Comparative Genomics of Burkholderia singularis sp. nov., a Low G+C Content, Free-Living Bacterium That Defies Taxonomic Dissection of the Genus Burkholderia

ABSTRACTIn most bacteria, cell division begins with the polymerization of the GTPase FtsZ at the mid-cell, which recruits the division machinery to initiate cell constriction. In the filamentous bacterium Streptomyces, cell division is positively controlled by SsgB, which recruits FtsZ to the future septum sites and promotes Z-ring formation. Here we show via site-saturated mutagenesis that various amino acid substitutions in the highly conserved SsgB protein result in the production of ectopically placed septa, that sever spores diagonally or along the long axis, perpendicular to the division plane. Ectopic septa were especially prominent when cells expressed SsgB variants with substitutions in residue E120. Biochemical analysis of SsgB variant E120G revealed that its interaction with - and polymerization of - FtsZ had been maintained. The crystal structure of S. coelicolor SsgB was resolved and the position of residue E120 suggests its requirement for maintaining the proper angle of helix α3, thus providing a likely explanation for the aberrant septa formed in SsgB E120 substitution mutants. Taken together, our work presents the first example of longitudinal division in a free living bacterium, which is explained entirely by changes in the FtsZ-recruiting protein SsgB.

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Msh Pilus Mutations Increase the Ability of a Free-Living Bacterium to Colonize a Piscine Host

10.20944/preprints202012.0391.v1 ◽

2020 ◽

Author(s):

Jarrett F. Lebov ◽

Brendan J. M. Bohannan

Keyword(s):

Dominant Role ◽

Shewanella Oneidensis ◽

Loss Of Function ◽

Surface Adhesion ◽

Free Living ◽

Environmental Surfaces ◽

Evolutionary Changes ◽

Novel Host ◽

Living Bacterium ◽

Free Living Bacterium

Symbioses between animals and bacteria are ubiquitous. To better understand these relationships, it is essential to unravel how bacteria evolve to colonize hosts. Previously, we serially passaged the free-living bacterium, Shewanella oneidensis, through the digestive tracts of germ-free larval zebrafish (Danio rerio) to uncover the evolutionary changes involved in the initiation of a novel symbiosis with a vertebrate host. After 20 passages, we discovered an adaptive missense mutation in the mshL gene of the msh pilus operon, which improved host colonization, increased swimming motility, and reduced surface adhesion. In the present study, we have determined that this mutation was a loss-of-function mutation and found that it improved zebrafish colonization by augmenting S. oneidensis representation in the water column outside larvae through a reduced association with environmental surfaces. Additionally, we found that strains containing the mshL mutation were able to immigrate into host digestive tracts at higher rates per capita. However, mutant and evolved strains exhibited no evidence of a competitive advantage after colonizing hosts. Our results demonstrate that bacterial behaviors outside the host can play a dominant role in facilitating the onset of novel host associations.

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Internal Membranes in the Nitrogen Fixing Organisms: Free-Living Azotobacter vinelandii and Rhizobium japonicum Bacteriods

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100050871 ◽

1974 ◽

Vol 32 ◽

pp. 172-173

Author(s):

D. Raveed ◽

D. W. Reed ◽

R. E. Toia

Keyword(s):

Cytoplasmic Membrane ◽

Azotobacter Vinelandii ◽

Molecular Nitrogen ◽

Membrane System ◽

Rhizobium Japonicum ◽

Intracellular Membrane ◽

Free Living ◽

Cytoplasmic Material ◽

Living Bacterium ◽

Free Living Bacterium

The free-living bacterium Azotobacter vinelandii carries out the fixation of molecular nitrogen under aerobic conditions. During growth at high oxygen concentrations, these bacteria exhibit high rates of both respiration and nitrogen fixation. Internal membranes are not easily seen in sections of intact bacteria but an extensive intracellular membrane system is apparent in osmotically-lysed cells (Fig. 1). Equilibration of the cells with 0.3 M glycerol and rapid dilution into ten volumes of 0.01 M Tris-HCl buffer, pH 7.4, permits the escape of electron dense cytoplasmic material. These intracellular membranes which contain the respiratory components of the cell are spherical invaginations of the cytoplasmic membrane and are completely separable from the smaller vesicular azotophore membranes which contain the nitrogenase in A. vinelandii.

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The novel shapeshifting bacterial phylum Saltatorellota

10.1101/817700 ◽

2019 ◽

Cited By ~ 3

Author(s):

Sandra Wiegand ◽

Mareike Jogler ◽

Timo Kohn ◽

Ram Prasad Awal ◽

Sonja Oberbeckmann ◽

...

Keyword(s):

Cell Wall ◽

Turgor Pressure ◽

The Novel ◽

Free Living ◽

E Coli ◽

Type Iv ◽

Peptidoglycan Cell Wall ◽

Living Bacterium ◽

Free Living Bacterium ◽

Shape Changes

AbstractOur current understanding of a free-living bacterium - capable of withstanding a variety of environmental stresses-is represented by the image of a peptidoglycan-armored rigid casket. The making and breaking of peptidoglycan greatly determines cell shape. The cytoplasmic membrane follows this shape, pressed towards the cell wall by turgor pressure. Consequently, bacteria are morphologically static organisms, in contrast to eukaryotic cells that can facilitate shape changes. Here we report the discovery of the novel bacterial phylum Saltatorellota, that challenges this concept of a bacterial cell. Members of this phylum can change their shape, are capable of amoeba-like locomotion and trunk-formation through the creation of extensive pseudopodia-like structures. Two independent Saltatorellota cells can fuse, and they employ various forms of cell division from budding to canonical binary fission. Despite their polymorphisms, members of the Saltatorellota do possess a peptidoglycan cell wall. Their genomes encode flagella and type IV pili as well as a bacterial actin homolog, the ‘saltatorellin’. This protein is most similar to MamK, a dynamic filament-forming protein, that aligns and segregates magnetosome organelles via treadmilling. We found saltatorellin to form filaments in both, E. coli and Magnetospirillum gryphiswaldense, leading to the hypothesis that shapeshifting and pseudopodia formation might be driven by treadmilling of saltatorellin.

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Phenotypic Parallelism during Experimental Adaptation of a Free-Living Bacterium to the Zebrafish Gut

mBio ◽

10.1128/mbio.01519-20 ◽

2020 ◽

Vol 11 (4) ◽

Author(s):

Jarrett F. Lebov ◽

Brandon H. Schlomann ◽

Catherine D. Robinson ◽

Brendan J. M. Bohannan

Keyword(s):

Experimental Evolution ◽

Bacterial Species ◽

Shewanella Oneidensis ◽

Free Living ◽

Content Type ◽

Larval Zebrafish ◽

Health And Development ◽

Living Bacterium ◽

Animal Hosts ◽

Free Living Bacterium

ABSTRACT Although animals encounter a plethora of bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. However, our understanding of how bacteria initiate symbioses with animal hosts remains underexplored, and this process is central to the assembly and function of gut bacterial communities. Therefore, we used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). After approximately 200 bacterial generations, isolates from evolved populations improved their ability to colonize larval zebrafish during competition against their unpassaged ancestor. Genome sequencing revealed unique sets of mutations in the two evolved isolates exhibiting the highest mean competitive fitness. One isolate exhibited increased swimming motility and decreased biofilm formation compared to the ancestor, and we identified a missense mutation in the mannose-sensitive hemagglutinin pilus operon that is sufficient to increase fitness and reproduce these phenotypes. The second isolate exhibited enhanced swimming motility but unchanged biofilm formation, and here the genetic basis for adaptation is less clear. These parallel enhancements in motility and fitness resemble the behavior of a closely related Shewanella strain previously isolated from larval zebrafish and suggest phenotypic convergence with this isolate. Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association. IMPORTANCE Although animals encounter many bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. We used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association.

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Msh Pilus Mutations Increase the Ability of a Free-Living Bacterium to Colonize a Piscine Host

Genes ◽

10.3390/genes12020127 ◽

2021 ◽

Vol 12 (2) ◽

pp. 127

Author(s):

Jarrett F. Lebov ◽

Brendan J. M. Bohannan

Keyword(s):

Dominant Role ◽

Shewanella Oneidensis ◽

Loss Of Function ◽

Surface Adhesion ◽

Free Living ◽

Environmental Surfaces ◽

Evolutionary Changes ◽

Novel Host ◽

Living Bacterium ◽

Free Living Bacterium

Symbioses between animals and bacteria are ubiquitous. To better understand these relationships, it is essential to unravel how bacteria evolve to colonize hosts. Previously, we serially passaged the free-living bacterium, Shewanella oneidensis, through the digestive tracts of germ-free larval zebrafish (Danio rerio) to uncover the evolutionary changes involved in the initiation of a novel symbiosis with a vertebrate host. After 20 passages, we discovered an adaptive missense mutation in the mshL gene of the msh pilus operon, which improved host colonization, increased swimming motility, and reduced surface adhesion. In the present study, we determined that this mutation was a loss-of-function mutation and found that it improved zebrafish colonization by augmenting S. oneidensis representation in the water column outside larvae through a reduced association with environmental surfaces. Additionally, we found that strains containing the mshL mutation were able to immigrate into host digestive tracts at higher rates per capita. However, mutant and evolved strains exhibited no evidence of a competitive advantage after colonizing hosts. Our results demonstrate that bacterial behaviors outside the host can play a dominant role in facilitating the onset of novel host associations.

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Phenotypic parallelism during experimental adaptation of a free-living bacterium to the zebrafish gut

10.1101/2020.03.18.997734 ◽

2020 ◽

Author(s):

Jarrett F. Lebov ◽

Brandon H. Schlomann ◽

Catherine D. Robinson ◽

Brendan J. M. Bohannan

Keyword(s):

Bacterial Species ◽

Shewanella Oneidensis ◽

Free Living ◽

Swimming Motility ◽

Larval Zebrafish ◽

Living Bacterium ◽

Animal Hosts ◽

Host Microbe Interactions ◽

And Function ◽

Free Living Bacterium

AbstractDespite the fact that animals encounter a plethora of bacterial species throughout their lives, only a subset are capable of colonizing vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. However, it is still unknown how bacteria evolve symbioses with animal hosts, and this process is central to both the assembly and function of gut bacterial communities. Therefore, we used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host. We serially passaged replicate populations of Shewanella oneidensis, through the digestive tracts of larval zebrafish (Danio rerio). After only 20 passages, representing approximately 200 bacterial generations, isolates from replicate evolved populations displayed an improved ability to colonize larval zebrafish digestive tracts during competition against their unpassaged ancestor. Upon sequencing the genomes of these evolved isolates, we discovered that the two isolates with the highest mean competitive fitness accumulated unique sets of mutations. We characterized the swimming motility and aggregation behavior of these isolates, as these phenotypes have previously been shown to alter host-microbe interactions. Despite exhibiting different biofilm characteristics, both isolates evolved augmented swimming motility. These enhancements are consistent with expectations based on the behavior of a closely related Shewanella strain previously isolated from the zebrafish digestive tract and suggest that our evolved isolates are pursuing a convergent adaptive trajectory with this zebrafish isolate. In addition, parallel enhancements in swimming motility among isolates from independently adapted populations implicates increased dispersal as an important factor in facilitating the onset of host association. Our results demonstrate that free-living bacteria can rapidly improve their associations with vertebrate hosts.

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Model communities hint to promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria

10.1101/103838 ◽

2017 ◽

Cited By ~ 2

Author(s):

Sarahi L Garcia ◽

Moritz Buck ◽

Joshua J. Hamilton ◽

Christian Wurzbacher ◽

Magnus Alm Rosenblad ◽

...

Keyword(s):

Time Series ◽

Comparative Genomics ◽

Mixed Cultures ◽

Biosynthetic Pathways ◽

Free Living ◽

Freshwater Bacteria ◽

Interaction Partners ◽

Microbial Associations ◽

Occurrence Patterns ◽

Freshwater Environments

AbstractFree-living microorganisms with streamlined genomes are very abundant in the environment. Genome streamlining results in losses in the cell’s biosynthetic potential generating physiological dependencies between microorganisms. However, there exists no consensus on the specificity of these microbial associations. To verify specificity and extent of these associations, mixed cultures were established from three different freshwater environments. These cultures contained free-living streamlined organisms lacking multiple biosynthetic pathways. Among the co-occurring members of the mixed cultures, there was no clear recurring pattern of metabolic complementarity and dependencies. This, together with weak temporal co-occurrence patterns observed using time-series metagenomics, suggests that free-living freshwater bacteria form loose and unspecific cooperative loops. Comparative genomics suggests that the proportion of accessory genes in populations of streamlined bacteria allows for flexibility in interaction partners. Altogether this renders these free-living bacterial lineages functionally versatile despite their streamlining tendencies.

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