Synergism of endophytic Bacillus subtilis and Klebsiella aerogenes modulates plant growth and bacoside biosynthesis in Bacopa monnieri

Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot

BACKGROUND

Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health.

RESULTS

Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease.

CONCLUSIONS

Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe's occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops. Video Abstract.

Unraveling the functional characteristics of endophytic bacterial diversity for plant growth promotion and enhanced secondary metabolite production in Pelargonium graveolens

The rich diversity of microbial endophytic communities associated with plants, often referred to as the second genome, serves as a compelling illustration of efficient co-evolution. This noteworthy partnership plays a pivotal role in sustaining plant well-being and enhancing plant adaptability across diverse habitats. Therefore, examining the diversity of endophytic microbes associated with their particular host plant is valuable for gaining insights into the vast spectrum of plant-microbe interactions. The present experiments aimed at investigating the bacterial endophytic diversity in both root and shoot tissues of Pelargonium graveolens, employing culture dependent and culture independent high-throughput metagenomics approach. A total of 614 and 620 operational taxonomic units (OTUs), encompassing 291 and 229 genera, were identified in the shoot and root tissues of P. graveolens, respectively. Furthermore, the subsequent classification of OTUs revealed 15 highly abundant phyla, with Proteobacteria dominating both root and shoot tissues. Notably, an exceptionally high abundance of Firmicutes phyla was observed in the shoot compared to the root. Additionally, 30 bacterial endophytes from the root, stem, petiole, and leaves were isolated and molecularly characterized, unveiling a consistent pattern of diversity distribution between the root and shoot of P. graveolens. Upon screening all isolates for plant growth promoting traits, Pseudomonas oryzihabitans was found to be positive for major biochemical test like nitrogen fixation, phosphate solubilization etc. and on inoculation resulted in about two-fold increase in content of essential oil accompanied by a significant rise in the geraniol and citronellol content. Diving deep into the genetic constitution of P. oryzihabitans unveiled a substantial number of genes directly and indirectly contributing to the endophyte's capability in colonizing host plants effectively. In summary, data obtained from metagenomics and culture dependent approaches including glass house trials suggest potential bacterial endophytes suitable for field applications for yield enhancement and in planta secondary metabolite enhancement investigations.

Response of Chinese cabbage (Brassica rapa subsp. pekinensis) to bacterial soft rot infection by change of soil microbial community in root zone

Chinese cabbage, scientifically known as Brassica rapa subsp. pekinensis, is a highly popular vegetable in China for its delectable taste. However, the occurrence of bacterial soft rot disease poses a significant threat to its growth and overall development. Consequently, this study aimed to explore the defense mechanisms employed by Chinese cabbage against bacterial soft rot disease. Specifically, the investigation focused on understanding the relationship between the disease and the microbial communities present in the soil surrounding the roots of Chinese cabbage. Significant disparities were observed in the composition of microbial communities present in the root-zone soil of healthy Chinese cabbage plants compared to those affected by Pectobacterium brasiliense-caused soft rot disease. The analysis of 16S rRNA gene high-throughput sequencing results revealed a lower abundance of Proteobacteria (8.39%), Acidobacteriot (0.85), Sphingomonas (3.51%), and Vicinamibacteraceae (1.48%), whereas Firmicutes (113.76%), Bacteroidota (8.71%), Chloroflexi (4.89%), Actinobacteriota (1.71%), A4b (15.52%), Vicinamibacterales (1.62%), and Gemmatimonadaceae (1.35%) were more prevalent in healthy plant soils. Similarly, the analysis of ITS gene high-throughput sequencing results indicated a reduced occurrence of Chytridiomycota (23.58%), Basidiomycota (21.80%), Plectosphaerella (86.22%), and Agaricomycetes (22.57%) in healthy soils. In comparison, Mortierellomycota (50.72%), Ascomycota (31.22%), Podospora (485.08%), and Mortierella (51.59%) were more abundant in healthy plant soils. In addition, a total of 15 bacterial strains were isolated from the root-zone soil of diseased Chinese cabbage plants. These isolated strains demonstrated the ability to fix nitrogen (with the exception of ZT20, ZT26, ZT41, ZT45, and ZT61), produce siderophores and indole acetic acid (IAA), and solubilize phosphate. Notably, ZT14 (Citrobacter freundii), ZT33 (Enterobacter cloacae), ZT41 (Myroides odoratimimus), ZT52 (Bacillus paramycoides), ZT58 (Klebsiella pasteurii), ZT45 (Klebsiella aerogenes), and ZT32 (Pseudomonas putida) exhibited significant growth-promoting effects as determined by the plant growth promotion (PGP) tests. Consequently, this investigation not only confirmed the presence of the soft rot pathogen in Chinese cabbage plants in Hangzhou, China, but also advanced our understanding of the defense mechanisms employed by Chinese cabbage to combat soft rot-induced stress. Additionally, it identified promising plant-growth-promoting microbes (PGPMs) that could be utilized in the future to enhance the Chinese cabbage industry.

Isolation of endophytes from Dioscorea nipponica Makino for stimulating diosgenin production and plant growth

KEY MESSAGE

Both bacterial and fungal endophytes exhibited one or more plant growth-promoting (PGP) traits. Among these strains, the Paenibacillus peoriae SYbr421 strain demonstrated the greatest activity in the direct biotransformation of tuber powder from D. nipponica into diosgenin. Endophytes play crucial roles in shaping active metabolites within plants, significantly influencing both the quality and yield of host plants. Dioscorea nipponica Makino accumulates abundant steroidal saponins, which can be hydrolyzed to produce diosgenin. However, our understanding of the associated endophytes and their contributions to plant growth and diosgenin production is limited. The present study aimed to assess the PGP ability and potential of diosgenin biotransformation by endophytes isolates associated with D. nipponica for the efficient improvement of plant growth and development of a clean and effective approach for producing the valuable drug diosgenin. Eighteen bacterial endophytes were classified into six genera through sequencing and phylogenetic analysis of the 16S rDNA gene. Similarly, 12 fungal endophytes were categorized into 5 genera based on sequencing and phylogenetic analysis of the ITS rDNA gene. Pure culture experiments revealed that 30 isolated endophytic strains exhibited one or more PGP traits, such as nitrogen fixation, phosphate solubilization, siderophore synthesis, and IAA production. One strain of endophytic bacteria, P. peoriae SYbr421, effectively directly biotransformed the saponin components in D. nipponica. Moreover, a high yield of diosgenin (3.50%) was obtained at an inoculum size of 4% after 6 days of fermentation. Thus, SYbr421 could be used for a cleaner and more eco-friendly diosgenin production process. In addition, based on the assessment of growth-promoting isolates and seed germination results, the strains SYbr421, SYfr1321, and SYfl221 were selected for greenhouse experiments. The results revealed that the inoculation of these promising isolates significantly increased the plant height and fresh weight of the leaves and roots compared to the control plants. These findings underscore the importance of preparing PGP bioinoculants from selected isolates as an additional option for sustainable diosgenin production.

Plants and endophytes interaction: a "secret wedlock" for sustainable biosynthesis of pharmaceutically important secondary metabolites

Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future.

Diversity and Exploration of Endophytic Bacilli for the Management of Head Scab (Fusarium graminearum) of Wheat

Fusarium graminearum causing head scab (HS) or head blight (HB) disease in wheat is one of the nasty fungi reported to cause significant grain quality and yield loss. Biological control using endophytic bacteria has emerged as a prospective option for containing fungal diseases in an environmentally benevolent, durable, and sustainable manner. In this regard, 112 endophytic bacilli were isolated from the anthesis stage (Zadok’s growth stage 65) from five different wheat genotypes with an aim to identify prospective antagonistic strains against F. graminearum. The molecular identity of the strains was confirmed by matching 16S rRNA sequences of bacterial strains with the gene sequences of type strains available in the National Center for Biotechnology Information database and reported 38 different species of Bacillus in all the five wheat cultivars. Further, it has been observed that only fourteen strains (B. clarus NOK09, B. mojavensis NOK16, B. subtilis NOK33, B. rugosus NOK47, B. mojavensis NOK52, B. clarus NOK59, B. coahuilensis NOK72, B. cabrialesii NOK78, B. cabrialesii NOK82, B. rugosus NOK85, B. amyloliquefaciens NOK89, B. australimaris NOK95, B. pumilus NOK103, and B. amyloliquefaciens NOK109) displayed in-vitro antagonistic effect against Fusarium graminearum fungus. Furthermore, the three endophytic Bacillus strains showing the strongest antagonistic effect (>70% of growth inhibition of fungal mycelium) under in-vitro antagonistic assay were selected for field experiments. In a two-year consecutive field study, a combination of three strains (B. clarus NOK09 + B. subtilis NOK33 + B. amyloliquefaciens NOK109) displayed a remarkable reduction in HS disease index by 81.47% and 77.85%, respectively. Polymerase chain reaction assay detected three genes (ituD, bmyC, and srfA) involved in antibiotic biosynthesis pathways. Additional attributes such as potassium solubilization, siderophore release, and hydrolytic enzyme (protease, lipase, amylase, chitinase, and pectinase) synthesis have been observed in these strains. Overall, the present study was successful in profiling endophytic bacilli and selecting the combination of effective antagonistic endophytic Bacillus strains that could be the best alternative for the sustainable and ecological sound management of HS disease in wheat under field conditions.