Identification of Genes Involved in Biogenesis of Outer Membrane Vesicles (OMVs) in Salmonella enterica Serovar Typhi

et al. 2020

Preprint

Background: Bacterial predation is an important selective force for microbial community structure and dynamics. However, only a limited number of predatory bacteria were reported, and their predatory strategies and evolutionary adaption remain elusive. We recently isolated a novel group of bacterial predator, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with other bacterial predators (e.g. Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales remain largely unknown.Results: Bradymonabacteria preyed on diverse bacteria but had a high preference on Bacteroidetes based on individual co-culture of Bradymonabacteria with 281 prey bacteria. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual-transcriptome analysis of co-culture of Bradymonabacteria and prey suggested the potential contact-dependent predation mechanism. Comparative genomic analysis with other 24 bacterial predators indicated Bradymonabacteria had different predatory and living strategies. Furthermore, we extracted Bradymonadales from 1552 public available 16S rRNA amplicon sequencing samples and found that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed there may be six proposed subgroups for this order and each subgroup occupied a different habitat. Conclusions: Bradymonabacteria have unique living strategies, which are different from so-called “obligate” or “facultative” predators. We propose a framework to categorize the current bacterial predators into 3 groups: (i) highly prey-dependent predators, (ii) facultative prey-dependent predators, and (iii) prey-independent predators. Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments.

Section: Dual-transcriptome Analysis Of Potential Predation Mechanismmentioning

confidence: 94%

Bradymonabacteria, a novel bacterial predator with versatile survival strategies in saline environments

et al. 2020

Preprint

“…3). Genes involved in OMV-like biosynthesis were also detected in most genomes, such as ompA (cell envelope biogenesis protein), envC (Murein hydrolase activator) and tolR (envelope stability) [32]. Vesicle membrane-related genes (DN745_03865, DN745_02930, and DN745_07125) were significantly upregulated during predation (Table S4, Fig.…”

Section: Dual-transcriptome Analysis Of the Potential Predation Mechamentioning

confidence: 99%

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

et al. 2020

Preprint

Background: Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ- Proteobacteria . Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales ), the predatory and living strategies of Bradymonadales are still largely unknown. Results: Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes . Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual-transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat. Conclusions: Bradymonabacteria have unique living strategies that differ from those of so-called “obligate” or “facultative” predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) highly prey-dependent predators, (ii) facultatively prey-dependent predators, and (iii) prey-independent predators. Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments.

“…3). Genes involved in outer membrane vesicles (OMV) biosynthesis were also detected in most genomes, such as ompA (cell envelope biogenesis protein), envC (Murein hydrolase activator) and tolR (envelope stability) [32]. Vesicle membrane-related genes (DN745_03865, DN745_02930, and DN745_07125) were signi cantly upregulated during predation (Table S4, Fig.…”

Section: Bradymonabacteria Are Polyauxotrophsmentioning

confidence: 99%

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

et al. 2020

Preprint

Abstract Background: Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales are still largely unknown.Results: Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual-transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat.Conclusions: Bradymonabacteria have unique living strategies that are transitional between the “obligate” and the so-called “facultative” predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) obligate predators (completely prey-dependent), (ii) facultative predators (facultatively prey-dependent), and (iii) opportunistic predators (prey-independent). Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments.