A Meta-Analysis Approach to Defining the Culturable Core of Plant Endophytic Bacterial Communities

Abstract

Endophytic bacteria are key members of the plant microbiome, which phylogenetic diversity has been widely described through next-generation sequencing technologies in the last decades. On the other side, a synopsis of culturable plant endophytic bacteria is still lacking in the literature. However, culturability is necessary for biotechnology innovations related to sustainable agriculture, such as biofertilizer and biostimulant agents’ development. In this review, 148 scientific papers were analyzed to establish a large dataset of cultured endophytic bacteria, reported at the genus level, inhabiting different compartments of wild and farmed plants, sampled around the world from different soil types and isolated using various growth media. To the best of our knowledge, this work provides the first overview of the current repertoire of cultured plant endophytic bacteria. Results indicate the presence of a recurrent set of culturable bacterial genera regardless of factors known to influence the plant bacterial community composition and the growth media used for the bacterial isolation. Moreover, a wide variety of bacterial genera that are currently rarely isolated from the plant endosphere was identified, demonstrating that culturomics can catch previously uncultured bacteria from the plant microbiome, widening the panorama of strains exploitable to support plant holobiont health and production.

Bacterial Endophytes Contribute to Rice Seedling Establishment Under Submergence

“…Only a few strains of bacteria were isolated from seedlings grown under dark submergence, confirming the stress imposed by this condition ( Table 3 ). These includes Pantoea , Bacillus , Microbacterium and Paenibacillus genera that have been suggested to be part of the culturable core of plant endophytic bacteria isolated in seeds ( Riva et al, 2022 ). P. ananatis , P. eucalypti and P. vagans related strains were found to produce indole-related compounds under hypoxia ( Table 3 ).…”

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

“…High-throughput genome sequencing has enabled less biased assessments of the microbial diversity, community composition, and dynamics in the endosphere, hence advancing state-of-the-art knowledge on the ecology of endophytes ( 54 , 58 , 59 ). Nonetheless, understanding the physiological role and in vivo interactions of seed endophytes requires studies with microbial isolates, whose diversity can be enhanced from developing novel culturing techniques ( 47 , 48 , 52 , 60 , 61 ). Plant tissues and their extracts provide a broad range of macromolecules, vitamins, and inorganic salts whose use, either as supplements to standard complex media or as unique nutritional sources, can improve culturing of endophytic bacteria and regeneration from glycerol stocks ( 62 , 63 ).…”

Acinetobacter baylyi Strain BD413 Can Acquire an Antibiotic Resistance Gene by Natural Transformation on Lettuce Phylloplane and Enter the Endosphere

“…Literature data indicate in fact that Acinetobacter spp. are abundant members of water, soil, phyllosphere, and endosphere microbiome [ 18 , 27 , 28 ], and the species A. baylyi , among others affiliated to this genus, was isolated from commercial lettuce [ 19 ]. During this study, we verified the ability of A. baylyi strain BD413 to survive on the lettuce leaf surface and enter the internal tissues when administered in a physiological solution simulating spray irrigation.…”

“…The genus Acinetobacter includes several human opportunistic pathogens, such as Acinetobacter baumannii , recognized as major causal agents of nosocomial infections and known for the propensity to develop resistance to the main groups of antibiotics [ 16 , 17 ]. On the other hand, different species of the Acinetobacter genus are typical members of the cultivable plant endophytic microbiome [ 7 , 18 ] and were isolated from fresh fruits and leafy vegetables, such as lettuce [ 19 ]. Recently, the opportunity to manage the microbiota composition of lettuce and other fresh produces has been proposed as a strategy to limit the invasion of potential human pathogens and to limit outbreaks related to the consumption of contaminated food [ 20 , 21 ].…”