Indigenous Nigerian Vegetables Harbour Plant Species‐Specific Seed Microbial Signatures for Bacteria and Fungi

ABSTRACT Introduction The seed microbiome is essential for plant health, development, and adaptation. Little is known regarding the constituents of seed microbiomes of Africa's indigenous vegetables, which enables the vertical transmission of a specific microbial heritage. Shedding light on this was the focus of the current study. Methodology Microbiome profiling using domain‐specific amplicon sequencing was performed to examine the seed microbiome of five economically important vegetable crops in Nigeria. The selection included not yet studied Amaranthus hybridus , Solanum macrocarpon , Corchorus olitorius , Celosia argentea , and Telfairia occidentalis . Results The seeds of the five plant species harboured a diverse microbiome comprised of 2877, 765, and 56 amplicon sequence variants (ASVs), for bacterial, fungal, and archaeal communities, respectively. Plant species‐specific seed microbial signatures were found for bacterial and fungal communities, which were highly abundant (i.e., 10 8 to 10 11 gene copy numbers for bacterial and 10 9 to 10 11 for fungal community). In contrast, there was no separation for the less abundant archaea across the different plant species. The core seed microbiota was comprised by potentially plant‐beneficial taxa including the archaeal genus Methanobrevibacter and bacterial genera like Methylobacterium , Burkholderia‐Caballeronia‐Paraburkholderia , Bacillus , Paenibacillus, Stenotrophomonas, Pseudomonas, Serratia, Pantoea, Shingomonas, and Lactobacillus ; as well as fungal genera Aspergillus and Fusarium . Random forest classification revealed that the seed microbiome profiles can resolve plant species‐specific differences. Conclusion Our study shows that indigenous African vegetables harbour diverse and abundant microbial communities which are potentially important for the sustenance of these plants, particularly in smallholder‐dependent food production systems, like in Sub‐Sahara Africa. The research also provides the basis for conservation of these unique plant genetic resources.