Abstract
Orders Oceanospirillales and Pseudomonadales play important roles in various ecosystems as the keystone taxa of microbiomes. However, the two orders present a close evolutionary relationship, which might have caused taxonomic misinterpretation and resulted in an incorrect understanding of their evolutionary history. In this study, first, we used the 16S rRNA gene sequences of 2,049 species of Gammaproteobacteria to build a phylogenetic tree, which demonstrated that reports regarding the evolutionary relationship of orders Cellvibrionales, Oceanospirillales, and Pseudomonadales based on a single conserved gene with a poor resolution have been conflicting; in particular, the major families Moraxellaceae and Pseudomonadaceae of order Pseudomonadales were separated from orders Cellvibrionales and Oceanospirillales Subsequently, we constructed the bac120 trees of all representative reference genomes of class Gammaproteobacteria based on 120 ubiquitous single-copy proteins from bacteria and a phylogenomic tree based on the 119 core genes of 257 reference genomes obtained from orders Cellvibrionales, Oceanospirillales, and Pseudomonadales to cross validate and infer their intrinsic evolutionary relationships. These results indicated that two novel orders, Moraxellales ord. nov. and Kangiellales ord. nov., and three novel families, Marinobacteraceae fam. nov., Perlucidibacaceae fam. nov., and Zooshikellaceae fam. nov., should be proposed. Additionally, orders Cellvibrionales and Oceanospirillales were merged into the order Pseudomonadales except for families Moraxellaceae and Kangiellaceae in class Gammaproteobacteria, which currently includes 18 families. Our work sheds some light on the evolutionary history of class Gammaproteobacteria, which could facilitate the detection and taxonomic analysis of natural communities.IMPORTANCE The orders Cellvibrionales, Oceanospirillales, and Pseudomonadales, as three major orders of the largest bacterial class, Gammaproteobacteria, play important roles in various ecosystems as the keystone taxa of microbiomes, but their evolutionary relationship is currently polyphyletic and chaotic. Here, we constructed a bac120 tree and core-genome tree and calculated the amino acid identity (AAI) value to explore their intrinsic evolutionary history. In this study, we proposed two novel orders and three novel families. This evolution study vastly reconstructed the taxonomic framework of class Gammaproteobacteria and could provide a more distinct perspective on global distribution and evolutionary patterns of these environmental microorganisms.
Highlights
Orders Oceanospirillales and Pseudomonadales play important roles in various ecosystems as the keystone taxa of microbiomes
The results indicated that genera Marinobacter, Mangrovitalea, and Tamilnaduibacter formed a monophyletic clade with family Oleiphilaceae (Fig. 1), which was shown by the Genome Taxonomy Database (GTDB) phylogeny reconstructed from 120 ubiquitous single-copy msystems.asm.org 3 protein-coding genes [3], and these genera were distantly related to order Alteromonadales, implying that the monophyletic clade could represent a novel family
We proved that two novel families, Marinobacteraceae and Perlucidibacaceae; families Alcanivoracaceae [40], Balneatrichaceae, Halomonadaceae [41], Hahellaceae [42], Oleiphilaceae [33], Oceanospirillaceae, Saccharospirillaceae [43], and Zooshikellaceae of order Oceanospirillales; Pseudomonadaceae and Ventosimonadaceae [28] of order Pseudomonadales; and Cellvibrionaceae, Halieaceae, Microbulbiferaceae, Porticoccaceae, and Spongiibacteraceae [5] of order Cellvibrionales shared a relatively recent ancestor and formed a robust branch based on two typical phylogenomic tree and amino acid identity (AAI) values in class Gammaproteobacteria
Summary
Orders Oceanospirillales and Pseudomonadales play important roles in various ecosystems as the keystone taxa of microbiomes. We constructed the bac120 trees of all representative reference genomes of class Gammaproteobacteria based on 120 ubiquitous single-copy proteins from bacteria and a phylogenomic tree based on the 119 core genes of 257 reference genomes obtained from orders Cellvibrionales, Oceanospirillales, and Pseudomonadales to cross validate and infer their intrinsic evolutionary relationships. These results indicated that two novel orders, Moraxellales ord. IMPORTANCE The orders Cellvibrionales, Oceanospirillales, and Pseudomonadales, as three major orders of the largest bacterial class, Gammaproteobacteria, play important roles in various ecosystems as the keystone taxa of microbiomes, but their evolutionary relationship is currently polyphyletic and chaotic. The order Pseudomonadales plays an important role in contaminated soil remediation and plant-associated microbiota [4], and many members of order Pseudomonadales present clear associations with human health as pathogens, such as Acinetobacter baumannii, Moraxella catarrhalis, and Pseudomonas aeruginosa
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