Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100

Abstract

Defining phenotypic and associated genotypic variation among Bdellovibrio may further our understanding of how this genus attacks and kills different Gram-negative bacteria. We isolated Bdellovibrio sp. NC01 from soil. Analysis of 16S rRNA gene sequences and average amino acid identity showed that NC01 belongs to a different species than the type species bacteriovorus. By clustering amino acid sequences from completely sequenced Bdellovibrio and comparing the resulting orthologue groups to a previously published analysis, we defined a 'core genome' of 778 protein-coding genes and identified four proteincoding genes that appeared to be missing only in NC01. To determine how horizontal gene transfer (HGT) may have impacted NC01 genome evolution, we performed genome-wide comparisons of Bdellovibrio nucleotide sequences, which indicated that eight NC01 genomic regions were likely acquired by HGT. To investigate how genome variation may impact predation, we compared protein-coding gene content between NC01 and the B. bacteriovorus type strain HD100, focusing on genes implicated as important in successful killing of prey. Of these, NC01 is missing ten genes that may play roles in lytic activity during predation. Compared to HD100, NC01 kills fewer tested prey strains and kills Escherichia coli ML35 less efficiently. NC01 causes a smaller log reduction in ML35, after which the prey population recovers and the NC01 population decreases. In addition, NC01 forms turbid plaques on lawns of E. coli ML35, in contrast to clear plaques formed by HD100. Linking phenotypic variation in interactions between Bdellovibrio and Gram-negative bacteria with underlying Bdellovibrio genome variation is valuable for understanding the ecological significance of predatory bacteria and evaluating their effectiveness in clinical applications.

A Metataxonomic Approach Reveals Diversified Bacterial Communities in Antarctic Sponges

“…ASV’s analysis of the three sponges, M. ( Oxymycale ) acerata , H. pilosus and H. ( Rhizoniera ) dancoi , displayed Deltaproteobacteria ( Figure 2 ; Tables S5–S7 ) belonging to the phylum Proteobacteria, that, as mentioned above, produce interesting bioactive metabolites [ 57 ]. For instance, H. pilosus exhibited some strains included into the genus Bdellovibrio ( Figure 3 ; Table S7 ), which is an obligate predator of other Gram-negative bacteria that was proposed for possible biotechnological applications toward medicinal, agricultural and industrial fields [ 113 , 114 , 115 ].…”

Bacterial predation transforms the landscape and community assembly of biofilms

“…A key example of such a predator is Bdellovibrio bacteriovorus, which is ubiquitous in natural environments. [56][57][58][59][60] B. bacteriovorus, a delta-proteobacterium approximately 1 mm in length, most often exhibits an obligate predatory lifestyle in which it targets Gram-negative prey, bores through the outer membrane into the periplasm, harvests resources to replicate, and lyses the host cell in search of new prey. [1][2][3][4][5][6][7] B. bacteriovorus can predate Escherichia coli and Pseudomonas fluorescens within biofilms in static culture and under flow, 61 and numerous studies have isolated B. bacteriovorus directly from biofilms on abiotic substrata and the surfaces of animals and plants in aquatic environments.…”

Phylogenomic insights into distribution and adaptation of Bdellovibrionota in marine waters

“…A total of 148 genomes of Bdellovibrionota were downloaded from GTDB database (Table S1), eight genomes were obtained from the NCBI to represent the model species that have been well studied previously (19, 20). After quality control (>70% completeness, < 10% contamination and average nucleotide identity ≽ 98.5%) (Tables S2 and S3), 82 genomes were retained for the subsequent study.…”