Genome-centric metagenomics reveals insights into the evolution and metabolism of a new free-living group in Rhizobiales

Abstract

Background The Rhizobiales (Proteobacteria) order is an abundant and diverse group of microorganisms, being extensively studied for its lifestyle based on the association with plants, animals, and humans. New studies have demonstrated that the last common ancestor (LCA) of Rhizobiales had a free-living lifestyle, but the phylogenetic and metabolism characterization of basal lineages remains unclear. Here, we used a high-resolution phylogenomic approach to test the monophyly of the Aestuariivirgaceae family, a new taxonomic group of Rhizobiales. Furthermore, a deep metabolic investigation provided an overview of the main functional traits that can be associated with its lifestyle. We hypothesized that the presence of pathways (e.g., Glycolysis/Gluconeogenesis) and the absence of pathogenic genes would be associated with a free-living lifestyle in Aestuariivirgaceae. Results Using high-resolution phylogenomics approaches, our results revealed a clear separation of Aestuariivirgaceae into a distinct clade of other Rhizobiales family, suggesting a basal split early group and corroborate the monophyly of this group. A deep functional annotation indicated a metabolic versatility, which includes putative genes related to sugar degradation and aerobic respiration. Furthermore, many of these traits could reflect a basal metabolism and adaptations of Rhizobiales, as such the presence of Glycolysis/Gluconeogenesis pathway and the absence of pathogenicity genes, suggesting a free-living lifestyle in the Aestuariivirgaceae members. Conclusions Aestuariivirgaceae (Rhizobiales) family is a monophyletic taxon of the Rhizobiales with a free-living lifestyle and a versatile metabolism that allows these microorganisms to survive in the most diverse microbiomes, demonstrating their adaptability to living in systems with different conditions, such as extremely cold environments to tropical rivers.

New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient

“…The MAGs classified in the TMED25 division of Rhizobiales [14], which are abundant in marine metagenomes (Table 2 and [15]), cluster together with Hyphomonadaceae and Robiginitomaculaceae (Figure 5), as expected from the highly derived genomes of these taxa. On the other hand, Parvibaculaceae are shown to be the earliest branching family of Rhizobiales (Figure 5), consistent with some studies [6,13], but apparently in contrast with another [7].…”

“…Their fundamental classification comprises various orders that have been defined since 2007 [2] but have a very different distribution in nature. The most common order is that of the Rhizobiales, which are widespread in earth environments and have been studied predominantly because of their economic (agricultural) and medical impact [6,7]. The second most common order is that of Rhodobacterales, including purple photosynthetic bacteria that have traditionally dominated the biochemical and genetic studies on Alphaproteobacteria [1,4], plus an ever-increasing number of marine non-photosynthetic bacteria [8,9].…”

Lithic bacterial communities: ecological aspects focusing onTintenstrich communities

“…While most of the sequences of the order Rhizobiales were unclassified (58 %), their higher relative abundance on siliceous rock is consistent with the fact that it is a more stable environment where roots system can develop, which are known to represent a good substrate for most of the genera belonging to this order [49] . The tight relation with root systems may also explain the decrease of Rhizobiales with elevation.…”

Impact of wine-grape continuous cropping on soil enzyme activity and the composition and function of the soil microbial community in arid areas

“…The main order of microorganisms were Rhizobiales , Propionibacteriales , Solirubrobacterales , Micrococcales , and Streptomycetales , The relative abundance of Rhizobiales significantly increased after land use, and the relative abundance varied across different planting years. Rhizobiales (Proteobacteria) represent a diverse and abundant microbiome taxa that establishes both mutualistic and pathogenic relationships with plants while playing a crucial role in nitrogen fixation processes ( Clúa et al, 2018 ; Lemos et al, 2021 ). After the land use for vineyards, the litter and animal residues increase the nitrogen fixation of the soil, consequently leading to a higher relative abundance of Rhizobiales .…”