Assessment of ecological role of bacterial endophytes in vegetable production for human nutrition

Abstract

Bacterial endophytes are a unique group of microbes inhabiting plant tissues for at least a part of their life cycle without causing any pathogenic symptoms. These microbes play significant roles in ecosystem functions and plant growth promotion (PGP) through biogeochemical cycling, biodegradation, nutrient solubilisation and production of phytohormones and bioactive compounds. These ecological roles impact the productivity and nutritional quality of plants and consequently, human health may be affected when plant materials are consumed. Being highly diverse in association and distribution, endophytes exist in every plant that has been investigated, including vegetable crops. Despite vegetables being an important component of a healthy diet and having substantial human health benefits, their endophytes are underexplored. Thus, using high-throughput sequencing, this study investigated the community composition and functional profile of bacterial endophytes inhabiting vegetables such as cabbage, lettuce, onion and spinach. The functional profile was investigated with PICRUSt2 or Tax4Fun pipelines. Additionally, endophytes were recovered from vegetables using the culture-dependent method and identified by sequencing the partial 16S rRNA gene employing Sanger sequencing. The PGP potential was assessed using in vitro and greenhouse experiments. Results revealed that vegetables are colonized by an abundant and diverse group of bacterial endophytes, with Proteobacteria, followed by Actinobacteriodes being the most abundant phyla accounting for over 80% of the communities. Pseudomonas, Pantoea, Bacillus, Serratia, Rahnella1, Rhodococcus, Xanthomonas and Streptomyces were the most relatively abundant genera. The abundance, diversity and richness of endophytic bacteria were lower in the leaves compared to the roots. In multivariate space, the non-metric multidimensional scaling plot revealed a substantial overlap in the bacterial communities of cabbage, lettuce and spinach, while onion samples clustered separately. Shared and unique bacterial communities vary between plant species and organ types, with onions having the highest number of unique amplicon sequence variants compared to other vegetables, suggesting plant structures may influence the composition and community structure of endophytes. Co-occurrence analysis showed that over 60% of the core genera belonged to the generalist, with the dominant taxa being Pseudomonas, Bacillus, Agromyces, Nocardioides and other unclassified genera in the