I have just added to the Wikipedia entry for Parakaryon myojinense. This name was given to a single specimen found on a polychaete worm from a hydrothermal vent on an underwater volcano south of Japan. The discoverers claimed it was a new domain of life, neither prokaryote nor eukaryote. No other specimen has ever been discovered.
I added some extra bits to the Wikipedia article that I thought could give readers a clue to the probable overenthusiasm that inspired the claim that this is a new form of life. Unfortunately, no microbiologists seem to have commented on the find, other than the team who discovered it. A pop biochemist called Nick Lane got very enthusiastic about it. Otherwise, there is a strange lack of any comment on the internet, positive or negative.
I had to stop myself commenting further as Wikipedia does not allow opinions unless they are properly citable and I am certainly not a microbiologist. I had to get my comments down somewhere. Who knows, someone might find this little rant if they do a search. This specimen just doesn't seem to live up to the interpretation that the authors proposed. Most of what I have written is off the top of my head, not as polished as my usual long articles.
Here is the main part I added to Wikipedia:
Yamaguchi et al proposed in their 2012 paper¹ that there were three reasons why the single frozen specimen they named Parakaryon myojinensis was not simply a result of parasitic or predatory bacteria living within another prokaryote host - which they acknowledged is known from several examples:
1) "It is difficult to imagine that multiple bacteria of different species attacked a host at the same time." They referred to Figure 2d, showing the isolated forms of the inclusions, one large helix with three turns (volume 2.3 μm³) and two much smaller pieces (volumes 0.2 & 0.1 μm³).
2) "Secondly, because the cytoplasms of the host and the endosymbionts show orderly and electron-dense cellular structures, no digestion in either host or endosymbionts appears to have occurred."
3) "Lastly, if P. myojinensis originated due to a current interaction between predators and hosts, then there must be dense populations of predators and hosts, because predators need to find hosts quickly for survival once they are released from the previous host."¹
Another paper with Masashi Yamaguchi as the lead author was published in 2016. Detailing the discovery of helical bacteria on polychaetes collected from the same location on Myojin Knoll, they named them "Myojin spiral bacteria".² In 2020, Yamaguchi and two others published a new short paper⁴ on their studies of the microbiota of polychaetes from Myojin Knoll. The authors stated "Among them, we often observed bacteria that contained intracellular bacteria on ultrathin sections." They studied one such specimen and concluded that the "host" bacterium was dead and its cell wall broken. The smaller bacteria could have been feeding on the larger bacterium but they also suggest "The association of the bacteria with dead bacteria could also have been artificially caused by the centrifugation steps used for the preparation of specimens for electron microscopy." In this paper, all five mentions of Parakaryon myojinensis were as a valid taxon without any doubt implied.⁴If you want pictures, I am afraid you will have to go to the links below.
Some people have read the 2020 paper as a retraction of the previous assertions. It is not. The authors give a detailed case of another specimen where you could mistake it for endosymbiosis but it was clearly a dead bacterium with other bacteria in and around it. They do not discuss how this relates to the purported new Domain of life that Parakaryon myojinense would represent if it were true. As I remarked on Wikipedia, the authors reference that specimen five times, each time carefully using wording that implies that it is a valid taxon.
The whole claim that this specimen was a part of a new domain of life rested on the apparent endosymbiosis of a bacterium-like organelle inside another bacterium-like organism. It would be a very big deal because there are prokaryotes that don't have mitochondria or any other organelles added and eukaryotes that do have mitochondria, some with some extra organelles like chloroplasts. This specimen did not have mitochondria so the inclusion of another organelle would make it a different fork on the evolutionary path. If the specimen is simply a bacterium with another bacterium eating it from the inside then it is not remarkable at all.
So, I will comment on the 3 reasons they gave in their 2012 paper in order.
1) Are those different bacteria? Could the tiny pieces be fragments of the invading bacterium that are part of its weaponry for breaching the cell wall of its prey? Could it have been damaged by being spun in the centrifuge? Remember that no parts of this specimen were sampled for their DNA. All the information comes from structure and the way the processing chemicals attach to the tissues.
The 2020 paper⁴ states that "The association of the bacteria with dead bacteria could also have been
artificially caused by the centrifugation steps used for the
preparation of specimens for electron microscopy." So, more than one type of bacterium could be accidentally mixed up together. Could that include shreds broken by scraping the skin of the scale worm?
2) Why assume that digestion has progressed to the point where the cytoplasm of the large bacterium will be obviously degraded? If the smaller bacterium has only just entered it may just be preparing to start its meal. The contents of the larger bacterium are clearly not exactly as would be expected from known bacteria. Could this be a reaction to the shock of entry of the predator bacterium?
In Figure 1 there is an apparent tear in the cell wall of the larger bacterium at the far right of the picture. If that was a structure produced by the "host" deliberately, it would surely be more regular. It looks more like a tear, especially as the helical bacterium is sitting just on the inside of it with a swirl of tissue between.
The usual predation of bacteria that I have seen on the Journey to the Microcosmos youtube channel leads to a very messy burst of cytoplasm exploding from the bacterium. However, is there a reason that some predatory bacteria could not seal the wound behind them so they can eat all the contents without other bacteria butting in? It would seem to be a good idea to be less profligate with all those nutrients, if they could manage that.
3) The authors claimed to have not found any micro-organisms like Parakaryon in 12 years of microbiological studies of the ocean depth off Japan. They state that this must mean that "Parakaryon myojinense" must live in very low densities. So an interaction with a bacterium just when they find it would be unlikely. This dodges a few obvious questions. Do we know what the bacterium that is being eaten would have looked like before it was attacked? Could it be more vulnerable to collection when it is being attacked? Did they check the skin on all the other worms? If predatory bacteria had to find another victim immediately, how could they spread to new areas? Could some have slow metabolisms? Could some eat so much, so efficiently from their prey that they can store reserves to carry them over a thin patch?
That last question brings up the later discoveries of microbiota from polychaete worms from the same location. The 2018 description³ of an amorphous bacterium shows they were still working their way through discovering the local bacteria. That one was only a quarter of the length of the "Parakaryon" but who knows how it would react if its cytoplasm was invaded? Obviously, it was amorphous, so could be the right shape sometimes.
The authors did find an organism remarkably like the supposed "endosymbiont" in their 2012 sample. They reported in 2016 that they found helical bacteria on the same polychaetes from Myojin Knoll.² The helical thing in the 2012 sample was reported as 10.4 μm long. This obviously can't be right as the host was 10.3 μm long. From the pictures it looks like it was about 3.8 μm. The longest of the nine specimens from 2016 was 2.386 μm long. Once those little helical bacteria were inside their prey the conditions would be quite different. Lots of food and different osmotic pressure. They might change their shape and length. If they are the same species. These weren't studied while alive either.
I really know nothing about microbiology except a little general knowledge. This is just a list of questions and doubts because it seems obvious to me that the raising of a whole new Domain of life should be questioned closely. Extraordinary claims require extraordinary evidence. One set of electron micrograph slices from one specimen frozen without any observation during life and no DNA analysis seems a little too thin a foundation on which to build a new Domain. Presumably, that is why it has been ignored for the last 12 years. There have been no other reports of examples found.
Nobody would be happier than I would if a new domain of life were to be found. Especially if it were found by the crew of a ship called Hyper-Dolphin. I love new discoveries. I spend a lot of time scrolling through endless new species discovered reported on the blog Species New to Science. Perhaps there will be a big announcement this year. I won't be holding my breath.
If you have read this far into my rant/pondering off the top of my head, thanks and sorry.
¹ Yamaguchi Masashi, et al "Prokaryote or eukaryote? A unique microorganism from the deep sea" Journal of Electron Microscopy (Tokyo) (2012) 61 (6): 423–431 Researchgate
² Yamaguchi, Masashi, et al "High-voltage electron microscopy tomography and structome analysis of unique spiral bacteria from the deep sea" Microscopy (2016) 65 (4): 363–369 https://www.academia.edu
³ Yamaguchi, Masashi, et al "Electron Microscopy and Structome Analysis of Unique Amorphous Bacteria from the Deep Sea in Japan". Cytologia (2018) 83 (3): 336–341 https://www.jstage.jst.go.jp
⁴ Yamaguchi, Masashi, et al "Deep-Sea Bacteria Harboring Bacterial Endosymbionts in a Cytoplasm?: 3D Electron Microscopy by Serial Ultrathin Sectioning of Freeze-Substituted Specimen". Cytologia (2020) 85 (3): 209–211 https://www.jstage.jst.go.jp
