Introduction Despite the long-held belief that reproductive and disseminative organs of plants are sterile, it is now well established that seeds host diverse microbial assemblages (Hardoim et al. 2015; Truyens et al. 2015). Some of these associated microorganisms contribute to plant health, plant growth, and seed survival while others are detrimental (Barret et al. 2016; Saikkonen et al. 2016). Seeds can facilitate the dispersal of microorganisms, providing for early colonization of a new plant generation. Although seeds are an important means of supporting microbial growth and dispersal, relatively little is known about the ecology of seed-associated microorganisms (Saikkonen et al. 1998; Compant et al. 2010; Truyens et al. 2015; Brader et al. 2017) in comparison with root- and leaf-associated microorganisms (Mercado-Blanco and Lugtenberg 2014; Mercado-Blanco 2015; Vacher et al. 2016; Compant et al. 2016). In many instances, the composition and structure of the seed microbiota of various plants species have yet to be characterized. This includes the microorganisms living on the surface as well as the inner tissues of the seeds. Furthermore, a thorough understanding of the specific routes of seed transmission of microorganisms needs to be developed. Whereas seed transmission has been thought to occur through three main routes: the internal, floral and external pathways (Maude 1996), the relative importance of these pathways in determining the composition of the seed microbiota remains to be explored. Moreover, the impact of vertical (derived from the mother plant) and horizontal transmission (derived from air-borne or soil-borne microorganisms) in the assembly of seed microbial communities is unclear for some taxa. As much needs to be understood about seed-associated microbes, perhaps among the most important are resolving the relative roles of horizontal and vertical transmission in establishing the seed microbiota, which could lead to a better understanding of the plant holobiont, its microbiome and functioning, and the potential use of seed-associated microbes for improving agricultural productivity. This understanding could like lead to insights into the evolution of specific microbial taxa within seeds and the relative contributions of various selective forces in shaping the seed microbiota. The unraveling of these processes could provide important knowledge about how beneficial, commensal, and pathogenic fungal and bacterial microorganisms establish and maintain intimate associations with their seeds and contribute to the health of the next plant generation, improving our abilities to develop successful application strategies for microbial inoculants and their integration into sustainable crop production and protection. Since the nineteenth century, advances have been made in our understanding of plant-associated microorganisms. However, for seeds and their microbiota, there remain large gaps in our knowledge. Seed transmission of some microorganisms like Epichloids in grasses (Kauppinen et al. 2016; Saikkonen et al. 2016) or phytopathogenic fungi and bacteria (Li et al. 2017; Brader et al. 2017) have been relatively well studied. However, seed transmission of many plant-associated microorganisms remains unknown. The contributions in this Special Issue have served to greatly improve our understanding of the mechanisms of seed-microbe-soil interactions, the nature of the microbiota and functioning of the microbiome present within various seeds, the evolution of the seed microbiota, and the routes of microbial colonization. The studies include different beneficial and detrimental microorganisms as fungi and bacteria thriving as endophytes in different kinds of plants. They further describe ways in which specific native or non-native seed microorganisms may be utilized for improving seed and seedling survival and plant health and productivity