Parent Group

Eubiota (“True Life”)

Sister Groups

Eukaryota (Eukaryotes)

Daughter Groups

Bacteria (Bacteria)
Archaea


D. J. Scott

Archaeons

(The Archaea)
Copyright © 2017-2018 by Dustin Jon Scott
[Last Update: September 15th, 2017]


Introduction

Prokaryotes are a paraphyletic group of organisms.



I.b-2A.) Archaeal Extremophiles


I.b-2Aα.) Acidophilic Archaeons

(Baker &al., 2006)
(Fashola &al., 2015)
(Zhang &al., 2015)

ARMAN group
-Micrarchaeota
--Diapherotrites
--Parvarchaeota
--Aenigmarchaeota
--Nanoarchaeota
--Nanohaloarchaeota. -Parvarchaeota

Domain Genus & Species OGpH Source Ratio σ (–ρ) ρ %>H0
Archaea Acidianus ambivalens <3 Johnson (1998) 39:25 25/64
(39%)
39/64
(61%)
22%
Acidianus brierleyi <3 Johnson (1998)
Acidianus convivator <4 ()
Acidianus infernus <3 Johnson (1998)
Acidianus manzaensis 1.5-2.5 (Ding &al. 2011)
Acidianus pozzuoliensis <4 ()
Acidianus tengchongensis <4 ()
Acidiplasma aeolicum <4 ()
Acidiplasma cupricumulans <4 ()
Ferroplasma acidiphilum <4 ()
Ferroplasma cyprexacervatum <4 ()
Ferroplasma acidarmanus <3 (Dopson &al.2003)
Halarchaeum acidiphilum <4 ()
Metallosphaera hakonensis <4 ()
Metallosphaera prunae <3 (Johnson 1998)
Metallosphaera sedula <3 Johnson (1998)
Metallosphaera yellowstonensis <4 ()
Picrophilus oshimae 2.2 Rampelotto (2013), Johnson (1998)
Picrophilus torridus 0.06-0.07 Rampelotto (2013), Johnson (1998)
Stygiolobus azoricus <3 (Johnson 1998)
Sulfolobus acidocaldarius <3 (Johnson 1998)
Sulfolobus hakonensis <3 (Johnson 1998)
Sulfolobus islandicus <4 ()
Sulfolobus metallicus <3 (Johnson 1998)
Sulfolobus mirabilis <3 (Johnson 1998)
Sulfolobus neozealandicus <4 ()
Sulfolobus shibatae <3 (Johnson 1998)
Sulfolobus solfataricus 2-4 Johnson (1998), Dopson (2003)
Sulfolobus tengchongensis <4 ()
Sulfolobus thuringiensis <4 ()
Sulfolobus tokodaii <3 Dopson 2003
Sulfolobus yangmingensis <4 ()
Sulfurisphaera ohwakuensis <4 ()
Sulfurococcus mirabilis <4 ()
Sulfurococcus yellowstonensis <4 ()
Sulfurococcus yellowstonii <3 Johnson (1998)
Thermogymnomonas acidocola <4 ()
Thermoplasma acidophilum 1.8 Johnson (1998)
Thermoplasma volcanium <3 Johnson (1998)
Bacteria Acidiphilium spp. <3 (Johnson 1998)
Acidiphilium acidophilum
(Thiobacillus acidophilus)
<3 (Johnson 1998)
Acidiphilium multivorum <3 (Dopson 2003)
Acidithiobacillus albertensis
(Thiobacillus albertis)
<3 (Johnson 1998)
Acidithiobacillus caldus
(Thiobacillus caldus)
<3 Johnson (1998)
Acidithiobacillus ferridurans <4 ()
Acidithiobacillus ferriphilus <4 ()
Acidithiobacillus ferrivorans <4 ()
Acidithiobacillus ferrooxidans
(Thiobacillus ferrooxidans)
<3 Johnson (1998)
Acidithiobacillus thiooxidans
(Thiobacillus thiooxidans)
<3 Johnson (1998)
Acidobacterium capsulatum <3 Johnson (1998)
Acidimicrobium ferrooxidans <3 Johnson (1998)
Acidocella spp. <3 Johnson (1998)
Acidomonas methanolica <3 Johnson (1998)
Alicyclobacillus thermosulfidooxidans spp. <3 Johnson (1998)
Alicyclobacillus thermosulfidooxidans
(Sulfobacillus thermosulfidooxidans)
<3 Johnson (1998)
Bryocella elongata <4 ()
Ferrimicrobium acidiphilum <3 Johnson (1998)
Leptospirillum ferrooxidans <3 Johnson (1998)
Leptospirillum thermoferrooxidans <3 Johnson (1998)
Sulfobacillus acidophilus <3 Johnson (1998)
Telmatobacter bradus <4 ()
Thiobacillus prosperus <3 Johnson (1998)
Thiobacillus acidophilus <4 ()
Thiobacillus organovorus <4 ()
Thiomonas cuprina
(Thiobacillus cuprinus)
<3 (Johnson 1998)
Life (Basel). 2013 Sep; 3(3): 482–485. Published online 2013 Aug 7. doi: 10.3390/life3030482 PMCID: PMC4187170 Extremophiles and Extreme Environments Pabulo Henrique Rampelotto https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187170/
MiniReview Biodiversity and ecology of acidophilic microorganisms D. Barrie Johnson FEMS Microbiology Ecology 27 (1998) 307^317 FEMS Microbiology Ecology Volume 27, Issue 4, Version of Record online: 17 JAN 2006 http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.1998.tb00547.x/pdf
Growth in sulfidic mineral environments: metal resistance mechanisms in acidophilic micro-organisms Mark Dopson, Craig Baker-Austin, P. Ram Koppineedi and Philip L. Bond Microbiology (2003), 149, 1959–1970 DOI 10.1099/mic.0.26296-0 http://mic.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.26296-0#tab2
A novel acidophilic, thermophilic iron and sulfur-oxidizing archaeon isolated from a hot spring of tengchong, yunnan, China Jiannan DingI, II, *; Ruiyong ZhangI; Yizun YuII; Decai JinI; Changli LiangI; Yang YiI; Wei ZhuI; Jinlan XiaI, Brazilian Journal of Microbiology Print version ISSN 1517-8382 Braz. J. Microbiol. vol.42 no.2 São Paulo Apr./June 2011 http://dx.doi.org/10.1590/S1517-83822011000200016
An Archaeal Iron-Oxidizing Extreme Acidophile Important in Acid Mine Drainage Katrina J. Edwards, 1,2 * Philip L. Bond, 1 Thomas M. Gihring, 1 Jillian F. Banfield 10 MARCH 2000 VOL 287 SCIENCE p. 1796-1799

I.b-2Aβ.) Alkaliphiles
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Archaea Halalkalicoccus 16:1 1/16 (6.25%) 15/16 (93.75%) 87.5%
Haloarcula
Halobaculum
Halobiforma
Haloferax
Halorubrum gandharaense
Nanobacterium gregoryi
Natronococcus amylolyticus
Natronococcus jeotgali
Natronococcus occultus
Natronolimnobius
Natronomonas pharaonis
Natronorubrum
Thermococcus alkaliphilus
Thermococcus acidaminovorans
Methanohalophilus
Bacteria (Coming Soon)


I.b-2Aγ.) Barophiles
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Archaea Pyrococcus abyssi 6:1 1/7 (14%) 6/7 (86%) 72%
Pyrococcus endeavori
Pyrococcus furiosis
Pyrococcus glycovorans
Pyrococcus horikoshii
Pyrococcus woesei
Bacteria Salinicola salarius

(Gareeb & Setati, 2009)
(Pikuta &al., 2017)

I.b-2Aδ.) Hyperthermophiles
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Archaea Aeropyrum pernix 6:1 1/7 (14%) 6/7 (86%) 72%
Pyrolobus fumaril
Pyrococcus furiosus
Archaeoglobus fulgidis
Methanococcus jannaschii
Stygiolobus azoricus
Sulfolobus acidocaldarius
Sulfolobus islandicus
Sulfolobus metallicus
Sulfolobus neozealandicus
Sulfolobus shibatae
Sulfolobus solfataricus
Sulfolobus tengchongensis
Sulfolobus thuringiensis
Sulfolobus tokodaii
Sulfolobus yangmingensis
Methanopyrus kandleri
"Strain 121"
Bacteria Aquifex aeolicus
Geothermobacterium ferrireducens
Theromotoga maritima


I.b-2Aε.) Totals for Planetary Extremes
Extreme Domain Number Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Acidity Archaea 18 18:7 7/25 (28%) 18/25 (72%) 44%
Bacteria 7
Alkalinity Archaea 6 16:1 1/16 (6.25%) 15/16 (93.75%) 87.5%
Bacteria 1
Salinity Archaea
Bacteria
High Pressure Archaea 6 6:1 1/7 (14%) 6/7 (86%) 72%
Bacteria 1
Heat Archaea 18 6:1 1/7 (14%) 6/7 (86%) 72%
Bacteria 3
Total Archaea
Bacteria


I.b-2Aζ.) Radioresistant Prokaryotes
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Archaea Pyrococcus furiosis 1:4 1/5 (20% 4/5 (80%) 60%
Haloferax volcanii
Natrialba magadii
Thermococcus gammatolerans
BacteriaBacillus subtilis
Bacillus atropheus
Bacillus thuringiensis
Bacillus cereus
Bacillus megaterium
Deinococcus radiodurans
Escherichia coli
Rubrobacter sp.
Achromobacter sp.
Acinetobacter sp.
Alcaligenes sp.
Enterococcus sp.
Micrococcus sp.
Pseudomonas sp.
Staphylococcus sp.
Streptococcus sp.

(Abrevaya &al., 2011)
(Bucker & Horneck, 1970)
(Horneck, 1971)
(Nicholson, &al. 2005)

I.b-2Aη.) Xerophilic Prokaryotes
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Bacteria Bacillus subtilis 2:0 0/2 (0%) 1/1 (100%) 100%
Escherichia coli


I.b-2Aη.) Cryophilic Prokaryotes
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Bacteria Bacillus subtilis 2:0 0/2 (0%) 1/1 (100%) 100%
Escherichia coli


I.b-2Aθ.) Totals for Spacial Extremes
Extreme Domain Number Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Radioactivity Archaea 4 4:1 1/5 (20%) 4/5 (80%) 60%
Bacteria 20
Hyperacceleration / Hypergravity Archaea
Bacteria 2
Low Pressure Archaea
Bacteria
Cold Archaea
Bacteria
Drouth Archaea 0 2:0 0/2 (0%) 1/1 (100%) 100%
Bacteria 2
Total Archaea
Bacteria


I.b-2Aι.) Totals for Prokaryotic Extremophiles
Extreme Type Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Acidity Planetary 18:7 7/25 (28%) 18/25 (72%) 44%
Alkalinity 16:1 1/16 (6.25%) 15/16 (93.75%) 87.5%
Salinity
High Pressure 6:1 1/7 (14%) 6/7 (86%) 72%
Heat 6:1 1/7 (14%) 6/7 (86%) 72%
Radioactivity Spacial 1:4 1/5 (20%) 4/5 (80%) 60%
Hyperacceleration / Hypergravity
Low Pressure
Cold
Drouth 2:0 0/2 (0%) 1/1 (100%) 100%


I.b-2A.) Problems with Independent Origins
"What we need is a second sample of life. We have only one at present. It would be- it would a disappointment, as you say, to find life based on DNA, or at least life on Mars based on the same DNA code. [You can] just about imagine DNA evolving twice, but you couldn't imagine the same, uh, four-letter code, um, uh, evolving twice." (Richard Dawkins to Neil Tyson, Dawkins & Tyson, 2016, 7:30-7:57 minutes in)

Since modern RNA can be used as a template to synthesize DNA, with the uracil in RNA matching the thyamine in DNA, it is entirely possible that what Dawkins refers to as “the same four-letter code" in DNA could have evolved twice, so long as the two DNA codes were derived from a common RNA code. This could be said to be dodging the issue of how DNA evolved twice in the same way that (most) panspermia hypotheses dodge the issue of how life began. This therefore begs the question: How could the same four-letter RNA code have evolved twice? The most obvious solution is that the same four-letter RNA code couldn’t have evolved twice, but must have come from a common RNA-based ancestor. The independently-derived DNA codes could thus be compatible with one another so long as the RNA codes on Earth and Mars had not yet greatly diverged since their common ancestor. That is to say, if in the early Solar system there was RNA-based life on both Mars and Earth, and these lifeforms (or quasi-lifeforms) were still very closely related and compatible with one another, and DNA originated roughly in this time period, independently on both worlds, then the DNA on either planet very well may have been compatible with the other simply by virtue of having been synthesized by nearly identical RNA codes.

Furthermore, there is, as noted earlier evidence indicating that the common ancestor of the Archaea and the Bacteria possessed an RNA-based genome (Leipe & al., 1999) and only after divergence was DNA acquired separately in the two lineages, possibly from DNA viruses in which DNA first arose (Leipe & al., 1999; Forterre, 2002).

Regardless, whether DNA evolved once, on either Earth or Mars, or twice, separately in the ancestors of the Archaea and the Bacteria, the fact that Archaea and Bacteria can experience LGT with one another and presumably would have been able to do so far more easily in the distant past, leaves us with the inescapable reality that there must have been a common origin for both of these groups. The Archaea and the Bacteria simply could not have evolved entirely independently ex nihilo.



I.b-2B.) Alternative Explanations for Apparent Evidence of Independent Origins

The apparent "biological" evidence for independent origins, which mainly has to do with various bacteria having adaptations which confer upon them survivability when exposed to spacial conditions as opposed to the archaea, may be explainable by known conditions in Earth's past.

To space and back during the LHB (Wells, &al., 2003).

Natural fission reactors (Davis &al., 2014) representing a “critical event” (Gauthier-Lafaye &al., 1996) possible formation of the Moon by a nuclear explosion at Earth's core-mantle boundary (CMB) (de Meijer &al., 2010).

Another possibility is that Earth and Mars were both seeded by a common source of biological life.



I.b-3.) The Protoplanetary Origin of Life

The earliest stages of life on Earth very likely antedate the Earth Herself. This idea has been variously referred to as “molecular panspermia", “quasi-panspermia", or “pseudo-panspermia".

"Essential to the spontaneous origin of life was the availability of organic molecules as building blocks. The famous ‘prebiotic soup’ experiment by Stanley Miller (Miller 1953, Miller-Urey experiment) had shown that amino acids, the building blocks of proteins, arose among other small organic molecules spontaneously by reacting a mixture of methane, hydrogen, ammonia and water in a spark discharge apparatus. These conditions were assumed to simulate those on the primitive Earth. Already in 1922 Oparin had proposed that the early Earth had such a reducing atmosphere (in his classic ‘The Origin of Life’ from 1936 he expanded on these ideas). Observations of Jupiter and Saturn had shown that they contained ammonia and methane, and large amounts of hydrogen were inferred to be present there as well (it is now known that hydrogen is the main atmospheric component of these planets). These reducing atmospheres of the giant planets were regarded as captured remnants of the solar nebula and the atmosphere of the early Earth was assumed by analogy to have been similar." -- The Origin of Life by Albrecht Moritz

(Moritz, 2010)

"Indigenous purines and pyrimidines have been detected in several carbonaceous chondrites. The pyrimidine uracil and the purines adenine, guanine, xanthine, and hypoxanthine (Stoks & Schwartz 1979, 1981) were detected in the CM carbonaceous chondrites Murchison and Murray, as well as in the CI meteorite Orgueil, in total concentrations of about 1.3 parts per million (ppm). Upper limits exist (detection limit of 0.01 ppm) for the concentrations of thymine and cytosine, as well as other heterocyclic compounds, in the Murchison meteorite (van der Velden & Schwartz 1977)."

(Peeters &al., 2003)

(Zita &al., 2008)

(Martins &al., 2008)

(Ehrenfreund & Cami, 2010)

(Ziurys, 2008)

(Coggins & Powner, 2017)

The conditions of the Miller-Urey experiments more closely resemble the conditions of the Solar nebular than the conditions of the primordial Earth (Hill & Nuth, 2003).

The purine bases adenine and guanine have been detected in meteorites, although the only pyrimidine-base compound formally reported in meteorites is uracil (Stoks & Schwartz, 1979), however cytosine cannot be ruled out (Shapiro, 1998; Peeters &al., 2003; Martins &al., 2006) and ultraviolet irradiation of low-temperature ices (the dominant phase of H2O in cold astrophysical environments is ice, and most ices in such environments are H2O-rich) has been shown to produce not only amino acids, quinones, and amphiphiles, but have also, with the introduction of pyrimidine, been shown to produce uracil (Nuevo &al., 2009), cytosine, and even thiamine, though the abiotic synthesis of thiamine is less straightforward compared to other pyrimidine-base compounds (Sandford &al., 2014). (That this would logically make the prebiotic synthesis of RNA easier than that of DNA could explain why RNA has a larger repertoire of functions than does DNA in modern cells.) Additionally, ribose and related sugars have been produced experimentally in interstellar ice analogues (Meinert &al., 2016).

Cytosine can be synthesized from cyano-acetylene and cayanate, this is unlikely to have occured in acqueous media as cayanate is rapidly hydrolized into CO2 and NH3.

Cyano-acetylene is an abundant interstellar molecule and can by produced by a spark discharge in a CH4/N2 environment.

hydrolysis of cyanoacetylene leads to cyanoacetaldehyde

reaction of cyanoacetaldehyde with urea produces cytosine in 30-50% yields

Hydrolysis of cytosine leads to uracil

(Robertson & Miller, 1995)

(Pudritz, 2016)

(Sandford, Bera &al., 2014)

(Kuga &al., 2015)

What all of this means is that hypothetical geochemical pathways for the production of key organic compounds here on Earth, though interesting, are completely superfluous, since the biochemical building blocks of life were already being produced astrochemically before the formation of the Earth. Occam's razor therefore dictates that such geochemical hypotheses for the prebiotic synthesis of organic compounds should be regarded as irrelevant to the origin of life problem.

Clear liquid turns brown as amino acids form peptides. Jennifer Blank. Experiment.

Amino acids + impact = peptides (Blank & al. 2001)



I.b-4.) Synthesis: Molecular Panspermia & Subsequent Mars-Earth Interplanetary Lithopanspermia

Rather than an “RNA world" on either Earth or Mars, the Last Universal Common Ancestor (LUCA) may have lain in the “RNA cloud" of the protoplanetary Solar nebula. The early RNA-based replicons wouldn't necessarily have been “life" in the modern sense of the word, and might have lacked lipid cell membranes as some researches (cite) have suggested for the LUCA even in purely terrestrial models, with the development of cell membranes being an example of parallel evolution. If the development of more modern features of life (or rather, the features we associate with “true life") such as cell-membranes, and possibly even thymine-using nucleic acid, occured separately on Earth and Mars, the result would be two independent evolutions of “true life" that would appear to be very closely related to one another by having shared a relatively recent amembranous RNA-based ancestor. DNA and cell membranes may have evolved separately in parallel simply because this was the most sensible way for the LUCA to respond to the two nearly identical new environments of early Earth and early Mars as the Solar nebula accreted into the terrestrial planets. (This also means it may not be a futile endeavor to search for past-life on Venus, as the environment of early Venus was very much like the environment of early Earth and early Mars, and a sort of “Bacteria from Mars, Archaea from Venus" scenario, with the eukarya developing on Earth, being most closely related to Venereal/Archaeal life but having incorporated Martian/Bacterial life in the form of mitochondria, isn't difficult to envision, either).

(Belbruno, 2012)

So while the first and most obvious objection to the idea of independent origins should be that all life on Earth appears to have descended from a common ancestor, it does not necessarily follow that all life on Earth must have originated on a single planetary body — this objection could only seem reasonable to researchers who wrongly assume that the environments of the planets have always been as isolated from one another as they presently appear to be, which is simply not the case. The early Solar system was a chaotic place; organic molecules were likely already present when the material that would later accrete into the planets were but a diffuse and relatively (compared to today) homogenous gas cloud, which “curdled" gradually into something like a vast asteroid field, the rocky, protoplanetary bodies growing larger and fewer in number as the material accreted until the planets we are now familiar with arose out of the chaos. When the planets were smaller and surrounded by yet-to-be-accreted debris, impacts would have logically been far more frequent, and the smaller sizes of the proto-planetary bodies relative to the modern planets would've meant that lower-speed impacts — and therefore a larger proportion of the impacts which occured — were kicking impact debris back into space.



II.b-1.) Prokaryotic Multicellularity

(Ereskovsky &al., 2013)


II.b-1A.) Bacterial Multicellularity

Bacterial multicellularity can be grouped into three general categories (Lyons & Kolter, 2015):

☣ Filaments —
☣ Aggregates —
☣ Biofilms —
☣ Swarms —
☣ MMPs (multicellular magnetotactic prokaryotes) —



II.b-1B.) Archaeal Multicellularity

(Fröls, 2013)

(Orell &al., 2013)



Works Cited