New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia

Abstract

Since early studies, the history of prokaryotes taxonomy has dealt with many changes driven by the development of new and more robust technologies. As a result, the number of new taxa descriptions is exponentially increasing, while an increasing number of others has been subject of reclassification, demanding from the taxonomists more effort to maintain an organized hierarchical system. However, expectations are that the taxonomy of prokaryotes will acquire a more stable status with the genomic era. Other analyses may continue to be necessary to determine microbial features, but the use of genomic data might be sufficient to provide reliable taxa delineation, helping taxonomy to reach the goal of correct classification and identification. Here we describe the evolution of prokaryotes’ taxonomy until the genomic era, emphasizing bacteria and taking as an example the history of rhizobia taxonomy. This example was chosen because of the importance of the symbiotic nitrogen fixation of legumes with rhizobia to the nitrogen input to both natural ecosystems and agricultural crops. This case study reports the technological advances and the methodologies used to classify and identify bacterial species and indicates the actual rules required for an accurate description of new taxa.

Efficiency of bacterial isolates on suppressing brown spot in rice plants

“…The taxonomic classification of prokaryotes has been carried out using techniques that have evolved and become more robust over the years, thus making it possible to adjust interest rates and their components. Expectations are that prokaryotic taxonomy will acquire a more stable status in the genomic era (Helene et al, 2022) and thus improve our understanding of microbiota populations and their constituents. For more details about the formed groups, see Table S2.…”

In Vitro Screening of Endophytic Micromonospora Strains Associated with White Clover for Antimicrobial Activity against Phytopathogenic Fungi and Promotion of Plant Growth

“…To reveal the relationship between the tested isolates and the most related reference strains at the species level, multilocus sequence analysis (MLSA) was carried out [31,32]. As a result, the maximum likelihood phylogenetic tree of the strains examined in this study and the valid taxa based on the concatenated 2620 bp of four housekeeping gene sequence fragments is presented in Figure 1.…”

Genomes of two type strains of the Rhizobium tropici group: R. calliandrae CCGE524 T and R. mayense CCGE526 T

“…Nowadays, the use of genomic parameters is highly encouraged in studies of taxonomy and phylogeny of bacteria, including rhizobia ( 5 ). As there were no genomes available for these two type strains, we performed next-generation sequencing to obtain high-quality genomes.…”