Chapter 7 Biodiversity, phylogenetic profiling, and mechanisms of colonization of seed microbiomes Kusam Lata Rana a , Divjot Kour a , Tanvir Kaur a , Rubee Devi a , Neelam Yadav b , Ali Asghar Rastegari c , and Ajar Nath Yadav a a Department of Biotechnology, Dr. KSG Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, India, b Gopi Nath P.G. College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh, India, c Department of Molecular and Cell Biochemistry, Falavarjan Branch, Islamic Azad University, Isfahan, Iran 7.1 Introduction Microbiomes which spend the whole or part of their life cycle residing inside the internal tissues of plants without causing any noticeable symptoms of infection to the host plants are referred to as endophytes. Endophytic lifestyle of microbes plays an essential role in maintaining the growth and health of plants by providing nutrients and protection to the plants both against biotic and abiotic stress factors. The main objective of exploration of the seed microbiomes is to have a better understanding of the transmission of seed endophytes from generation to generation, their assured presence in new plants, their influence on the overall structure and function of plant microbiomes, and the impact of these interactions on the plant ecology. While discussing the seed microbiomes, it is very essential to differentiate between those microbial species which reside in the internal tissues of the seeds and are transmitted directly from parent to the progeny seedlings and those species which reside on the surface of the seeds and may or may not colonize the seed tissue with either vertical or horizontal transmission, though this differentiation is an artificial one because endophytes can become epiphytes and vice versa. But, this division is rather important as endophytic microbial communities may either originate from the seed tissues or be transmitted through various environmental sources such as vertical transmission and horizontal transmission; those microbes that are associated with endosperm and embryo will more likely be transmitted vertically and those that are asso- ciated with the seed coat will be transmitted horizontally (Barret et al., 2016). The evolving view of the seed microbiomes is that they are rich in consortium of bacteria and fungi (Hodgson et al., 2014; Malfanova et al., 2013; Rodriguez et al., 2009; Truyens et al., 2015) though there may also be presence of various viruses (Sastry, 2013) as well as oomycetes (Thines, 2014), but still most of the studies have focused on the endophytic fungi of seeds. Further, different conditions during the maturation of the seeds directly affect the microbial community. Some specific characteristic features are found in seed endophytes rather than in other plant tissue endophytes such as accumulation of starch and loss of water during maturation of seeds which directly favor those endophytes that are able to tolerate high osmotic pressure (Elbeltagy et al., 2000; Mano et al., 2006). It has been demonstrated in the study by Mano et al. (2006) that Gram-negative isolates predominated in the early stages of seed development, whereas Gram-positive isolates predominated during the seed maturation. It has been reported that in the very early stages, Methylobacterium sp. and Sphingomonas sp. are abundant while Bacillus sp. and Curtobacterium sp. are more abundant in the later stages (Mano et al., 2006). Mostly the seed-associated bacterial diversity has been found belonging to phyla Actinobacteria, Bacteroidetes, Pro- teobacteria, and Firmicutes (Barret et al., 2015; Bulgarelli et al., 2013; Johnston-Monje et al., 2016; Liu et al., 2012b). Epichl € oe and their asexual forms Neotyphodium are the most well-studied fungal seed endophytes. They possess affinities for members of the family Poaceae and benefit the plants by protecting them from pathogenic infection (P erez et al., 2016; Saikkonen et al., 2016). Further, many ascomycete and basidiomycete fungal and yeast species have been demonstrated to be associated with seeds (Barret et al., 2015; Links et al., 2014; Rodriguez et al., 2009). In the study by Barret et al. (2015), the seeds of plants Brassicaceae plants were demonstrated to be dominated by ascomycetes and also by the basidiomycete New and Future Developments in Microbial Biotechnology and Bioengineering. https://doi.org/10.1016/B978-0-12-820526-6.00007-5 © 2020 Elsevier Inc. All rights reserved. 99