A Whiff of Taxonomy – Among Vampires

by Christoph
 

Elio wrote A Table for Two many years ago, about the surprising observation that the Gram‑negative bac­terium Vibrio vulnificus can be preyed upon simultaneously by a bacteriophage and a "bacteriovorous" bacterium. He could hardly have figured that the single image in his piece is a perfect vignette for the greatly increased interest in phages and "Bdellovibrio and like organisms" (BALOs) today.
 

Bacteriophages and predatory bacteria appear as promising alternatives to antibiotic therapy at a time when physicians dread that bacterial in­fectious diseases will soon no longer be as defeatable as they were for much of the last century. The spread of resistances to virtually all thera­peutically re­le­vant antibiotics in all major human pathogens, including but not restricted to the ESKAPE patho­gens, and the almost complete lack of newly developed antibiotics have led to this dire situation, worldwide. (In Germany alone, the number of hospital patients who die each year from non-treatable infections already significantly exceeds the number of traffic fatalities, and the trend is upward.)
 

Figure 1. Electron micrographs showing predatory at­tach­ment of Bdellovibrio to Escherichia coli prey (fron­tispiece) and replication of Bdellovibrio within prey (here). Source

STC has covered phage therapy earlier (see here and here), and predatory bacteria only spuri­ously. Here, now, I will not review the existing research projects on the therapeutic use of pre­datory bacteria, but will wrap-up their diversity across the different bacterial and archaeal clades. Here it goes.
 

Recently starring in the remake of Le bal des vampires, Bdellovibrio exovorus JSS^T (the super­script T stands for "type strain"), was renamed Pseudobdellovibrio exo­vorus JSS^T by Waite et al. (2020) to indicate that its similarity to the better known Bdellovibrio bacterio­vorus (Figure 1) is not sufficient to place both in the same genus. However, it will take a while for the renaming to take hold in the literature.
 

An aside. The prefix "Pseudo..." is often used by taxono­mists to avoid complete name changes, and not to devalue the newly baptized as "Fake...". For the same reason, for example, the genus Alteromonas was split into Alteromonas and Pseudoaltero­monas. The history of the genus name Pseudomonas is more complicated, though, if not obscure (if you like detective work, dive into the linked paper (Open Access)).
 

Predatory bacteria have been found among many of the known bacterial phyla − check the somewhat intimidating Figure 1 in the review by Ka­ma­da et al. (2023) (Open Access) − but it is not clear in many cases to what extent their "lifestyle" resembles the vampire habits of "Bdellovibrio and like organisms" (BALOs). For the latter, Waite et al. (2020) sought to bring some order into the cluttered drawer "Delta­pro­teobacteria" and pro­posed the creation of the new phylum Bdellovibrionota, which comprises the (mostly non‑pre­da­tory) class Oligoflexia and the predatory classes Bacteriovoracia and Bdellovibrionia. As you crawl through these new, now tidy drawers − already slightly weary, probably − you'll even­tually find both species Pseudo­bdel­lovi­brio exo­vorus and Bdellovibrio bacterio­vorus in the family Pseudobdellovibrionaceae, from the order Bdellovi­brio­nales in − back to square 1 − the class Bdellovibrionia (the usual hierarchical stacking).
 

Figure 2. Microscopy observation of Vampirococcus cells. (d–f) Closer microscopy view of anoxygenic photo­syn­thetic bacteria infected by epibiotic Vampirococcus cells and few-cell filaments (indicated by yellow ar­rows). (g) Scanning electron microscopy image (SEM) of a host cell infected by two stacking Vampirococcus cells (yel­low arrow). (h) Transmission electron microscopy (TEM) image of a thin section of a host cell infected by Vampi­rococcus (yellow arrow). Scale bars: 0.5 µm. Source

What use is such knowledge about taxonomic drawers to you anyway? Little, except that it gives you a vague qualitative hint on genomic similarity of the species you study. And it is im­portant in which direction you make your comparisons and build your hypotheses. Referring to Le bal des vampires, Santin et al. (2023) could not infer the predation mechanism of P. exo­vorus from its taxonomic and phylogenetic relationship to B. bacterio­vorus, but could, after its elucidation, safely conclude that mech­a­nis­ti­cal­ly different predation mechanisms occur in clo­sely related, that is, genetically very similar species. I'll spare you and myself from specifying exactly in which drawers you'll find Bacteriovorax, Peredi­bacter and all the other >50 BALOs.
 

The predatory Deltaproteobacterium Myxococcus xanthus and its ilk, which stalk Gram-ne­ga­tive bacteria by a "wolf-pack hunting" strategy rather than vampirism are now grouped with other orders into a new phylum, Myxococcota (check out this YouTube clip recorded over se­ven days). There are "hunters" known from other phyla too, but since their predatory lifestyle does not involve temporary, intimate attachment to their victims as it is the hallmark of vampires, I will omit them here. However, I can't resist suggesting a short video clip for you to watch, by the Dutch photographer Wim van Egmond, "(unidentified) bacteria engulfing Spirogyra alga", a case of "cross-kingdom hunting".
 

Since their discovery, it has been suspected that the majority of CPR bacteria (now Patescibacteria) cannot live autotrophically because their re­duced genomes, mostly <1 Mb in length, generally do not encode complete sets of biosynthetic genes. It is certainly premature to simply call the entire (super)phylum Patescibacteria an enormous bat cave, but a few vampires are now known, for example from the Saccharibacteria. Both "Candidatus Mycosyn­bacter amalyticus JR1" and Nanosynbacter lyticus only grow in co‑cultures with their actinobacterial hosts, which they pre­sumably "poke" with a type IV secretion (T4SS) apparatus to suck up leaking cell material (similar to Vampirovibrio, see last paragraph). Another vampire of the Patescibacteria, Vampirococcus lugosii (class Absconditabacteria) has made it into Wikipedia, and you find more details of its lifestyle there. It survives free-floating but only grows and replicates when firmly attached to its host Chromatium spp. (H₂S-oxidising, photo­autotrophic gammapro­teobacterium) that it sucks empty to produce up to six daughter cells (Figure 2).
 

Le bal des vampires doesn't end here, quite the contrary! It is not limited to bacteria vampirizing among themselves, as told above, or archaea among themselves. Think of A Happy Hot Couple, Nanoarchae­on equi­tans (DPANN, Nanoarchaeota) taking a nutritious ride on Ignicoccus hos­pitalis (Thermoproteota). This is no exception, as I just learned from a preprint in late October describing the cultivated DPANN archaeon Nano­bdella aerobiophila MJ1^T that grows as epibiont on Metallosphaera sedula MJ1HA (Thermoproteota). To what degree this symbiosis leans more on the parasitic or vampiric side is not clear at this time.
 

(click to enlarge)
Figure 3. Proposed conjugative mechanism. T4SS oper­ons are found on two conjugative plasmids in V. chlorel­lavorus. The T-strands of the plasmids are predicted to be made single-stranded by plasmid-encoded relaxa­ses, nicking the DNA at the origin of transfer and transporting the T-strands to the C. vulgaris cell via the mating pair formation. We predict that effector proteins (hydrolytic enzymes) synthesized in the bacterium are also transported via the mating pair formation. The T-strand enters the algal nucleus through a nuclear po­re complex and is incorporated into a C. vulgaris chro­mosome. The effector pro­teins degrade the algae con­tents which are transported out of the algal cell via T-strand encoded trans­porters. The algal lysates are imported into the V. chlorellavorus cell providing ener­gy and nutrients for replication. Source

Meanwhile, a few cases of "cross-kingdom dances" have also been found. Kizina et al. (2022) report their observation of the tiny bacterium "Candidatus Velamenicoccus archaeovorus" (Candidatus Omnitrophica, previously Candidate division OP3/WOR‑2) that thrives as epibiont on the archaeon Metha­nosaeta sp. (Euryarchaeota).
 

A stunner among of "cross-kingdom dances", however, is the story of Vampirovibrio chlo­rel­lavorus, a non‑photosynthetic distant relative of cyanobacteria that preys on the eukaryotic microal­gae Chlorella vulgaris. Stunning because it merges a vampire story with a zombie story. Soo et al. (2015) failed to resurrect Vampirovibrio from 36 year-old lyophilized material, but could nevertheless se­quence its genome and confirm its identity as a member of the Melai­nabacteria, a non‑photosyn­the­tic sister clade of the Cyanobacteria in the phylum Terra­bac­teria. The genome analysis suggested that V. chlorellavorus is likely an obligate predator of the photosynthetic microalga Chlorella, and predicts that it uses a conjugative type IV secretion system (T4SS) to inject DNA in its host (Figure 3). A footnote: soon after, it was found that a V. chlo­rellavorus strain can efficiently "clear" com­mercial 1.000 L Chlorella cultures within days. Thus, the lyophilized zombie was not "the last of us" and, ap­parently, not all vam­pires shy away from sunlight.
 

"Vampirism" is not a properly defined scientific term − and certainly not a taxonomically re­le­vant one − but it is fondly used by microbiologists versed in film history who follow the fate of prey bacteria upon infestation with predatory bac­teria in the microscope or on culture media (plaque formation!). It is certainly useful to distinguish bacterial "vampires" (and their relatives among the archaea) from other predatory bacteria in that the vampires attach themselves firmly to their prey before and while "sip­ping" on them, or even suck them completely (like B. exovorus leaving just a "ghost" host cell, or like V. lugosii). In contrast, predatory bacteria of the Myxococ­cus‑type tend to kill their prey from a distance before ingesting the debris.
 

Another characteristic of vampires is that they grow and reproduce only as long as they are firmly attached to their prey (or hanging inside, like B. bacteriovorus). This is a rather weak criterion, however, because all epibionts/ectosymbionts do this, and many of them are commensals or symbionts without which their host cannot thrive, think Thiosymbion oneisti that covers its host, a marine nematode, with a furry coat. It is an easy observation to make but certainly not more than a curiosity: symbiotic epibionts like T. oneisti grow and divide longitudinally so that daughter cells do not lose intimate contact with the host. Vampires like B. exovorus or V. lugosii form daughter cells at the pole opposite to the attach­ment site, which then have no connection to the host; in the case of V. lugosii, this looks like a tiny stack perpendicular to the host at­tach­ment site (Figure 2). Since no significant differences are apparent between the attachment mechanisms of symbiotic epibionts and vampires, there will be a gray area in the distinction until experiments allow for a decision. Not a pleasant prospect for order-conscious microbiologists, but here we are.
 

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