Rare microbes lead scientists to discover new branch on the tree of life | Hacker News Reader

Rare microbes lead scientists to discover new branch on the tree of life

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157 pointstosh17 comments

The old way was to culture whatever earth you grabbed. The trouble is, most of it did not grow, although some did. When they perfected high speed sequencing they could then lyze out all the DNA from all the organisms living there and sequence and catalog them. They then take all the organisms they could grow from the same sample (representational sample), and then deduct all those sequences from the total. That was when they realized that they had only grown 10-15% of all the various organisms. There are hundreds of growth media, all painstakingly crafted by trial and error to grow particular organisms. Some organisms only grow by parasitism of others, some by eating others, and thus will only grow on a special media to fit this. It can take years to craft a growth medium. To this day we have many organisms that affect mankind that we can not grow in culture. The amassed sequence data can be analysed to see what sort of proteins they will grow. They can then try to make them - if they can - some need chaperone proteins that lead them into their correct folding pattern. No chaperone protein = no correct fold = wrong activity etc. It is very hard to 'uncook' the soup that made the amassed sequence data, but you may be able to identify promising proteins and tag those sequences in the living bacteria with a fluorescent dye that is taken up by the organism. Shine the right light on it and that organism will light up and you may be able to isolate it or hopefully, many of it. Repeat again and again gradually tease out these new organisms. With number to play with you can try to make them grow by analyzing their metabolism to see what might feed them and well fed ones will reproduce.

If this is interesting to you, I just started reading "Tangled Tree" [1] which examines the history of phylogeny and molecular bio and the current state if the art, I recommend it. I want to go home and read it right now but alas, work. (lo I'm on HN, but also WFH, modern life It's Complicated..)

[1] https://lccn.loc.gov/2018004356

Link to download the original paper in Nature "Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes":

http://libgen.io/scimag/ads.php?doi=10.1038%2Fs41586-018-070...

A bit of a let-down after "Canadian researchers have discovered a new kind of organism" to read "Hemimastigotes were first seen and described in the 19th century. ...About 10 species of hemimastigotes have been described over more than 100 years."

A description is one thing. What this article describes is a genetic analysis that places a mystery on the rather broken 'tree of life'.

Basically they solved a long-running mystery, and it turns out to be stranger than anyone thought.

On the contrary, I read through the open-access paper and went down the rabbit hole for several hours. It’s astonishing that a single celled creature could be so complex. But, it’s had over a billion years to evolve since it split off from the rest of the eucaryotes.

Most weird organisms have been noticed long before their genetic weirdness was known. Darwin mentioned in "The Voyage of the Beagle" that a salt lake in South America was reddish due to microbes, but only in the late 20th century did people recognize that these were very unusual microbes -- members of the Archaea.

Interesting stuff. The talk of a new kingdom or supra-kingdom (domain? empire?) prompted me to see how we currently model the tree of life. (Something I probably haven't known since elementary school!)

Within the life of some readers here: kingdoms.count() -> 4, 5, 6, 3, 8, 6, 7, ...

Currently, seven kingdoms: animalia, fungi, plantae, chromista, protozoa, archaea, bacteria [1]

https://en.wikipedia.org/wiki/Kingdom_(biology)

Note that "domain" has been added on top of "kingdom" for quite some time now; that's probably why they went with "supra-kingdom", as this division seems to be above kingdom but below domain (since these creatures are still eukaryotes).

There was some tantalizing evidence that there may be a fourth domain besides bacteria,archaea and eukaryotes. Was news couple of years ago, but I didn't hear anything about it since. https://www.newscientist.com/article/dn20265-biologys-dark-m...

So, uh ... plants and animals wasn't enough? I feel so last millennium.

2 rare organism in a small sample of dirt picked up at whim. Maybe they're not so rare anymore?

Cool, do they fight tardigrades? :-)

From a science perspective the process of grab some soil and analyze it is remarkably fruitful. If you have any budding biologists it is always interesting to do this experiment, one tablespoon of soil in a 1/2 cup of water, leave covered overnight and then put it under a microscope.

>It'll be the one time in my lifetime that we find this sort of thing

I wouldn't be so sure. Especially given how recently we've had the technology to find and analyse these things.

The world is a wild wonderful place. We think we know a lot about it, but there's so so much we don't know. It's nice to get a reminder of that every so often.

>Were found in dirt collected on a whim during a hike

I internally thought about dirt as soon as I read the headline. There is so much biodiversity in soil that is still unknown but goes unobserved due to the anaerobic nature of the microbes.

I met a grad student who was randomly sequencing whatever nucleotides he could find in dirt and was finding new sequences all over the place.

Archaea are also interesting as they are simple Prokaryotes but lack a nucleus.

If this tree gets too many more branches, I doubt she'll last the winter

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