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 data set 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.

Keywords: culturomics; endophytes; plant microbiome.

FIG 1

Number of shared bacterial genera and the correspondent record percentage for each comparison. Venn diagrams represent the bacterial genera shared between the categories when comparing (A) plant compartments, (B) isolation media, (C) soil types, and (D) growing conditions. Bar charts indicate, for each comparison, the percentage of records referred to the bacterial genera shared among all the categories (filled bars) or isolated only from some categories (empty bars). Venn diagrams were generated using the open software InteractiVenn at http://www.interactivenn.net/.

FIG 2

Representation of the genera most represented in the data set. Comparison of the endophytic bacteria isolated (A) from different plant compartments, (B) with different isolation media, (C) from plants grown in different soil types, and (D) from wild and farmed plants. In each panel, the graph shows the phylogenetic affiliation of the most represented bacterial genera up to 50% of records for each category. Each genus is represented with the same color in the different graphs. The gray portion of the bars is the 50% of records that includes the less represented bacterial genera in the categories.

FIG 3

Current situation of culturability in plant endosphere. The scheme indicates the results of this bibliographic study that investigated the taxonomy of culturable endophytes associated to a wide range of plants, and considered different information, i.e., plant compartment, isolation medium, soil type, and plant growing condition. Data elaboration indicates the presence of both a recurrent set of cultured bacterial genera and a wide range of bacterial genera that are rarely isolated under laboratory conditions, revealing the pivotal role of culturomics for the future studies on plant microbiome.