The domestication of plants has played a crucial role in the cultural and economic advancement of societies across the globe. Through domestication, humanity has cultivated plants that provide several benefits, including food, beverages, medicine, raw materials for industry, and even elements that have cultural or social significance (Milla et al., 2015; Purugganan, 2019).

The biological origin, diversification, and domestication of maize occurred in Mesoamerica, located in the center of Mexico. This grass of the Poaceae family had a seminal role in the origin, extension of agriculture, and culture of pre-Hispanic civilizations (Smith et al., 1981). One of the species of actual teosintes, Zea mays subsp. parviglumis, is the progenitor of all derivative Zea mays subsp. mays modern races. The human-driven domestication that started around 9,000 years ago is one of the most critical events in the history of agriculture (Doebley, 2004; Piperno et al., 2009; Sahoo et al., 2021).

Numerous groups of bacteria and fungi establish interactions with plants. It has been discovered that the overall health of plants is closely associated with the specific composition of microorganisms present both in the soil and the plants themselves (Gherbi et al., 2008; Miyambo et al., 2016; van der Heijden and Hartmann, 2016; Dastogeer et al., 2020). Plants maintain associations with microorganisms both outside and within their tissues. Endophytic microorganisms within the root, stem, leaves, flowers, and seeds maintain mutualistic symbiosis with the plant host (Frey-Klett et al., 2011; Mishra et al., 2015; De Mandal et al., 2021). Seed endophyte microorganisms can be transferred vertically to plant offspring, ensuring their permanence in favorable environments (Johnston-Monje & Raizada, 2011).

Few studies of culturable fractions of teosinte bacteria have been performed. Nitrogen-fixing Paraburkholderia tropica (formerly Burkholderia tropica) was isolated from the rhizosphere and stem of teosinte (Caballero-Mellado et al., 2004; Reis et al., 2004). Although this species has not been reported again associated with teosinte, other species and strains isolated from maize and sugarcane express plant growth promotion (PGP) and antifungal phenotypic features (Tenorio-Salgado et al., 2013; Bernabeu et al., 2018; Schlemper et al., 2018; Kuramae et al., 2020; Vio et al., 2022). Also, endophytic Bacillus, Enterobacter, Methylobacterium, and Pantoea, with variable PGP features, were repeatedly isolated from three different teosinte species (Johnston-Monje & Raizada, 2011). Paenibacillus polymyxa and Citrobacter sp. obtained from the same teosinte seeds inhibited fungal growth and mycotoxin production and maintained a potential to combat phytopathogens (Mousa et al., 2015). Currently, an important research topic is to elucidate how much of a plant’s phenotype, adaptive capacities, evolution, and productivity are due to its endospheric and rhizospheric microbiome (Santoyo et al., 2017; Kaur et al., 2021).

In that sense, next-generation sequencing (NGS) technologies have revolutionized the field of microbiology and have become an essential tool for studying the plant holobiont, which encompasses the plant and all its associated microorganisms. Identifying microbial species or microbiomes present in the plant holobiont is the first step to studying the complexity of the existing symbiosis (Simon et al., 2019; Marco et al., 2022).

In this work, the bacteriome of seeds of three teosinte species was explored by NGS of 16S rRNA gene. The alpha and beta diversities of bacterial genera, the core bacteriome of the teosinte species, and metabolic prediction of the main bacteria were documented. Many previously potential PGPB associated with maize were detected in teosintes. This work may lead efforts to isolate the cultivable fraction of these plant species that may be a reservoir of PGPB for use as biofertilizers and for biocontrol.

The diversity of bacterial communities associated with the seed of three teosinte species: Z. diploperennis, Z. perennis, and Z. mays subsp. mexicana races Nobogame, Balsas, Mesa Central, and Chalco were explored in this work with culture-independent methods of NGS. Only some works have addressed the issue of bacterial diversity in the teosinte endosphere from the perspective of culture-independent methods. In this sense, previous efforts focused on using bacterial DNA fingerprinting (16S rDNA TRFLP) detected a core bacteriome composed of Clostridium, Paenibacillus, and two other unidentified genera in seeds and stems of three teosinte species (Johnston-Monje & Raizada, 2011). Additionally, 18 bacteria genera were isolated and cultured from the same samples, expanding the core bacteriome of teosinte with members of the Enterobacter, Methylobacterium, Pantoea, and Pseudomonas genres. In contrast, in this work, the core bacteriome detected with NGS includes 38 bacterial genera only in seeds, confirming the presence of all previously detected but adding 36 bacteria genera for the first time. However, although the investigation of bacterial diversity is just the beginning and the comparisons between works carried out with different experimental strategies should be taken carefully, previous research using TRFLP has raised crucial questions regarding maize domestication, evolution, ethnography, geographic migration, and ecology (Johnston-Monje & Raizada, 2011; Johnston-Monje et al., 2014), all legitimate questions that can now be reconsidered with the use of NGS.

Some of the bacterial genera found in this work have been previously described as culturable endophytes in maize and teosinte plants with relevant phenotypic traits for plant-microorganism interaction, plant growth promotion, biological control, and adaptation to the environment (Chowdhury et al., 2019; Mehta et al., 2021; Wallace, 2023). However, many non-cultured bacteria genera no previously associated with teosinte and maize endophytes were also detected in the seed endosphere of teosinte, such as Nitrospira, Scalindua, and Phytoplasma, among others. These bacteria expand the potential of the teosinte microbiome for developing PGPB and biocontrol agents. The work results may be the basis for renewing efforts for isolating bacterial genera and species in specific culture media and ambiental conditions designed for those bacteria that have yet to be isolated in pure cultures.

The dynamic symbiotic relationship of endophytes with the host has essential implications for adaptation, stress tolerance, evolution, and plant domestication (Hardoim et al., 2015). Most of 38 genera of central bacteriome (core) have been recognized as PGPB, and some are also among the most abundant microorganisms found in native landrace maize samples, such as the case of Burkholderia, Methylobacterium, Pseudomonas, Paenibacillus, Clostridium, Stenotrophomonas, Streptomyces, and Luteibacter (Johnston-Monje & Raizada, 2011). As has been suggested in previous works performed with the seeds of other plants, teosinte seeds are also a vast reservoir of microorganisms of evolutionary and biotechnological interest that remain in their host despite geographic and genetic differences (Chen et al., 2018; Hamonts et al., 2018; Koskella and Bergelson, 2020; Kuźniar et al., 2020; Noble et al., 2020; Rodríguez et al., 2020). The accessory bacteriome of teosintes is possibly related to the specialization of the bacteria with their particular host. Depending on the plant host’s sampling moment, geography, or ecology, it could also be a transitory event.

The UniFrac in β-diversity analysis unveiled two clades, one that included Z. mays subsp. mexicana and another to the rest of the species and races. The association between these bacteriomes, phylogenetic proximity, and geographical distribution highlight the significance of plant genotype in influencing microbiome selection and alterations, emphasizing the role of host genetics in shaping the microbial communities associated with these plant species (Yadav et al., 2023).

The phylogeny of Mexican annual teosintes performed with microsatellite analysis recognizes two clusters Zea mays subsp. mexicana and Z. mays subsp. parviglumis on one side; meanwhile, Z. diploperennis, and Z. perennis on the other share an earlier common ancestor (Matsuoka et al., 2002; Fukunaga et al., 2005). This phylogenetic scenario could be related to the greater bacterial diversity associated with earlier teosinte species since a longer available evolutionary time to establish a symbiosis and co-evolve with free-living bacteria than the other races. However, other geographic, ecological, or evolutive scenarios cannot be discarded.

The taxonomic microbial interaction network, constructed using representative bacterial genera from the core bacteriome in teosinte samples, exhibited a complex and extensive structure. These findings indicate that the seeds of teosinte act as a “Noah’s Ark,” which possibly facilitates the vertical transmission of essential symbiotic bacteria for the survival and growth of the subsequent plant generation in new and challenging environments. When considering the assumption that the teosinte seeds originate from diverse conditions, it becomes evident that the microbial interaction network within these seeds is crucial for the plants’ adaptation and resilience. This intricate network of interactions among microbial taxa suggests a cooperative and interdependent relationship between bacteria and their plant host (Li et al., 2019; Verma & White, 2019; Bomfim et al., 2020).

By implementing caution and considering the current state of knowledge, identifying bacteria at the genus level can provide valuable insights into their phenotypic characteristics and their ability to establish symbiotic relationships with plants (Fitzpatrick et al., 2020; Liu et al., 2020; Morella et al., 2020; Trivedi et al., 2020). The outstanding similarity in the diversity and relative abundance of bacterial genera among teosintes indicates the presence of a functional and stable microbiome despite variations in recognized bacterial taxonomy. By conducting a thorough analysis of bacterial diversity and their phenotypic traits, we can better understand the role and symbiotic interactions of these bacterial communities throughout the plants’ life cycle (Berg et al., 2010; Reinhold-Hurek and Hurek, 2011; Sessitsch et al., 2012; Belimov et al., 2015; Khatabi et al., 2019).

The prediction of the functional profiles of teosinte endophytes focuses on three critical components in the plant-microorganism symbiosis: adaptation to the host environment, specific symbiotic activities, and biological control of plant pathogens. The endophyte seed bacteria of teosinte participate in the potential establishment and development of the plant holobiont through the secretion of enzymes that break down complex organic matter, allowing adequate access to nutrients and bacterial motility to enable and facilitate colonization and establishing beneficial interactions and chemical communication systems such as quorum sensing to synchronize bacteria-bacteria interaction and production of phytohormones that lead plant-bacteria communication (Vandana et al., 2021). Also, bacterial genera with a potential capacity for degradation of xenobiotic compounds commonly present in contaminated soils, such as atrazine, xylene, chloroalkanes, and polycyclic aromatic compounds, were detected. These bacteria detoxify the soil, recirculate carbon from generally recalcitrant compounds, and offer the plant an adaptative advantage during colonization and initial growth of plants (Li et al., 2012; Pandey et al., 2013; Thelusmond et al., 2016; Regar et al., 2019; Huang X. et al., 2022).

Besides, the bacterial digestion of starch, sucrose metabolism, biosynthesis of amino acids, phytohormones, and intermediate compounds of vital biochemical cycles are metabolic activities that promote the development of plants from germination to advanced phenological stages (Hunting et al., 2015; Cui et al., 2019; Rehman et al., 2019; Yuan et al., 2021; Mishra et al., 2022). Finally, the biosynthesis of antibiotic compounds such as streptomycin, cephalosporin, tetracycline, polyketides, and non-ribosomal peptides such as siderophores can function as antifungals and protect the seed before and during germination and early growth (Abbas et al., 2022; Huang B. et al., 2022; Yadav et al., 2022), although they could also interfere with the establishment of mutualistic mycorrhizae (Schrey et al., 2012).

The microbiome of other plants highlights the importance of diversity, structure, composition, and core bacteriomes for the production of essential metabolites for ecology and plant-microorganism interaction, as is the example of Salvia miltiorrhiza (Chen et al., 2018), Hordeum vulgare L. (Rahman et al., 2018), Brassica napus (Rybakova et al., 2017), among others.

These efforts help lay the foundations for understanding the specific interactions between plants and microorganisms from an evolutionary and ecological point of view, complementing these studies with more precise tools such as holo-omics sciences (Xu et al., 2021).

The knowledge of the bacterial diversity in the progenitor plants of modern maize can allow us to propose lines of research that will explore the domestication, evolution, ecology, and biogeography of the different races of the plant to the symbiosis-plant microorganism that will allow us to recognize the bacteria that harbor a potential to improve agricultural productivity under more environmentally friendly conditions.

The endophytic bacterial diversity of seed teosintes, encompassing Z. diploperennis, Z. perennis, and Z. mays, displays a rich array of dozens of bacterial genera, forming a strict core. In contrast, many others reside in accessory bacteriomes specific to each plant species. Numerous PGB bacterial genera have been identified, alongside several previously unassociated with maize or teosinte. However, it is essential to acknowledge that further experiments are needed to demonstrate the reproducibility of these findings. The results also suggest that teosinte seeds are a reservoir of many important culturable and non-culturable bacteria, potentially microorganisms with exciting properties in plant-microorganism interaction as plant growth promoters or bio-control agents. These results lay the groundwork for future research on the functional role of members of the core bacteriome in symbiosis and their possible biotechnological applications in the intelligent design of bioinoculants. This work is the first step toward defining holobiont, holohabitat, and holoniche as previously defined (Malard and Guisan, 2023).

The datasets presented in this study can be found in online repositories.The accesion number of the Bioproject in NCBI is PRJNA952205.

ED-L-V-C and JH-G performed the DNA extraction, data analysis, and bioinformatics performances; ED-L-V-C, JH-G, LV-T, and CH-R designed and coordinated the study; ED-L-V-C wrote the first draft manuscript; ED-L-V-C, JH-G, LV-T, and CH-R contributed to the manuscript editing. All authors read and approved the final manuscript.