Talk:Deep biosphere/GA1

GA Review

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Reviewer: Jens Lallensack (talk · contribs) 15:39, 8 November 2019 (UTC)[reply]

Sounds interesting, will start soon! --Jens Lallensack (talk) 15:39, 8 November 2019 (UTC)[reply]

@RockMagnetist (DCO visiting scholar): – This is great work, I am impressed. Comments below are mainly minor issues (not all is needed to reach GA level). I hope they will help to improve the article further. Consider nominating this at FAC.

The subsurface accounts for about 90% of the biomass in two domains of life, Archaea and Bacteria, and 15% of the total for the biosphere. Eukarya are also found, including some multicellular life (nematodes, fungi, flatworms, rotifers, annelids and arthropods). Viruses are also present and infect the microbes. – So this info is on the entire subsurface, not only the deep biosphere? Are there numbers for the deep biosphere only? Partly done

I used some sloppy wording: most of the information refers to the deep subsurface. Unfortunately, the only source that gives the most common taxa in the continental subsurface does not make it clear whether it is exclusively deep, although its introduction emphasizes the deep biosphere. I have clarified which parts refer to the deep biosphere. RockMagnetist (DCO visiting scholar) (talk) 04:35, 11 November 2019 (UTC)[reply]

numerous advances in technology for sample collection, field analysis, molecular science, cultivation, imaging and analysis. – The last item in the list, "analysis", is very general and "field analysis" is included? Would be more specific. Done

Chikyu 1 drilling ship (figure caption) – needs the special character (ū). Also consider linking stuff like this again in the figure captions. Done

roll front development – can you link link/explain? Done

serpentinization – as this is quite central for the article, I would explain (gloss) briefly. Done

hydrogen sulfide (H2S) – I think this is a good idea to add the chemical formulae, helps with the understanding. Maybe do with the other chemical compounds mentioned in the article as well? Partly done

I'm a little afraid that the text will become too cluttered if formulas are added in lists of compositions. However, maybe a middle ground would be to add formulae when they are simple and restricted to one compound (e.g., methane) but not groups like "reduced sulfur compounds". How does that sound? RockMagnetist (DCO visiting scholar) (talk) 23:36, 10 November 2019 (UTC)[reply]

iron oxyhydroxides – link/explain? Done

However, between room temperature and 200°C, the dielectric constant decreases by half, and the water becomes less polarized, changing the solubility of biomolecules. Changes in the structures of proteins, lipids and DNA can make them more stable. – I do not understand the connection between these two sentences. What do the microbes to cope with the different solubility of biomolecules/whats the significance of this? Done

I agree, this was not clear, and I'm not even sure it's worth talking about the dielectric constant. I rewrote this and added new info. RockMagnetist (DCO visiting scholar) (talk) 18:45, 14 November 2019 (UTC)[reply]

Temperature is named as an important constrain for life. But are there other constrain? Is any combination of temperature and pressure possible as long as water does not boil? Done

I have added a section on pressure, but the article already stated that the theoretical maximum temperature for life is 150 deg C. RockMagnetist (DCO visiting scholar) (talk) 22:57, 14 November 2019 (UTC)[reply]

An advanced version of CORK is able to seal off multiple regions using packers – not clear to me: multiple regions of what? Done

death phase follows in which almost all the cells die off – Why is this? Is this specific to subsurface bacteria? ? Maybe

The whole paragraph discusses the life cycle in laboratory studies of bacteria under conditions at the surface, but concludes that this is far from the conditions experienced in the subsurface. I thought this paragraph would provide some context, but maybe it's just confusing. RockMagnetist (DCO visiting scholar) (talk) 04:50, 11 November 2019 (UTC)[reply]

However, laboratory estimates are several orders of magnitude greater than those that appear to sustain life underground. – Confused, where is "those" referring to? Done

Wow, I didn't word that well. I added some text to make it clear. RockMagnetist (DCO visiting scholar) (talk) 04:50, 11 November 2019 (UTC)[reply]

In rock, chemicals are mainly carried through an aquifer system that cycles all of the ocean's water every 200,000 years. – "Rock" is not only igneous rocks but all sorts of solid aggregated minerals, including sediments. Here, and in some other parts of the article, I get the impressions that sediments are excluded from the definition of "rock". Another thing: These regions under influence of the aquifer (and thus sea water) are not part of the deep biosphere given the definitions? Done

I think a lot of the articles on the ocean floor lump sediments and sedimentary rocks together. On the continents, the Magnabosco et al. article basically says that microbes are in every kind of environment, and some figures list a variety of sedimentary rocks. So far, I haven't found much to say about sedimentary rocks. RockMagnetist (DCO visiting scholar) (talk) 23:11, 14 November 2019 (UTC)[reply]
That definition was from an encyclopedia article, and it clearly contradicts much of the rest of the literature, so I have removed it. RockMagnetist (DCO visiting scholar) (talk) 23:11, 14 November 2019 (UTC)[reply]
On a second look, I realized that I have a whole paragraph on sedimentary rocks in the section on continents. RockMagnetist (DCO visiting scholar) (talk) 18:16, 18 November 2019 (UTC)[reply]

depends on the rate of deposition – would name it "Sediment deposition" for clarity. Done

Where it is rapid, oxygen is taken up rapidly as organic matter is consumed; where slow, oxygen can persist much deeper. – But why, because organic matter does not reach the deep subsurface? Done

that serve as an energy sources – "an" too much? Done

Characterized by hydrothermal circulation, they extend to about 80 million years in age. – What cycles where? A bit more explanation could be helpful. Done

There is little evidence of microbe activity in older (more than 10 million year old) crust. – because the hydrothermal circulation is declining? Done

The source doesn't say why. RockMagnetist (DCO visiting scholar) (talk) 01:30, 15 November 2019 (UTC)[reply]

The subjecting plate – possibly the "subducting" plate? Done

Hotspot volcanoes also occur in the middle of oceanic plates. – Not necessarily in the middle? There are hotspots under continental crust. Done

Hydrothermal fluids are cooler and less sulfides – Don't understand; "contain" missing or something? Done

The "Habitats" section has little on how the habitats are exploited by organisms, and what kind of organisms they support. Partly done

You spotted one of the biggest concerns I have with the content! I started on this section thinking that it was important to describe the habitats, and it took a while for me to notice that the sources don't say much about how the habitats influence the organisms. I think that's because not much is known yet, so I see this section as a place holder for future scientific progress. RockMagnetist (DCO visiting scholar) (talk) 01:13, 11 November 2019 (UTC)[reply]
I am happy to report that I found a new source with good information on taxa in ocean sediments, so at least I have made some progress on this issue. RockMagnetist (DCO visiting scholar) (talk) 18:45, 19 November 2019 (UTC)[reply]

in the high temperature and salinity – should "the" be removed? Done

"Candidatus Desulforudis audaxviator" – why in brackets, and why not all in italics as in the paper? Done

I'm following the usage described in Candidatus#Usage. RockMagnetist (DCO visiting scholar) (talk) 01:13, 11 November 2019 (UTC)[reply]

I miss some information on ecosystem composition. How many species in a given ecosystem? Are there food chains? In the Candidatus Desulforudis audaxviator, they argue that this is the only species on earth that is alone in its habitat; maybe stuff like this deserves some discussion in the article. --Jens Lallensack (talk) 22:24, 10 November 2019 (UTC) Partly done[reply]

I have added a section on ecology. It's not FA-level comprehensive, but it lays down some of the concepts. RockMagnetist (DCO visiting scholar) (talk) 17:56, 22 November 2019 (UTC)[reply]

I would remove the red link from the "See also", this is not how this section is used in other Wikipedia articles. Done

I'm confused about the section "Sources". What is the difference to the "references"? Should this be named "Further reading" or similar? Done --Jens Lallensack (talk) 22:35, 10 November 2019 (UTC)[reply]

@Jens Lallensack: Thank you for your kind remarks on this page! I'll start with the easier questions above, and move on to the others.

Comment from a page watcher. I am also impressed with the article. Nice work over the months. My main comment would be that the last section Diversity reads differently from the rest of the article in the sense that it is dense with unexplained latinate names, more scientific review than layperson-accessible summary. Perhaps some common names associated with the taxonomic names could help the reader make sense of what is being talked about. My guess, for instance, is that the second para is mostly about bacteria, but then Archaea is mentioned, too. Clarity might more of an FA thing than a GA thing, so feel free to think of fixing this as optional for a GA pass. --{{u|Mark viking}} {Talk} 00:21, 11 November 2019 (UTC)[reply]

@Mark viking: Thank you for your kind remarks. I'm not very happy with this section, but I don't know what to do about it. By its nature, this is a subject with few common names: many of the phyla were not even cultured ten years ago. I felt it necessary to add a little history, even though it adds to the thicket, because otherwise it's really hard to interpret sources from more than ten years ago. I considered adding some taxonomic trees, but I'm not sure if that would shed more light.

More fundamentally, the difficulty with this section is it's about how the taxa are related, not what they do. But the functions (like, say, methanogenesis) cut across taxa. Any ideas for making all of this more readable would be very welcome. RockMagnetist (DCO visiting scholar) (talk) 01:25, 11 November 2019 (UTC)[reply]

@Jens Lallensack: I have addressed all your issues. RockMagnetist (DCO visiting scholar) (talk) 17:57, 22 November 2019 (UTC)[reply]

Great, thanks for the many improvements, looking very good now. Promoting now, congrats for the new GA! There appears to be one regression that you might want to fix:

Other non-equlibrium processes include hydrothermal vents, volcanism, geothermal activity, and Other processes that – and what? Something missing here? --Jens Lallensack (talk) 23:08, 23 November 2019 (UTC)[reply]

@Jens Lallensack: Thank you for an excellent review; I think the article really benefited from it. I fixed that last problem. RockMagnetist (DCO visiting scholar) (talk) 00:30, 24 November 2019 (UTC)[reply]