, RF1, C1 were identified as Bacillus subtilis with >99% sequence identity, two EBs viz., SB3, and CS1 were identified as B. subtilis subsp. subtilis, two EBs viz., SB1, and CS4 were identified as B. licheniformis. The SB2 isolate was identified as Bacillus sp., whereas SB4 as Brevibacillus borstelensis, TH1 as B. velezensis, TH2 as B. tequilensis, CS3 as B. pumilus and MS1 as Micrococcus luteus were identified.

Conclusion

The phylogenetic analysis of 16S rRNA sequence revealed eight distinct clades and showed the close clustering of identified species with the reference species retrieved from NCBI GenBank. The current investigation provides the scope for further field evaluations of these endophytic microbes for managing anthracnose disease.

Emissions of volatile organic compounds from aboveground and belowground parts of rapeseed (Brassica napus L.) and tomato (Solanum lycopersicum L.)

Root systems represent a source of Volatile Organic Compounds (VOCs) that may significantly contribute to the atmospheric VOC emissions from agroecosystems and shape soil microbial activity. To gain deeper insights into the role of roots in the VOC emissions from crops, we developed a dynamic chamber with isolated aboveground and belowground compartments, allowing for simultaneous measurements of VOC fluxes from both compartments in controlled conditions. We continuously monitored VOC emissions from intact plants of rapeseed (Brassica napus L.) and tomato (Solanum lycopersicum L.) i) over 24 h when plants were rooted in soil, and ii) over 6 h following soil removal. The measurements were performed using a highly sensitive Proton Transfer Reaction - Time of Flight - Mass Spectrometer and a Thermic Desorption- Gas Chromatography - Mass Spectrometer. Net VOC emissions measured at the soil surface represented <5 % of the aboveground emissions and were higher during the day than at night. However, when soil was removed, belowground VOC emissions became up to two times higher than aboveground emissions. This large increase in VOC emissions from roots observed after soil removal was almost exclusively due to methanol emissions. Differences in VOC composition between plant species were also detected with and without soil: rapeseed emitted more sulphurous and nitrogenous compounds and tomato more mono- and poly-unsaturated hydrocarbons. Our results suggest that roots may be a largely underestimated VOC source and that the soil is a strong sink for root-borne methanol. Root VOC emissions should be considered when agricultural practices involve roots excavation.

Bacterial and fungal root endophytes alter survival, growth, and resistance to grazing in a foundation plant species

Plants host an array of microbial symbionts, including both bacterial and fungal endophytes located within their roots. While bacterial and fungal endophytes independently alter host plant growth, response to stress and susceptibility to disease, their combined effects on host plants are poorly studied. To tease apart interactions between co-occurring endophytes on plant growth, morphology, physiology, and survival we conducted a greenhouse experiment. Different genotypes of Spartina alterniflora, a foundational salt marsh species, were inoculated with one bacterial endophyte, Kosakonia oryzae, one fungal endophyte, Magnaporthales sp., or co-inoculated. Within the greenhouse, an unplanned herbivory event occurred which allowed insight into the ways bacteria, fungi, and co-inoculation of both endophytic microbes alters plant defense chemicals and changes herbivory. Broadly, the individual inoculation of the bacterial endophyte increased survival, whereas the fungal endophyte increased plant growth traits. Following the herbivory event, the proportion of stems grazed was reduced when plants were inoculated with the individual endophytes and further reduced when both endophytes were present. Across genotypes, anti-herbivore defense chemicals varied by individual and co-inoculation of endophytes. Bacterial inoculation and genotype interactively affected above:below-ground biomass and S. alterniflora survival of ungrazed plants. Overall, our results highlight the variable outcomes of endophyte inoculation on Spartina growth, morphology, phenolics, and survival. This study furthers our understanding of the combined effects of symbionts and plant multitrophic interactions. Further, exploring intra and inter specific effects of plant--microbe symbiosis may be key in better predicting ecosystem level outcomes, particularly in response to global change.

Disclosing the key role of Fe/As/Cu in community co-occurrence and microbial recruitment in metallurgical ruins

Mining activities have led to the persistent presence of substantial heavy metals at metallurgical sites. However, the impact of long-term and complex heavy metal pollution in metallurgical ruins on the structure and spatial shift of microbiome remains unclear. In this study, we focused on various types of metallurgical sites to uncover the occurrence of heavy metals in abandoned mines and the response patterns of microbial communities. The results indicate that mining activities have caused severe exceedances of multiple heavy metals, with AsBio, CuBio, and FeBio being the primary factors affecting community structure and function. Co-occurrence network analyses suggest that several genera, including Ellin6515, Cupriavidus, Acidobacteria genus RB41, Vicinamibacteraceae, Blastococcus, and Sphingomonas, may play significant roles in the synergistic metabolism of communities responding to Fe-Cu-As stress. Although random dispersal contributed to community migration, null models emphasized that variable selection predominates in the spatial turnover of community composition. Additionally, metagenomic prediction (PICRUSt2) identified key genes involved in stress and detoxification strategies of heavy metals. The composite heavy metal stress strengthened the relationship between network structure and the potential function of the community, along with critical ecosystem functions. Our findings demonstrated that microbial interactions were crucial for ecosystem management and the ecological consequences of heavy metal pollution remediation.

Exploration of a multifunctional biocontrol agent Streptomyces sp. JCK-8055 for the management of apple fire blight

Apple fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple and pear trees. Biological control methods have attracted much attention from researchers to manage plant diseases as they are eco-friendly and viable alternatives to synthetic pesticides. Herein, we isolated Streptomyces sp. JCK-8055 from the root of pepper and investigated its mechanisms of action against E. amylovora. Streptomyces sp. JCK-8055 produced aureothricin and thiolutin, which antagonistically affect E. amylovora. JCK-8055 and its two active metabolites have a broad-spectrum in vitro activity against various phytopathogenic bacteria and fungi. They also effectively suppressed tomato bacterial wilt and apple fire blight in in vivo experiments. Interestingly, JCK-8055 colonizes roots as a tomato seed coating and induces apple leaf shedding at the abscission zone, ultimately halting the growth of pathogenic bacteria. Additionally, JCK-8055 can produce the plant growth regulation hormone indole-3-acetic acid (IAA) and hydrolytic enzymes, including protease, gelatinase, and cellulase. JCK-8055 treatment also triggered the expression of salicylate (SA) and jasmonate (JA) signaling pathway marker genes, such as PR1, PR2, and PR3. Overall, our findings demonstrate that Streptomyces sp. JCK-8055 can control a wide range of plant diseases, particularly apple fire blight, through a combination of mechanisms such as antibiosis and induced resistance, highlighting its excellent potential as a biocontrol agent. KEY POINTS: • JCK-8055 produces the systemic antimicrobial metabolites, aureothricin, and thiolutin. • JCK-8055 treatment upregulates PR gene expression in apple plants against E. amylovora. • JCK-8055 controls plant diseases with antibiotics and induced resistance.

Fertilizer reduction and biochar amendment promote soil mineral-associated organic carbon, bacterial activity, and enzyme activity in a jasmine garden in southeast China

Reducing chemical fertilizers and biochar amendment is essential for achieving carbon neutrality, addressing global warming, and promoting sustainable agricultural development. Biochar amendment, a carbon rich soil additive produced through biomass pyrolysis, enhances soil fertility, increases crop yield, and improves soil carbon storage. However, research on the combined effect of fertilizer reduction and biochar amendment on soil mineral associated organic carbon (MAOC) in jasmine gardens is limited. This study aims to determine if biochar can reduce industrial fertilizer usage without compromising soil quality. This study focuses on jasmine cultivation in southeastern China, employing four treatments: conventional fertilization (CK), biochar amendment without fertilizer (BA), fertilizer reduction (FR), and fertilizer reduction with biochar amendment (FRBA). The effects on MAOC, microbial abundance, and enzyme activity were investigated. The FRBA treatment significantly increased MAOC content by 19.98 % compared to CK (P < 0.05). The BA and FRBA treatments enhanced the diversity of soil bacteria, including Lactobacillus, Azospirillum, and Cutibacterium, which are associated with soil organic carbon sequestration and nutrient decomposition. The RandomForest model identified β-N-acetyl-glucosaminidase (NAG), electric conductivity (EC), β-1, 4-Glucosidase (BG), soil potential of Hydrogen (pH), soil bulk density (BD), and β-D-cellobiosidase (CBH) as key soil traits promoting MAOC accumulation (P < 0.05). The results indicate that BA and FRBA improve soil bacterial community structure, enzyme activity, and MAOC content, promoting soil carbon accumulation through environmental factors and dominant bacteria. This study encourages future fertilization protocols that enhance fertilizer efficiency and carbon storage in crop soils.

Root inoculation with soil-borne microorganisms alters gut bacterial communities and performance of the leaf-chewer Spodoptera exigua

Soil-borne microorganisms can impact leaf-chewing insect fitness by modifying plant nutrition and defence. Whether the altered insect performance is linked to changes in microbial partners of caterpillars remains unclear. We investigated the effects of root inoculation with soil bacteria or fungi on the gut bacterial community and biomass of the folivore Spodoptera exigua. We also explored the potential correlation between both parameters. We performed herbivory bioassay using leaves of tomato plants (Solanum lycopersicum), measured caterpillar weight gain and characterized the gut bacterial communities via 16S rRNA gene metabarcoding. All soil microbes modified the gut bacterial communities, but the extent of these changes depended on the inoculated species. Rhizophagus irregularis and Bacillus amyloliquefaciens had opposite effects on S. exigua weight. While plant inoculation with the fungus influenced gut bacterial diversity, B. amyloliquefaciens also affected the community composition. A reduced abundance of two S. exigua enterococcal symbionts correlated with decreased insect biomass. Our results show that soil microorganisms can induce plant-mediated changes in the gut bacterial community of foliar-feeding caterpillars. We propose that the impact of these alterations on insect performance might rely on specific adaptations within the gut bacteria, rather than solely on the occurrence of changes.

Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple

A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.

Correlation Analysis of Soil Microbial Communities and Physicochemical Properties with Growth Characteristics of Sageretia thea Across Different Habitats

This study aimed to investigate the growth characteristics of Sageretia thea and analyze the correlations between soil physicochemical properties and microbial communities in its native habitats. Soil physicochemical properties were characterized by organic matter (0.37-36.43%), available phosphate (57.96-315.90 mg/kg), potassium (0.11-1.17 cmol+kg-1), calcium (1.23-25.97 cmol+kg-1), magnesium (0.43-15.01 cmol+kg-1), sodium (0.04-6.16 cmol+kg-1), and pH (4.68-7.05), indicating slightly acidic to neutral conditions. S. thea exhibited variable growth characteristics across habitats; leaf length and width were largest in Jangnam-ri and Hacka-ri, respectively, whereas Docheong-ri promoted higher fruit growth. The soil microbial community composition was dominated by Proteobacteria, Actinobacteria, and Acidobacteria at the phylum level (76.09%) and by Alphaproteobacteria, Actinobacteria_c, and Vicinamibacter_c at the class level (40%). Soil physicochemical properties were significantly correlated with Actinobacteria, Acidobacteria, and Chloroflexi at the phylum level, and all microbial groups except Spartobacteria at the class level. Furthermore, growth characteristics were significantly correlated with all microbial communities except Acidobacteria and Firmicutes at the phylum level, and Acidobacteria, Thermoleophilia, and Rubrobacteria at the class level. These findings provide a foundation for developing efficient cultivation techniques for S. thea based on its soil microbiome and habitat conditions.

Effects of intercropping with legume forage on the rhizosphere microbial community structure of tea plants

Context

Intercropping in agriculture is crucial for addressing challenges in intensive tea farming. Forage legumes reduce fertilizer dependence and significantly boost productivity. Currently, intercropping with legumes enhances the environmental conditions of tea plantations and improves tea quality.

Objective

However, the comprehension of the rhizosphere's impact on the associated microbes and the community structure of tea plants is still somewhat constrained.

Methods

Hence, four distinct planting methodologies were examined: Monoculture cultivation of Tieguanyin tea plants (MT), Laredo forage soybean (Glycine max Linn.) without partitioning in conjunction with tea (IT), intercropping with tea using plastic partitions (PPIT), and intercropping with tea facilitated by net partitions (NPIT). An absolute quantitative analysis of soil phospholipid fatty acids, labeled with the rhizosphere microbial characteristics of tea plants, was conducted through multi-ion reaction monitoring (MRM). The bacterial and fungal communities were anticipated utilizing the FAPROTAX and FUNG databases, respectively. Gas chromatography was employed to ascertain greenhouse gas emissions across diverse root interaction cultivation systems.

Results and conclusion

The rhizospheric influence culminated in a 44.6% increase in total phospholipid fatty acids (PLFAs) and a remarkable 100.9% escalation in the ratio of unsaturated to saturated fatty acids. This rhizospheric enhancement has significantly potentiated the ecological functionalities within the bacterial community, including xylanolysis, ureolysis, nitrogen respiration, nitrogen fixation, nitrite respiration, nitrite ammonification, and nitrate reduction. Mycorrhizomonas, encompassing both ectomycorrhizal and arbuscular forms, has notably colonized the rhizosphere. The interspecific mutualistic interactions within the rhizosphere have resulted in a significant enhancement of plant growth-promoting bacteria, including allorhizobium, bradyrhizobium, rhizobium, burkholderia, gluconacetobacter, and gluconobacter, while concurrently reducing the prevalence of pathogenic microorganisms such as xanthomonas, ralstonia, fusarium, and opportunistic fungi responsible for white and soft rot. The intercropping system showed lower total greenhouse gas emissions than monocultured tea plants, particularly reducing soil CO2 emissions due to complex interspecific rhizosphere interactions. This tea/legume intercropping approach promotes a sustainable ecosystem, enhancing microbial biomass and vitality, which helps suppress rhizospheric pathogens.

Significance

These findings are instrumental in enhancing our comprehension of the pivotal practical implications of rhizosphere intercropping, thereby optimizing the structure of rhizosphere communities and alleviating the impact of greenhouse gases within croplands.

Compost mediates the recruitment of core bacterial communities in alfalfa roots to enhance their productivity potential in saline-sodic soils

Introduction

Composting is one of the effective environmental protection and sustainable measures for improving soil quality and increasing crop yield. However, due to the special physical and chemical properties of saline-sodic soil and the complex rhizosphere microecological environment, the potential mechanism of regulating plant growth after applying compost in saline-sodic soil remains elusive.

Methods

Here, we investigated the effects of different compost addition rates (0, 5, 15, 25%) on plant growth traits, soil chemical properties, and rhizosphere bacterial community structure.

Results

The results showed that compost promoted the accumulation of plant biomass and root growth, increased soil nutrients, and enhanced the diversity and complexity of the rhizosphere bacterial communities. Moreover, the enriched core bacterial ASVs (Amplicon Sequence Variants) in compost treatment could be reshaped, mainly including dominant genera, such as Pseudomonas, Devosia, Novosphingobium, Flavobacterium, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. The functions of these ASVs were energy resources and nitrogen cycle functions, suggesting the roles of these ASVs in improving plant root nutrient resource acquisition for alfalfa growth. The contents of available potassium, available phosphorus, total nitrogen, and organic carbon of the soil surrounding the roots, the root length, root surface area, root volume, and root tips affected the abundance of the core bacterial ASVs, and the soil chemical properties contributed more to the effect of plant biomass.

Discussion

Overall, our study strengthens the understanding of the potentially important taxa structure and function of plant rhizosphere bacteria communities, and provides an important reference for developing agricultural microbiome engineering techniques to improve root nutrient uptake and increase plant productivity in saline-sodic soils.

Swimming Modes of Bacteria Escaping from a Soft Confined Space

Navigating through soft and highly confined environments is crucial for bacteria moving within living organisms' tissues, yet this topic has been less explored. In our study, we experimentally harnessed the unique biconcave geometry of red blood cells (RBCs) to enable real-time visualization of swimming Escherichia coli interacting with soft RBCs. Our findings show that RBCs adhering to a rigid surface can enclose spaces comparable to the size of bacteria, effectively entrapping them. Remarkably, we found that bacteria can escape from this extremely confined space through three newly defined escape modes: Bundling, Unbundling, and Flipping, each mode relying on the specific states of bacterial flagella. A quantitative analysis uncovers significant differences among these modes in terms of scattering angle, escaping speed, and trapping duration. We used two methods to alter the rigidity and adhesion strength of RBCs, and we studied their effects on the detailed bacterial escape process. Our results contribute to the knowledge of bacterial migration in soft, confined spaces, thereby enhancing our understanding of similar processes in biological tissue environments.

Arsenic-induced enhancement of diazotrophic recruitment and nitrogen fixation in Pteris vittata rhizosphere

Heavy metal contamination poses an escalating global challenge to soil ecosystems, with hyperaccumulators playing a crucial role in environmental remediation and resource recovery. The enrichment of diazotrophs and resulting nitrogen accumulation promoted hyperaccumulator growth and facilitated phytoremediation. Nonetheless, the regulatory mechanism of hyperaccumulator biological nitrogen fixation has remained elusive. Here, we report the mechanism by which arsenic regulates biological nitrogen fixation in the arsenic-hyperaccumulator Pteris vittata. Field investigations and greenhouse experiments, based on multi-omics approaches, reveal that elevated arsenic stress induces an enrichment of key diazotrophs, enhances plant nitrogen acquisition, and thus improves plant growth. Metabolomic analysis and microfluidic experiments further demonstrate that the upregulation of specific root metabolites plays a crucial role in recruiting key diazotrophic bacteria. These findings highlight the pivotal role of nitrogen-acquisition mechanisms in the arsenic hyperaccumulation of Pteris vittata, and provide valuable insights into the plant stress resistance.

Enhancing Photosynthetic Carbon Transport in Rice Plant Optimizes Rhizosphere Bacterial Community in Saline Soil

Saline soils exert persistent salt stress on plants that inhibits their ability to carry out photosynthesis and leads to photosynthetic carbon (C) scarcity in plant roots and the rhizosphere. However, it remains unclear how a rhizosphere environment is shaped by photosynthetic C partitioning under saline conditions. Given that sucrose is the primary form of photosynthetic C transport, we, respectively, created sucrose transport distorted (STD) and enhanced (STE) rice lines through targeted mutation and overexpression of the sucrose transporter gene OsSUT5. This approach allowed us to investigate different scenarios of photosynthate partitioning to the rhizosphere. Compared to the non-saline soil, we found a significant decrease in soil dissolved organic carbon (DOC) in the rhizosphere, associated with a reduction in bacterial diversity when rice plants were grown under moderate saline conditions. These phenomena were sharpened with STD plants but were largely alleviated in the rhizosphere of STE plants, in which the rhizosphere DOC, and the diversity and abundances of dominant bacterial phyla were measured at comparable levels to the wildtype plants under non-saline conditions. The complexity of bacteria showed a greater level in the rhizosphere of STE plants grown under saline conditions. Several salt-tolerant genera, such as Halobacteroidaceae and Zixibacteria, were found to colonize the rhizosphere of STE plants that could contribute to improved rice growth under persistent saline stresses, due to an increase in C deposition.

Exploring Plant-Bacterial Symbiosis for Eco-Friendly Agriculture and Enhanced Resilience

This review explores the intricate relationship between plants and bacterial endophytes, revealing their multifaceted roles in promoting plant growth, resilience, and defense mechanisms. By selectively shaping their microbiome, plants harness diverse endophytic bacterial strains to enhance nutrient absorption, regulate hormones, mitigate damage, and contribute to overall plant health. The review underscores the potential of bacterial endophytes in self-sustaining agricultural systems, offering solutions to reduce reliance on fertilizers and pesticides. Additionally, the review highlights the importance of endophytes in enhancing plant tolerance to various environmental stresses, such as drought, salinity, extreme temperatures, and heavy metal toxicity. The review emphasizes the significance of understanding and harnessing the mutualistic relationship between plants and endophytes for maximizing agricultural yields and promoting sustainable farming practices.

Evaluation and identification of metabolites produced by Cytobacillus firmus in the interaction with Arabidopsis thaliana plants and their effect on Solanum lycopersicum

Currently, the use of bio-inputs is increasing due to the need to reduce the use of agrochemicals. However, one of the limitations is to preserve the viability of the living microorganisms, so it is important to find an alternative that allows us to obtain different metabolites to produce it. We evaluated three different interactions (contact, diffusible and volatile compounds) in vitro in Arabidopsis thaliana (At) seedlings with the strain Cytobacillus firmus M10 and its filtered secondary metabolites (M10F). The results showed that the seedlings inoculated by contact with the filtrate (AtM10F) presented increases in root length (30 %) and leaf area (33 %), as well as in the volatile interaction (At/M10F) with respect to the uninoculated treatment. For both interactions, the seedlings inoculated with the bacteria by contact (AtM10) and volatile (At/M10) obtained greater biomass (48 and 57 %). Subsequently, an evaluation at the end of the A. thaliana cycle showed that the treatments obtained by contact and distance when reinoculated with the bacteria and the filtrate (AtM10, At-M10 and AtM10F) obtained 50 % more seed yield than the control treatment, while AtM10F presented 72 %, while At/M10F presented the highest no. of siliques and seeds, which increased the yield by 65 %. In the Solanum lycopersicum (Sl) experiment, the filtrate (SlM10F) showed significant differences in seedling height, leaf length and width (23, 24 and 36 %, respectively). It also promoted an increase in fresh and dry weight, producing a greater root area and larger leaves compared to the control (Sl) and the bacteria (SlM10). We performed a qualitative characterization of the secondary metabolites present in the filtrate, where we found 2,4-DTBP, sylvopinol, isophthaladehyde, and eicosane of interest with possible growth-promoting effects on A. thaliana and tomato. We identified volatile compounds present in plant-microorganism and plant-filtrate interactions as possible precursors in the induction of plant growth, among which phenols, alcohols, aldehydes, alkanes, and alkenes stand out. Most of the analyzed compounds have not been found in the literature with reports of growth promoters, is important to mention that due to their characteristic functional groups they can derive and trigger the synthesis of new molecules with agronomic application.

Microbes in Agriculture: Prospects and Constraints to Their Wider Adoption and Utilization in Nutrient-Poor Environments

Microbes such as bacteria and fungi play important roles in nutrient cycling in soils, often leading to the bioavailability of metabolically important mineral elements such as nitrogen (N), phosphorus (P), iron (Fe), and zinc (Zn). Examples of microbes with beneficial traits for plant growth promotion include mycorrhizal fungi, associative diazotrophs, and the N2-fixing rhizobia belonging to the α, β and γ class of Proteobacteria. Mycorrhizal fungi generally contribute to increasing the surface area of soil-root interface for optimum nutrient uptake by plants. However, when transformed into bacteroids inside root nodules, rhizobia also convert N2 gas in air into ammonia for use by the bacteria and their host plant. Thus, nodulated legumes can meet a high proportion of their N requirements from N2 fixation. The percentage of legume N derived from atmospheric N2 fixation varies with crop species and genotype, with reported values ranging from 50-97%, 24-67%, 66-86% 27-92%, 50-92%, and 40-75% for soybean (Gycine max), groundnut (Arachis hypogea), mung bean (Vigna radiata), pigeon pea (Cajanus cajan), cowpea (Vigna unguiculata), and Kersting's groundnut (Macrotyloma geocarpum), respectively. This suggests that N2-fixing legumes require little or no N fertilizer for growth and grain yield when grown under field conditions. Even cereals and other species obtain a substantial proportion of their N nutrition from associative and endophytic N2-fixing bacteria. For example, about 12-33% of maize N requirement can be obtained from their association with Pseudomonas, Hebaspirillum, Azospirillum, and Brevundioronas, while cucumber can obtain 12.9-20.9% from its interaction with Paenebacillus beijingensis BJ-18. Exploiting the plant growth-promoting traits of soil microbes for increased crop productivity without any negative impact on the environment is the basis of green agriculture which is done through the use of biofertilizers. Either alone or in combination with other synergistic rhizobacteria, rhizobia and arbuscular mycorrhizal (AM) fungi have been widely used in agriculture, often increasing crop yields but with occasional failures due to the use of poor-quality inoculants, and wrong application techniques. This review explores the literature regarding the plant growth-promoting traits of soil microbes, and also highlights the bottle-necks in tapping this potential for sustainable agriculture.

Prairie soil improves wheat establishment and accelerates the developmental transition to flowering compared to agricultural soils

Less than 1% of native prairie lands remain in the United States. Located in eastern Washington, the rare habitat called Palouse prairie was largely converted to wheat monocropping. With this conversion came numerous physical, chemical, and biological changes to the soil that may ultimately contribute to reduced wheat yields. Here, we explored how wheat (Tritcum aestivum L.) seedling establishment, plant size, and heading, signifying the developmental transition to flowering, were affected by being planted in prairie soil versus agricultural soils. We then sought to understand whether the observed effects were the result of changes to the soil microbiota due to agricultural intensification. We found that prairie soil enhanced both the probability of wheat seedling survival and heading compared to agricultural soil; however, wheat growth was largely unaffected by soil source. We did not detect effects on wheat developmental transitions or phenotype when inoculated with prairie microbes compared with agricultural microbes, but we did observe general antagonistic effects of microbes on plant size, regardless of soil source. This work indicates that agricultural intensification has affected soils in a way that changes early seedling establishment and the timing of heading for wheat, but these effects may not be caused by microbes, and instead may be caused by soil nutrient conditions.

Modulating phytoremediation: How drip irrigation system affect performance of active green wall and microbial community changes

A recent innovation in air phytoremediation is active green walls, which utilises biofiltration technology with airflow from mechanical ventilation. While this novel technology is gaining traction, the influence of irrigation on soil moisture, and subsequently the microbial communities that play a role in air filtration is untested. In this study, the application of drip irrigation techniques in active green walls were investigated for their influence on system performance. A modular green wall system was tested, with tests across 7 different plant species, as well as a substrate only control. Water distribution across the modules, the water-carrying capacity and airflow through the substrate were measured. The microbial community present, which is critical to the phytoremediation process, was quantified by identifying individual microbial phospholipid fatty acids (PLFA) within the substrate. Results demonstrated that the lower-speed drip irrigation reduced water consumption compared to the rapid system, and had generally more uniform moisture distribution. High flow drip irrigation resulted in a water pathway phenomenon, leading to uneven moisture distribution within the green wall, and this effect was accentuated with fibrous root plant species. Drip irrigation did not change microbial community composition across planted modules, apart from increasing fungi by 6%, but did wash out bacteria at the high flow rate used (-56.67%), thus low flow rate irrigation rate is more beneficial for both plant growth and microbial community composition. The current work provides evidence that drip irrigation has considerable effects on both substrate airflow rate and substrate microbial density: both key to system air cleaning performance.

Protein Involved in Tip Elongation (PITE) regulates root hair growth in rice

Polar tip growth in plants occurs only in root hairs and pollen tubes. In particular, root hair growth is considered very important in the growth of plants, as it is critical for water and nutrient absorption. Polar tip growth is regulated by various factors, including plant hormones such as abscisic acid (ABA) and gibberellin (GA) and cell wall modifications. We aimed to elucidate the effects and mechanisms on tip growth of a novel gene containing the domain of unknown function (DUF) 3511. We found that Protein Involved in Tip Elongation (PITE) is involved in root hair development in rice (Oryza sativa L.). PITE protein was observed in the plasma membrane and cytoplasm of root hairs. Pite mutants generated by the CRISPR/Cas9 system showed a shorter root hair phenotype compared to the wild type. Through RNA sequencing and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis, we found that the expression of genes that affect cell wall rigidity and GA metabolism-related genes were differently regulated in pite mutants. PITE could interact with acyl transferase and haloacid dehalogenase-like hydrolase (HAD9) in the nucleus and cytoplasm. Our study suggests that PITEs containing the DUF3511 domain regulate root hair growth in rice by mediating the expression of genes that can regulate cell wall rigidity or cause changes in GA metabolism through interactors such as HAD9.

Bacterial endophyte Pseudomonas mosselii PR5 improves growth, nutrient accumulation, and yield of rice (Oryza sativa L.) through various application methods

BACKGROUND

Pseudomonas spp. have drawn considerable attention due to their rhizospheric abundance and exceptional plant growth-promoting attributes. However, more research is needed on the optimal application methods of Pseudomonas mosselii for rice growth, nutrient accumulation, and yield improvement. This research explored the application of the endophytic bacterium P. mosselii PR5 on rice cultivar BRRI dhan29 with four treatments: control, seedling priming, root drenching, and bacterial cell-free culture (CFC) foliar application.

RESULTS

PR5 led to better rice growth, improved nutrient acquisition, and higher yields compared to the control, regardless of the application method used. The highest results in fresh weight of root (146.93 g/pot), shoot (758.98 g/pot), and flag leaf (7.88 g/pot), dry weight of root (42.16 g/pot), shoot (97.32 g/pot), and flag leaf (2.69 g/pot), and grains/panicle (224.67), were obtained from seedling priming treatment, whereas root drenching resulted in maximum plant height (105.67 cm), root length (49.0 cm), tillers/pot (23.7), and panicles/pot (17.67). In all three application methods, rice grain yield per pot was higher in PR5 inoculated treatments, compared to the control. The amount of P, Mg and Zn in the shoot and N, P, Ca, Mg and Si content in the flag leaf was significantly increased along with effective suppression of naturally occurring blast disease in bacterial CFC foliar application, validated by multivariate analysis.

CONCLUSION

Our results indicated that rice seedlings priming with PR5 improved rice growth, yield and nutrient uptake, whereas CFC foliar application significantly increased the concentration of most nutrients in the rice plant and suppressed the naturally occurring rice blast disease. This research highlights the significant potential of P. mosselii PR5 in enhancing rice growth, yield, and nutrient uptake, particularly through seedling priming and CFC foliar application methods.

Mechanisms of Cannabis Growth Promotion by Bacillus velezensis S141

Cannabis sativa L. has a variety of uses, including fiber production, food, oil, and medicine. In response to environmental concerns regarding chemical fertilizers, Bacillus velezensis S141 was examined as a plant-growth-promoting bacterium (PGPB) for cannabis. This study evaluated the effects of S141 on cannabis growth and utilized transcriptomic analysis to identify the responsive pathways. Inoculation with S141 significantly increased growth in laboratory and field environments, with most of the bacteria residing in the leaves, followed by the stems and roots, as determined by quantitative polymerase chain reaction (qPCR). Transcriptomic analysis revealed 976 differentially expressed genes. Upregulated genes were associated with metabolism, cellular processes, and catalytic activities, especially in the biosynthesis of phenylpropanoid, plant-pathogen interactions, and hormone signaling pathways. S141 mutants deficient in the production of auxin and cytokinin displayed reduced growth enhancement, which affirmed the roles of these hormones in cannabis development. These findings emphasize the potential of S141 as a sustainable growth promoter for cannabis and provide insights into the underlying pathways it influences.

Comparison between bacterial bio-formulations and gibberellic acid effects on Stevia rebaudiana growth and production of steviol glycosides through regulating their encoding genes

Stevia rebaudiana is associated with the production of calorie-free steviol glycosides (SGs) sweetener, receiving worldwide interest as a sugar substitute for people with metabolic disorders. The aim of this investigation is to show the promising role of endophytic bacterial strains isolated from Stevia rebaudiana Egy1 leaves as a biofertilizer integrated with Azospirillum brasilense ATCC 29,145 and gibberellic acid (GA3) to improve another variety of stevia (S. rebaudiana Shou-2) growth, bioactive compound production, expression of SGs involved genes, and stevioside content. Endophytic bacteria isolated from S. rebaudiana Egy1 leaves were molecularly identified and assessed in vitro for plant growth promoting (PGP) traits. Isolated strains Bacillus licheniformis SrAM2, Bacillus paralicheniformis SrAM3 and Bacillus paramycoides SrAM4 with accession numbers MT066091, MW042693 and MT066092, respectively, induced notable variations in the majority of PGP traits production. B. licheniformis SrAM2 revealed the most phytohormones and hydrogen cyanide (HCN) production, while B. paralicheniformis SrAM3 was the most in exopolysaccharides (EPS) and ammonia production 290.96 ± 10.08 mg/l and 88.92 ± 2.96 mg/ml, respectively. Treated plants significantly increased in performance, and the dual treatment T7 (B. paramycoides SrAM4 + A. brasilense) exhibited the highest improvement in shoot and root length by 200% and 146.7%, respectively. On the other hand, T11 (Bacillus cereus SrAM1 + B. licheniformis SrAM2 + B. paralicheniformis SrAM3 + B. paramycoides SrAM4 + A. brasilense + GA3) showed the most elevation in number of leaves, total soluble sugars (TSS), and up-regulation in the expression of the four genes ent-KO, UGT85C2, UGT74G1 and UGT76G1 at 2.7, 3.3, 3.4 and 3.7, respectively. In High-Performance Liquid Chromatography (HPLC) analysis, stevioside content showed a progressive increase in all tested samples but the maximum was exhibited by dual and co-inoculations at 264.37% and 289.05%, respectively. It has been concluded that the PGP endophytes associated with S. rebaudiana leaves improved growth and SGs production, implying the usability of these strains as prospective tools to improve important crop production individually or in consortium.

Impact of biopolymer-based Trichoderma harzianum seed coating on disease incidence and yield in oilseed crops

The use of microbe-based biological control for crop pests is recognized as an environmentally safe substitute for conventional chemical pesticides. However, the practical application of microbial inoculants in large-scale agriculture is underexplored, impeding their widespread commercial adoption. This study addresses the scarcity of research on effective delivery methods for microbial inoculants, particularly through seed coating, which has the potential to be a cost- and time-efficient strategy in crop management. In this research, the Trichoderma harzianum strain Th4d, a biological control agent (BCA), was incorporated into specially formulated biopolymeric compositions based on chitosan and cellulose. The efficacy of this seed coating approach was tested against various soil- and seed-borne pathogens in oilseed crops, including soybean, groundnut, and safflower. Results indicate that safflower treated with the biopolymer chitosan-based T. harzianum Th4d 1 % liquid formulation blend exhibited a higher seed yield of 793 kg/ha, seed germination of 84.7 %, and a significant reduction in wilt and root rot by 64.7 %. In groundnut crops, the seed coating led to a seed germination rate of 88.6 %, a 72 % reduction in root rot incidence, and a seed yield of 3040 kg/ha. Similarly, soybean crops treated with the biopolymer chitosan and T. harzianum Th4d displayed 83.4 % seed germination, a 70.9 % reduction in root rot, and a seed yield of 1239 kg/ha. Further on-farm evaluations demonstrated promising results, with the biopolymer chitosan-based T. harzianum Th4d 1 % liquid formulation blend seed treatment showing a high incremental cost-benefit ratio in safflower (1:4.5), soybean (1:2.5), and groundnut crops (1:3.3). This study underscores the potential of microbe-based seed coating as a sustainable and economically viable strategy for pest management in oilseed crops."

Maize Endophytic Plant Growth-Promoting Bacteria Peribacillus simplex Can Alleviate Plant Saline and Alkaline Stress

Soil salinization is currently one of the main abiotic stresses that restrict plant growth. Plant endophytic bacteria can alleviate abiotic stress. The aim of the current study was to isolate, characterize, and assess the plant growth-promoting and saline and alkaline stress-alleviating traits of Peribacillus simplex M1 (P. simplex M1) isolates from maize. One endophytic bacterial isolate, named P. simplex M1, was selected from the roots of maize grown in saline-alkali soil. The P. simplex M1 genome sequence analysis of the bacteria with a length of 5.8 Mbp includes about 700 genes that promote growth and 16 antioxidant activity genes that alleviate saline and alkaline stress. P. simplex M1 can grow below 400 mM NaHCO3 on the LB culture medium; The isolate displayed multiple plant growth-stimulating features, such as nitrogen fixation, produced indole-3-acetic acid (IAA), and siderophore production. This isolate had a positive effect on the resistance to salt of maize in addition to the growth. P. simplex M1 significantly promoted seed germination by enhancing seed vigor in maize whether under normal growth or NaHCO3 stress conditions. The seeds with NaHCO3 treatment exhibited higher reactive oxygen species (ROS) levels than the maize in P. simplex M1 inoculant on maize. P. simplex M1 can colonize the roots of maize. The P. simplex M1 inoculant plant increased chlorophyll in leaves, stimulated root and leaf growth, increased the number of lateral roots and root dry weight, increased the length and width of the blades, and dry weight of the blades. The application of inoculants can significantly reduce the content of malondialdehyde (MDA) and increase the activity of plant antioxidant enzymes (Catalase (CAT), Superoxide Dismutase (SOD), and Peroxidase (POD)), which may thereby improve maize resistance to saline and alkaline stress. Conclusion: P. simplex M1 isolate belongs to plant growth-promoting bacteria by having high nitrogen concentration, indoleacetic acid (IAA), and siderophore, and reducing the content of ROS through the antioxidant system to alleviate salt alkali stress. This study presents the potential application of P. simplex M1 as a biological inoculant to promote plant growth and mitigate the saline and alkaline effects of maize and other crops.

Prescribed fire regimes influence responses of fungal and bacterial communities on new litter substrates in a brackish tidal marsh

Processes modifying newly deposited litter substrates should affect fine fuels in fire-managed tidal marsh ecosystems. Differences in chemical composition and dynamics of litter should arise from fire histories that generate pyrodiverse plant communities, tropical cyclones that deposit wrack as litter, tidal inundation that introduces and alters sediments and microbes, and interactions among these different processes. The resulting diversity and dynamics of available litter compounds should affect microbial (fungal and bacterial) communities and their roles in litter substrate dynamics and ecosystem responses over time. We experimentally examined effects of differences in litter types produced by different fire regimes and litter loads (simulating wrack deposition) on microbial community composition and changes over time. We established replicated plots at similar elevations within frequent tidal-inundation zones of a coastal brackish Louisiana marsh. Plots were located within blocks with different prescribed fire regimes. We deployed different measured loads of new sterilized litter collected from zones in which plots were established, then re-measured litter masses at subsequent collection times. We used DNA sequencing to characterize microbial communities, indicator families, and inferred ecosystem functions in litter subsamples. Differences in fire regimes had large, similar effects on fungal and bacterial indicator families and community compositions and were associated with alternate trajectories of community development over time. Both microbial and plant community compositional patterns were associated with fire regimes, but in dissimilar ways. Differences in litter loads introduced differences in sediment accumulation associated with tidal inundation that may have affected microbial communities. Our study further suggests that fire regimes and tropical cyclones, in the context of frequent tidal inundation, may interactively generate substrate heterogeneities and alter microbial community composition, potentially modifying fine fuels and hence subsequent fires. Understanding microbial community compositional and functional responses to fire regimes and tropical cyclones should be useful in management of coastal marsh ecosystems.

Genetic diversity, stress tolerance and phytobeneficial potential in rhizobacteria of Vachellia tortilis subsp. raddiana

BACKGROUND

Soil bacteria often form close associations with their host plants, particularly within the root compartment, playing a significant role in plant growth and stress resilience. Vachellia tortilis subsp. raddiana, (V. tortilis subsp. raddiana)a leguminous tree, naturally thrives in the harsh, arid climate of the Guelmim region in southern Morocco. This study aims to explore the diversity and potential plant growth-promoting (PGP) activities of bacteria associated with this tree.

RESULTS

A total of 152 bacterial isolates were obtained from the rhizosphere of V. tortilis subsp. raddiana. Rep-PCR fingerprinting revealed 25 distinct genomic groups, leading to the selection of 84 representative strains for further molecular identification via 16 S rRNA gene sequencing. Seventeen genera were identified, with Bacillus and Pseudomonas being predominant. Bacillus strains demonstrated significant tolerance to water stress (up to 30% PEG), while Pseudomonas strains showed high salinity tolerance (up to 14% NaCl). In vitro studies indicated variability in PGP activities among the strains, including mineral solubilization, biological nitrogen fixation, ACC deaminase activity, and production of auxin, siderophores, ammonia, lytic enzymes, and HCN. Three elite strains were selected for greenhouse inoculation trials with V. tortilis subsp. raddiana. Strain LMR725 notably enhanced various plant growth parameters compared to uninoculated control plants.

CONCLUSIONS

The findings underscore the potential of Bacillus and Pseudomonas strains as biofertilizers, with strain LMR725 showing particular promise in enhancing the growth of V. tortilis subsp. raddiana. This strain emerges as a strong candidate for biofertilizer formulation aimed at improving plant growth and resilience in arid environments.

Mechanism of microbial action of the inoculated nitrogen-fixing bacterium for growth promotion and yield enhancement in rice (Oryza sativa L.)

The use of nitrogen-fixing bacteria in agriculture is increasingly recognized as a sustainable method to boost crop yields, reduce chemical fertilizer use, and improve soil health. However, the microbial mechanisms by which inoculation with nitrogen-fixing bacteria enhance rice production remain unclear. In this study, rice seedlings were inoculated with the nitrogen-fixing bacterium R3 (Herbaspirillum) at the rhizosphere during the seedling stage in a pot experiment using paddy soil. We investigated the effects of such inoculation on nutrient content in the rhizosphere soil, plant growth, and the nitrogen-fixing microbial communities within the rhizosphere and endorhizosphere. The findings showed that inoculation with the R3 strain considerably increased the amounts of nitrate nitrogen, ammonium nitrogen, and available phosphorus in the rhizosphere by 14.77%, 27.83%, and 22.67%, respectively, in comparison to the control (CK). Additionally, the theoretical yield of rice was enhanced by 8.81% due to this inoculation, primarily through a 10.24% increase in the effective number of rice panicles and a 4.14% increase in the seed setting rate. Further analysis revealed that the structure of the native nitrogen-fixing microbial communities within the rhizosphere and endorhizosphere were altered by inoculation with the R3 strain, significantly increasing the α-diversity of the communities. The relative abundance of key nitrogen-fixing genera such as Ralstonia, Azotobacter, Geobacter, Streptomyces, and Pseudomonas were increased, enhancing the quantity and community stability of the nitrogen-fixing community. Consequently, the nitrogen-fixing capacity and sustained activity of the microbial community in the rhizosphere soil were strengthened. Additionally, the expression levels of the nitrogen absorption and transport-related genes OsNRT1 and OsPTR9 in rice roots were upregulated by inoculation with the R3 strain, potentially contributing to the increased rice yield. Our study has revealed the potential microbial mechanisms through which inoculation with nitrogen-fixing bacteria enhances rice yield. This finding provides a scientific basis for subsequent agricultural practices and is of critical importance for increasing rice production and enhancing the ecosystem services of rice fields.

Pseudomonas thivervalensis K321, a promising and effective biocontrol agent for managing apple Valsa canker triggered by Valsa mali

Plant growth-promoting rhizobacteria (PGPR) have been reported to suppress various diseases as potential bioagents. It can inhibit disease occurrence through various means such as directly killing pathogens and inducing systemic plant resistance. In this study, a bacterium isolated from soil showed significant inhibition of Valsa mali. Morphological observations and phylogenetic analysis identified the strain as Pseudomonas thivervalensis, named K321. Plate confrontation assays demonstrated that K321 treatment severely damaged V. mali growth, with scanning electron microscopy (SEM) observations showing severe distortion of hyphae due to K321 treatment. In vitro twigs inoculation experiments indicated that K321 had good preventive and therapeutic effects against apple Valsa canker (AVC). Applying K321 on apples significantly enhanced the apple inducing systemic resistance (ISR), including induced expression of apple ISR-related genes and increased ISR-related enzyme activity. Additionally, applying K321 on apples can activate apple MAPK by enhancing the phosphorylation of MPK3 and MPK6. In addition, K321 can promote plant growth by solubilizing phosphate, producing siderophores, and producing 3-indole-acetic acid (IAA). Application of 0.2% K321 increased tomato plant height by 53.71%, while 0.1% K321 increased tomato fresh weight by 59.55%. Transcriptome analysis revealed that K321 can inhibit the growth of V. mali by disrupting the integrity of its cell membrane through inhibiting the metabolism of essential membrane components (fatty acids) and disrupting carbohydrate metabolism. In addition, transcriptome analysis also showed that K321 can enhance plant resistance to AVC by inducing ISR-related hormones and MAPK signaling, and application of K321 significantly induced the transcription of plant growth-related genes. In summary, an excellent biocontrol strain has been discovered that can prevent AVC by inducing apple ISR and directly killing V. mali. This study indicated the great potential of P. thivervalensis K321 for use as a biological agent for the control of AVC.

Chemical fertilizers promote dissemination of ARGs in maize rhizosphere: An overlooked risk revealed after 37-year traditional agriculture practice

Bacterial communities in soil and rhizosphere maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs and antibiotic resistant bacteria (ARB) are well-characterized under traditional farming practices. Here we compared the ARG profiles of maize rhizosphere and their bulk soils using metagenomic analysis to identify the ARG dissemination and explored the potential impact of chemical fertilization on ARB. Results showed a relatively lower abundance but higher diversity of ARGs under fertilization than straw-return. Moreover, the abundance and diversity of MGEs were significantly promoted by chemical fertilizer inputs in the rhizosphere compared to bulk soil. Machine learning and bipartite networks identified three bacterial genera (Pseudomonas, Bacillus and Streptomyces) as biomarkers for ARG accumulation. Thus we cultured 509 isolates belonging to these three genera from the rhizosphere and tested their antimicrobial susceptibility, and found that multi-resistance was frequently observed among Pseudomonas isolates. Assembly-based tracking explained that ARGs and four class I integrons (LR134330, LS998783, CP065848, LT883143) were co-occurred among contigs from Pseudomonas sp. Chemical fertilizers may shape the resistomes of maize rhizosphere, highlighting that rhizosphere carried multidrug-resistant Pseudomonas isolates, which may pose a risk to animal and human health. This study adds knowledge of long-term chemical fertilization on ARG dissemination in farmland systems and provides information for decision-making in agricultural production and monitoring.

Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes

Plants have coevolved together with the microbes that surround them and this assemblage of host and microbes functions as a discrete ecological unit called a holobiont. This review outlines plant-driven assembly of disease-suppressive microbiomes. Plants are colonized by microbes from seed, soil, and air but selectively shape the microbiome with root exudates, creating microenvironment hot spots where microbes thrive. Using plant immunity for gatekeeping and surveillance, host-plant genetic properties govern microbiome assembly and can confer adaptive advantages to the holobiont. These advantages manifest in disease-suppressive soils, where buildup of specific microbes inhibits the causal agent of disease, that typically develop after an initial disease outbreak. Based on disease-suppressive soils such as take-all decline, we developed a conceptual model of how plants in response to pathogen attack cry for help and recruit plant-protective microbes that confer increased resistance. Thereby, plants create a soilborne legacy that protects subsequent generations and forms disease-suppressive soils.

Characteristics of Rhizosphere Microbiome, Soil Chemical Properties, and Plant Biomass and Nutrients in Citrus reticulata cv. Shatangju Exposed to Increasing Soil Cu Levels

The prolonged utilization of copper (Cu)-containing fungicides results in Cu accumulation and affects soil ecological health. Thus, a pot experiment was conducted using Citrus reticulata cv. Shatangju with five Cu levels (38, 108, 178, 318, and 388 mg kg-1) to evaluate the impacts of the soil microbial processes, chemistry properties, and citrus growth. These results revealed that, with the soil Cu levels increased, the soil total Cu (TCu), available Cu (ACu), organic matter (SOM), available potassium (AK), and pH increased while the soil available phosphorus (AP) and alkali-hydrolyzable nitrogen (AN) decreased. Moreover, the soil extracellular enzyme activities related to C and P metabolism decreased while the enzymes related to N metabolism increased, and the expression of soil genes involved in C, N, and P cycling was regulated. Moreover, it was observed that tolerant microorganisms (e.g., p_Proteobacteria, p_Actinobacteria, g_Lysobacter, g_Sphingobium, f_Aspergillaceae, and g_Penicillium) were enriched but sensitive taxa (p_Myxococcota) were suppressed in the citrus rhizosphere. The citrus biomass was mainly positively correlated with soil AN and AP; plant N and P were mainly positively correlated with soil AP, AN, and acid phosphatase (ACP); and plant K was mainly negatively related with soil β-glucosidase (βG) and positively related with the soil fungal Shannon index. The dominant bacterial taxa p_Actinobacteriota presented positively correlated with the plant biomass and plant N, P, and K and was negatively correlated with plant Cu. The dominant fungal taxa p_Ascomycota was positively related to plant Cu but negatively with the plant biomass and plant N, P, and K. Notably, arbuscular mycorrhizal fungi (p_Glomeromycota) were positively related with plant P below soil Cu 108 mg kg-1, and pathogenic fungi (p_Mortierellomycota) was negatively correlated with plant K above soil Cu 178 mg kg-1. These findings provided a new perspective on soil microbes and chemistry properties and the healthy development of the citrus industry at increasing soil Cu levels.

Plant growth-promoting rhizobacterium Bacillus megaterium modulates the expression of antioxidant-related and drought-responsive genes to protect rice (Oryza sativa L.) from drought

Global climate change poses a significant threat to plant growth and crop yield and is exacerbated by environmental factors, such as drought, salinity, greenhouse gasses, and extreme temperatures. Plant growth-promoting rhizobacteria (PGPR) help plants withstand drought. However, the mechanisms underlying PGPR-plant interactions remain unclear. Thus, this study aimed to isolate PGPR, Bacillus megaterium strains CACC109 and CACC119, from a ginseng field and investigate the mechanisms underlying PGPR-stimulated tolerance to drought stress by evaluating their plant growth-promoting activities and effects on rice growth and stress tolerance through in vitro assays, pot experiments, and physiological and molecular analyses. Compared with B. megaterium type strain ATCC14581, CACC109 and CACC119 exhibited higher survival rates under osmotic stress, indicating their potential to enhance drought tolerance. Additionally, CACC109 and CACC119 strains exhibited various plant growth-promoting activities, including phosphate solubilization, nitrogen fixation, indole-3-acetic acid production, siderophore secretion, 1-aminocyclopropane-1-carboxylate deaminase activity, and exopolysaccharide production. After inoculation, CACC109 and CACC119 significantly improved the seed germination of rice (Oryza sativa L.) under osmotic stress and promoted root growth under stressed and non-stressed conditions. They also facilitated plant growth in pot experiments, as evidenced by increased shoot and root lengths, weights, and leaf widths. Furthermore, CACC109 and CACC119 improved plant physiological characteristics, such as chlorophyll levels, and production of osmolytes, such as proline. In particular, CACC109- and CACC119-treated rice plants showed better drought tolerance, as evidenced by their higher survival rates, greater chlorophyll contents, and lower water loss rates, compared with mock-treated rice plants. Application of CACC109 and CACC119 upregulated the expression of antioxidant-related genes (e.g., OsCAT, OsPOD, OsAPX, and OsSOD) and drought-responsive genes (e.g., OsWRKY47, OsZIP23, OsDREB2, OsNAC066, OsAREB1, and OsAREB2). In conclusion, CACC109 and CACC119 are promising biostimulants for enhancing plant growth and conferring resistance to abiotic stresses in crop production. Future studies should conduct field trials to validate these findings under real agricultural conditions, optimize inoculation methods for practical use, and further investigate the biochemical and physiological responses underlying the observed benefits.