Insights into the structure and role of seed-borne bacteriome during maize germination

Implications of Domestication in Theobroma cacao L. Seed-Borne Microbial Endophytes Diversity

The study of plant-microbe interactions is a rapidly growing research field, with increasing attention to the role of seed-borne microbial endophytes in protecting the plant during its development from abiotic and biotic stresses. Recent evidence suggests that seed microbiota is crucial in establishing the plant microbial community, affecting its composition and structure, and influencing plant physiology and ecology. For Theobroma cacao L., the diversity and composition of vertically transmitted microbes have yet to be addressed in detail. We explored the composition and diversity of seed-borne endophytes in cacao pods of commercial genotypes (ICS95, IMC67), recently liberated genotypes from AGROSAVIA (TCS01, TCS19), and landraces from Tumaco (Colombia) (AC9, ROS1, ROS2), to evaluate microbial vertical transmission and establishment in various tissues during plant development. We observed a higher abundance of Pseudomonas and Pantoea genera in the landraces and AGROSAVIA genotypes, while the commercial genotypes presented a higher number of bacteria species but in low abundance. In addition, all the genotypes and plant tissues showed a high percentage of fungi of the genus Penicillium. These results indicate that domestication in cacao has increased bacterial endophyte diversity but has reduced their abundance. We isolated some of these seed-borne endophytes to evaluate their potential as growth promoters and found that Bacillus, Pantoea, and Pseudomonas strains presented high production of indole acetic acid and ACC deaminase activity. Our results suggest that cacao domestication could lead to the loss of essential bacteria for seedling establishment and development. This study improves our understanding of the relationship and interaction between perennial plants and seed-borne microbiota.

Insight into the composition and differentiation of endophytic microbial communities in kernels via 368 maize transcriptomes

INTRODUCTION

Kernels are important reproductive organs in maize, yet there is a lack of systematic investigation on the differences in the composition of endophytic microorganisms in plants from a population perspective.

OBJECTIVES

We aimed to elucidate the composition of endophytic microorganisms in developing maize kernels, emphasizing differences among various inbred lines.

METHODS

The transcriptomic data of 368 maize inbred lines were used to explore the composition and diversity of endophytic microorganisms.

RESULTS

The findings revealed a higher abundance of fungi than bacteria in developing maize kernels, followed by protozoa, while viruses were less abundant. There were significant differences in the composition and relative abundance of endophytic microorganisms among different maize lines. Diversity analysis revealed overall similarity in the community composition structure between tropical/subtropical (TST) and temperate (NSS) maize germplasm with apparent variations in community richness and abundance. The endophytic microorganisms network in the kernels from TST genotypes exhibited higher connectivity and stability compared to NSS kernels. Bacteria dominated the highly connected species in the networks, and different core species showed microbial phylum specificity. Some low-abundance species acted as core species, contributing to network stability. Beneficial bacteria were predominant in the core species of networks in TST kernels, while pathogenic bacteria were more abundant in the core species of networks in NSS kernels.

CONCLUSION

Tropical maize germplasm may have advantages in resisting the invasion of pathogenic microorganisms, providing excellent genetic resources for disease-resistant breeding.

Heterosis of endophytic microbiomes in hybrid rice varieties improves seed germination

Seed endophytic microbiomes are shaped by host and environmental factors and play a crucial role in their host growth and health. Studies have demonstrated that host genotype, including hybridization, affects seed microbiomes. Heterosis features are also observed in root-associated microbiomes. It remains unclear, however, whether heterosis exists in seed endophytic microbiomes and whether hybrid microbiota provide noticeable advantages to host plant growth, especially to seed germination. Here, we investigated the structure of seed endophytic bacterial and fungal communities from three hybrid rice varieties and their respective parents using amplicon sequencing targeting 16S rRNA and ITS2 genes. Heterosis was found in diversity and composition of seed endophytic microbiomes in hybrids, which hosted more diverse communities and significantly higher abundances of plant growth-promoting taxa, such as Pseudomonas and Rhizobium genera compared with their parental lines. Co-occurrence network analysis revealed that there are potentially tighter microbial interactions in the hybrid seeds compared with their parent seeds. Finally, inoculation of seed-cultivable endophytes, isolated from hybrids, resulted in a greater promotion of seed germination compared with those isolated from parent lines. These findings suggest that heterosis exists not only in plant traits but also in seed endophytic microbiota, the latter in turn promotes seed germination, which offers valuable guidance for microbiome-assisted rice breeding.IMPORTANCEGenetic and physiological changes associated with plant hybridization have been studied for many crop species. Still, little is known about the impact of hybridization on the seed microbiota. In this study, we indicate that hybridization has a significant impact on the endophytic bacterial and fungal communities in rice seeds. The seed endophytic microbiomes of hybrids displayed distinct characteristics from those of their parental lines and exhibited potential heterosis features. Furthermore, the inoculation of seed-cultivable endophytes isolated from hybrids exhibited a greater promotion effect on seed germination compared with those isolated from the parents. Our findings make a valuable contribution to the emerging field of microbiome-assisted plant breeding, highlighting the potential for a targeted approach that aims to achieve not only desired plant traits but also plant-beneficial microbial communities on the seeds.

Seedling microbiota engineering using bacterial synthetic community inoculation on seeds

Synthetic Communities (SynComs) are being developed and tested to manipulate plant microbiota and improve plant health. To date, only few studies proposed the use of SynCom on seed despite its potential for plant microbiota engineering. We developed and presented a simple and effective seedling microbiota engineering method using SynCom inoculation on seeds. The method was successful using a wide diversity of SynCom compositions and bacterial strains that are representative of the common bean seed microbiota. First, this method enables the modulation of seed microbiota composition and community size. Then, SynComs strongly outcompeted native seed and potting soil microbiota and contributed on average to 80% of the seedling microbiota. We showed that strain abundance on seed was a main driver of an effective seedling microbiota colonization. Also, selection was partly involved in seed and seedling colonization capacities since strains affiliated to Enterobacteriaceae and Erwiniaceae were good colonizers while Bacillaceae and Microbacteriaceae were poor colonizers. Additionally, the engineered seed microbiota modified the recruitment and assembly of seedling and rhizosphere microbiota through priority effects. This study shows that SynCom inoculation on seeds represents a promising approach to study plant microbiota assembly and its consequence on plant fitness.

Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization

IMPORTANCE

Synthetic communities (SynComs) are an invaluable tool to characterize and model plant-microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increase enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of "just add buffer and apply to sterilized seeds or seedlings" and thus can save time applied in multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to those of freshly constructed SynComs and thus allow for significant time savings when working with SynComs.

The Role of Silica Nanoparticles in Promoting the Germination of Tomato (Solanum lycopersicum) Seeds

The addition of nanoparticles has been reported to be an effective strategy for enhancing seed germination, but the underlying mechanisms whereby this occurs are unclear. In the present study, we added silica nanoparticles (SiNPs) to an aqueous growth medium in which tomato seeds were germinated. We examined the effects of SiNPs on growth and possible mechanisms of action. SiNPs had a diameter of 10-17 nm and 110-120 nm. SiNPs shortened the mean germination time from 5.24 ± 0.29 days to 4.64 ± 0.29 days. Seedling vigor, measured by criteria including length and weight, was also improved compared to the control condition. The presence of SiNPs in the seedlings was assessed using an X-ray fluorescence spectrometer. The nanoparticles may have promoted germination by enhancing water imbibition by the seeds or altering the external microenvironment. Scanning electron microscopy revealed changes in the seed coat during germination, many of which were only observed in the presence of nanoparticles. Soil bacteria affect germination; specifically, Bacillus sp. may promote germination. The number of Bacillus sp. changed in the germination medium with SiNPs compared to the control. This suggested that these bacteria could interact with SiNPs to promote germination.

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.

Temporal Dynamics of Endogenous Bacterial Composition in Rice Seeds During Maturation and Storage, and Spatial Dynamics of the Bacteria During Seedling Growth

Seed endophytes are of interest because they are believed to affect seed quality, and ultimately, plant growth and fitness. A comprehensive understanding of the assembly of the seed microbiome during seed development and maturation, the fate of microbes during storage, and the migration of microbes during seedling growth are still lacking. In this study, to understand the assembly and fate of endogenous bacteria in rice seeds from the ripening stage to the storage and seedling stages, we employed culture-dependent and metagenomic analyses. Bacterial communities in rice seeds were composed of a few dominant taxa that were introduced at the milky and dough stages, and they persisted during seed maturation. The culturable bacterial population gradually increased during the ripening stage, whereas there was a gradual decrease during storage. Bacteria that persisted during storage proliferated after imbibition and were distributed and established in the shoots and roots of rice seedlings. The storage temperature influenced the abundance of bacteria, which consequently changed the bacterial composition in the shoots and roots of seedlings. Pantoea, Pseudomonas, and Allorhizobium were consistently abundant from seed development to the germination stage. Some endogenous bacterial strains significantly promoted the growth of Arabidopsis and rice plants. Overall, our results indicate that rice seeds are colonized by a few bacterial taxa during seed development, and their relative abundance fluctuates during storage and contributes significantly to the establishment of endophytes in the stems and roots of rice plants. The selected bacterial isolates can be used to improve the growth and health of rice plants. To the best of our knowledge, this is the first study to reveal the dynamics of bacterial populations during storage of rice seeds at different temperatures. The temporal dynamics of the bacterial community during seed storage provide clues for the manipulation of endogenous bacteria in rice plants.

Diversity of endophytic bacteria in hybrid maize seeds and Bacillus mojavensis J2416-7 may be capable of vertical transmission

The diversity of endophytic bacteria in the progeny is related to the parental lines. In this study, the traditional separation method was used to study the dominant endophytic bacteria of the shared paternal line and its pollen, different maternal lines and their F1 progeny. And the results showed that the dominant endophytic bacteria in maize seeds and the pollen were Bacillus and Pantoea. The Bacillus diversity of the progeny JMC121 and JN728 were the same as both the paternal line and the maternal line, including Bacillus subtilis, Bacillus velezensis, Bacillus mojavensis, and Bacillus licheniformis. The Bacillus subtilis and Bacillus velezensis in JN828 were the same as both the paternal line and the maternal line, while Bacillus licheniformis was only the same as the paternal line. Through the RAPD molecular typing, there was the same strain of Bacillus mojavensis existed in the paternal line J2416, the pollen and the progeny JN728; this meant that the paternal line passed its dominant endophytic bacteria to the progeny through pollen in vertical transmission. This study showed that the dominant endophytic bacteria in maize seeds and the pollen were Bacillus, and the diversity of F1 progeny was related to both the paternal line and the maternal line.