Cristina Bez1, Ivana Galic2*, Iris Bertani1, Nada Stankovic2, Vittorio Venturi1
1International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
2Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
ivanagalic [at] imgge.bg.ac.rs
Abstract
In terms of agricultural sustainability, herbicide-resistant, plant growth promoting (PGP) bacteria that can improve crop yield are valuable resource. To exhibit PGP traits, the bacteria must be able to colonize and survive in the rhizosphere.
Upon screening the herbicide-resistant bacterial collection, candidates with the highest PGP potential were grouped into three consortia to evaluate their ability to colonize roots and persist in the natural/local plant microbiome in the pot. Experiments were conducted with seeds of commercial maize hybrids under controlled conditions, with and without herbicide. Colonization ability was evaluated by examining multiple plants from each treatment at two-time points during the experiment. 16S rRNA amplicon community profiling was performed to precisely target the bacterial strains used in the three consortia and investigate how the local microbiome might be altered by the application of the consortia. Bioinformatic analysis was performed using qiime2, clustering of reads into amplicon sequence variants ASVs using the DADA2 plugin, and the taxonomic assignment was based on a customized dataset formed from the 16S rRNA gene sequences of the ten isolates used in this study or by using the Silva rRNA database. For clustering and comparison of ASVs based on sequence similarity, the program cd-hit was used, with the sequence similarity parameter set to 98% to be considered part of the same cluster. The obtained dataset was imported into R using the package qiime2R, and subsequent analyzes and graphs were generated using either the R packages phyloseq, microbiome, or reshape2. We identified seven out of ten inoculated strains in both time points tested and with comparable abundance, indicating that most of the bacterial isolates tested have the ability to colonize the root system of maize. Furthermore, the natural/local microbiome of maize plants is not disturbed by the three consortia used in this study, implying that they are good candidates for future biotechnological applications.
Keywords: metabarcoding, 16S, consortium, bacteria, PGP
Acknowledgement: FEMS Research and Training Grant ID: 1818; IMGGE work program for 2022 (Ministry of Education, Science and Technological Development of the Republic of Serbia, 451-03-68/2022-14/200042)
