Talk:Lokiarchaeota

DYK

I suggest that this be nominated for DYK. AshLin (talk) 16:30, 8 May 2015 (UTC)

I have sent it to In the news. Please feel free to comment there. If that fails, I'll send it to DYK. --ThaddeusB (talk) 19:18, 9 May 2015 (UTC)

Posted via ITN. --ThaddeusB (talk) 18:34, 10 May 2015 (UTC)

RfC: Are the claims about archaeal primacy in evolution scientifically accurate?

The consensus is that the alteration of the text here resolves the RfC initiator's concerns. Cunard (talk) 02:54, 25 May 2015 (UTC)

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

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There is a claim that Archaea are "the most ancient of lineages". This is not a widespread view amongst my scientific colleagues. This debatable assertion is not essential for this article describing Lokiarchaeota, nor is it essential to describe Lokiarchaeota as the sister group most closely related to eukaryotes. As far as I know, the most unequivocal evidence of early life is stromatolite fossils dating 3.4-3.6 billion years, which are thought to be bacterial as opposed to archaeal. DrJHuff (talk) 17:23, 8 May 2015 (UTC)

• Yeah, that doesn't reflect consensus. I have altered the text. There is no real need to do an RfC on this, so I suppose you must be new to Wikipedia. Please feel free to edit the article as you see fit. Abductive (reasoning) 19:55, 8 May 2015 (UTC)

I am pleased to see that the issue has been dealt with, correctly in my view. But I am surprised to have been summoned to a RfC that was resolved three days ago. While I am here I will point out that the while article goes into a lot of technical details, it does not make it clear what it is about. Lokiarchaeota is a "proposed phylum" - but what will it contain? Any living species? I suspect that the answer is "none that we know of", but the article ought to say. Maproom (talk) 07:07, 11 May 2015 (UTC)

Looks like someone addressed this too - thanks for the feedback. I have removed the RfC tag. --ThaddeusB (talk) 15:08, 11 May 2015 (UTC)

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The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Jargon, misused

I am not completely confident in my understanding of the subject matter, but I have some concerns about the (mis)use of jargon in the article. For example,

1. "It was sequenced by deep metagenomics, and reconstructed by binning." I feel that it was sequenced by ordinary methods, and deep metagenomics describes the singling out of housekeeping genes for analysis/tree building. Binning is standard practive too, correct? Abductive (reasoning) 19:59, 8 May 2015 (UTC)

   Agreed, this sentence does not seem to add anything - I'll remove it. --ThaddeusB (talk) 19:27, 9 May 2015 (UTC)

2. "The analysis of the genome of Lokiarchaeum revealed about 175 proteins that were most similar to eukaryotic proteins." My reading is that 175 genes were selected beforehand, because they are conserved, and the analysis run on their sequences. Abductive (reasoning) 20:01, 8 May 2015 (UTC)

   It looks like all proteins were compared, of which 175 were closer to eukaryote versions that prokaryote versions. I will edit accordingly. --ThaddeusB (talk) 19:27, 9 May 2015 (UTC)

Metagnome?

Is the word used in the Description section meant to be "metagnome" or "metagenome"?

CBHA (talk) 03:26, 11 May 2015 (UTC)

metagenome; looks like someone fixed the typo already. --ThaddeusB (talk) 15:09, 11 May 2015 (UTC)

Article structure

I feel the article would benefit from changing its structure: The "taxonomic history" (which should be renamed "Discovery" should come first, and the "Description" should be next, and finally the evolutionary significance. The sentence about Lokiarchaeum not being isolated should go at the end of the "discovery" section. LionelGuy (talk) 19:06, 11 May 2015 (UTC)

Well, I just did it in the end, and it sounds better to me. Hope it's OK. LionelGuy (talk) 19:36, 11 May 2015 (UTC)

Gakkel Ridge is in Arctic Ocean, not Atlantic

The Gakkel Ridge has also been known as the Arctic Ocean Ridge. They got the ocean ID wrong. Tmangray (talk) 05:49, 12 May 2015 (UTC)

Correct. I edited accordingly LionelGuy (talk) 07:09, 12 May 2015 (UTC)

@Tmangray: Feel free to correct such errors yourself in the future - the person who added the line probably just had a mental lapse when doing so. --ThaddeusB (talk) 14:18, 12 May 2015 (UTC)

Is this the correct word---genes, or proteins?

In #Description, the subject is 'proteins'---mentioned 3 times; then the subject shifts to 'genes'. Is this (shift) correct? If so, what is the connection between the two, 'proteins' v 'genes'?

"A small, but significant portion of the proteins (175, 3.3%) are most similar to eukaryotic proteins. A number of factors made sample contamination an unlikely explanation for the unusual proteins including: the genes were always flanked by prokaryotic genes; no genes of ..." Jbeans (talk) 02:29, 13 May 2015 (UTC)

• Scientists speak imprecisely when it comes to genes, alleles and proteins. In this case, the genes were recovered out of the muck, and the proteins that the genes code for do things within cells (we know what the proteins do in species other than Lokiarchaeum, since Lokiarchaeum has never been grown in the lab). If any particular case of the use of the words genes and proteins could use clarification, please either fix it or ask. Abductive (reasoning) 04:38, 13 May 2015 (UTC)

Hmmm---and thank you--- //tho an engineer-scientist in a different field, I instinctively take up for the lay-reader, which is my own status for 98% of my reading on wp, and I would this narrative simpler and more clear.

But first.. if I restate---(while not my intention to edit)(right now)---as thus:

"A small, but significant portion of the proteins (175, 3.3%) 'that the recovered genes code for' are most similar to eukaryotic proteins. A number of factors made sample contamination an unlikely explanation for these unusual proteins including: the genes were always flanked by prokaryotic genes; no genes of ..."

This, or something like is more comprehensible because it connnects the two terms--- Is it correct? Thanks. Jbeans (talk) 15:53, 13 May 2015 (UTC)

Yes. Bondegezou (talk) 17:08, 13 May 2015 (UTC)

Breaking news for article

Links can be found here. If that source is correct -- one would need to examine the Science & Nature articles linked there -- a revised version of this article would qualify for Wikipedia: In the News. (I'm not adding the material because I don't consider myself informed enough to do an adequate job.) -- llywrch (talk) 20:54, 13 August 2019 (UTC)

I think this material has already been added in these edits, although more work could be done to further improve the additions. Bondegezou (talk) 09:51, 14 August 2019 (UTC)

Wiki Education assignment: Marine Microbial Ecology

This article was the subject of a Wiki Education Foundation-supported course assignment, between 21 February 2022 and 25 April 2022. Further details are available on the course page. Student editor(s): Ocean.n18 (article contribs).

2 species cultivated now

Besides Candidatus Prometheoarchaeum syntrophicum MK-D1 another species, Candidatus Lokiarchaeum ossiferum = Ca. Lokiarchaeum B-35 = Loki-B25, has now been cultivated:

• doi:10.1038/s41586-022-05550-y Actin cytoskeleton and complex cell architecture in an Asgard archaeon (see esp. Fig. 2)
• doi:10.1038/d41586-022-04450-5 Mysterious Asgard archaea microbes reveal their inner secrets
• https://medienportal.univie.ac.at/en/media/recent-press-releases/detailansicht-en/artikel/shedding-light-on-the-origin-of-complex-life-forms/
• https://www.eurekalert.org/news-releases/975017
• https://www.sci.news/biology/asgard-archaea-cellular-architecture-cytoskeleton-11503.html
• https://www.science.org/content/article/strange-tentacled-microbe-may-resemble-ancestor-complex-life
• https://www.sciencedaily.com/releases/2022/12/221221121318.htm Shedding light on the origin of complex life forms
• https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2951803&lvl=3
• https://lpsn.dsmz.de/family/lokiarchaeota-no-family LPSN Lokiarchaeota: genera w/o family
• https://lpsn.dsmz.de/search?word=Lokiarchae LPSN lookup for Lokiarchae*

A further member is Ca. Harpocratesius repetitus FW102:

• doi:10.1038/s41564-021-01039-y Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes
• doi:10.1038/s41586-022-05550-y Actin cytoskeleton and complex cell architecture in an Asgard archaeon

Family membership: The article here places both genera into a family "Lokiarchaeaceae" Vanwonterghem et al. 2016, but wihout giving a reference to Vanwonterghem (2016). Same at Asgard (archaea) and List of Archaea genera. GTDB locates strain HM1_B6_4 into species Prometheoarchaeum sp018238965, family MK-D1 (prov. name). However, according to the new study, HM1_B6_4 next known relative is Candidatus Lokiarchaeum ossiferum, but not Prometheoarchaeum syntrophicum. Threrfore Prometheoarchaeum (as given in GTDB) is either polyphyletic or both genera are synonyms. Anyway "Lokiarchaeaceae" Vanwonterghem et al. 2016 should be a synonmy for GRDB-family MK-D1; List of Archaea genera telling them apart may be in error. So I tried to lookup a paper Vanwonterghem (2016). Unfortunately I was not successful in finding Lokiarchaeaceae in any of the hits. Can you pleas add a reference for family "Lokiarchaeaceae" Vanwonterghem et al 2016? Thanks in advance!

Besides of family and order names, synonymies seem to be as follows:

• superphylum Asgard (NCBI) = phylum Asgardarchaeota (GTDB)
  • clade Lokiarchaeota-Helarchaeota = class Lokiarchaeia (GTDB)
    • phylum Helarchaeota (NCBI) = order Helarchaeales (GTDB)
    • phylum Lokiarchaeota (NCBI) = order CR-4 (GTDB)

LPSN is essentially the same as NCBI, except for an additional orphaned entry Lokiarchaeia. --Ernsts (talk) 06:40, 22 December 2022 (UTC). Last update: 04:37, 29 December 2022 (UTC)

GTDB should be monophyletic in its own tree. I wouldn't be too surprised if a different method (such as the one used by doi:10.1038/s41586-022-05550-y fig 2) turns out something else. In this case, GTDB's 53 markers are giving a different tree compared to some 23 ribosomal protein markers (see also doi:10.1038/s41467-019-13443-4, which uses even more markers and report some differences from GTDB; in particular Supplementary Figs. 15b, d, 16). I don't have a time machine, so I can't really tell which one is more correct. Is more length to compare with better? Maybe, maybe not. (Oh right, GTDB is also known to synonymize based on its "RED" metric. We really can't know why without GTDB adding the strain in a future version or someone running GTDB-tk.) --Artoria2e5 🌉 16:04, 10 December 2023 (UTC)

There is an assembly for Ca. "L. ossiferum" GCA_025839675, but it's also too new for GTDB. (If it fails quality check, it would still show up in search; example.) --Artoria2e5 🌉 16:17, 10 December 2023 (UTC)

So if two species have been cultured now, why are they still called Candidatus? And why is the name Lokiarchaeota being changed? Is there a source to explain the reason why Lokiarchaeota is still deprecated? 2601:441:5000:13E0:E9A3:5446:3044:580C (talk) 22:06, 12 November 2024 (UTC)