To celebrate our two hundredth Talmudic Question "What is the leading cause of bacterial or archaeal death?" we made a poll on Twitter. Thanks to our followers we received more than 100 votes, wow! We suggested the following possible answers, presented here with the results:
I will be wary of scoring the choices made by our Twitter followers, and just leave it at that. Think about it yourself ─ in good talmudic tradition! In the following, I will make some remarks on what is known about each of our proposed death causes. Since my "remarks" add up to a calculated reading time of just under 8 minutes, I suggest that you simply jump to the numbered items that interest you the most; the numbering follows that of the poll.
1. Suicide Bacterial cells can commit suicide, take Bacillus subtilis for example. Sporulation of this bacterium is a cell density‑dependent response to nutrient deprivation that results in the formation of an endospore within the so-called "mother cell." The release of the mature spore happens by lysis of the mother cell. Membrane fissions in the mother cell releases the chromosomal DNA into the environment and preceeds degradation of the peptidogylcan. The expression of an extracellular nuclease, NucB, that degrades the released chrDNA is triggered by the mother cell-specific sigma factor σK, a clear sign that this is not an accident but programmed cell death (PCD). (An aside: the term 'apoptosis' should be avoided here, since cell biologists have reserved it for multicellular organisms with very distinct conserved pathways for apoptosis that haven't yet been traced down to bacteria and archaea.) The suicide of a sporulating Bacillus mother cell is thus quite comparable to Japanese seppuku (often called harakiri in the West), in which the self-slayer rams a short sword into his stomach and intestines to cause himself to leak and bleed to death. It could very well be that the self‑dissolution of the mother cell evolved to give the mature spore a chance to spread and not be trapped, so to speak, in the cytoplasmic soup and viscous chrDNA surrounding it (experimental evidence for this is still missing). Most certainly, however, suicide is not the leading death cause among bacilli, because in wild-type strains the proportion of sporulating cells in a population tends to be low, in the <30% range, and is high in laboratory strains (>80%) only because they have been selected for to study, you guessed it, sporulation.
In multicellular organisms, it is common for individual cells to commit suicide for the benefit of the whole tissue, for example, during tissue remodeling in development ─ think of the "disappearance" of the initially existing webs between the fingers of the hands in embryos. A comparable process also exists in bacteria, another case of programmed cell death (PCD) and distinct from sporulation.
When polymorphonuclear leukocytes of the human immune system sense nearby bacteria, they secrete hydrogen peroxide, H2O2, in a burst to kill them during phagocytosis ("bleach" is mentioned in: death cause 6. "other"). If these bacteria happen to be related to E. coli STEC or Shigella dysenteriae carrying a 933W or H‑19B prophage (phage lambda relatives), the hydrogen peroxide released by the leukocytes triggers the induction of the prophage in a small part of the bacterial population, as studied by Loś et al. (2013). During phage propagation in the host, the phage‑encoded stxAB genes are expressed and Shiga toxin synthesized. When phage propagation finally results in host lysis, the phage progeny is released together with Shiga toxin.
That's when the counter attack starts: while the B subunit of Shiga toxin docks to the membrane of human cells carrying the cognate receptor and triggers its uptake, the A subunit, once internalized, attacks the cytosolic ribosomes, cutting and thus inactivating the ribosomal 28S rRNA, thus blocking translation. And as it is with toxins, they are not consumed by one-time use. Cells with inactivated ribosomes are doomed. Whether one can speak of "altruism" here remains to be discussed. What is clear, however, is that the self‑sacrifice of a few bacterial cells promotes the survival of the entire population.
2. Exhaustion In the disqus comments section for TQ #200, our reader Morris39 remarked (complained?) that "starvation" is missing from the list of death causes. There is no doubt that for bacteria in the laboratory, "starvation" is the primary cause of death after nutrients are depleted. In E. coli, for example, the death phase begins after approximately one week into stationary phase with successive lysis of the culture. Note that it is not so much the lack of nutrients that causes death, but the lack of efficient disposal of toxic metabolic end products in a contained culture and shifts in pH. But then, and this is noteworthy, there is a small percentage of cells that keep themselves alive for long time periods in the mass grave of a culture by gorging on cadavers, "GASPing for life in stationary phase" as Mechas Zambrano and Roberto termed this habit. In such a stationary culture, feeble growth and death balance each other such that the cell number remains almost constant over many months.
Unlike E. coli, bacteria like Deinococcus radiodurans and a number of cyanobacteria cannot be starved to death. Filamentous cyanobacteria like Nostoc or Anabaena form so-called Akinetes within strings of cells (Figure 1) under unfavorable growth conditions. Akinetes come close to Bacillus spores with respect to long-term resistance to adverse physical conditions, they're not heat resistant though. The survival skills of Deinococcus are by all means extreme (see here STC). In a recent post from 2021, Elio wrote:" D. radiodurans [also] placed outside the International Space Station, revealed that cells in pellets 500 microns thick stayed alive after 3 years in space. Once cultivated, they repaired their damaged DNA via the products of uvrA gene (nucleotide excision repair) and uvdE gene (UV-damage excision repair)." Under space conditions there is certainly no such thing as "dormancy" or "hibernation" or even "suspended animation," and biology lacks an apt term for this form of unlife.
"Exhaustion" in bacteria could also mean the decline of their "reproductive output," in other words senescence. That's exactly what Martin Ackermann studied in Caulobacter crescentus, a bacterium with a dimorphic life cycle (see here is STC). Briefly, a "stalked cell" attaches to a substrate via the holdfast on the tip of its stalk, grows, and subsequently divides, with the mother cell remaining attached while the flagellated daughter cell, the "swarmer cell," takes flight (and turns into a stalked cell once it finds a suitable substrate, thus completing the cycle). By flushing away the swarmers with fresh medium and counting division events in the stalkers, he found that Caulobacter cells do indeed gradually age and cease dividing after 60 generations, on average. While some cells produced up to 130 progeny cells in 300 hours, most stopped dividing or divided more slowly with increasing age.
Yet, what is true for Caulobacter must not necessarily be true for elephants or E. coli. Wang et al. (2010) seeded cells of two distantly related E. coli strains, B/r and MG1655, into microfluidic channels and followed the steady-state growth of ~105 individual "mother" cells over >100 generations, that is, cell divisions visible by microscopic inspection. They found strikingly constant growth rates of mother cells and their immediate sister cells for hundreds of generations. Despite this robust growth, cells died due to accumulation of damages during the course of the experiments. This was most evident in MG1655 lexA3 mutant cells that are unable to respond to damage via the SOS response and had a constant mortality rate of ~3% from the start. In contrast, the death rate wild type MG1655 cells gradually increased from <0.1% at start to reach <2% after 150 generations. The authors concluded:"from the qualitative difference in death rate between MG1655 and its lexA3 mutant derivative (...) that death of E. coli cells cannot be due to random events such as DNA damage but must be a consequence of growth-independent accumulation of lethal element." Death by a "lethal element" but not senescence or "exhaustion" ─ this isn't easy to comprehend.
3. Murder by kin I was a bit surprised at how few of our survey participants considered "murder by kin" to be a relevant cause of death for bacteria. It is now well known that bacteria and archaea in the wild prefer to congregate in biofilms. And such aggregates are the venue for every conceivable form of cooperation and competition, and this applies to mixed‑species and mono‑species biofilms alike. When it comes to co‑inhabitants in biofilms, Vibrio cholerae, for example, are not squeamish: all other bacteria that come close enough to them are first shot on suspect ─ with their T6SS ─ and only if those hit have an antidote to the injected toxin do they survive this "identity check." This may well be kin, that is, a genetically almost identical Vibrio cholerae lacking the antidote. We had described this murder in the family setting in detail here, and mentioned that it is by no means restricted to the Vibrios. Several "secretion systems" ─ we currently know nine ─ are widespread among bacteria, and they probably all serve the purpose of keeping unwanted neighbors at arm's length, whether they are from the closer or more distant family.
4. Predation by phages By a wide margin, the preferred cause of death of bacteria and archaea in our poll (see frontispiece). And indeed, to my knowledge, there are no described bacteria and archaea that are not preyed upon by well over a dozen species‑specific phages (including those with a broad host range). Not even those that sport multiple sophisticated phage defense systems escape phage predation, but individual cells may. And this is also true for those species that we know only from their genome sequences, which usually contain integrated prophage genomes or telltale remnants thereof.
I pick here only one particularly impressive example, the phage WO, which has accompanied Wolbachia since this bacterium infected more than half of all known arthropods and settled there as endosymbiont (and has dramatic influences on the sex of the host's offspring). It is difficult to estimate, let alone measure, the contribution of phage WO to the death rate of intracellular Wolbachia (Figure 2).
5. Predation by protists In the lab, protists are most often successfully fed with bacteria, well‑ known examples being Acanthamoeba (see here in STC) and, of course, Dictyostelium. The latter eats away holes in a bacterial lawn that look like clear phage plaques at first glance (Figure 3). From such artificial lab conditions, under which "killing by protists" is the main cause of death for bacteria, it is of course not possible to extrapolate to conditions in the wild, or even in the human gut.
In the upper layers of the oceans, the number of picocyanobacteria doubles about every 2 days, but since their concentrations remain quite stable for weeks, regardless of seasonal fluctuations, half of them must either die and lyse, or fall prey to predators, mostly both the ubiquitous cyanophages and protists. Although by orders of magnitude less abundant than phages and bacteria, both heterotrophic and phototrophic protists, which often go "sideways" in their feeding, are efficient hunters. For example, a single Prorocentrum dinoflagellate ─ more a trapper than a hunter ─ can easily catch ~50 prokaryotic cells per day in its mucosphere for immediate consumption (see here in STC).
It is only anecdotal and therefore not really scientifically relevant, but I vividly remember the horror that haunted Blanca Perez Sepulveda during her PhD in David Scanlan's lab at Warwick University, UK, that the "grazers," the omnivorous protists, would decimate her precious long-term Synechococcus cultures; she found it much easier to tame the phages.
6. Other causes Alex Bisson (@Archaeon_Alex) suggested bleach as one of "other causes," and that was indeed appropriate as physicians and microbiologists often use it for efficient surface disinfection. In more natural settings, chlorine-based bleaches won't play a large role as chlorine is simply too reactive with anything that is even remotely oxidizable. This is different for peroxide-based bleaches as hydrogen peroxide (H2O2) and superoxide (•O2−), which belong to the reactive oxygen species (ROS), are byproducts of cell metabolism in all domains of life.
Many bacteria avoid being killed by ROS by the production of catalases, enzymes with among the highest known turnover numbers. Unless they can't, which is the case in picocyanobacteria. This deficiency in catalase in Prochlorococcus and Synechococcus results in their failure to form colonies on solid media unless they are grown in the presence of "helper" bacteria like catalase-positive Alteromonas (first explored by Morris et al. (2008) and also briefly mentioned here in STC).
Conclusion For all the death causes we asked about, they do occur in nature and in the lab. Each of them is the main death cause of individual bacterial cells under certain conditions. But it is perhaps presumptuous to try to pin down a single cause of death as the predominant one among bacteria and archaea in general. This could also be a valid answer to our Talmudic Question, but was not given as a choice in the poll. Our fault. Or, was it?