Legumes Regulate Symbiosis with Rhizobia via Their Innate Immune System

The Small Key to the Treasure Chest: Endogenous Plant Peptides Involved in Symbiotic Interactions

Plant growth and development are inextricably connected with rhizosphere organisms. Plants have to balance between strong defenses against pathogens while modulating their immune responses to recruit beneficial organisms such as bacteria and fungi. In recent years, there has been increasing evidence that regulatory peptides are essential in establishing these symbiotic relationships, orchestrating processes that include nutrient acquisition, root architecture modification, and immune modulation. In this review, we provide a comprehensive summary of the peptide families that facilitate beneficial relationships between plants and rhizosphere organisms.

Differential responses of Bradyrhizobium sp. SUTN9-2 to plant extracts and implications for endophytic interactions within different host plants

Bradyrhizobium sp. strain SUTN9-2 demonstrates cell enlargement, increased DNA content, and efficient nitrogen fixation in response to rice (Oryza sativa) extract. This response is attributed to the interaction between the plant's cationic antimicrobial peptides (CAMPs) and the Bradyrhizobium BacA-like transporter (BclA), similar to bacteroid in legume nodules. The present study reveals that SUTN9-2 can also establish functional endophytic interactions with chili (Capsicum annuum) and tomato (Solanum lycopersicum) plants. When exposed to extracts from chili and tomato, SUTN9-2 exhibits cell elongation, polyploidy, and reduced cell viability, with the effects being less pronounced for tomato extract. Transcriptomic and cytological analyses revealed that genes associated with CAMP resistance, nitrogen metabolism, nitrogen fixation, defense responses, and secretion systems were upregulated, while genes related to the cell cycle and certain CAMP-resistance mechanisms were downregulated, particularly in response to chili extract. This study suggests that SUTN9-2 likely evolves resistance mechanisms against CAMPs found in rice, chili, and tomato plants through mechanisms involving the protease-chaperone DegP, AcrAB-TolC multidrug efflux pumps, and polysaccharides. These mechanisms facilitate efflux, degradation, and the formation of protective barriers to resist CAMPs. Such adaptations enable SUTN9-2 to persist and colonize host plants despite antimicrobial pressures, influencing its viability, cell differentiation, and nitrogen fixation during endophytic interactions with various plant hosts.

Plant Colonization by Biocontrol Bacteria and Improved Plant Health: A Review

The use of biological control agents is one of the best strategies available to combat the plant diseases in an ecofriendly manner. Biocontrol bacteria capable of providing beneficial effect in crop plant growth and health, have been developed for several decades. It highlights the need for a deeper understanding of the colonization mechanisms employed by biocontrol bacteria to enhance their efficacy in plant pathogen control. The present review deals with the in-depth understanding of steps involved in host colonization by biocontrol bacteria. The colonization process starts from the root zone, where biocontrol bacteria establish initial interactions with the plant's root system. Moving beyond the roots, biocontrol bacteria migrate and colonize other plant organs, including stems, leaves, and even flowers. Also, the present review attempts to explore the mechanisms facilitating bacterial movement within the plant such as migrating through interconnected spaces such as vessels or in the apoplast, and applying quorum sensing or extracellular enzymes during colonization and what is needed to establish a long-term association within a plant. The impacts on microbial community dynamics, nutrient cycling, and overall plant health are discussed, emphasizing the intricate relationships between biocontrol bacteria and the plant's microbiome and the benefits to the plant's above-ground parts, the biocontrol 40 bacteria confer. By unraveling these mechanisms, researchers can develop targeted strategies for enhancing the colonization efficiency and overall effectiveness of biocontrol bacteria, leading to more sustainability and resilience.

Suppression of Nodule Formation by RNAi Knock-Down of Bax inhibitor-1a in Lotus japonicus

BACKGROUND/OBJECTIVES

The balanced regulation of innate immunity plays essential roles in rhizobial infection and the establishment and maintenance of symbiosis. The evolutionarily conserved cell death suppressor Bax inhibitor-1 plays dual roles in nodule symbiosis, providing a valuable clue in balancing immunity and symbiosis, while it remains largely unexplored in the legume Lotus japonicus.

METHODS/RESULTS

In the present report, the BI-1 gene family of L. japonicus was identified and characterized. We identified 6 BI-1 genes that translate into peptides containing 240-255 amino acids with different structural characteristics and isoelectric points. We performed phylogenetic analyses and detected evolutionary conservation and divergence among BI-1 proteins from L. japonicus, Glycine max, Medicago truncatula, Arabidopsis thaliana, and Oryza sativa. Expression profiles among different roots indicated that the inoculation of MAFF303099 significantly increased the expression of most of the L. japonicus BI-1 family genes. We down-regulated the transcripts of LjBI-1a by RNA interference and observed that LjBI-1a promotes nodulation and nodule formation.

CONCLUSIONS

These discoveries shed light on the functions of BI-1 genes in L. japonicus, and simultaneously emphasize the potential application of LjBI-1a in enhancing the symbiotic nitrogen fixation ability of legumes.

Symphony of survival: Insights into cross-talk mechanisms in plants, bacteria, and fungi for strengthening plant immune responses

Plants coexist with a diverse array of microorganisms, predominantly bacteria and fungi, in both natural and agricultural environments. While some microorganisms positively influence plant development and yield, others can cause harm to the host, leading to significant adverse impacts on the environment and the economy. Plant growth-promoting microorganisms (PGPM), including plant growth-promoting bacteria, arbuscular mycorrhizal fungus (AMF), and rhizobia, have been found to increase plant biomass production by synthesizing hormones, fixing nitrogen, and solubilizing phosphate and potassium. Numerous studies have contributed to unraveling the complex process of plant-microbe interactions in recent decades. In light of the increasing global challenges such as population growth, climate change, and resource scarcity, it has become imperative to explore the potential of plant-bacteria-fungi crosstalk in promoting sustainability. This review aims to bridge existing knowledge gaps, providing a roadmap for future research in this dynamic field by synthesizing current knowledge and identifying emerging trends.

Omics approaches in understanding the benefits of plant-microbe interactions

Plant-microbe interactions are pivotal for ecosystem dynamics and sustainable agriculture, and are influenced by various factors, such as host characteristics, environmental conditions, and human activities. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revolutionized our understanding of these interactions. Genomics elucidates key genes, transcriptomics reveals gene expression dynamics, proteomics identifies essential proteins, and metabolomics profiles small molecules, thereby offering a holistic perspective. This review synthesizes diverse microbial-plant interactions, showcasing the application of omics in understanding mechanisms, such as nitrogen fixation, systemic resistance induction, mycorrhizal association, and pathogen-host interactions. Despite the challenges of data integration and ethical considerations, omics approaches promise advancements in precision intervention and resilient agricultural practices. Future research should address data integration challenges, enhance omics technology resolution, explore epigenomics, and understand plant-microbe dynamics under diverse conditions. In conclusion, omics technologies hold immense promise for optimizing agricultural strategies and fortifying resilient plant-microbe alliances, paving the way for sustainable agriculture and environmental stewardship.

Targeted knockout of early nodulin-like 3 (MusaENODL3) gene in banana reveals its function in resistance to Xanthomonas wilt disease

Nodulins and nodulin-like proteins play an essential role in the symbiotic associations between legumes and Rhizobium bacteria. Their role extends beyond the leguminous species, as numerous nodulin-like proteins, including early nodulin-like proteins (ENODL), have been identified in various non-leguminous plants, implying their involvement in functions beyond nodulation, such as nutrient transport and growth modulation. Some ENODL proteins have been associated with plant defense against pathogens, as evident in banana infected with Xanthomonas campestris pv. musacearum (Xcm) causing banana Xanthomonas wilt (BXW) disease. Nonetheless, the specific role of ENODL in plant defense remains to be fully elucidated. The MusaENODL3 gene was found to be repressed in BXW-resistant banana progenitor 'Musa balbisiana' and 20-fold upregulated in BXW-susceptible cultivar 'Gonja Manjaya' upon early infection with Xcm. To further unravel the role of the ENODL gene in disease resistance, the CRISPR/Cas9 system was employed to disrupt the MusaENODL3 gene in 'Gonja Manjaya' precisely. Analysis of the enodl3 edited events confirmed the accurate manipulation of the MusaENODL3 gene. Disease resistance and gene expression analysis demonstrated that editing the MusaENODL3 gene resulted in resistance to BXW disease, with 50% of the edited plants remaining asymptomatic. The identification and manipulation of the MusaENODL3 gene highlight its potential as a critical player in plant-pathogen interactions, offering new opportunities for enhancing disease resistance in crops like banana, an important staple food crop and source of income for resource-poor farmers in the tropics. This study provides the first evidence of the direct role of the ENODL3 gene in developing disease-resistant plants.

Autophagy and Symbiosis: Membranes, ER, and Speculations

The interaction of plants and soil bacteria rhizobia leads to the formation of root nodule symbiosis. The intracellular form of rhizobia, the symbiosomes, are able to perform the nitrogen fixation by converting atmospheric dinitrogen into ammonia, which is available for plants. The symbiosis involves the resource sharing between two partners, but this exchange does not include equivalence, which can lead to resource scarcity and stress responses of one of the partners. In this review, we analyze the possible involvement of the autophagy pathway in the process of the maintenance of the nitrogen-fixing bacteria intracellular colony and the changes in the endomembrane system of the host cell. According to in silico expression analysis, ATG genes of all groups were expressed in the root nodule, and the expression was developmental zone dependent. The analysis of expression of genes involved in the response to carbon or nitrogen deficiency has shown a suboptimal access to sugars and nitrogen in the nodule tissue. The upregulation of several ER stress genes was also detected. Hence, the root nodule cells are under heavy bacterial infection, carbon deprivation, and insufficient nitrogen supply, making nodule cells prone to autophagy. We speculate that the membrane formation around the intracellular rhizobia may be quite similar to the phagophore formation, and the induction of autophagy and ER stress are essential to the success of this process.

Bacterial Endophytes from Legumes Native to Arid Environments Are Promising Tools to Improve Mesorhizobium-Chickpea Symbiosis under Salinity

Symbiotic nitrogen fixation is a major contributor of N in agricultural ecosystems, but the establishment of legume-rhizobium symbiosis is highly affected by soil salinity. Our interest is focused on the use of non-rhizobial endophytes to assist the symbiosis between chickpea and its microsymbiont under salinity to avoid loss of production and fertility. Our aims were (1) to investigate the impact of salinity on both symbiotic partners; including on early events of the Mesorhizobium-chickpea symbiosis, and (2) to evaluate the potential of four non-rhizobial endophytes isolated from legumes native to arid regions (Phyllobacterium salinisoli, P. ifriqiyense, Xanthomonas translucens, and Cupriavidus respiraculi) to promote chickpea growth and nodulation under salinity. Our results show a significant reduction in chickpea seed germination rate and in the microsymbiont Mesorhizobium ciceri LMS-1 growth under different levels of salinity. The composition of phenolic compounds in chickpea root exudates significantly changed when the plants were subjected to salinity, which in turn affected the nod genes expression in LMS-1. Furthermore, the LMS-1 response to root exudate stimuli was suppressed by the presence of salinity (250 mM NaCl). On the contrary, a significant upregulation of exoY and otsA genes, which are involved in exopolysaccharide and trehalose biosynthesis, respectively, was registered in salt-stressed LMS-1 cells. In addition, chickpea co-inoculation with LMS-1 along with the consortium containing two non-rhizobial bacterial endophytes, P. salinisoli and X. translucens, resulted in significant improvement of the chickpea growth and the symbiotic performance of LMS-1 under salinity. These results indicate that this non-rhizobial endophytic consortium may be an appropriate ecological and safe tool to improve chickpea growth and its adaptation to salt-degraded soils.

Microbial Colonization of the Host Plant: Cellular and Molecular Mechanisms of Symbiosis

Nitrogen is an essential element for all plants, animals, and microorganisms in the Earth's biosphere [...].

Screening of compound-formulated Bacillus and its effect on plant growth promotion

Bacillus bacteria can produce abundant secondary metabolites that are useful for biocontrol, especially in maintaining plant root microecology, and for plant protection. In this study, we determine the indicators of six Bacillus strains for colonization, promotion of plant growth, antimicrobial activity, and other aspects, with the aim of obtaining a compound bacteriological agent to construct a beneficial Bacillus microbial community in plant roots. We found that there was no significant difference in the growth curves of the six Bacillus strains over 12 h. However, strain HN-2 was found to have the strongest swimming ability and the highest bacteriostatic effect of n-butanol extract on the blight-causing bacteria Xanthomonas oryzae pv. oryzicola. The hemolytic circle produced by the n-butanol extract of strain FZB42 was the largest (8.67 ± 0.13 mm) and had the greatest bacteriostatic effect on the fungal pathogen Colletotrichum gloeosporioides, with a bacteriostatic circle diameter of 21.74 ± 0.40 mm. Strains HN-2 and FZB42 can rapidly form biofilms. Time-of-flight mass spectrometry and hemolytic plate tests showed that strains HN-2 and FZB42 may have significantly different activities because of their ability to produce large quantities of lipopeptides (i.e., surfactin, iturin, and fengycin). Different growth-promoting experiments revealed that the strains FZB42, HN-2, HAB-2, and HAB-5 had better growth-promoting potential than the control, and therefore these four strains were compounded in an equal ratio and used to treat pepper seedlings through root irrigation. We found an increase in the stem thickness (13%), leaf dry weight (14%), leaf number (26%), and chlorophyll content (41%) of pepper seedlings treated with the composite-formulated bacterial solution compared to the optimal single-bacterial solution treatment. Furthermore, several of these indicators increased by an average of 30% in the composite solution-treated pepper seedlings compared with the control water treatment group. In conclusion, the composite solution obtained by compounding strains FZB42 (OD₆₀₀ = 1.2), HN-2 (OD₆₀₀ = 0.9), HAB-2 (OD₆₀₀ = 0.9), and HAB-5 (OD₆₀₀ = 1.2) in equal parts highlights the advantages of a single bacterial solution, which includes achieving good growth promotion and antagonistic effects against pathogenic bacteria. The promotion of this compound-formulated Bacillus can reduce the application of chemical pesticides and fertilizers; promote plant growth and development; avoid the imbalances of soil microbial communities and thus reduce the risk of plant disease; and provide an experimental basis for the production and application of various types of biological control preparations in the future.

A Novel Rhizobium sp. Chiba-1 Strain Exhibits a Host Range for Nodule Symbiosis in Lotus Species

Rhizobia are soil bacteria that induce the formation of nodules in the roots of leguminous plants for mutualistic establishment. Although the symbiotic mechanism between Lotus japonicus and its major symbiotic rhizobia, Mesorhizobium loti, has been extensively characterized, our understanding of symbiotic mechanisms, such as host specificity and host ranges, remains limited. In the present study, we isolated a novel Rhizobium strain capable of forming nodules on L. burttii from agricultural soil at Iwate prefecture in Japan. We conducted genomic and host range ana-lyses of various Lotus species. The results obtained revealed that the novel isolated Rhizobium sp. Chiba-1 was closely related to R. leguminosarum and had a wide host range that induced nodule development, including L. burttii and several L. japonicus wild-type accessions. However, L. japonicus Gifu exhibited an incompatible nodule phenotype. We also identified the formation of an epidermal infection threads that was dependent on the Lotus species and independent of nodule organ development. In conclusion, this newly isolated Rhizobium strain displays a distinct nodulation phenotype from Lotus species, and the results obtained herein provide novel insights into the functional mechanisms underlying host specificity and host ranges.