Abstract
PurposeThe plant Solanaceae family is one of the most important for global agriculture and nutrition. Within this plant family, two plant species stand out for their economic importance and for human consumption, which are tomato (Solanum lycopersicum) and chili pepper (Capsicum annuum). Moreover, those plants support diverse and characteristic microbial communities that are uniquely suited to the plant habitat and intimately connected to plant health. The main objective of this work is the bacterial community characterization in the rhizobiome of tomato and chili pepper, cultivated in arid environments.MethodsFive crop fields located in the south of the peninsula of Baja California, Mexico, were sampled. Total DNA was extracted from rhizosphere, rhizoplane, and endophytic root compartment and sequenced by Illumina MiniSeq platform technology applied to 16S rRNA gene V3 region.ResultsWe were able to obtain 1,195,426 total reads and 1,725,258 total reads for tomato and chili pepper samples, respectively. The analysis of the bacterial community structures confirmed that the two plant species showed differences in their microbial community structures. Nonetheless, the microbial community structures were directly and equally influenced by the crop field localization of each plant species. Interestingly, we determined that in both plant species, the Proteobacteria was the main phylum.ConclusionIn conclusion, we found that several bacterial families are part of the core rhizobiome (28 OTUs) for both tomato and chili pepper, but the most abundant were the Pseudomonadaceae family and the Pseudomonas genus, which most probably play a pivotal role in the microbial ecology to benefit both crop plants.
Highlights
Plants are capable to support diverse microbial communities
In conclusion, we found that several bacterial families are part of the core rhizobiome (28 operational taxonomic unit (OTU)) for both tomato and chili pepper, but the most abundant were the Pseudomonadaceae family and the Pseudomonas genus, which most probably play a pivotal role in the microbial ecology to benefit both crop plants
From the core microbiome analysis for both plant Solanaceae species and related samples taking the OTU presence in at least 50%, 75%, and 100% of the samples, we found that the Pseudomonadaceae family and the genus Pseudomonas were present at 100% of the samples, and this genus was the most abundant in the core microbiome at 100% criteria
Summary
Plants are capable to support diverse microbial communities. Those are specific to the plant habitat and are intimately coupled with plant requirements. The rhizosphere (defined as microbes living in the zone around root (Sasse et al 2018)) is rich in nutrients due to the accumulation of plant exudates, and these contain amino acids and sugars that provide a nitrogen and carbon source required for colonizing bacteria. This induces the bacterial community to colonize the rhizoplane and rhizosphere (Qiao et al 2017; Posada et al 2018). Some bacteria from the rhizoplane can colonize intercellular spaces in several internal plant tissues without causing any harm or disease, and some bacteria enhance plant growth and increase plant resistance to pathogens; those bacteria are collectively known as endophytic bacteria (defined as microbe living within plant tissue in the endosphere (Sasse et al 2018)) (Lopez et al 2011; Passari et al 2016)
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