Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters

Abstract

Bdellovibrionota is composed of obligate predators that can consume some Gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies using 132 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from the ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ATP-binding cassette (ABC) transporters and penicillin-binding protein were necessary for the predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, and all the marine genomes have a number of genes for adaptation to marine environments. The genes encoding chitinase and chitin-binding protein were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey on a wider spectrum of microbes. This study expands our knowledge on adaption strategies of Bdellovibrionota inhabiting deep seas and the potential usage of Oligoflexia for biological control.

Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes

“…In addition, fourteen rare phyla (i.e., representing less than 1% of ASVs across samples) were also found in more than 50% of the samples and are therefore well represented across sub-Saharan African soils. These include the predatory bacterial phylum Bdellovibrionota, previously classified as members of the class Oligoflexia [62], members of which have been proposed to be biocontrol agents in marine environments [63], and Fribrobacteres, a phylum that includes several cellulose-degrading genera [64]. Another rare phylum identified in 589 (of 810) samples, Eremiobacterota (previously known as WS-2), includes several members capable of anoxygenic phototrophy [65] and has been recently associated with the ability to use trace gases such as hydrogen and carbon monoxide as energy sources in exothermic reactions capable of sustaining life in extreme environments [66,67].…”

The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone

“…Cand . Puniceispirillum and Pseudofulvibacter (Figure 7B) were probably sustained by decaying phytoplankton (Choi et al, 2015; Gros et al, 2023), whereas Chitinophagales and Oligoflexales might utilize chitinous aggregates (Fontanez et al, 2015; Li et al, 2021; Martínez‐García et al, 2022). Aureispira can be attached to gel particles, and feed on bacterial cells or cell debris (Furusawa et al, 2015; Bunse et al, 2021).…”

Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp.

“…Phylogenomic inference showed that both MAGs B11 and B12 fell in the Bdello-group2 in the phylum Bdellovibrionota but form two separate deep branches ( Figure 5 ). Bdello-group2 comprised of the representative Bdellovibrio predators including Bdellovibrio exovorus JSS, Bdellovibrio bacteriovorus HD100, Bdellovibrio bacteriovorus Tiberius, and Bdellovibrio bacteriovorus 109J (Li et al, 2021 ), suggesting that B11 and B12 may also represent bacterial predators. The Bdellovibrionota MAGs B11 and B12 have remarkably smaller genome sizes and lower GC contents than those free-living Bdellovibrionota species ( Supplementary Figure 2 ).…”

“…Bdellovibrio (in the phylum Bdellovibrionota) and Bdellovibrio -like bacteria (BALOs) are gram-negative bacterial predators living in various environments (Jurkevitch et al, 2000 ; Sockett, 2009 ) and mainly consists of four groups: Bacteriovoracia, Oligoflexia, Bdello-group1, and Bdello-group2 (Li et al, 2021 ). Till now, sponge-associated BALO had only been reported in the shallow-water sponge Cymbastela concentrica , and this predator was proposed to live with cyanobacteria (Tian et al, 2017 ).…”

“…Phylogenomic inference showed that both MAGs B11 and B12 fell in the Bdello-group2 in the phylum Bdellovibrionota but form two separate deep branches (Figure 5). Bdello-group2 comprised of the representative Bdellovibrio predators including Bdellovibrio exovorus JSS, Bdellovibrio bacteriovorus HD100, Bdellovibrio bacteriovorus Tiberius, and Bdellovibrio bacteriovorus 109J (Li et al, 2021), suggesting that B11 and B12 may also represent Global distribution of the sponge symbiont Nitrososphaerota B . To investigate the distribution of B in sponges and surrounding environmental samples, its S rRNA gene sequence as a query was searched against the Sponge Microbiome Project (SMP) using BLASTN, and the target sequences with identity values of > % were selected and assigned to Id (identity = %), Id (identity ≥ % but < %), Id , Id , and Id groups.…”