Abstract:

Fruits have long been recognized for their role in seed dispersal, yet their influence after falling to the ground has remained largely unexplored. Our new study published in New Phytologist challenges this view by demonstrating that fruit decomposition itself can actively shape the soil and plant microbiome with potential implications for seedling establishment, plant health, and ecological inheritance. Using tomato and chili as model systems, we show that decomposing fruits significantly alter soil chemistry and drive shifts in bacterial community composition, increasing diversity and enriching specific microbial functions. The consequences were that fruit presence reduced seed germination rates and affected early plant growth. By highlighting fruit decomposition as an overlooked but ecologically meaningful process, our work expands the classical view of fruit function and opens new directions for understanding microbial inheritance, early plant microbiome assembly, and the broader ecological role of fruit traits. For more info see our publication.

Abstract:

Seeds are reservoirs of beneficial microbes that shape early plant development. However, their functional roles and mechanisms remain poorly understood. We isolated 23 SEB from three maize varieties and characterized their plant growth-promoting traits, including auxin production, phosphate solubilization, nitrogen fixation, and extracellular enzyme activity. Among these, Lysinibacillus sp. (ZM1) significantly enhanced root architecture, auxin levels, and nitrogen metabolism in maize seedlings, even under nitrogen-deficient conditions. Additionally, Bacillus velezensis (ZMW8) exhibited strong antifungal activity against Fusarium verticillioides and Rhizoctonia solani through lipopeptide production (bacillomycin D, fengycin), improving seedling survival and defense gene expression. Our findings address a critical gap in understanding how seed-associated microbes contribute to both growth promotion and disease protection, highlighting their potential as bioinoculants for sustainable maize cultivation. For more info see our publication.

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Biological control of seed-borne pathogens such as the bacterium Paracidovorax (formerly Acidovorax citrulli) offers a sustainable option for disease management. Questions remain, however, whether bacterial interactions can prevent initial seed infection from flowers, and whether arrival order (i.e. priority effects) impacts interaction outcomes. Here, we used a synthetic community (SynCom) experiment in commercial watermelon (Citrullus lanatus) to test the following questions: 1) does bacterial arrival order on stigmas impact pathogen transmission to seeds, 2) are there effects on seed quality, germination and seedling emergence, and 3) are there effects on microbiota composition in offspring seedlings? Through strain specific qPCR, we found that detection and copy abundance of the pathogen Paracidovorax citrulli was higher when inoculated before or concurrently with the SynCom compared to inoculations after other SynCom strains. Through seed/seedling phenotyping, we found that germination and seedling size were higher when Paraburkholderia phytofirmans was inoculated first during pollination. Finally, through amplicon sequencing of seedling shoots, we found that bacterial and fungal communities differed in diversity and composition between inoculation treatments. This initial data suggests that priority effects can impact floral transmission of bacteria to seeds, and that these effects can be transgenerational. Such findings have implications for the timing of seed inoculation with biocontrol or beneficial bacteria in agriculture.

Abstract:

Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health. For more info, please see our recent paper.”

Abstract:

Although evidence of antibiotic resistance spreading through the plant microbiome is growing, research on the antibiotic resistome in seeds, a key reproductive organ and food source, remains limited. We integrate findings from microcosm and field experiments to investigate how environmental factors, including long-term organic fertilization and elevated CO₂, shape the seed resistome. We detected diverse antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in seed endophytes, with organic fertilization enhancing their numbers and abundance, and further impacted the relative abundance of ARGs in progeny rhizosphere. Furthermore, elevated CO₂ significantly increased seed ARG abundance, altered bacterial and fungal communities, and strengthened bacteria–fungi interactions, further influencing resistome dynamics. Structural equation models revealed that seed resistomes play a pivotal role in ARG transmission to progeny rhizosphere soils, emphasizing their potential as resistome reservoirs. These findings highlight the overlooked contribution of plant seeds to antibiotic resistance dissemination and underscore the need for further research on their role in microbial resistance evolution within agroecosystems and under climate change. For more info, please see our papers on organic fertilization and free-air CO₂ enrichment.

Abstract:

Seed germination critically determines successful plant establishment and agricultural productivity. In the plant holobiont’s life cycle, seeds are hubs for microbial communities’ assembly, but what exactly shapes the holobiont during germination remains unknown. Here, 16S rRNA gene amplicon sequencing characterized the bacterial communities in embryonic compartments (cotyledons and axes) and on seed coats pre- and post-germination of four soybean (Glycine max) cultivars, in the presence or absence of exogenous abscisic acid (ABA), which prevented germination and associated metabolism of seeds that had imbibed. Embryonic compartments were metabolically profiled during germination to design minimal media mimicking the seed endosphere for bacterial growth assays. The distinction between embryonic and seed coat bacterial microbiomes of dry seeds weakened during germination, resulting in the plumule, radicle, cotyledon, and seed coat all hosting the same most abundant and structurally influential genera in germinated seeds of every cultivar. Treatment with ABA prevented the increase of bacterial microbiomes’ richness, but not taxonomic homogenization across seed compartments. Growth assays on minimal media containing the most abundant metabolites that accumulated in germinated seeds revealed that seed reserve mobilization promoted enrichment of copiotrophic bacteria. Our data show that seed imbibition enabled distribution of seed-coat-derived epiphytes into embryos irrespective of germination, while germinative metabolism promoted proliferation of copiotrophic taxa, which predominated in germinated seeds. For more info, please see our paper.

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Rice bakanae disease, caused by Fusarium fujikuroi, nowadays represents the main threat for rice seed producers. With recent European guidelines progressively reducing the use of chemical fungicides, new disease management strategies are urgently needed. The plant endosphere constitutes a source of potential microbial biocontrol agents (BCAs) against fungal pathogens. Endophytic antagonists, with their close association with the host, are more likely to withstand harsh field conditions, the main bottleneck of BCAs selection. This represents the first report of E. layuense, E. catenisporum, M. testaceum and M. oryzae strains with biocontrol potential against F. fujikuroi as promising biological seed dressing alternatives to chemical fungicides. For more info, please see our recent paper.

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Abstract:

The microbial communities associated with seeds, known as seed microbiota, are involved in seed germination, seedling emergence, and seedling health. Understanding the assembly, composition, and function of seed microbiota is therefore essential for optimizing agricultural practices and increasing crop productivity. Recent advances in seed microbiota engineering allow the manipulation of seed microbiota to better understand the role of selected strains and representative microbiota on seed germination, seedling emergence and seedling phenotype. The seed microbiota is a low-diversity community with dominant strains found across multiple species and agricultural conditions. Here, we evidence the role of bean seed natural microbiota in seed germination and seedling emergence ability across eight genotypes grown in field conditions and identify bacterial (Microbacteriaceae, Rhizobiales, Pseudomonadaceae) and fungal taxa (Leotiomycetes, Dothideomycetes, Sordariomycetes) associated with seed emergence potential. Then, using synthetic communities inoculations, we confirm the influence of seed-borne microorganisms and soil-dependent effect of seed inoculation on seedling phenotypes. We show associations between seed or seedling microbiota and specific plant metabolites at different early developmental stages likely involved in plant-microbe interactions. Ultimately, this approach could be used to design and inoculate synthetic microbiota based on desired plant phenotype traits, such as resistance against phytopathogens.

Abstract:

While often disregarded and not as well understood as microbe-root or microbe-shoot interactions, microbe-seed interactions can have important impacts on plant health. Weed seed persistence in the soil seed bank depends on dormancy, longevity and defence as key traits. Although it is generally understood that soil microorganisms contribute to weed seed decay, clear and strong relationships and mechanisms are largely unknown. It is posited that certain soil management practices increase the rate of weed seed decay by microbial activity, but neither specific microbial species nor practical strategies have been rigorously studied or confirmed. While there is some research on soil microbial effects on weed seeds, few (if any) studies have investigated how innate seed microbiomes may modulate persistence in the soil seed bank. Our experimental work in collaboration with Syngenta (UK, USA, Switzerland) as industrial partner aims to deliver an improved understanding of how soil and seed microbiomes are formed and their potential to affect weed seed persistence in distinct agricultural practices. A model, based on observations, to predict seed decay and germination and, by extension, improve weed management will be proposed.

Abstract:

Seeds provide a unique environment shaped by co-evolutionary processes, hosting diverse microbial communities. While metagenomic studies have uncovered an extended diversity of microorganisms, culture-based approaches remain crucial for understanding microbial potential and functional interactions. However, the factors influencing microbial culturability within seeds are not well understood. Our findings highlight the limitations of culture-based methods in capturing the full microbial diversity of Cannabis seeds and emphasize the importance of microbial interactions in determining culturability. A strong network connectivity within uncultured bacteria suggests that interdependencies and competition within the seed microbiome may have a role hindering isolation of key bacterial groups. These insights provide a framework for refining cultivation strategies to recover ecologically significant microbes with potential agricultural applications.

Abstract:

Flower-sourced assembly of seed microbiota remains an understudied ecological process. Here, we investigated the floral transmission pathway for bacterial acquisition by developing seeds of watermelon (Citrullus lanatus). Comparison of stigma- and seed-associated bacterial communities from field-grown C. lanatus revealed significant overlap: up to 40% of the bacterial diversity that was detected in seed was also found on stigmas. In a field pollinator exclusion experiment, honeybee visitation to flower stigmas had no significant effect on bacterial community composition in seeds. Among a collection of bacterial isolates from stigmas and seeds in the field, more than half (57%) were able to transmit to seeds after inoculation onto stigmas under laboratory conditions. Interestingly, for most bacterial strains, fruit set rates increased after floral inoculation, and in some cases even in the absence of transmission to the seed. We also found that bacterial isolates from watermelon stigmas and seeds had variable (i.e. positive or negative) effects on seed germination and seedling emergence. Our findings highlight the contribution of floral transmission to seed microbiota assembly and its consequences for plant fitness. For more info, please see our preprint on BioRxiv.

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Abstract:

Species’ distributions and abundances are shifting in response to ongoing global climate change. Mutualistic microbial symbionts can provide their hosts with protection from environmental stress that may contribute towards resilient responses to environmental change, however these changes may also disrupt species interactions and lead to declines in hosts and/or symbionts. Symbionts preserved within natural history specimens offer a unique opportunity to quantify changes in microbial symbiosis across broad temporal and spatial scales. We asked how the prevalence of seed-transmitted fungal symbionts of grasses (Epichloë endophytes) have changed over time in response to climate change, and how these changes vary across host species’ ranges. Our results provide novel evidence for a cryptic biological response to climate change that may contribute to the resilience of host-microbe symbiosis through context-dependent benefits that confer a fitness advantage to symbiotic hosts under environmental change. For more info, please see our preprint on BioRxiv.

Abstract:

Bacteria associated with plants can enhance the plants’ growth and resistance against phytopathogens. Today, growers aim to reduce the use of mineral fertilizers and pesticides. Since phytopathogens cause severe yield losses in crop production systems, biological alternatives gain more attention. Plant and also seed endophytes have the potential to influence the plant, especially seed-borne bacteria may express their beneficiary impact at initial plant developmental stages. In the current study, we assessed the endophytic seed microbiome of seven genetically diverse barley accessions by 16S rRNA gene amplicon sequencing and verified the in vitro plant beneficial potential of isolated seed endophytes. Furthermore, we investigated the impact of the barley genotype and its seed microbiome on the rhizosphere microbiome at an early growth stage by 16S rRNA gene amplicon sequencing. Although barley accessions representing high genetic diversity displayed a genotype-dependent endophytic seed microbiome, a core seed microbiome with high relative abundances was identified. Endophytic isolates were affiliated to members of the core seed microbiome and many of them showed plant beneficial properties. We propose therefore that new breeding strategies should consider genotypes with high abundance of beneficial microbes. For more info, please see our paper.

Abstract:

Seed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays. Overall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs. For more info, please see our recent paper.

Abstract:

Seed is a critically important basic input of agriculture, because sowing healthy seeds is essential to food production. Using high quality seed enables less use of synthetic pesticides in the field. Seedborne pathogens can reduce yield quantity and quality of the crops produced. Seed treatments protect plant seedlings from pathogen attacks at emergence and at the early growth stages, contributing to healthy crop plants and good yield. However, there is increased concern about the application of synthetic pesticides to seeds, while alternatives are becoming increasingly addressed in seedborne pathogen research. A series of strategies based on synthetic fungicides, natural compounds, biocontrol agents (BCAs), and physical means has been developed to reduce seed contamination by pathogens. The volume of research on seed treatment has increased considerably in the past decade, along with the search for green technologies to control seedborne diseases. This review focuses on recent research results dealing with protocols that are effective in the management of seedborne pathogens. Moreover, the review illustrated an innovative system for routine seed health testing and need-based cereal seed treatment implemented in Norway. For more info, please see our recent paper.

Abstract:

Quinoa is a promising crop for food security, due to its high nutritional content and adaptation to climate change. Most of the world yield comes from Peru and Bolivia and is exported to the US to produce manufactured food supplements. However, some regions in Peru are polluted with cadmium and quinoa grains absorb toxic quantities. The main objective of this project is to identify how cadmium changes the bacteria and fungi found inside the quinoa grains and if those microorganisms could have beneficial activities to decrease cadmium concentration in quinoa and final consumersʼ uptake. Microbes were isolated in vitro to assess biochemical activities which are beneficial to plant growth and decrease cadmium concentration in grains and tested in quinoa plants to assess a new approach to decrease cadmium pollution and produce healthier quinoa crops.