Prey Range and Genome Evolution of Halobacteriovorax marinus Predatory Bacteria from an Estuary

Phylogenetic Revisit to a Review on Predatory Bacteria

Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, such as the role of outer membrane vesicles in myxobacterial predation, but provides an overview of the classification and newly described taxa of predatory bacteria since 2016, particularly with regard to phylogenetic aspects. Among them, it is noteworthy that in 2020 there was a major phylogenetic reorganization that the taxa hosting Bdellovibrio and Myxococcus, formerly classified as Deltaproteobacteria, were proposed as the new phyla Bdellovibrionota and Myxococcota, respectively. Predatory bacteria have been reported from other phyla, especially from the candidate divisions. Predatory bacteria that prey on cyanobacteria and predatory cyanobacteria that prey on Chlorella have also been found. These are also covered in this mini-review, and trans-phylum phylogenetic trees are presented.

Environmental Regulation of the Distribution and Ecology of Bdellovibrio and Like Organisms

The impact of key environmental factors, salinity, prey, and temperature, on the survival and ecology of Bdellovibrio and like bacteria (BALOs), including the freshwater/terrestrial, non-halotolerant group and the halophilic Halobacteriovorax strains, has been assessed based on a review of data in the literature. These topics have been studied by numerous investigators for nearly six decades now, and much valuable information has been amassed and reported. The collective data shows that salinity, prey, and temperature play a major role in, not only the growth and survival of BALOs, but also the structure and composition of BALO communities and the distribution of the predators. Salinity is a major determinant in the selection of BALO habitats, distribution, prey bacteria, and systematics. Halophilic BALOs require salt for cellular functions and are found only in saltwater habitats, and prey primarily on saltwater bacteria. To the contrary, freshwater/terrestrial BALOs are non-halotolerant and inhibited by salt concentrations greater than 0.5%, and are restricted to freshwater, soils, and other low salt environments. They prey preferentially on bacteria in the same habitats. The halophilic BALOs are further separated on the basis of their tolerance to various salt concentrations. Some strains are found in low salt environments and others in high salt regions. In situ studies have demonstrated that salinity gradients in estuarine systems govern the type of BALO communities that will persist within a specific gradient. Bacterial prey for BALOs functions more than just being a substrate for the predators and include the potential for different prey species to structure the BALO community at the phylotype level. The pattern of susceptibility or resistance of various bacteria species has been used almost universally to differentiate strains of new BALO isolates. However, the method suffers from a lack of uniformity among different laboratories. The use of molecular methods such as comparative analysis of the 16S rDNA gene and metagenomics have provided more specific approaches to distinguished between isolates. Differences in temperature growth range among different BALO groups and strains have been demonstrated in many laboratory experiments. The temperature optima and growth range for the saltwater BALOs is typically lower than that of the freshwater/terrestrial BALOs. The collective data shows not only that environmental factors have a great impact on BALO ecology, but also how the various factors affect BALO populations in nature.

Halobacteriovorax vibrionivorans sp. nov., a novel prokaryotic predator isolated from coastal seawater of China

Three prokaryotic predator strains, BL9^T, BL10 and BL28, were isolated with Vibrio alginolyticus from coastal seawater of PR China. Cells of the strains were Gram-negative, vibrioid-shaped and motile with a single sheathed flagellum (25-28 nm wide). Cells were around 0.3×0.5-1.0 µm in size. The three strains were obligate predators that exhibited a biphasic life cycle: a free-swimming attack phase and an intraperiplasmic growth phase within the prey. Bdelloplasts were formed. NaCl was required for growth. Optimum growth occurred at ~37 °C, with 2-4 % (w/v) NaCl and at pH 7.0-8.0. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the three strains shared 99.9 % similarity to each other, were affiliated with the genus Halobacteriovorax in the class Oligoflexia, and represented the same new species. Strain BL9^T (=MCCC 1K03527^T=JCM 32962^T) was designated as the type strain. Genome sequencing of strain BL9^T revealed a genome size of 3.14 Mb and a G+C content of 35.8 mol%. The estimated digital DNA-DNA hybridization (dDDH) values and the whole genome average nucleotide identity (gANI) values between the genome of strain BL9^T and those of Bdellovibrionales and Bacteriovoracales were 12.5-19 and 63.49-76.15 %, respectively. On the basis of life cycle features, results of physiological analyses, gANI data and dDDH data, strain BL9^T represents a new species within the genus Halobacteriovorax, for which the name Halobacteriovoraxvibrionivorans sp. nov. is proposed.

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

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 protein-coding 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.

Complete Genome Sequence of Escherichia coli ML35

We report here the complete genome sequence of Escherichia coli strain ML35. We assembled PacBio reads into a single closed contig with 169× mean coverage and then polished this contig using Illumina MiSeq reads, yielding a 4,918,774-bp sequence with 50.8% GC content.

Complete Genome Sequence of Pseudomonas sp. Strain NC02, Isolated from Soil

We report here the complete genome sequence of Pseudomonas sp. strain NC02, isolated from soil in eastern Massachusetts. We assembled PacBio reads into a single closed contig with 132× mean coverage and then polished this contig using Illumina MiSeq reads, yielding a 6,890,566-bp sequence with 61.1% GC content.