Root exudates and chemotactic strains mediate bacterial community assembly in the rhizosphere soil of Casuarina equisetifolia L

Rhizosphere microbiome regulation: Unlocking the potential for plant growth

Rhizosphere microbial communities are essential for plant growth and health maintenance, but their recruitment and functions are affected by their interactions with host plants. Finding ways to use the interaction to achieve specific production purposes, so as to reduce the use of chemical fertilizers and pesticides, is an important research approach in the development of green agriculture. To demonstrate the importance of rhizosphere microbial communities and guide practical production applications, this review summarizes the outstanding performance of rhizosphere microbial communities in promoting plant growth and stress tolerance. We also discuss the effect of host plants on their rhizosphere microbes, especially emphasizing the important role of host plant species and genes in the specific recruitment of beneficial microorganisms to improve the plants' own traits. The aim of this review is to provide valuable insights into developing plant varieties that can consistently recruit specific beneficial microorganisms to improve crop adaptability and productivity, and thus can be applied to green and sustainable agriculture in the future.

Endophytic bacteria with allelopathic potential regulate gene expression and metabolite production in host Casuarina equisetifolia

Introduction

Casuarina equisetifolia is a common protective forest in coastal areas. However, artificial C. equisetifolia forests cannot self-renew, mainly due to the accumulation of allelochemicals. Endophytic bacteria may alleviate the root growth inhibition caused by allelochemicals in C. equisetifolia seedlings. B. amyloliquefaciens and B. aryabhattai were endophytic bacteria with strong allelopathy in C. equisetifolia root. The allelopathy mechanism of these two endophytes and their interaction with C. equisetifolia remains to be studied.

Methods

Whole-genome sequencing of B. amyloliquefaciens and B. aryabhattai isolated from the roots of allelochemical-accumulating C. equisetifolia was performed using Illumina Hiseq and PacBio single-molecule sequencing platforms. Sterile seedlings of C. equisetifolia were treated with either individual or mixed bacterial cultures through root drenching. Transcriptional and metabolomics analyses were conducted after 3 days of infection.

Results and discussion

Whole-genome sequencing of Bacillus aryabhattai and Bacillus amyloliquefaciens showed that the two strains contained various horizontal gene transfer elements such as insertion sequence, prophage and transposon. In addition, these two strains also contain numerous genes related to the synthesis and catabolism of allelochemicals. After these two strains of bacteria were individually or mixed infected with C. equisetifolia, metabolomics and transcriptomic analysis of C. equisetifolia showed the 11 important secondary metabolite biosynthesis among them alkaloids biosynthesis, phenylpropanoid and terpenes biosynthesis and related genes were putatively regulated. Correlation analysis revealed that 48 differentially expressed genes had strong positive correlations with 42 differential metabolites, and 48 differentially expressed genes had strong negative correlations with 36 differential metabolites. For example, CMBL gene showed positive correlations with the allelochemical (-)-Catechin gallate, while Bp10 gene showed negative correlations with (-)-Catechin gallate.

Conclusion

The intergenerational accumulation of allelochemicals may induce horizontal gene transfer in endogenic bacteria of Casuarina equisetifolia root. Endophytic Bacillus plays an allelopathic role by assisting the host in regulating gene expression and the production and/or variety of allelochemicals. This comprehensive study sheds light on the intricate genetic and metabolic interactions between Bacillus endophytes and C. equisetifolia. These findings provide insights into endophyte-mediated allelopathy and its potential uses in plant biology and forest sustainability.

Advancements in bacterial chemotaxis: Utilizing the navigational intelligence of bacteria and its practical applications

The fascinating world of microscopic life unveils a captivating spectacle as bacteria effortlessly maneuver through their surroundings with astonishing accuracy, guided by the intricate mechanism of chemotaxis. This review explores the complex mechanisms behind this behavior, analyzing the flagellum as the driving force and unraveling the intricate signaling pathways that govern its movement. We delve into the hidden costs and benefits of this intricate skill, analyzing its potential to propagate antibiotic resistance gene while shedding light on its vital role in plant colonization and beneficial symbiosis. We explore the realm of human intervention, considering strategies to manipulate bacterial chemotaxis for various applications, including nutrient cycling, algal bloom and biofilm formation. This review explores the wide range of applications for bacterial capabilities, from targeted drug delivery in medicine to bioremediation and disease control in the environment. Ultimately, through unraveling the intricacies of bacterial movement, we can enhance our comprehension of the intricate web of life on our planet. This knowledge opens up avenues for progress in fields such as medicine, agriculture, and environmental conservation.

Effects of varying nano-ZnO concentrations on the physiology, biochemistry, root exudate, and root microbial community of Agrostis stolonifera

This study investigates the adsorption and transport of nano-ZnO in Agrostis stolonifera, focusing on its effects on plant physiology, biochemistry, root exudate, and root microbial community.

Characterisation of Soil Bacterial Communities That Exhibit Chemotaxis to Root Exudates from Phosphorus-Limited Plants

The ability to sense and direct movement along chemical gradients is known as 'chemotaxis' and is a common trait among rhizosphere microorganisms, which are attracted to organic compounds released from plant roots. In response to stress, the compounds released from roots can change and may recruit symbionts that enhance host stress tolerance. Decoding this language of attraction could support the development of microbiome management strategies that would enhance agricultural production and sustainability. In this study, we employ a culture-independent bait-trap chemotaxis assay to capture microbial communities attracted to root exudates from phosphorus (P)-sufficient and P-deficient Arabidopsis thaliana Col-0 plants. The captured populations were then enumerated and characterised using flow cytometry and phylogenetic marker gene sequencing, respectively. Exudates attracted significantly more cells than the control but did not differ between P treatments. Relative to exudates from P-sufficient plants, those collected from P-deficient plants attracted a significantly less diverse bacterial community that was dominated by members of the Paenibacillus, which is a genus known to include powerful phosphate solubilisers and plant growth promoters. These results suggest that in response to P deficiency, Arabidopsis exudates attract organisms that could help to alleviate nutrient stress.

Certain Tomato Root Exudates Induced by Pseudomonas stutzeri NRCB010 Enhance Its Rhizosphere Colonization Capability

Plant growth-promoting rhizobacteria (PGPR) can colonize plant root surfaces or form biofilms to promote plant growth and enhance plant resistance to harsh external environments. However, plant-PGPR interactions, especially chemical signaling molecules, are poorly understood. This study aimed to gain an in-depth understanding of the rhizosphere interaction mechanisms between PGPR and tomato plants. This study found that inoculation with a certain concentration of Pseudomonas stutzeri significantly promoted tomato growth and induced significant changes in tomato root exudates. Furthermore, the root exudates significantly induced NRCB010 growth, swarming motility, and biofilm formation. In addition, the composition of the root exudates was analyzed, and four metabolites (methyl hexadecanoate, methyl stearate, 2,4-di-tert-butylphenol, and n-hexadecanoic acid) significantly related to the chemotaxis and biofilm formation of NRCB010 were screened. Further assessment showed that these metabolites positively affected the growth, swarming motility, chemotaxis, or biofilm formation of strain NRCB010. Among these, n-hexadecanoic acid induced the most remarkable growth, chemotactic response, biofilm formation, and rhizosphere colonization. This study will help develop effective PGPR-based bioformulations to improve PGPR colonization and crop yields.

Is allelochemical synthesis in Casuarina equisetifolia plantation related to litter microorganisms?

Productivity decline of Casuarina equisetifolia plantation and difficulty in natural regeneration remains a serious problem because of allelopathy. Previous studies have confirmed that 2,4-di-tert-butylphenol (2,4-DTBP) are the major allelochemicals of the C. equisetifolia litter exudates. The production of these allelochemicals may derive from decomposition of litter or from the litter endophyte and microorganisms adhering to litter surfaces. In the present study, we aimed to evaluate the correlation between allelochemicals in litter and endophytic and epiphytic fungi and bacteria from litter. A total of 100 fungi and 116 bacteria were isolated from the interior and surface of litter of different forest ages (young, half-mature, and mature plantation). Results showed that the fermentation broth of fungal genera Mycosphaerella sp. and Pestalotiopsis sp., and bacterial genera Bacillus amyloliquefaciens, Burkholderia-Paraburkholderia, and Pantoea ananatis had the strongest allelopathic effect on C. equisetifolia seeds. Allelochemicals, such as 2,4-DTBP and its analogs were identified in the fermentation broths of these microorganisms using GC/MS analysis. These results indicate that endophytic and epiphytic fungi and bacteria in litters are involved in the synthesis of allelochemicals of C. equisetifolia. To further determine the abundance of the allelopathic fungi and bacteria, Illumina MiSeq high-throughput sequencing was performed. The results showed that bacterial genera with strong allelopathic potential were mainly distributed in the young and half-mature plantation with low abundance, while the abundance of fungal genera Mycosphaerella sp. and Pestalotiopsis sp. were higher in the young and mature plantations. In particular, the abundance of Mycosphaerella sp. in the young and mature plantations were 501.20% and 192.63% higher than in the half-mature plantation, respectively. Overall, our study demonstrates that the litter fungi with higher abundance in the young and mature plantation were involved in the synthesis of the allelochemical 2,4-DTBP of C. equisetifolia. This finding may be important for understanding the relationship between autotoxicity and microorganism and clarifying the natural regeneration problem of C. equisetifolia.