Signal communication during microbial modulation of root system architecture

Decoding bacterial communication: Intracellular signal transduction, quorum sensing, and cross-kingdom interactions

This review provides a comprehensive analysis of the intricate architecture of bacterial sensing systems, with a focus on signal transduction mechanisms and their critical roles in microbial physiology. It highlights quorum sensing (QS), quorum quenching (QQ), and quorum sensing interference (QSI) as fundamental processes driving bacterial communication, influencing gene expression, biofilm formation, and interspecies interactions. The analysis explores the importance of diffusible signal factors (DSFs) and secondary messengers such as cAMP and c-di-GMP in modulating microbial behaviors. Additionally, cross-kingdom signaling, where bacterial signals impact host-pathogen dynamics and ecological balance, is systematically reviewed. This review introduces "signalomics", an novel interdisciplinary framework integrating genomics, proteomics, and metabolomics to offer a holistic framework for understanding microbial communication and evolution. These findings hold significant implications for various domains, including food preservation, agriculture, and human health.

Root RADAR: how 'rhizocrine' signals allow roots to detect and respond to their soil environment and stresses

Agricultural intensification coupled with changing climate are causing soils to become increasingly vulnerable to stresses such as drought, soil erosion, and compaction. The mechanisms by which roots detect and respond to soil stresses remain poorly understood. Recent breakthroughs show that roots release volatile and soluble hormone signals into the surrounding soil, then monitor their levels to sense soil stresses. Our review discusses how hormones can act 'outside the plant' as 'rhizocrine' signals that function to improve plant resilience to different soil stresses. We also propose a novel signalling paradigm which we term 'root RADAR' where 'rhizocrine' levels change in soil in response to environmental stresses, feeding back to roots and triggering adaptive responses.

Synthetic Microbial Community Isolated from Intercropping System Enhances P Uptake in Rice

Changes in root traits and rhizosphere microbiome are important ways to optimize plant phosphorus (P) efficiency and promote multifunctionality in intercropping. However, whether and how synthetic microbial communities isolated from polyculture systems can facilitate plant growth and P uptake are still largely unknown. A field experiment was first carried out to assess the rice yield and P uptake in the rice/soybean intercropping systems, and a synthetic microbial community (SynCom) isolated from intercropped rice was then constructed to elucidate the potential mechanisms of growth-promoting effects on rice growth and P uptake in a series of pot experiments. Our results showed that the yield and P uptake of intercropped rice were lower than those of rice grown in monoculture. However, bacterial networks in the rice rhizosphere were more stable in polyculture, exhibiting more hub nodes and greater modularity compared to the rice monoculture. A bacterial synthetic community (SynCom) composed of four bacterial strains (Variovorax paradoxus, Novosphingobium subterraneum, Hydrogenophaga pseudoflava, Acidovorax sp.) significantly enhanced the biomass and P uptake of potted rice plants. These growth-promoting effects are underpinned by multiple pathways, including the direct activation of soil available P, increased root surface area and root tip number, reduced root diameter, and promotion of root-to-shoot P translocation through up-regulation of Pi transporter genes (OsPht1;1, OsPht1;2, OsPht1;4, OsPht1;6). This study highlights the potential of harnessing synthetic microbial communities to enhance nutrient acquisition and improve crop production.

Deciphering the ABA and GA biosynthesis approach of Bacillus pumilus, mechanistic approach, explaining the role of metabolic region as an aid in improving the stress tolerance

Bacillus pumilus plays an essential role in agricultural applications as a beneficial microbe and for sustainable agriculture production. However, the underlying mechanisms of B. pumilus strains remain unclear as to how they are beneficial for plants as stress tolerant and growth promoters. Bacillus pumilus was isolated from the rhizosphere soil of Artemisia vulgaris. NGS (next-generation sequencing) was performed for the strain to gain new insights into the molecular mechanisms underlying plant-microbial interactions. NGS revealed 3,910 genes, 3294 genes with protein-coding, and 11 functional genomic regions related to diverse agronomic traits including stress tolerance. We identified the two possible phytohormone biosynthesis approaches from metabolic regions1(terpense→diterpense→betacarotene→xanthoxin→ABA)2(terpense→diterpense→geranyl diphosphate →C20 →GA). Several gene clusters related to the biosynthesis of phytohormones, stress tolerance, and agricultural diversification were predicted. The genome provides insights into the possible mechanisms of this bacterium for stress tolerance and its future applications. The genomic organization of B. pumilus revealed several hallmarks of its plant growth promotion and pathogen suppression activities. Our results provide detailed genomic information for the strain and reveal its potential stress tolerance mechanisms, laying the foundation for developing effective stress tolerance strategies against abiotic stress.

Soil Microbiota Modulates Root Transcriptome With Divergent Effect on Maize Growth Under Low and High Phosphorus Inputs

Plant growth can be promoted by beneficial microorganisms, or inhibited by detrimental ones. Although the interaction process between a single microbial species and its host has been extensively studied, the growth and transcriptional response of the host to soil microbiota is poorly understood. We planted maize in natural or sterile soil collected from a long-term experimental site with two different soil phosphate (P) regimes. We examined the composition of microbial communities inhabiting root-associated niches in natural soil. In parallel, we determined the biomass, ionomes, and root transcriptome profiling of maize grown in natural or sterile soil. Soil microbiota could promote or inhibit different P starvation-responsive (PSR) genes, as well as induce several defense-related metabolic processes independently of external P levels. Soil microbiota accompanied by long-term application of P fertilizer induced lower intensity of PSR and defense responses, inhibiting maize growth. Under a low P regime, the PSR and defense responses were induced to a higher extent, promoting P absorption and growth. Our findings suggest a soil P-dependent effect of microbiota on maize growth by integrating PSR and defense responses and provide a more refined understanding of the interaction between root growth and soil microbiota.

Genome-wide identification and expression analysis of CASPL gene family in Zea mays (L.)

Casparian strip membrane domain proteins like (CASPL), exhibit profound associations with root development, stress responsiveness and mineral element uptake in plants. Nonetheless, a comprehensive bioinformatics analysis of the ZmCASPL gene family in maize remains unreported. In the study, we have identified 47 ZmCASPL members at the whole-genome level, systematically classifying them into six distinct groups. Furthermore, our analysis revealed that the same group of ZmCASPL contains similar gene structures and conserved motifs. Duplication events showed whole genome duplication (WGD) and tandem duplication (TD) contribute to the generation of the ZmCASPL gene family together in maize, but the former plays a more prominent role. Furthermore, we observed that most ZmCASPL genes contain MYB-binding sites (CAACCA), which are associated with the Casparian strip. Utilizing RNA-seq data, we found that ZmCASPL21 and ZmCASPL47 are specifically highly expressed only in the roots. This finding implies that ZmCASPL21 and ZmCASPL47 may be involved in the Casparian strip development. Additionally, RNA-seq analysis illuminated that drought, salt, heat, cold stresses, low nitrogen and phosphorus conditions, as well as pathogen infection, significantly impact the expression patterns of ZmCASPL genes. RT-qPCR revealed that ZmCASPL 5/13/25/44 genes showed different expression patterns under PEG and NaCl treatments. Collectively, these findings provide a robust theoretical foundation for further investigations into the functional roles of the ZmCASPL gene family in maize.

Metabolomic Analyses Reveal That IAA from Serratia marcescens Lkbn100 Promotes Plant Defense during Infection of Fusarium graminearum in Sorghum

Global sorghum production has been significantly reduced due to the occurrence of sorghum root rot caused by the fungus Fusarium graminearum. The utilization of biocontrol microorganisms has emerged as an effective strategy. However, the underlying mechanisms remain unclear. Therefore, the aim of this study was to investigate the effectiveness of biocontrol bacteria in inducing sorghum resistance against sorghum root rot and explore the potential induced resistance mechanisms through metabolomics analysis. The results revealed that the biocontrol bacteria Lnkb100, identified as Serratia marcescens (GenBank: PP152264), significantly enhanced the resistance of sorghum against sorghum root rot and promoted its growth, leading to increased seed weight. Targeted metabolomics analysis demonstrated that the highest concentration of the hormone IAA (indole-3-acetic acid) was detected in the metabolites of Lnkb100. Treatment with IAA enhanced the activity of disease-related enzymes such as SOD, CAT, POD and PPO in sorghum, thereby improving its resistance against sorghum root rot. Further untargeted metabolomic analysis revealed that IAA treatment resulted in higher concentrations of metabolites involved in the resistance against F. graminearum, such as geniposidic acid, 5-L-Glutamyl-taurine, formononetin 7-O-glucoside-6″-O-malonate, as well as higher concentrations of the defense-related molecules volicitin and JA. Additionally, "secondary bile acid biosynthesis" and "glycerophospholipid metabolism" pathways were found to play significant roles in the defense response of sorghum against fungal infection. These findings provide a reliable theoretical basis for utilizing biocontrol microorganisms to control sorghum root rot.

Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture

The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant-beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment-dominated and plant genetic-dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment-dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic-dominated rhizosphere microbiome for breeding microbiome-assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome.

The Influence of Piriformospora indica Colonization on the Root Development and Growth of Cerasus humilis Cuttings

Numerous studies have shown that the endophytic fungus Piriformospora indica has a broad range of promoting effects on root development and plant growth in host plants. However, there are currently no reports on the application of this fungus on Cerasus humilis. This study first compared the colonization ability of P. indica on 11 C. humilis varieties and found that the colonization rate of this fungus on these varieties ranged from 90% to 100%, with the colonization rate of the varieties '09-01' and 'Nongda 7' being as high as 100%. Subsequently, the effect of P. indica on root development and plant growth of C. humilis was investigated using cuttings of '09-01' and 'Nongda 7' as materials. P. indica colonization was found to increase the biomass of '09-01' and 'Nongda 7' plants; root activity, POD enzymes, and chlorophyll content were also significantly increased. In addition, indole-3-acetic acid (IAA) content in the roots of C. humilis plants increased after colonization, while jasmonic acid (JA) and 1-aminocyclopropane-1-car- boxylic acid (ACC) content decreased. In conclusion, it has been demonstrated that P. indica can promote the growth of C. humilis plants by accelerating biomass accumulation, promoting rooting, and enhancing the production of photosynthetic pigments, as well as regulating hormone synthesis.

Trichoderma-secreted anthranilic acid promotes lateral root development via auxin signaling and RBOHF-induced endodermal cell wall remodeling

Trichoderma spp. have evolved the capacity to communicate with plants by producing various secondary metabolites (SMs). Nonhormonal SMs play important roles in plant root development, while specific SMs from rhizosphere microbes and their underlying mechanisms to control plant root branching are still largely unknown. In this study, a compound, anthranilic acid (2-AA), is identified from T. guizhouense NJAU4742 to promote lateral root development. Further studies demonstrate that 2-AA positively regulates auxin signaling and transport in the canonical auxin pathway. 2-AA also partly rescues the lateral root numbers of CASP1pro:shy2-2, which regulates endodermal cell wall remodeling via an RBOHF-induced reactive oxygen species burst. In addition, our work reports another role for microbial 2-AA in the regulation of lateral root development, which is different from its better-known role in plant indole-3-acetic acid biosynthesis. In summary, this study identifies 2-AA from T. guizhouense NJAU4742, which plays versatile roles in regulating plant root development.

Root architecture and rhizosphere-microbe interactions

Plant roots fulfil crucial tasks during a plant's life. As roots encounter very diverse conditions while exploring the soil for resources, their growth and development must be responsive to changes in the rhizosphere, resulting in root architectures that are tailor-made for all prevailing circumstances. Using multi-disciplinary approaches, we are gaining more intricate insights into the regulatory mechanisms directing root system architecture. This Special Issue provides insights into our advancement of knowledge on different aspects of root development and identifies opportunities for future research.

Warm Temperature Increments Strengthen the Crosstalk between Roots and Soil in the Rhizosphere of Soybean Seedlings

The plant rhizosphere underlies the crosstalk between plant and soil and has a crucial role in plant growth and development under various environments. We examined the effect of temperature rise on the rhizosphere environment of soybean roots to clarify the rhizosphere crosstalk between roots and soil in response to warm temperature rises in a global warming background. The in situ results of root enzyme activity revealed that soybean roots secrete β-glucosidase, and enzyme spectrum imaging demonstrated different enzymatic activities under different temperature environments. The soil enzyme kinetics results showed that soil enzymatic activity increased with increasing temperature, and soybean rhizosphere soil enzymatic activity was higher than that of non-rhizosphere soil. Rhizosphere soil and non-rhizosphere soil showed that the dominant bacterial phylum in soybean rhizosphere soil was Acidobacteria, and the dominant bacterial genus was JG30-KF-AS9. Compared with non-rhizosphere soil, rhizosphere soil was more nutrient-rich, and root secretions provided abundant carbon sources and other nutrients for soil microorganisms in the rhizosphere. Rhizosphere microorganisms affect plant growth by influencing the decomposition of soil organic carbon. The organic carbon content of rhizosphere soil was higher than that of non-rhizosphere soil under high temperatures.

Communication between Plants and Rhizosphere Microbiome: Exploring the Root Microbiome for Sustainable Agriculture

Plant roots host numerous microorganisms around and inside their roots, forming a community known as the root microbiome. An increasing bulk of research is underlining the influences root-associated microbial communities can have on plant health and development. However, knowledge on how plant roots and their associated microbes interact to bring about crop growth and yield is limited. Here, we presented (i) the communication strategies between plant roots and root-associated microbes and (ii) the applications of plant root-associated microbes in enhancing plant growth and yield. This review has been divided into three main sections: communications between root microbiome and plant root; the mechanism employed by root-associated microbes; and the chemical communication mechanisms between plants and microbes and their application in plant growth and yield. Understanding how plant root and root-associated microbes communicate is vital in designing ecofriendly strategies for targeted disease suppression and improved plant growth that will help in sustainable agriculture. Ensuring that plants become healthy and productive entails keeping plants under surveillance around the roots to recognize disease-causing microbes and similarly exploit the services of beneficial microorganisms in nutrient acquisition, stress mitigation, and growth promotion.