Maternal effects shape the seed mycobiome in Quercus petraea

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.

Pitting the olive seed microbiome

BACKGROUND

The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in the same orchard through amplicon sequencing to test whether the olive genotype is a major driver in shaping the seed microbial community, and to identify the origin of the latter. Therefore, we have developed a methodology for obtaining samples from the olive seed's endosphere under sterile conditions.

RESULTS

A diverse microbiota was uncovered in olive seeds, the plant genotype being an important factor influencing the structure and composition of the microbial communities. The most abundant bacterial phylum was Actinobacteria, accounting for an average relative abundance of 41%. At genus level, Streptomyces stood out because of its potential influence on community structure. Within the fungal community, Basidiomycota and Ascomycota were the most abundant phyla, including the genera Malassezia, Cladosporium, and Mycosphaerella. The shared microbiome was composed of four bacterial (Stenotrophomonas, Streptomyces, Promicromonospora and Acidipropionibacterium) and three fungal (Malassezia, Cladosporium and Mycosphaerella) genera. Furthermore, a comparison between findings obtained here and earlier results from the root endosphere of the same trees indicated that genera such as Streptomyces and Malassezia were present in both olive compartments.

CONCLUSIONS

This study provides the first insights into the composition of the olive seed microbiota. The highly abundant fungal genus Malassezia and the bacterial genus Streptomyces reflect a unique signature of the olive seed microbiota. The genotype clearly shaped the composition of the seed's microbial community, although a shared microbiome was found. We identified genera that may translocate from the roots to the seeds, as they were present in both organs of the same trees. These findings set the stage for future research into potential vertical transmission of olive endophytes and the role of specific microbial taxa in seed germination, development, and seedling survival.

Wheat fungal endophyte communities are inseparable from the host and influence plant development

Plants harbor complex and highly diverse fungal endophyte communities (FECs), making it difficult to evaluate the functional role of individual taxa, subsets of the community, or the FEC as a whole. To reduce the complexity of this system, we aimed to produce fungi-null wheat (Triticum aestivum) plants. To this end, we treated seeds with heat and fungicides and generated plants from rescued embryos and callus tissue. A culture-based approach and reverse transcription PCR analysis were negative, indicating that all treatments produced plants apparently free of fungi. However, the analysis of DNA using digital droplet PCR and next-generation sequencing revealed that tissues from all treatments retained low levels but diversity-rich FECs. While the FECs varied in composition across treatments and tissues, they all included core taxa of the mycobiome. The reduced fungal biomass, along with the changes in FEC composition, negatively affected plant development, supporting a FEC contribution to proper plant development and fitness. Our discovery that a large part of the FEC cannot be separated from plants and can be transmitted through seeds and tissue culture calls for reevaluation of particular microbiome paradigms, such as core taxa concepts, transmission modes, and functional species.IMPORTANCEThe native microbiome in a given plant must be considered when evaluating the effect of a single taxon or synthetic community. The pre-existing microbiome can interact with artificially added microbial cargo, which affects the final outcome. Such issues can be at least partially solved by the use of endophyte-free plants, which provide a clean background that should be useful in determining the effect of a single taxon, taxa combinations, or the entire microbiome on plant performance. Previous reports regarded plants as endophyte-free or axenic by the lack of fungal growth on culture media or the generation of plants from tissue cultures. We showed here that while fungi could not be isolated from fungicide-treated or tissue culture-regenerated plants, nevertheless, all plants contained rich fungal endophyte communities; namely, it was impossible to create fungi-free wheat plants. Our results call for rethinking fundamental microbiome-related concepts, such as core taxa, transmission mode, and functional species.

Fungal Endophytes: Discovering What Lies within Some of Canada's Oldest and Most Resilient Grapevines

Plant diseases and pests reduce crop yields, accounting for global crop losses of 30% to 50%. In conventional agricultural production systems, these losses are typically controlled by applying chemical pesticides. However, public pressure is mounting to curtail agrochemical use. In this context, employing beneficial endophytic microorganisms is an increasingly attractive alternative to the use of conventional chemical pesticides in agriculture. A multitude of fungal endophytes are naturally present in plants, producing enzymes, small peptides, and secondary metabolites due to their bioactivity, which can protect hosts from pathogens, pests, and abiotic stresses. The use of beneficial endophytic microorganisms in agriculture is an increasingly attractive alternative to conventional pesticides. The aim of this study was to characterize fungal endophytes isolated from apparently healthy, feral wine grapes in eastern Canada that have grown without agrochemical inputs for decades. Host plants ranged from unknown seedlings to long-lost cultivars not widely propagated since the 1800s. HPLC-MS was used to identify unique endophyte-derived chemical compounds in the host plants, while dual-culture competition assays showed a range in endophytes' ability to suppress the mycelial growth of Botrytis, which is typically controlled in viticulture with pesticides. Twelve of the most promising fungal endophytes isolated were identified using multilocus sequencing and morphology, while DNA barcoding was employed to identify some of their host vines. These fungal endophyte isolates, which consisted of both known and putative novel strains, belonged to seven genera in six families and five orders of Ascomycota. Exploring the fungal endophytes in these specimens may yield clues to the vines' survival and lead to the discovery of novel biocontrol agents.

Seeds Act as Vectors for Antibiotic Resistance Gene Dissemination in a Soil-Plant Continuum

Though the evidence for antibiotic resistance spread via plant microbiome is mounting, studies regarding antibiotic resistome in the plant seed, a reproductive organ and important food resource, are still in their infancy. This study investigated the effects of long-term organic fertilization on seed bacterial endophytes, resistome, and their intergenerational transfer in the microcosm. A total of 99 antibiotic resistance genes (ARGs) and 26 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR. The amount of organic fertilizer applied was positively correlated to the number and relative abundance of seed-associated ARGs and MGEs. Moreover, the transmission of ARGs from the rhizosphere to the seed was mainly mediated by the shared bacteria and MGEs. Notably, the rhizosphere of progeny seedlings derived from seeds harboring abundant ARGs was found to have a higher relative abundance of ARGs. Using structural equation models, we further revealed that seed resistome and MGEs were key factors affecting the ARGs in the progeny rhizosphere, implying the seed was a potential resistome reservoir for rhizosphere soil. This study highlights the overlooked role of seed endophytes in the dissemination of resistome in the soil-plant continuum, and more attention should be paid to plant seeds as vectors of ARGs within the "One-Health" framework.

Assembly and Function of Seed Endophytes in Response to Environmental Stress

Seeds are colonized by diverse microorganisms that can improve the growth and stress resistance of host plants. Although understanding the mechanisms of plant endophyte-host plant interactions is increasing, much of this knowledge does not come from seed endophytes, particularly under environmental stress that the plant host grows to face, including biotic (e.g., pathogens, herbivores and insects) and abiotic factors (e.g., drought, heavy metals and salt). In this article, we first provided a framework for the assembly and function of seed endophytes and discussed the sources and assembly process of seed endophytes. Following that, we reviewed the impact of environmental factors on the assembly of seed endophytes. Lastly, we explored recent advances in the growth promotion and stress resistance enhancement of plants, functioning by seed endophytes under various biotic and abiotic stressors.

Integrated microbiology and metabolomics analysis reveal responses of cotton rhizosphere microbiome and metabolite spectrum to conventional seed coating agents

Fludioxonil (FL) and metalaxyl-M·fludioxonil·azoxystrobin (MFA) are conventional seed coating agents for controlling cotton seedling diseases. However, their effects on seed endophytic and rhizosphere microecology are still poorly understood. This study aimed to assess the effects of FL and MFA on cotton seed endophytes, rhizosphere soil enzymatic activities, microbiome and metabolites. Both seed coating agents significantly changed seed endophytic bacterial and fungal communities. Growing coated seeds in the soils originating from the Alar (AL) and Shihezi (SH) region inhibited soil catalase activity and decreased both bacterial and fungal biomass. Seed coating agents increased rhizosphere bacterial alpha diversity for the first 21 days but decreased fungal alpha diversity after day 21 in the AL soil. Seed coating reduced the abundance of a number of beneficial microorganisms but enriched some potential pollutant-degrading microorganisms. Seed coating agents may have affected the complexity of the co-occurrence network of the microbiome in the AL soil, reducing connectivity, opposite to what was observed in the SH soil. MFA had more pronounced effects on soil metabolic activities than FL. Furthermore, there were strong links between soil microbial communities, metabolites and enzymatic activities. These findings provide valuable information for future research and development on application of seed coatings for disease management.

Reciprocal influence of soil, phyllosphere, and aphid microbiomes

BACKGROUND

The effect of soil on the plant microbiome is well-studied. However, less is known about the impact of the soil microbiome in multitrophic systems. Here we examined the effect of soil on plant and aphid microbiomes, and the reciprocal effect of aphid herbivory on the plant and soil microbiomes. We designed microcosms, which separate below and aboveground compartments, to grow oak seedlings with and without aphid herbivory in soils with three different microbiomes. We used amplicon sequencing and qPCR to characterize the bacterial and fungal communities in soils, phyllospheres, and aphids.

RESULTS

Soil microbiomes significantly affected the microbial communities of phyllospheres and, to a lesser extent, aphid microbiomes, indicating plant-mediated assembly processes from soil to aphids. While aphid herbivory significantly decreased microbial diversity in phyllospheres independent of soil microbiomes, the effect of aphid herbivory on the community composition in soil varied among the three soils.

CONCLUSIONS

This study provides experimental evidence for the reciprocal influence of soil, plant, and aphid microbiomes, with the potential for the development of new microbiome-based pest management strategies.

The Influence of Cone Age and Urbanisation on the Diversity and Community Composition of Culturable Seed Fungal Endophytes within Native Australian Banksia ericifolia L.f. subsp. ericifolia

Seed fungal endophytes play a crucial role in assisting the overall health and success of their host plant; however, little is known about the factors that influence the diversity and composition of these endophytes, particularly with respect to how they change over time and within urban environments. Using culturing techniques, morphological analyses, and Sanger sequencing, we identified the culturable seed fungal endophytes of Banksia ericifolia at two urban and two natural sites in Sydney, New South Wales, Australia. A total of 27 Operational Taxonomic Units were obtained from 1200 seeds. Older cones were found to contain, on average, more colonised endophytes than younger cones. Species richness was also significantly influenced by cone age, with older cones being more speciose. Between urban and natural sites, the overall community composition did not change, although species richness and diversity were greatest at urban sites. Understanding how these endophytes vary in time and space may help provide an insight into the transmission pathways used and the potential role they play within the development and survival of the seed. This knowledge may also be crucial for restoration purposes, especially regarding the need to consider endophyte viability in ex situ seed collection and storage in seed-banking practices.

Insights into the seed microbiome and its ecological significance in plant life

In recent years, the microbiome has attracted much attention because of the multiple roles and functions that microbes play in plants, animals, and human beings. Seed-associated microbes are of particular interest in being the initial microbial inoculum that affects the critical early life stages of a plant. The seed-microbe interactions are also known to improve nutrient acquisition, resilience against pathogens, and resistance against abiotic stresses. Despite these diverse roles, the seed microbiome has received little attention in plant ecology. Thus, we review the current knowledge on seed microbial diversity, community structure, and functions obtained through culture-dependent and culture-independent approaches. Furthermore, we present a comprehensive synthesis of the ecological literature on seed-microbe interactions to better understand the impact of these interactions on plant health and productivity. We suggest that future research should focus on the role of the seed microbiome in the establishment, colonization and spread of plant species in their native and non-native ranges as it may provide new insights into conservation biology and invasion ecology.

From seed to seed: the role of microbial inheritance in the assembly of the plant microbiome

Despite evidence that the microbiome extends host genetic and phenotypic traits, information on how the microbiome is transmitted and maintained across generations remains fragmented. For seed-bearing plants, seeds harbor a distinct microbiome and play a unique role by linking one generation to the next. Studies on microbial inheritance, a process we suggest including both vertical transmission and the subsequent migration of seed microorganisms to the new plant, thus become essential for our understanding of host evolutionary potential and host-microbiome coevolution. We propose dividing the inheritance process into three stages: (i) plant to seed, (ii) seed dormancy, and (iii) seed to seedling. We discuss the factors affecting the assembly of the microbiome during the three stages, highlight future research directions, and emphasize the implications of microbial inheritance for fundamental science and society.

Antifungal Activity and Effect of Plant-Associated Bacteria on Phenolic Synthesis of Quercus robur L

Europe's forests, particularly in Ukraine, are highly vulnerable to climate change. The maintenance and improvement of forest health are high-priority issues, and various stakeholders have shown an interest in understanding and utilizing ecological interactions between trees and their associated microorganisms. Endophyte microbes can influence the health of trees either by directly interacting with the damaging agents or modulating host responses to infection. In the framework of this work, ten morphotypes of endophytic bacteria from the tissues of unripe acorns of Quercus robur L. were isolated. Based on the results of the sequenced 16S rRNA genes, four species of endophytic bacteria were identified: Bacillus amyloliquefaciens, Bacillus subtilis, Delftia acidovorans, and Lelliottia amnigena. Determining the activity of pectolytic enzymes showed that the isolates B. subtilis and B. amyloliquefaciens could not cause maceration of plant tissues. Screening for these isolates revealed their fungistatic effect against phytopathogenic micromycetes, namely Fusarium tricinctum, Botrytis cinerea, and Sclerotinia sclerotiorum. Inoculation of B. subtilis, B. amyloliquefaciens, and their complex in oak leaves, in contrast to phytopathogenic bacteria, contributed to the complete restoration of the epidermis at the sites of damage. The phytopathogenic bacteria Pectobacterium and Pseudomonas caused a 2.0 and 2.2 times increase in polyphenol concentration in the plants, respectively, while the ratio of antioxidant activity to total phenolic content decreased. Inoculation of Bacillus amyloliquefaciens and Bacillus subtilis isolates into oak leaf tissue were accompanied by a decrease in the total pool of phenolic compounds. The ratio of antioxidant activity to total phenolic content increased. This indicates a qualitative improvement in the overall balance of the oak leaf antioxidant system induced by potential PGPB. Thus, endophytic bacteria of the genus Bacillus isolated from the internal tissues of unripe oak acorns have the ability of growth biocontrol and spread of phytopathogens, indicating their promise for use as biopesticides.

Quercus rubra invasion of temperate deciduous forest stands alters the structure and functions of the soil microbiome

Invasive plants can modify the diversity and taxonomical structure of soil microbiomes. However, it is difficult to generalize the underlying factors as their influence often seems to depend on the complex plant-soil-microbial interactions. In this paper, we investigated how Quercus rubra impacts on the soil microbiome across two soil horizons in relation to native woodland. Five paired adjacent invaded vs native vegetation plots in a managed forest in southern Poland were investigated. Soil microbial communities were assessed along with soil enzyme activities and soil physicochemical parameters, separately for both organic and mineral horizons, as well as forest stand characteristics to explore plant-soil-microbe interactions. Although Q. rubra did not significantly affect pH, organic C, total N, available nutrients nor enzymatic activity, differences in soil abiotic properties (except C to N ratio) were primarily driven by soil depth for both vegetation types. Further, we found significant differences in soil microbiome under invasion in relation to native vegetation. Microbial richness and diversity were lower in both horizons of Q. rubra vs control plots. Moreover, Q. rubra increased relative abundance of unique amplicon sequence variants in both horizons and thereby significantly changed the structure of the core soil microbial communities, in comparison to the control plots. In addition, predicted microbial functional groups indicated a predominant soil depth effect in both vegetation plots with higher abundance of aerobic chemoheterotrophic bacteria and endophytic fungi in the organic horizon and greater abundance of methanotrophic and methylotrophic bacteria, and ectomycorrhizal fungi in the mineral horizon. Overall, our results indicate strong associations between Q. rubra invasion and changes in soil microbiome and associated functions, a finding that needs to be further investigated to predict modifications in ecosystem functioning caused by this invasive species.

Influence of Geographical Orchard Location on the Microbiome from the Progeny of a Pecan Controlled Cross

Carya illinoinensis (Wangenh.) K.Koch production has expanded beyond the native distribution as the genetic diversity of the species, in part, has allowed the trees to grow under broad geographic and climatic ranges. Research in other plant species has demonstrated that the phytobiome enhances their ability to survive and thrive in specific environments and, conversely, is influenced by the prevailing environment and plant genetics, among other factors. We sought to analyze the microbiota of pecan seedlings from the controlled cross 'Lakota' × 'Oaxaca' that were made in Georgia and Texas, respectively, to determine if the maternal geographical origin influences the microbiome of the resulting progeny. No significant differences in bacterial communities were observed between the seeds obtained from the two different states (p = 0.081). However, seed origin did induce significant differences in leaf fungal composition (p = 0.012). Results suggest that, in addition to some environmental, epigenetics, or host genetic components, ecological processes, such as dispersal mechanisms of the host, differentially impact the pecan microbiome, which may have ramifications for the health of trees grown in different environments. Future studies on the role of the microbiome in plant health and productivity will aid in the development of sustainable agriculture for improved food security.

Understanding the sugar beet holobiont for sustainable agriculture

The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.

Characterization of Seed Mycobiota Using Culture-Dependent and Culture-Independent Approaches

Seed fungi are potentially important for their roles in seedling microbiome assembly and seedling health, but surveys of full seed fungal communities remain limited. While culture-dependent methods have been used to characterize some members of the seed mycobiota, recent culture-independent studies have improved the ease in identifying and characterizing full seed fungal communities. In this chapter, we describe how to survey seed fungi using both traditional culture-based methods and culture-free metabarcoding. We first describe protocols for the isolation and long-term preservation of fungal strains from individual seeds and for the extraction and amplification of DNA from such fungal isolates for identification with Sanger sequencing. We also detail how to extract, amplify, and sequence fungal DNA directly from individual seeds. Finally, we provide suggestions for troubleshooting media choices, PCR inhibition by isolates and plant tissue, and PCR limitation by low fungal DNA.

Single Seed Microbiota: Assembly and Transmission from Parent Plant to Seedling

The seed acts as the primary inoculum source for the plant microbiota. Understanding the processes involved in its assembly and dynamics during germination and seedling emergence has the potential to allow for the improvement of crop establishment. Changes in the bacterial community structure were tracked in 1,000 individual seeds that were collected throughout seed developments of beans and radishes. Seeds were associated with a dominant bacterial taxon that represented more than 75% of all reads. The identity of this taxon was highly variable between the plants and within the seeds of the same plant. We identified selection as the main ecological process governing the succession of dominant taxa during seed filling and maturation. In a second step, we evaluated the seedling transmission of seed-borne taxa in 160 individual plants. While the initial bacterial abundance on seeds was not a good predictor of seedling transmission, the identities of the seed-borne taxa modified the phenotypes of seedlings. Overall, this work revealed that individual seeds are colonized by a few bacterial taxa of highly variable identity, which appears to be important for the early stages of plant development. IMPORTANCE Seeds are key components of plant fitness and are central to the sustainability of the agri-food system. Both the seed quality for food consumption and the seed vigor in agricultural settings can be influenced by the seed microbiota. Understanding the ecological processes involved in seed microbiota assembly will inform future practices for promoting the presence of important seed microorganisms for plant health and productivity. Our results highlighted that seeds were associated with one dominant bacterial taxon of variable taxonomic identity. This variety of dominant taxa was due to (i) spatial heterogeneity between and within plants and (ii) primary succession during seed development. According to neutral models, selection was the main driver of microbial community assembly for both plant species.

The Recruitment of the Recalcitrant-Seeded Cryptocarya alba (Mol.) Looser, Established via Direct Seeding Is Mainly Affected by the Seed Source and Forest Cover

Natural regeneration of recalcitrant-seeded tree species is strongly limited in Mediterranean-type climate zones due to increasing droughts imposed by climate change. Direct seeding can be a low-cost alternative to seedling establishment, but there is still limited information for some species. This study aimed to assess the effects of the seed source and forest cover on the germination and survival of the endemic Cryptocarya alba Mol. established through direct seeding. Three habitat types differing in forest cover were identified within the natural park Reserva Natural Altos de Cantillana, Metropolitan Region, Chile. The forest cover corresponded to open (canopy density <25%), semi-dense (canopy density around 50%), and dense forest (canopy density >75%). All forest cover had C. alba as one of the dominant species. At each habitat type, 38 families from four seed sources (Cuesta La Dormida (CD), Antumapu (AN), Cantillana (CA, local seed source) and Cayumanque (CY)) were directly seeded. Germination (Germin) and survival (Surv) were evaluated weekly during one growing season. There were significant differences between seed sources in Germin and Surv, with means values varying from 7.8% to 37% for Germin and 0% to 20% for Surv. The local seed source CA had the highest values in both traits. A significant variation was also observed between families within seed sources only for Germin. The dense forest cover had the highest Germin (22%) and Surv (55%) results compared to the other forest cover types, which was partially associated with differences in soil moisture, temperature, and bulk density. Due to the most frequent droughts in these Mediterranean-type climate zones, the use of local seeds on dense forest cover is recommended for the direct seeding of the species in the initial recruitment.

Tailored Media Are Key to Unlocking the Diversity of Endophytic Bacteria in Distinct Compartments of Germinating Seeds

Seeds offer an internal microbial niche, termed the endosphere, colonized by communities of endophytic bacteria. To elucidate the functions of seed endophytes during germination and early plant growth, studies with culturable isolates are essential. Conventional growth media favor few fast-growing taxa, while micro organisms with restricted nutrient requirements are usually outcompeted prior to isolation. Consequently, current knowledge of the interaction between seeds and their endophytes remains limited to only few bacterial taxa, despite a "black box" of unculturable isolates colonizing the endosphere. Here, we designed various solid media to mimic the endosphere of germinating soybean (Glycine max L.) seeds and assessed their effect on the diversity of culturable endophytic bacteria. The embryonic axis (i.e., the future plant) possessed higher richness and harbored more unique genera (i.e., Brevundimonas, Methylobacterium, Microbacterium, Pseudoclavibacter, and Rathayibacter) than cotyledons (i.e., seed storage organs). Overall, media containing germinating and ground seeds enabled culturing and isolation of the broadest diversity of endophytic bacteria, viewed through the molecular identification of 246 isolates. The use of multiple tailored media helped uncover trophic adaptation of the core taxa. Furthermore, comparison of seeds from four lots of distinct cultivars and origin revealed few overlapping taxa, indicating that the parental environment, including soil and fertilization regime, influenced seed endophytic diversity. Extended diversity of native seed endophytic bacteria revealed the functional relevance of unique Arthrobacter, Bacillus, and Curtobacterium strains to seed germination under salt stress, exemplifying the importance of enhanced culturing approaches to elucidate the role of microbiota in seed germination. IMPORTANCE Plant growth-promoting endophytic isolates that appear to advance seed germination are often obtained from plant niches other than the seed endosphere. Isolating pure cultures of native endophytes from seeds during germination is crucial to investigate their function during early plant growth. Here, the diversity of endophytic bacteria isolated from seeds during soybean germination was enhanced by combining media tailored to the nutritional composition of the seed endosphere, including pregerminated seeds themselves. Our results show that isolation from distinct soybean seed compartments affected such diversity, with the embryonic axis harboring more unique taxa while displaying higher endophytic richness. Furthermore, using pools of seeds from separate lots, each corresponding to a certain cultivar and field site, supported isolation of further unique strains that often unveiled substantial effects on germination performance. Such findings are relevant to assist studies on the interactions between seeds and their native endophytic bacteria.

A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds

Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.

Epichloë Fungal Endophytes Influence Seed-Associated Bacterial Communities

Seeds commonly harbour diverse bacterial communities that can enhance the fitness of future plants. The bacterial microbiota associated with mother plant’s foliar tissues is one of the main sources of bacteria for seeds. Therefore, any ecological factor influencing the mother plant’s microbiota may also affect the diversity of the seed’s bacterial community. Grasses form associations with beneficial vertically transmitted fungal endophytes of genus Epichloë. The interaction of plants with Epichloë endophytes and insect herbivores can influence the plant foliar microbiota. However, it is unknown whether these interactions (alone or in concert) can affect the assembly of bacterial communities in the produced seed. We subjected Lolium multiflorum plants with and without its common endophyte Epichloë occultans (E+, E-, respectively) to an herbivory treatment with Rhopalosiphum padi aphids and assessed the diversity and composition of the bacterial communities in the produced seed. The presence of Epichloë endophytes influenced the seed bacterial microbiota by increasing the diversity and affecting the composition of the communities. The relative abundances of the bacterial taxa were more similarly distributed in communities associated with E+ than E- seeds with the latter being dominated by just a few bacterial groups. Contrary to our expectations, seed bacterial communities were not affected by the aphid herbivory experienced by mother plants. We speculate that the enhanced seed/seedling performance documented for Epichloë-host associations may be explained, at least in part, by the Epichloë-mediated increment in the seed-bacterial diversity, and that this phenomenon may be applicable to other plant-endophyte associations.

Endophytic Bacterial Communities of Ginkgo biloba Leaves During Leaf Developmental Period

Plant-specialized secondary metabolites have ecological functions in mediating interactions between plants and their entophytes. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from Ginkgo leaves at five different sampling times. The results indicated that the bacterial community structure varied during leaf developmental stage. Bacterial diversity was observed to be the highest at T2 stage and the lowest at T1 stage. Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes were found as the dominant phyla. The major genera also showed consistency across sampling times, but there was a significant variation in their abundance, such as Bacillus, Lysinibacillus, and Staphylococcus. Significant correlations were observed between endophytic bacteria and flavonoids. Especially, Staphylococcus showed a significant positive correlation with quercetin, and changes in the abundance of Staphylococcus also showed a strong correlation with flavonoid content. In order to determine the effect of flavonoids on endophytic bacteria of Ginkgo leaves, an extracorporeal culture of related strains (a strain of Staphylococcus and a strain of Deinococcus) was performed, and it was found that the effect of flavonoids on them remained consistent. The predicted result of Tax4Fun2 revealed that flavonoids might lead to a lower abundance of endophytic microorganisms, which further proved the correlation between bacterial communities and flavonoids. This study provided the first insight into the bacterial community composition during the development of Ginkgo leaves and the correlation between the endophytic bacteria and flavonoids.

Culturable Seed Microbiota of Populus trichocarpa

Plants harbor a diverse community of microbes, whose interactions with their host and each other can influence plant health and fitness. While microbiota in plant vegetative tissues has been extensively studied, less is known about members of the seed microbiota. We used culture-based surveys to identify bacteria and fungi found in the seeds of the model tree, Populus trichocarpa, collected from different sites. We found that individual P. trichocarpa seeds typically contained zero or one microbe, with common taxa including species of Cladosporium, Aureobasidium, Diaporthe, Alternaria, and Pseudomonas, a bacterium. Pseudomonas isolates were associated with seed mortality and were negatively associated with the occurrence of fungal isolates within Epicoccum, Alternaria, and Aureobasidium from the same seed. Next, we conducted an inoculation experiment with one of the isolated seed microbes, Pseudomonas syringae pv. syringae, and found that it reduced seed germination and increased seedling mortality for P. trichocarpa. Our findings highlight common fungi and bacteria in the seeds of P. trichocarpa, prompting further study of their functional consequences. Moreover, our study confirms that P. syringae pv. syringae is a seed pathogen of P. trichocarpa and is the first report that P. syringae pv. syringae is a lethal seedling pathogen of P. trichocarpa, allowing for future work on the pathogenicity of this bacterium in seedlings and potential antagonism with other seed microbes.

Impact of Thermotherapy and Short-Term Storage on Quercus robur L. Acorn Mycobiota and Germination

When natural regeneration of Quercus robur stands is hampered by an insufficient acorn yield, human assisted sowing of acorns collected in non-affected stands and stored for some period of time is performed. To inhibit the development of fungi and acorn deterioration during storage, thermotherapy is usually applied by submerging acorns for 2.5 h in water heated to 41 °C. This research aimed to test the effect of four thermotherapy treatments of different durations and/or applied temperatures as well as short-term storage at −1 °C or 3 °C on acorn internal mycobiota and germination. Fungal presence in cotyledons was analyzed in 450 acorns by isolation of mycelia on artificial media, followed by a DNA-based identification. Germination of 2000 acorns was monitored in an open field trial. Thermotherapy significantly decreased fungal diversity, while storage at 3 °C increased the isolation frequency of several fungi, mainly Penicillium spp. The most frequently isolated fungi did not show a negative impact on acorn germination after short-term storage. The study confirmed the efficiency of thermotherapy in the eradication of a part of acorn internal mycobiota, but also its effect on the proliferation of fast-colonizing fungi during storage. However, the latter showed to be more stimulated by storage conditions, specifically by storage at 3 °C.