Shifts in seed‐associated endophytic bacterial communities from parental lines to advanced generations in lima bean

Root endophytic microbial communities play a key role in plant health and productivity, yet the extent to which these communities vary across different crop species remains underexplored. This study aimed to investigate the root endophytic bacterial diversity of two important crops—hybrid tomato (Lycopersicon esculentum Mill. var. TNAU CO3) and finger millet (Eleusine coracana L. var. TNAU CO13)—to understand how crop-specific microbiomes contribute to agricultural sustainability and productivity. Targeted 16S rDNA amplicon sequencing was performed on tomato and finger millet root samples. A total of 165,772 and 181,327 16S rRNA gene sequences were generated from tomato and finger millet roots, respectively. These sequences were processed to identify amplicon sequence variants (ASVs), which were then classified taxonomically to assess community composition and functional prediction. Across the two hybrid crops, 1400 ASVs were detected in tomato and 1838 in finger millet. Proteobacteria (52.61–62.09%) were the dominant phylum in both, followed by Actinobacteria, Firmicutes, Bacteroidota, unidentified bacteria, Myxococcota, Verrucomicrobiota, Acidobacteriota, Fusobacteriota, and Chloroflexi. Finger millet roots harbored a more diverse and robust microbial assemblage, particularly enriched with nitrogen-fixing and oxidative stress-mitigating bacteria. In contrast, tomato roots showed a higher abundance of phosphate-solubilizing and biofilm-forming taxa, potentially enhancing resilience to environmental stress. These findings highlight the crop-specific nature of endophytic bacterial communities and their diverse functional capabilities. By revealing distinct microbial profiles in tomato and finger millet, this work provides a valuable foundation for developing strategies to optimize soil health, crop performance, and abiotic stress tolerance.

The mechanisms behind the unique capacity of the vine Boquila trifoliolata to mimic the leaves of several tree species remain unknown. A hypothesis in the original leaf mimicry report considered that microbial vectors from trees could carry genes or epigenetic factors that would alter the expression of leaf traits in Boquila. Here we evaluated whether leaf endophytic bacterial communities are associated with the mimicry pattern. Using 16S rRNA gene sequencing, we compared the endophytic bacterial communities in three groups of leaves collected in a temperate rainforest: (1) leaves from the model tree Rhaphithamnus spinosus (RS), (2) Boquila leaves mimicking the tree leaves (BR), and (3) Boquila leaves from the same individual vine but not mimicking the tree leaves (BT). We hypothesized that bacterial communities would be more similar in the BR–RS comparison than in the BT–RS comparison. We found significant differences in the endophytic bacterial communities among the three groups, verifying the hypothesis. Whereas non-mimetic Boquila leaves and tree leaves (BT–RS) showed clearly different bacterial communities, mimetic Boquila leaves and tree leaves (BR–RS) showed an overlap concerning their bacterial communities. The role of bacteria in this unique case of leaf mimicry should be studied further.

The Food and Agriculture Organization of the United Nations (FAO) has identified hybrid rice as ideal for addressing food scarcity in poor nations. A comprehensive investigation of the endophytic bacteria in hybrid rice seeds is essential from a microecological perspective to illuminate the mechanisms underlying its high yield, high quality, and multi-resistance. The endophytic bacterial diversity and community structures of 11 genetically correlated hybrid rice seeds with different rice blast resistance levels were studied using high-throughput sequencing (HTS) on the Illumina MiSeq platform to reveal their "core microbiota" and explore the effect of genotypes, genetic relationships, and resistance. Proteobacteria (78.15-99.15%) represented the most abundant group in the 11 hybrid rice cultivars, while Pantoea, Pseudomonas, and Microbacterium comprised the "core microbiota." Hybrid rice seeds with different genotypes, genetic correlations, and rice blast resistance displayed endophytic bacterial community structure and diversity variation. In addition, the network relationships between the rice seed endophytic bacteria of "the same female parent but different male parents" were more complex than those from "the same male parent but different female parents." Matrilineal inheritance may be the primary method of passing on endophytic bacteria in rice from generation to generation. The endophytic bacterial interaction network in rice blast-resistant hybrid rice seed varieties was more complicated than in susceptible varieties. In summary, this study demonstrated that the genotype, genetic relationship, and rice blast resistance were important factors affecting the community structures and diversity of endophytic bacteria in hybrid rice seeds, which was vital for revealing the interaction between endophytic bacteria and the host. KEY POINTS: • Pantoea, Pseudomonas, and Microbacterium represent the main endophytic bacteria in hybrid rice seeds. • Genotype is the primary factor affecting endophytic bacterial diversity in hybrid rice seeds. • The diversity of the endophytic bacterial community in hybrid rice seeds is related to their genotypes, genetic relationships, and rice blast resistance.

This research aimed to investigate the composition and diversity of endophytic bacterial community in seeds of four hybrid maize and their parental lines, which was used to reveal the potential relationship and association of endophytic bacteria between maize genotypes and their genetic relevance. High-throughput sequencing (HTS) technology showed that a total of 1419 OTUs (46.6%) were parental lines unique and 1052 OTUs (34.5%) were hybrid varieties unique, with only 575 core OTUs revealed in all the samples. Most OTUs belonged to Proteobacteria. Enterobacter (23.2%), Shigella (21.2%), Pseudomonas (15.8%) and Achromobacter (10.1%) were the major genera; the bacterial community composition and diversity of endophytic bacteria were inconsistent among different seed genotypes. Based on principal component analysis (PCA), the results referred that the endophytic composition of hybrid sample showed obvious correlation with their female parental lines, and in 'Jingke968' and 'MC738' with the same female line the endophytic community was more similar than other hybrid samples. This was the first ever use of HTS technology for investigating the endophytic bacterial diversity and community structures in seeds of genetically related maize genotypes, it was shown that, there were core microbes shared among all genotypes of seed samples, and the female parental line was more significant to impact on the composition of their hybrid seeds than male parental line. This study would provide scientific clues for the future research on the vertical transmission of endophytes among maize generations.

A wide range of microorganisms, including endophytes, frequently interact with forest trees. The role of endophytes in industrial conifers has not been fully investigated. The Yezo spruce Picea jezoensis is widely used for logging in Russia and Japan. In this work, the endophytic communities of bacteria and fungi in healthy needles, branches, and fresh wood of P. jezoensis from Primorsky Territory were analyzed using metagenomic analysis. The results indicate that the diversity of endophytic communities in P. jezoensis is predominantly influenced by the specific tree parts (for both bacteria and fungi) and by different tree specimens (for fungi). The most abundant bacterial classes were Alphaproteobacteria, Gammaproteobacteria and Actinobacteria. Functional analysis of KEGG orthologs (KOs) in endophytic bacterial community using PICRUSt2 and the PLaBAse PGPT ontology revealed that 59.5% of the 8653 KOs were associated with plant growth-promoting traits (PGPTs), mainly, colonization, stress protection, bio-fertilization, bio-remediation, vitamin production, and competition. Metagenomic analysis identified a high abundance of the genera Pseudomonas and Methylobacterium-Methylorubrum in P. jezoensis, which are known for their potential growth-promoting activity in other coniferous species. The dominant fungal classes in P. jezoensis were Dothideomycetes, Sordariomycetes, and Eurotiomycetes. Notably, the genus Penicillium showed a pronounced increase in relative abundance within the fresh wood and needles of Yezo spruce, while Aspergillus displayed elevated abundance specifically in the fresh wood. It is known that some of these fungi exhibit antagonistic activity against phytopathogenic fungi. Thus, our study describes endophytic communities of the Yezo spruce and provides a basis for the production of biologicals with potential applications in forestry and agriculture.

Effect of Arbuscular mycorrhizal fungi (AMF) inoculation on endophytic bacteria of lettuce

Bisphenol A (BPA) is widely acknowledged as an endocrine disruptor, and its toxicological effects have garnered considerable research interest. In this investigation, a soil pot experiment was conducted to examine the consequences of sustained BPA exposure on the growth of soybean seedlings, the transcriptome, and the endophytic bacterial community. We observed a substantial inhibition in soybean seedling growth. Transcriptome analysis showed that growth-related genes in both leaves and roots were markedly downregulated following BPA treatment. Intriguingly, BPA considerably increased the abundance and diversity of endophytic bacteria in leaves while suppressing beta diversity in roots. A significant association was identified between amplicon sequence variants and differentially expressed genes under BPA treatment in the leaves and roots. These findings illuminate the effects of continuous exposure to BPA on the transcriptome and endophyte of soybean seedlings, which may collectively impair soybean seedling growth, offering valuable insights into BPA toxicity in plants.

Responses of endophytic bacterial communities in rice roots to phosphorus deficiency at the seedling stages

Endophytic bacteria have a complex coevolutionary relationship with their host macroalgae. Dioecious macroalgae are important producers in marine ecosystems, but there is still a lack of research on how sex influences their endophytic bacteria. In this study, the endophytic bacterial communities in male and female S. thunbergii and their reproductive tissues (receptacles) were compared using culture methods and high-throughput sequencing. The endophytic bacterial communities detected by the two methods were different. Among the 78 isolated strains, the dominant phylum, genus, and species were Bacillota, Alkalihalobacillus, and Alkalihalobacillus algicola, respectively, in the algal bodies, while in the receptacles, they were Bacillota, Vibrio, and Vibrio alginolyticus. However, 24 phyla and 349 genera of endophytic bacteria were identified by high-throughput sequencing, and the dominant phylum and genus were Pseudomonadota and Sva0996_ Marine_ Group, respectively, in both the algal body and the receptacles. The two methods showed similar compositions of endophytic bacterial communities between the samples of different sexes, but the relative abundances of dominant and specific taxa were different. The high-throughput sequencing results showed more clearly that the sex of the host alga had an effect on its endophyte community assembly and a greater effect on the endophytic bacterial community in the receptacles. Moreover, most specific bacteria and predicted functional genes that differed between the samples from the males and females were related to metabolism, suggesting that metabolic differences are the main causes of sex differences in the endophytic bacterial community. Our research is the first to show that host sex contributes to the composition of endophytic bacterial communities in dioecious marine macroalgae. The results enrich the database of endophytic bacteria of dioecious marine macroalgae and pave the way for better understanding the assembly mechanism of the endophytic bacterial community of algae.

Plant-associated microbial communities play a central role in the plant response to biotic and abiotic stimuli, improving plant fitness under challenging growing conditions. Many studies have focused on the characterization of changes in abundance and composition of root-associated microbial communities as a consequence of the plant response to abiotic factors such as altered soil nutrients and drought. However, changes in composition in response to abiotic factors are still poorly understood concerning the endophytic community associated to the phyllosphere, the above-ground plant tissues. In the present study, we applied high-throughput 16S rDNA gene sequencing of the phyllosphere endophytic bacterial communities colonizing wild Populus trichocarpa (black cottonwood) plants growing in native, nutrient-limited environments characterized by hot-dry (xeric) riparian zones (Yakima River, WA), riparian zones with mid hot-dry (Tieton and Teanaway Rivers, WA) and moist (mesic) climates (Snoqualmie, Skykomish and Skagit Rivers, WA). From sequencing data, 587 Amplicon Sequence Variants (ASV) were identified. Surprisingly, our data show that a core microbiome could be found in phyllosphere-associated endophytic communities in trees growing on opposite sides of the Cascades Mountain Range. Considering only taxa appearing in at least 90% of all samples within each climatic zone, the core microbiome was dominated only by two ASVs affiliated Pseudomonadaceae and two ASVs of the Enterobacteriaceae family. Alpha-diversity measures indicated that plants colonizing hot-dry environments showed a lower diversity than those from mid hot-dry and moist climates. Beta-diversity measures showed that bacterial composition was significantly different across sampling sites. Accordingly, we found that specific ASV affiliated to Pseudomonadaceae and Enterobacteriaceae were significantly more abundant in the phyllosphere endophytic community colonizing plants adapted to the xeric environment. In summary, this study highlights that sampling site is the major driver of variation and that only a few ASV showed a distribution that significantly correlated to climate variables.

Seed endophytic bacterial (SEB) communities have been little studied to date, although these microorganisms may assist seeds and seedlings to cope with environmental stresses. Hyperaccumulators have become models for studying plant adaptation to extreme environments, such as metalliferous soils. This work aims to characterize the endophytic bacterial communities associated with hyperaccumulating seeds collected from their native ecosystems (nonmetalliferous or calamine soils). Using 16S rRNA metabarcoding, endophytic bacterial communities were characterized for seeds from 14 Noccaea caerulescens populations. Plant genomes and environmental properties of the sites had previously been described. In all plant populations the metabarcoding revealed a large SEB core microbiome composed of the main phyla and sub-phyla: ɣ-Proteobacteria (56.56%) > α-Proteobacteria (32.23%) > Actinobacteria (7.93%) > Firmicutes (3.78%). According to the literature, some operational taxonomic units (OTUs) found in the core microbiome may be related to “plant growth promoting endophytes” (PGPE). The changes in the relative abundance of phyla/subphyla were correlated to altitude, pH, and soil exchangeable elements (Al, Mg, Cd, Mn, Zn), yet the main parameters observed to drive SEB diversity were the plants’ genetics. The distinction between populations based on calamine soils and nonmetalliferous soils failed to explain the SEB communities’ structural dissimilarities. In fact, the factor that best explained these dissimilarities was the plant’s genetic subunit. Future research, based on transcriptomic approaches, should study the ecological roles of the SEB communities and their involvement in the adaptation of hyperaccumulators to metalliferous soils.

Super hybrid rice is one of the important research achievements in the field of rice super-high yield breeding in China. Compared with general high-yield rice, the yield potential of super hybrid rice is relatively high, and the average yields per hectare can exceed 10.5 t. This study aimed to study the endophytic bacterial community among a super hybrid rice combination and its parental lines and to reveal the potential relationship and association of endophytic bacteria between rice genotypes and their genetic relevance. In this research, through high-throughput sequencing based on Illumina Hiseq 2500 platform, the seeds of super hybrid rice variety ‘Shenliangyou 5814’ (sample C) and its parental lines ‘Y58S’ (sample M) and ‘C4114’ (sample F) independently cultivated by China were used as plant materials to study their endophytic bacterial structure and diversity. The number of OTUs for sample M, F and C was 327, 288 and 283 respectively, and among them 218 endophytic OTUs coexisted in the 3 samples. Pantoea (18.6–31.1%) was the first dominant groups shared in all three samples, and other dominant shared groups belonged to Methylobacterium (4.48%~17.65%), Sphingomonas (4.0%~11.4%), Rhizobium (5.69–8.78%), Microbacterium (3.85%~9.41%) and Pseudomonas (4.13%~5.68%). Although Principal Coordinates Analysis (PCoA) and Non-metric Multidimensional Scaling (NMDS) analysis showed that there were obvious differences in endophytic bacterial community composition and structure among the 3 samples, the dominant endophytic bacterial genus sample C and its parental lines remained consistency. This study would provide scientific clues for the future research on the vertical transmission of endophytes between rice generations.

Sorghum is the second most cultivated crop in Africa and is a staple food source in many African communities. Exploiting the associated plant growth-promoting bacteria (PGPB) has potential as an agricultural biotechnology strategy to enhance sorghum growth, yield and nutritional properties. Therefore this study aimed to evaluate factors that shape bacterial communities associated with sorghum farmed in South Africa, and to detect bacteria consistently associated with sorghum which may impart PGP activities. Terminal-Restriction Fragment Length Polymorphism (T-RFLP) was used to assess factors that potentially shape rhizospheric (rhizosphere and rhizoplane) and endophytic (root, shoot, stem) bacterial communities associated with South African sorghum, and together with Denaturing Gradient Gel Electrophoresis (DGGE) to identify consistently sorghum-associated bacterial taxa. The sorghum rhizospheric communities were less variable than the endophytic ones. Geographical location was the main driver in describing bacterial community assemblages found in rhizospheric sorghum-linked niches, with total NO3-N, NH4-N, nitrogen, carbon, pH and, to a lesser extent, clay content identified as the main abiotic factors shaping sorghum-associated soil communities. Endophytic communities presented rather stochastic assemblages, with pH being the main variable explaining their structures. Despite community variations, specific bacterial taxa were consistently detected in sorghum-created rhizospheric and endophytic environments, irrespective of environmental factor effects. Soil structure and composition, which are influenced by agricultural practices, played major roles in shaping sorghum-associated edaphic bacterial communities. In contrast, endophytic bacterial communities displayed more variation. Nevertheless, potentially agronomically relevant (cyano)bacterial taxa constantly associated with sorghum were identified which is suggestive of their deterministic recruitment.

Soil microbial community encompasses a perplexing range of physiological, metabolic and genomic diversity which can be explored through direct cultivation-based techniques or indirect molecular approaches. As cultivation-based methods are limited to only the culturable microorganisms, information about the majority of the unculturable diversity is missing. To circumvent this problem, molecular approaches based on the analysis of total DNA isolated from the environmental samples, often termed as metagenomic DNA, are employed. These molecular approaches can study the rare bacterial populations present in low abundance in soil. Though molecular approaches can study the soil diversity much better than the traditional culturable approaches, the success of any metagenomic study depends on the quality and quantity of DNA isolated from the metagenomic sample. In this chapter, metagenomic approaches have been employed to study the diversity of rhizospheric, root endophytic and root nodule bacterial communities of Vigna radiata. Results indicated that in rhizospheric and root nodule bacterial communities, Proteobacteria were predominant while in root endophytic communities, Actinobacteria were predominant. Deltaproteobacteria predominated rhizospheric community, whereas Gammaproteobacteria and Alphaproteobacteria dominated root endophytic and root nodule communities, respectively. Coupling traditional approaches with advanced next-generation sequencing techniques for accessing bacterial community ecology and physiology may bring new insights in understanding the microbial life in the rhizosphere and their further progression as root or nodule endophytes.

Regardless of their growth locations and species diversity, plants have endophytic bacterial communities. Bilberry (Vaccinium myrtillus L.) is valuable for human health because of its antioxidant properties, and the plant has adapted to stressful growing conditions in forests. Here, we aimed to describe the composition of the community of endophytic microorganisms in bilberry leaves and to determine whether the diversity of endophytic bacteria varies depending on the geographical location of the plants. In this study, we evaluated the significance of endophytes in the host plant and the potential use of such bacteria. Twenty-five culturable bacterial isolates were identified in V. myrtillus leaves based on 16S rRNA gene sequencing and phylogenetic analysis. For the first time, we report upon the diversity of endophytic communities coexisting in bilberry leaves in different geographical locations of the Nordic-Baltic region. Under harsh conditions, the bilberry plants had a greater diversity of bacteria. The bacterial families Bacillaceae, Paenibacillaceae and Micrococcaceae were the most common endophytes in leaves of bilberry. Strains of Staphylococcaceae, Lactobacillaceae, Pseudomonaceae, Corynebacteriaceae and Planococcaceae were identified in samples from Finland and Norway. Plant growth-promoting genes (acdS and AcPho) and/or enzymatic activity were identified in many isolates.