SEED BACTERIAL ENDOPHYTES: COMMON GENERA, SEED-TO-SEED VARIABILITY AND THEIR POSSIBLE ROLE IN PLANTS

Seed-Borne Bacterial Diversity of Fescue (Festuca ovina L.) and Properties Study

Rich endophytic bacterial communities exist in fescue (Festuca ovina L.) and play an important role in fescue growth, cold tolerance, drought tolerance and antibiotic tolerance. To screen for probiotics carried by fescue seeds, seven varieties were collected from three different regions of China for isolation by the milled seed method and analyzed for diversity and motility, biofilm and antibiotic resistance. A total of 91 bacterial isolates were obtained, and based on morphological characteristics, 36 representative dominant strains were selected for 16S rDNA sequencing analysis. The results showed that the 36 bacterial strains belonged to four phyla and nine genera. The Firmicutes was the dominant phylum, and Bacillus, Paenibacillus and Pseudomonas were the dominant genera. Most of the strains had motility (80%) and were biofilm-forming (91.7%). In this study, 15 strains were capable of Indole-3-acetic acid (IAA) production, 24 strains were capable of nitrogen fixation, and some strains possessed amylase and protease activities, suggesting their potential for growth promotion. Determination of the minimum inhibitory concentration (MIC) against the bacteria showed that the strains were not resistant to tetracycline and oxytetracycline. Pantoea (QY6, LH4, MS2) and Curtobacterium (YY4) showed resistance to five antibiotics (ampicillin, kanamycin, erythromycin, sulfadiazine and rifampicin). Using Pearson correlation analysis, a significant correlation was found between motility and biofilm, and between biofilm and sulfadiazine. In this study, we screened two strains of Pantoea (QY6, LH4) with excellent growth-promoting ability as well as broad-spectrum antibiotic resistance. which provided new perspectives for subsequent studies on the strong ecological adaptations of fescue, and mycorrhizal resources for endophytic bacteria and plant interactions.

Revealing the seed microbiome: Navigating sequencing tools, microbial assembly, and functions to amplify plant fitness

Microbial communities within seeds play a vital role in transmitting themselves to the next generation of plants. These microorganisms significantly impact seed vigor and early seedling growth, for successful crop establishment. Previous studies reported on seed-associated microbial communities and their influence on processes like dormancy release, germination, and disease protection. Modern sequencing and conventional methods reveal microbial community structures and environmental impacts, these information helps in microbial selection and manipulation. These studies form the foundation for using seed microbiomes to enhance crop resilience and productivity. While existing research has primarily focused on characterizing microbiota in dried mature seeds, a significant gap exists in understanding how these microbial communities assemble during seed development. The review also discusses applying seed-associated microorganisms to improve crops in the context of climate change. However, limited knowledge is available about the microbial assembly pattern on seeds, and their impact on plant growth. The review provides insight into microbial composition, functions, and significance for plant health, particularly regarding growth promotion and pest control.

Effect of Epichloë gansuensis Endophyte on Seed-Borne Microbes and Seed Metabolites in Achnatherum inebrians

The seed-borne microbiota and seed metabolites of the grass Achnatherum inebrians, either host to Epichloë gansuensis (endophyte infected [EI]) or endophyte free (EF), were investigated. This study determined the microbial communities both within the seed (endophytic) and on the seed surface (epiphytic) and of the protective glumes by using Illumina sequencing technology. Epichloë gansuensis decreased the richness of the seed-borne microbiota except for the epiphytic fungi of glumes and also decreased the diversity of seed-borne microbiota. In addition, metabolites of seeds and glumes were detected using liquid chromatography-mass spectrometry (LC-MS). Unlike with the seeds of EF plants, the presence of E. gansuensis resulted in significant changes in the content of 108 seed and 31 glume metabolites. A total of 319 significant correlations occurred between seed-borne microbiota and seed metabolites; these correlations comprised 163 (147 bacterial and 16 fungal) positive correlations and 156 (136 bacterial and 20 fungal) negative correlations. Meanwhile, there were 42 significant correlations between glume microbiota and metabolites; these correlations comprised 28 positive (10 bacterial and 18 fungal) and 14 negative (9 bacterial and 5 fungal) correlations. The presence of E. gansuensis endophyte altered the communities and diversities of seed-borne microbes and altered the composition and content of seed metabolites, and there were many close and complex relationships between microbes and metabolites. IMPORTANCE The present study was to investigate seed-borne microbiota and seed metabolites in Achnatherum inebrians using high-throughput sequencing and LC-MS technology. Epichloë gansuensis decreased the richness of the seed-borne microbiota except for the epiphytic fungi of glumes and also decreased the diversity of seed-borne microbiota. Compared with endophyte-free plants, the content of 108 seed and 31 glume metabolites of endophyte-infected plants was significantly changed. There were 319 significant correlations between seed-borne microbiota and seed metabolites and 42 significant correlations between glume microbiota and metabolites.

Interaction networks reveal highly antagonistic endophytic bacteria in native maize seeds from traditional milpa agroecosystems

Milpas are traditional Mesoamerican agroecosystems maintained with ancestral practices. Maize landraces are grown in polyculture, creating highly productive and diverse ecosystems. Recent studies suggest that milpas maintain beneficial plant-microbe interactions that are probably absent in modern agroecosystems; however, direct comparisons of the microbiome of plants between traditional and modern agroecosystems are still needed. Here, we studied seed endophytic bacterial communities from native maize landraces from milpas (NME) and hybrid varieties (HME). First, we quantified the abundance of culturable endophytic microbes; next, we assessed pairwise antagonistic interaction networks between bacterial isolates; finally, we compared bacterial community structure by 16S rRNA amplicon sequencing. We found that seeds from native maize landraces harbor a higher endophytic microbial load, including more bacterial strains with antagonistic activity against soil-borne bacteria, and overall harbor more diverse bacterial communities than the hybrid varieties. Noteworthy, most of the seed-endophytic strains with antagonistic activity corresponded to Burkholderia spp. that were only found in native maize seeds, through both culture-dependent and independent strategies. Altogether, our results support that crop modernization alters the functions and structure of plant-associated microbes; we propose native maize from milpas could serve as a model for understanding plant-microbe interactions and the effect of modernization.

Seed-Derived Microbial Community of Wild Cicer Seedlings: Composition and Augmentation to Domesticated Cicer

Seed-borne bacteria are a unique group of microorganisms capable of maintaining stable populations within plant tissues and seeds. These bacteria may benefit their host from germination to maturation and are of great interest for basic and applied plant-microbe interaction studies. Furthermore, many such beneficial bacteria present in wild plant species are missing in their respective congeneric domesticated forms. The objectives of this study were to explore the bacterial communities within the seeds of wild Cicer species and to select beneficial bacteria which could be used to improve production of domesticated chickpea (C. arietinum). We analyzed the composition of seed-borne bacteria of chickpea (Cicer spp.), comparing wild and domesticated species from different geographic locations. Subsequently, we isolated the dominant and prevalent seed-borne bacteria from wild Cicer judaicum and assessed their ability to colonize and affect the growth of domesticated chickpea and other legume crops. The composition and structure of seed-borne bacteria, determined by amplicon sequencing of the 16S rRNA gene, differed between wild and domesticated chickpea and varied among geographic locations. The genus Burkholderia dominated samples from domesticated chickpea at all examined sites, while Bacillus or Sphingomonas dominated cultures isolated from wild C. judaicum, dependent on geographic location. A particular Bacillus strain, Bacillus sp. CJ, representing the most prevalent bacterium in wild C. judaicum, was further isolated. Bacillus sp. CJ, applied by seed coating, successfully inhabited domesticated chickpea plants and improved plant growth parameters. These results demonstrate the potential for reconstructing the microbiota of crop plants using the wild microbiota reservoir.

IMPORTANCE Chickpea (garbanzo bean, hummus, Cicer arietinum) representing the third legume crop produced globally. As is the case for many other domesticated crops, the adaptation and resistance of chickpea to biotic and abiotic stresses is inferior compared to that of their wild progenitors and relatives. Re-establishing desirable characteristics from wild to domesticated species may be achieved by reconstructing beneficial microbiota. In this study, we examined the seed-associated microbiota of both wild and domesticated chickpea and applied isolated beneficial bacteria originating from wild Cicer judaicum to domesticated chickpea by seed coating. This isolate, Bacillus sp. CJ, was successfully established in the crop and enhanced its growth, demonstrating effective and efficient manipulation of the chickpea microbiota as a potential model for future application in other crop plants.

Analysis of seed-associated bacteria and fungi on staple crops using the cultivation and metagenomic approaches

One of the key factors affecting seed quality is microbial communities residing on and in the seeds. In this study, microbial populations of seeds of conventionally and organically produced wheat, barley, and maize were analyzed using two different approaches: the cultivation method and metagenomics. For cultivation, three basic media were used: DG18 (for fungi), and nutrient agar or tryptic soy agar supplemented with cycloheximide or nystatin (for bacteria). Metagenomic sequencing was performed using the Illumina MiSeq platform. A total of 452 bacterial isolates comprising 36 genera and 5 phyla and 90 fungal isolates comprising 10 genera and 3 phyla were obtained from the seed surfaces. Among bacteria, representatives from the genera Bacillus, Pantoea, Paenibacillus, and Curtobacterium predominated, and among fungi, Aspergillus predominated. A total of 142 fungal OTUs and 201 bacterial OTUs were obtained from all the samples. Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria comprised most of the bacterial OTUs, and Ascomycota comprised most of the fungal OTUs. Only 3 fungal OTUs (representatives of Curvibasidium, Venturia, and Dermateaceae) were exclusively present only within seeds and not on the seed surfaces. Barley seeds had the highest microbial load and richness, whereas corn had the lowest. Wheat and barley shared a higher number of OTUs than either of them did with corn with higher overlap between conventionally grown cereals than between organically grown cereals. Some OTUs were farming specific. This study demonstrates that the microbiome of cereal seeds is greatly dependent on the species of the host and is less affected by agricultural practices.

Spatiotemporal Assembly of Bacterial and Fungal Communities of Seed-Seedling-Adult in Rice

Seeds harbor not only genetic information about plants but also microbial communities affecting plants’ vigor. Knowledge on the movement and formation of seed microbial communities during plant development remains insufficient. Here, we address this knowledge gap by investigating endophytic bacterial and fungal communities of seeds, seedlings, and adult rice plants. We found that seed coats act as microbial niches for seed bacterial and fungal communities. The presence or absence of the seed coat affected taxonomic composition and diversity of bacterial and fungal communities associated with seeds and seedlings. Ordination analysis showed that niche differentiation between above- and belowground compartments leads to compositional differences in endophytic bacterial and fungal communities originating from seeds. Longitudinal tracking of the composition of microbial communities from field-grown rice revealed that bacterial and fungal communities originating from seeds persist in the leaf, stem, and root endospheres throughout the life cycle. Our study provides ecological insights into the assembly of the initial endophytic microbial communities of plants from seeds.

The cypsela (achene) of Echinacea purpurea as a diffusion unit of a community of microorganisms

Echinacea purpurea is a plant cultivated worldwide for its pharmaceutical properties, mainly related to the stimulation of the immune system in the treatment of respiratory infections. The cypselas (fruits) of E. purpurea were examined in order to investigate the presence, localization and potential function(s) of endophytic microorganisms. Electron and confocal microscopy observations showed that three different components of microorganisms were associated to cypselas of E. purpurea: (i) one endocellular bacterial component in the cotyledons, enclosed within the host membrane; (ii) another more generic bacterial component adhering to the external side of the perianth; and (iii) a fungal component inside the porous layer of the perianth, the woody and porous modified residual of the flower, in the form of numerous hyphae able to cross the wall between adjacent cells. Isolated bacteria were affiliated to the genera Paenibacillus, Pantoea, and Sanguibacter. Plate tests showed a general resistance to six different antibiotics and also to an antimicrobial-producing Rheinheimera sp. test strain. Finally, microbiome-deprived E. purpurea seeds showed a reduced ability to germinate, suggesting an active role of the microbiome in the plant vitality. Our results suggest that the endophytic bacterial community of E. purpurea, previously found in roots and stem/leaves, might be already carried at the seed stage, hosted by the cotyledons. A further microbial fungal component is transported together with the seed in the perianth of the cypsela, whose remarkable structure may be considered as an adaptation for fungal transportation, and could influence the capability of the seed to germinate in the soil.Key Points• The fruit of Echinacea purpurea contains fungi not causing any damage to the plant.• The seed cotyledons contain endocellular bacteria.• Seed/fruit deprived of the microbiome showed a reduced ability to germinate.

Quantitative proteomic analysis reveals altered enzyme expression profile in Zea mays roots during the early stages of colonization by Herbaspirillum seropedicae

The use of plant growth-promoting bacteria as agricultural inoculants of plants should be encouraged because of their prominent role in biological nitrogen fixation, the increase of nutrient uptake by roots, abiotic stress mitigation, and disease control. The complex mechanisms underlying the association between plant and beneficial bacteria have been increasingly studied, and proteomic tools can expand our perception regarding the fundamental molecular processes modulated by the interaction. In this study, we investigated the changes in protein expression in maize roots in response to treatment with the endophytic diazotrophic Herbaspirillum seropedicae and the activities of enzymes related to nitrogen metabolism. To identify maize proteins whose expression levels were altered in the presence of bacteria, a label-free quantitative proteomic approach was employed. Using this approach, we identified 123 differentially expressed proteins, of which 34 were upregulated enzymes, in maize roots cultivated with H. seropedicae. The maize root colonization of H. seropedicae modulated the differential expression of enzymes involved in the stress response, such as peroxidases, phenylalanine ammonia-lyase, and glutathione transferase. The differential protein profile obtained in the inoculated roots reflects the effect of colonization on plant growth and development compared with control plants.

IDENTIFICATION OF ENDOPHYTIC BACTERIA OF SEEDS FROM Cedrela odorata L. (Meliaceae) WITH BIOTECHNOLOGICAL CHARACTERISTICS

In the present study, 62 endophytic bacterial strains of cedar seeds (Cedrela odorataL.), collected in the municipalities of Huehuetán, Motozintla, and Pijijiapan in the state of Chiapas, Mexico were isolated. The goal was to identify characteristics of biotechnological interest such as biocontrol, promotion of plant growth, and growth in aromatic compounds. The strains were identified by the partial sequence of the 16S ribosomal gene as belonging to the Bacillusgenus. The biocontrol capacity of phytopathogenic fungi, production of indoleacetic acid (IAA), solubilization of phosphate, and growth in xenobiotic compounds (phenanthrene, benzene, anthracene, or phenol) were detected in 26 strains of the 62 isolates. 21 % of the strains inhibited the mycelial growth of Alternaria solaniand Fusariumsp., and 13 % of the Phytophthora capsicioomycete. IAA production was detected in 24 isolates, phosphate solubilizing activity was identified in 18 isolates, while the ability to grow in the presence of phenanthrene and benzene was found in 26 isolates; 24 isolates grew in the presence of anthracene and only two isolates grew in phenol as the only carbon sources. This is the first report of the isolation and identification of endophytic bacteria from cedar seeds, where biotechnological characteristics were detected for biological control, promotion of plant growth, and growth in the presence of xenobiotic compounds.

Plant microbiota modified by plant domestication

Human life became largely dependent on agricultural products after distinct crop-domestication events occurred around 10,000 years ago in different geographical sites. Domestication selected suitable plants for human agricultural practices with unexpected consequences on plant microbiota, which has notable effects on plant growth and health. Among other traits, domestication has changed root architecture, exudation, or defense responses that could have modified plant microbiota. Here we present the comparison of reported data on the microbiota from widely consumed cereals and legumes and their ancestors showing that different bacteria were found in domesticated and wild plant microbiomes in some cases. Considering the large variability in plant microbiota, adequate sampling efforts and function-based approaches are needed to further support differences between the microbiota from wild and domesticated plants. The study of wild plant microbiomes could provide a valuable resource of unexploited beneficial bacteria for crops.

New Insight into the Composition of Wheat Seed Microbiota

Endophytes are associated with host plants throughout their life history from seed germination to fruit development. One of the most important plant organs colonized by endophytic microbiota is the seed. The aim of this study was to determine the structure of the seed core microbiome inhabiting the endosperms and embryos of eight wheat cultivars with the use of a culture-independent technique. The seeds of Triticum aestivum L. cv. Hondia, Wilejka, STH, Opcja, Tybalt, Euforia and Triticum spelta L. cv. Rokosz and Schwabencorn (producer: Plant Breeding Strzelce Sp. z o.o. Group IHAR) were studied. Rokosz and Hondia were cultured in vitro and in vivo to identify obligatory bacterial endophytes. A restrictive analysis of reads originating from the in vitro plants has demonstrated that the bacterial genera Paenibacillus and Propionibacterium inhabiting Rokosz and Hondia plants have a status of obligatory microorganisms. Greater biodiversity of seed-borne endophytes was found in the seed endosperms than in the embryos. The multiple comparison analysis of the OTU abundance indicated that the seed part significantly influenced the relative abundance. The seed-born microbiome is not statistically significantly dependent on the wheat cultivars; however, it cannot be claimed that every wheat seed is the same.

The ecological role of bacterial seed endophytes associated with wild cabbage in the United Kingdom

Endophytic bacteria are known for their ability in promoting plant growth and defense against biotic and abiotic stress. However, very little is known about the microbial endophytes living in the spermosphere. Here, we isolated bacteria from the seeds of five different populations of wild cabbage (Brassica oleracea L) that grow within 15 km of each other along the Dorset coast in the UK. The seeds of each plant population contained a unique microbiome. Sequencing of the 16S rRNA genes revealed that these bacteria belong to three different phyla (Actinobacteria, Firmicutes, and Proteobacteria). Isolated endophytic bacteria were grown in monocultures or mixtures and the effects of bacterial volatile organic compounds (VOCs) on the growth and development on B. oleracea and on resistance against a insect herbivore was evaluated. Our results reveal that the VOCs emitted by the endophytic bacteria had a profound effect on plant development but only a minor effect on resistance against an herbivore of B. oleracea. Plants exposed to bacterial VOCs showed faster seed germination and seedling development. Furthermore, seed endophytic bacteria exhibited activity via volatiles against the plant pathogen F. culmorum. Hence, our results illustrate the ecological importance of the bacterial seed microbiome for host plant health and development.

Nitrogen Fixation in Cereals

Cereals such as maize, rice, wheat and sorghum are the most important crops for human nutrition. Like other plants, cereals associate with diverse bacteria (including nitrogen-fixing bacteria called diazotrophs) and fungi. As large amounts of chemical fertilizers are used in cereals, it has always been desirable to promote biological nitrogen fixation in such crops. The quest for nitrogen fixation in cereals started long ago with the isolation of nitrogen-fixing bacteria from different plants. The sources of diazotrophs in cereals may be seeds, soils, and even irrigation water and diazotrophs have been found on roots or as endophytes. Recently, culture-independent molecular approaches have revealed that some rhizobia are found in cereal plants and that bacterial nitrogenase genes are expressed in plants. Since the levels of nitrogen-fixation attained with nitrogen-fixing bacteria in cereals are not high enough to support the plant’s needs and never as good as those obtained with chemical fertilizers or with rhizobium in symbiosis with legumes, it has been the aim of different studies to increase nitrogen-fixation in cereals. In many cases, these efforts have not been successful. However, new diazotroph mutants with enhanced capabilities to excrete ammonium are being successfully used to promote plant growth as commensal bacteria. In addition, there are ambitious projects supported by different funding agencies that are trying to genetically modify maize and other cereals to enhance diazotroph colonization or to fix nitrogen or to form nodules with nitrogen-fixing symbiotic rhizobia.

Endophytes of industrial hemp (Cannabis sativa L.) cultivars: identification of culturable bacteria and fungi in leaves, petioles, and seeds

Plant endophytes are a group of microorganisms that reside asymptomatically within the healthy living tissue. The diversity and molecular and biochemical characterization of industrial hemp-associated endophytes have not been previously studied. This study explored the abundance and diversity of culturable endophytes residing in petioles, leaves, and seeds of three industrial hemp cultivars, and examined their biochemical attributes and antifungal potential. A total of 134 bacterial and 53 fungal strains were isolated from cultivars Anka, CRS-1, and Yvonne. The number of bacterial isolates was similarly distributed among the cultivars, with the majority recovered from petiole tissue. Most fungal strains originated from leaf tissue of cultivar Anka. Molecular and phylogenetic analyses grouped the endophytes into 18 bacterial and 13 fungal taxa, respectively. The most abundant bacterial genera were Pseudomonas, Pantoea, and Bacillus, and the fungal genera were Aureobasidium, Alternaria, and Cochliobolus. The presence of siderophores, cellulase production, and phosphorus solubilization were the main biochemical traits. In proof-of-concept experiments, re-inoculation of tomato roots with some endophytes confirmed their migration to aerial tissues of the plant. Taken together, this study demonstrates that industrial hemp harbours a diversity of microbial endophytes, some of which could be used in growth promotion and (or) in biological control designed experiments.

What Is There in Seeds? Vertically Transmitted Endophytic Resources for Sustainable Improvement in Plant Growth

Phytobeneficial microbes, particularly endophytes, such as fungi and bacteria, are concomitant partners of plants throughout its developmental stages, including seed germination, root and stem growth, and fruiting. Endophytic microbes have been identified in plants that grow in a wide array of habitats; however, seed-borne endophytic microbes have not been fully explored yet. Seed-borne endophytes are of great interest because of their vertical transmission; their potential to produce various phytohormones, enzymes, antimicrobial compounds, and other secondary metabolites; and improve plant biomass and yield under biotic and abiotic stresses. This review addresses the current knowledge on endophytes, their ability to produce metabolites, and their influence on plant growth and stress mitigation.

Ecological patterns of seed microbiome diversity, transmission, and assembly

Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently act as the initial inoculum for the plant microbiota. The purpose of this mini-review is to provide an overview of current knowledge on the diversity, structure and role of the seed microbiota. The relative importance of the mode of transmission (vertical vs horizontal) of the microbial entities composing the seed microbiota as well as the potential connections existing between seed and other plant habitats such as the anthosphere and the spermosphere is discussed. Finally the governing processes (niche vs neutral) involved in the assembly and the dynamics of the seed microbiota are examined.