Spherical bundle of Dictyoglomus thermophilum, from Saiki et al. (1985).

Contains: Euryarchaeota, Eukaryota, Crenarchaeota, Reitlingerellidae, Fusobacteria, Gracilicutes, Terrabacteria, Deinococci, Thermotogaceae.

This is the source page to begin following the tree of all life on this planet. The total group of living organisms can be divided for convenience between eukaryotes, in which the greater part of the cell’s genetic material is contained within a nuclear membrane, and the prokaryotes which lack a distinct nucleus. It is generally agreed that the prokaryotes are paraphyletic with regard to the monophyletic eukaryotes. Prokaryotes may be divided between the Bacteria, in which the cytoplasmic membranes are composed of acyl ester lipids, and the Archaea, in which membranes are composed of prenyl ether lipids (Cavalier-Smith 2002).

The nature of Nanoarchaeum
Published 1 May 2008
Ignicoccus cell with four ‘Nanoarchaeum’ cells attached. Scale bar = 1 μm. Image from Huber et al. (2002) via MicrobeWiki.

The Archaea have received a great deal of attention in recent years as the supposed Third Domain of life. They are a group of prokaryotes that differ from all others (the Eubacteria) in a number of significant ways—they have a RNA-protein translation system more similar to that of eukaryotes than Eubacteria, they lack the murein that makes up the cell wall of most Eubacteria, and they have a unique tetraether cell membrane that differs from that of the other domains. The study of Archaea has also been influenced by the association of most cultured representatives with extreme environments as thermophiles or halophiles, though environmental PCR studies suggest that Archaea may be much more abundant in the general environment than the cultured diversity suggests (Forterre et al. 2002).

Compared to the dog’s breakfast that is our current understanding of eubacterial phylogeny, the phylogeny of Archaea seems much clearer. Most studies indicate a basal division of cultured Archaea between two major clades, the Crenarchaeota and Euryarchaeota. Crenarchaeota is the smallest of the two groups and the cultured representatives are all hyperthermophiles, though again PCR samples indicate uncultured mesophilic examples. The Euryarchaeota are much more diverse, including halophiles and methanogens as well as thermophiles. Environmental PCR sequences suggesting archaeal taxa lying outside these two major clades, and one group of them has received the provisional name of Korarchaeota, but until these taxa are properly characterised their existence remains uncertain.

So far, the only well-characterised archaeum that has been suggested to lie outside the two main clades is ‘Nanoarchaeum equitans’* (Huber et al. 2002). ‘Nanoarchaeum’ is a minute (400 nm) organism that lives in hyperthermophilic environments as an obligate associate of another archaeum, Ignicoccus. Attempts to culture ‘Nanoarchaeum’ independently have failed—even growth on a medium of puréed Ignicoccus or separated from an Ignicoccus culture by a semipermeable membrane proved impossible. ‘Nanoarchaeum’ can only grow in direct cell-to-cell contact with living Ignicoccus. ‘Nanoarchaeum’ also has the one of the smallest genomes of any organism known, with only about 490,000 base pairs. For comparison, the human genome includes about 3000,000,000 base pairs, that of a lungfish 130,000,000,000 base pairs, and that of the largest known virus, Mimivirus, 1200,000.

*I haven’t italicised ‘Nanoarchaeum’ because it’s not yet a technically valid taxon. To be valid, a prokaryote name requires publication or validation in the International Journal of Systematic and Evolutionary Microbiology, and this doesn’t seem to have happened for ‘Nanoarchaeum’. Because of the stringent culture requirements of the Prokaryote Code of Nomenclature, ‘Nanoarchaeum’ may not be eligible for validation, though it may be recognisable as a Candidatus, the Prokaryote Code’s provisional class for a taxon that cannot be cultured independently but can be well-characterised environmentally.

The reduced genome of ‘Nanoarchaeum’ is reflective of its inability to synthesise many of the metabolites it requires to survive, which it draws instead from its Ignicoccus host. This is not unusual among parasitic organisms, though ‘Nanoarchaeum’ is unusual among super-reduced parasites in its extracellular rather than intracellular position relative to the host, probably as a consequence of the general absence of phagocytosis among prokaryotes. ‘Nanoarchaeum’ is also comparable to other super-reduced parasites in another way. When it was first described, analysis of ribosomal genes suggested a position for ‘Nanoarchaeum’ divergent from all other Archaea, which lead to its promotion as a new archaeal phylum. However, studies of comparable eukaryotic parasites have indicated that they have usually undergone exceedingly rapid evolution that has exaggerated their differences from their more mediocre relatives. Ribosomal genes in particular seem to be very prone to such long-branch distortion. The prime example in recent years has been the Microsporidia, intracellular parasites that were once thought on the basis of ribosomal genes to be one of the earliest-diverging branches of eukaryotes, but have since been reinterpreted as highly-evolved fungi.

Phylogenetic analysis results from Brochier et al. (2005) showing association between ‘Nanoarchaeum’ and Thermococcales. Unconstrained unrooted maximum likelihood trees of (a) elongation factor EF-1α, (b) elongation factor EF-2, (c) subunit A of topoisomerase VI, and (d) Bayesian tree of reverse gyrase. Bold numbers at nodes are bootstrap values; the other numbers are the Bayesian posterior probabilities. Scale bars represent the number of changes per position for a unit branch length.

With this in mind, I was not overly surprised to see the results of Brochier et al. (2005). Brochier et al. took a slightly different tack to understanding the phylogeny of ‘Nanoarchaeum’—as well as using a wider range of genes, Brochier et al. also calculated the open reading frames (ORFs) of the entire ‘Nanoarchaeum’ genome (an ORF is a section of the genome that could potentially code for a protein) and compared them to those of other Archaea. The ORF analysis found that ‘Nanoarchaeum’ shared the majority of its ORFs with Euryarchaeota, and was particularly similar to members of the order Thermococcales. This result was corroborated by a number of the gene analyses. The basal position of ‘Nanoarchaeum’ in the ribosomal trees would therefore appear to be due to long-branch attraction, possibly exacerbated by lateral gene transfer with its Crenarchaeota host.

The endosymbiotic hammer strikes again
Published 21 August 2009

I was going to write a post here about Lake’s (2009) proposal in yesterday’s Nature that double-membraned (Gram-negative) bacteria could be derived from an endosymbiotic relationship between two single-membraned bacteria, and why I found it decidedly unconvincing. But I’ve spent today trying (unsuccessfully, I might add) to look at seminal receptacles in harvestman ovipositors and overexposure to the smell of clove oil has left me feeling decidedly crook and put my brain into shutdown. So I’ll just give you the link and the abstract, and a few things to keep in mind when reading the article (if you can get access to it):

Lake, J. A. 2009. Evidence for an early prokaryotic endosymbiosis. Nature 460: 967–971.

Endosymbioses have dramatically altered eukaryotic life, but are thought to have negligibly affected prokaryotic evolution. Here, by analysing the flows of protein families, I present evidence that the double-membrane, Gram-negative prokaryotes were formed as the result of a symbiosis between an ancient actinobacterium and an ancient clostridium. The resulting taxon has been extraordinarily successful, and has profoundly altered the evolution of life by providing endosymbionts necessary for the emergence of eukaryotes and by generating Earth’s oxygen atmosphere. Their double-membrane architecture and the observed genome flows into them suggest a common evolutionary mechanism for their origin: an endosymbiosis between a clostridium and actinobacterium.

Point 1: If such an endosymbiosis had occurred, then both partners would have probably had cell walls (peptidoglycan layers) outside their membrane (the only single-membraned eubacteria lacking cell walls are Mollicutes, which are parasites of eukaryotes*). Why did the external partner lose its cell wall rather than the internal partner?

*I originally referred to Mollicutes as intracellular—thankfully, Elio Schaechter put me right (they’re extracellular). I did say that my brain had stopped working.

Point 2: The endosymbiosis scenario requires that the genetic complement of the external partner be entirely lost or transferred to the inner partner (as well as the greater part of its cytoplasm). While unusual, this would not be unique. Transfer of genes from one partner to the other is a common (if not universal) event in endosymbioses. The hydrogenosomes found in some anaerobic eukaryotes are generally accepted to be derived from mitochondria, but most have entirely lost their genomes (as far as we know). Also, in most secondary or tertiary chloroplasts, the eukaryotic genome of the endosymbiont has disappeared. However:

Point 3: In all established cases of endosymbiosis, gene transfer or loss has been mostly (if not entirely) to the cost of the internal partner. This applies not just to mutualist endosymbionts, but also to intracellular parasites. Lake’s proposed endosymbiosis requires the transfer to happen the other way, at the cost of the external partner (offhand, the same objection applies to scenarios that propose an endosymbiotic origin for the eukaryotic nucleus).

Point 4: Even if Lake’s premise that double-membraned bacteria carry genes from two phylogenetically separate ancestors is correct (I have to confess that I don’t feel knowledgeable enough to critique that point), that doesn’t necessarily require an endosymbiosis. A simple symbiosis might possibly be sufficient. Many bacteria form closely-linked ectosymbiotic consortia, and the well-established propensity of bacteria to swap genetic material like trading cards could result in a substantial transfer in such an arrangement over time. Also:

Point 5: Among eukaryotes, the endosymbiosis theory receives something of a boost from the point that eukaryotes are absolutely lousy with endosymbionts at all stages of interdependence. Lake mentions the proteobacterium Buchnera in aphids; there are also zooxanthellae in corals and clams, Perkensiella in amoebae, a whole universe of intracellular parasites… the list goes on. Prokaryotes, in contrast, just don’t seem to carry endosymbionts to the same degree. Lake mentions in his support that the aforementioned Buchnera carries its own endosymbiont; what he doesn’t mention is that this is the only well-established case of an endosymbiont inside a prokaryote. Lake claims that the Chlorochromatium consortium is very close to an endosymbiotic relationship. It’s still ectosymbiotic nonetheless. Contrast this with the extreme general diversity and versatility of prokaryotes, which is leagues ahead of that of eukaryotes—you’d think that if they could easily do it, they would be.

Point 6: The presence of a nucleus of sorts in Planctomycetaceae indicates that bacteria are not incapable of developing new membrane systems.

Point 7: I really, really hate this paragraph:

In fact, the membrane organization of double-membrane prokaryotes fundamentally differs from that found in single-membrane prokaryotes. In the former, the peptidoglycan layer is sandwiched between the outer and inner membranes, so that it surrounds the inner membrane: in contrast, in the latter there is no inner membrane, and the peptidoglycan layer, located outside the cell, surrounds the outer membrane. Also, double-membrane prokaryotes contain their flagellar motors in the inner membrane, whereas single-membrane prokaryotes contain their flagellar motors in the outer membrane. And the photosynthetic apparatus in double-membrane prokaryotes is in the inner membrane, rather than in the outer membranes as in single-membrane prokaryotes. In other words, the organization of the inner membrane of the double-membrane prokaryotes resembles that of the outer membranes of typical single-membrane prokaryotes. The inner membranes of double-membrane prokaryotes are organized almost as if they were derived from the outer membrane of an engulfed single-membrane prokaryote.

This, ladies and gentlemen, is a classic case of semantic silly buggers. Lake obfuscates the difference between single- and double-membrane bacteria by noting that double-membrane bacteria have an outer and inner membrane, then referring to the membrane in single-membrane bacteria as the outer membrane even though it is positionally comparable to the inner membrane (pause to wipe foam from frothing mouth and allow bulging eyeballs to return to their sockets). His referral to the supposed difference between flagella of the two types of bacteria looks a little different when you consider that what he is saying is that both anchor their flagella on the membrane inside the cell wall. (noooo! the family curse!)

Point 8:

There is currently much discussion of the prokaryotic ‘tree of life’, but there are few points of agreement regarding its topology, except that it is not a tree.

While the idea that a tree is not an appropriate expression of prokaryote evolution is increasingly popular, I think it’s jumping the gun a little to present it as a consensus. Take a look at the number of trees in an average issue of the International Journal of Systematic and Evolutionary Microbiology, for a start (and yes, now I am just picking at minor details).

Point 9: And just on a final quibble, this line from the supplementary info:

I propose the name Domain Synergia (Gr. Synergia—joint work) for those prokaryotes that possess the Gram negative, double membrane organization, and are derived from large, statistically significant gene flows from both the Actinobacteria (as defined in Table S1) and the Clostridia (also as defined in Table S1).

Not only would I consider it fairly unacceptable to bury the publication of a new taxon name within the online-only supplementary info of a print-based article, but under Lake’s proposed scenario this “new” taxon would be circumscriptionally equivalent to the already-available name of Didermata.

The attack of Mega-Matrix
Published 10 September 2010

The last two decades have seen a great deal of discussion about the role of horizontal gene transfer (HGT) in phylogenetic reconstruction of prokaryotes. That HGT occurs among prokaryotes, occassionally between members of far distant lineage, is undeniable; the question is whether HGT is a common event in bacterial evolution or whether it is mere occasional noise. Some researchers have gone so far as to argue that HGT is so rampant among prokaryotes that the reconstruction of a reliable tree of life for bacteria is an impossibility. As I’ve noted elsewhere, I have to admit to a certain degree of hostility towards this idea, but I immediately have to confess that this hostility is entirely due to personal prejudice (I really want there to be a tree of life for prokaryotes) and not supported by anything rational.

Attempts to reconstruct the prokaryote tree of life have usually attempted to circumvent the issue of HGT by focusing on a small subset of genes that are believed to be resistant to this problem, such as ribosomal RNA genes. However, this method carries two major issues: (1) the assumption that horizontal transfer of these genes is not possible may not be as robust as believed (some have suggested that there may be no such thing as a truly HGT-free gene), and (2) the smaller the data set used, the greater the chance that other complicating factors may interfere with results. For instance, it is now generally accepted that high-level phylogenetic reconstructions of eukaryotes using rRNA are very vulnerable to the effects of inequal evolutionary rates, with many supposedly ‘basal’ branches being shown to in fact be highly derived. There is no a priori reason to assume that the same problem would not apply to rRNA phylogenies of prokaryotes.

A paper just published in Cladistics (Lienau et al. 2010) takes the opposite approach to the problem: it uses an absolutely enormous amount of data to see whether a coherent tree can still be recovered. Two main data sets were used analysing 166 genomes from taxa throughout the tree of life (mostly prokaryotes). One concatenated direct amino acid sequences from 12,381 genes to provide 846,999 phylogeny-informative characters (out of a potential 4,540,579 characters). The other compared presence vs absence of genes from the 166 genomes. Analysis was done using parsimony, which is potentially problematic for sequence data but probably necessary to simply work with this amount of data. One analysis was run on the sequence data alone; another was run using the combined sequence and gene presence/absence data (the gene presence/absence data alone had been analysed by an earlier study).

The heartening result of this analysis is that a coherent phylogeny was recovered, particularly using the combined data set (shown above from the paper; a few anomalies were present using the sequence data alone). Most previously recognised major bacterial groups analysed were recovered by the combined data as monophyletic* (the only exception being the spirochaetes, with Leptospira failing to associate with the two Spirochaetaceae). Many of the higher-level relationships were also congruent with earlier proposals: α-proteobacteria as sister to the clade of β- and γ-proteobacteria, with δ-proteobacteria the next group out; a clade of the sphingolipid-producing bacteria (Chlorobium + Bacteroidales; and a clade uniting ε-proteobacteria with Aquifex + Thermotoga, which would then include all known hydrogen-oxidising Eubacteria. It appears unlikely that HGT fatally compromises large-scale analyses.

*Or perhaps I should say ‘congruent’. As far as I can see, the study glosses over the question of the rooting of the tree of life; the tree shown is rooted between Neomura (Archaea + eukaryotes) and Eubacteria but no discussion is given on that position.

Of course, the tree is not without warning signs. The aforementioned polyphyletic spirochaetes are a bit worrying in light of the distinctive spirochaete ultrastructure. Some of the relationships within the major clades are a bit off: Gloeobacter is nested well within other cyanobacteria rather than being the most divergent (Gloeobacter is the only known cyanobacterium to lack thylakoids), and the arrangement of eukaryotes is all wrong. However, it must be stressed that, as large as this study was, the taxa analysed still represent only a small proportion of the world’s total diversity. What is more, the choice of organisms to have their whole genome sequenced (a necessary pre-requisite for this study) has not been evenly distributed through prokaryote diversity. Many little-studied but potentially phylogenetically significant taxa (such as many of the low-diversity bacterial ‘divisions’) are significant by their absence, as are many significant subgroups of those divisions that are represented. This story is not yet over.

Systematics of Life
LIFE (see below for synonymy)
|--Neomura (see below for synonymy)C-S02
| | i. s.: 0--+--Candidatus Micrarchaeum acidiphilumSS15
| | | `--Candidatus IainarchaeumRS13 [DiapherotritesSS15]
| | | `--I. andersoniiSS15
| | `--+--+--Candidatus Nanoarchaeum Huber, Hohn et al. 2002HH02 [NanoarchaeotaSS15]
| | | | `--*N. equitans Huber, Hohn et al. 2002HH02
| | | `--Candidatus Parvarchaeum [Parvarchaeota]SS15
| | | `--P. acidophilusSS15
| | `--+--Candidatus Aenigmarchaeum [Aenigmarchaeota]SS15
| | | `--A. subterraneumSS15
| | `--NanohaloarchaeotaRS13
| | |--Candidatus NanosalinaSS15
| | |--Candidatus NanosalinarumRS13
| | `--Candidatus HaloredivivusRS13
| |--EuryarchaeotaIN20
| `--+--AsgardZ-NC17
| | |--OdinarchaeotaZ-NC17
| | `--+--LokiarchaeotaIN20
| | | |--Candidatus LokiarchaeumSS15
| | | `---Candidatus Prometheoarchaeum syntrophicumIN20
| | `--+--ThorarchaeotaZ-NC17
| | `--+--HeimdallarchaeotaZ-NC17
| | `--EukaryotaSS15
| `--+--Candidatus Korarchaeum [Korarchaeota]SS15
| | `--K. cryptofilumSS15
| `--+--CrenarchaeotaSS15
| `--+--BathyarchaeotaZ-NC17
| `--+--Candidatus Caldiarchaeum [Aigarchaeota]SS15
| | `--C. subterraneumSS15
| `--ThaumarchaeotaSS15
| |--NitrososphaeraIN20
| | |--Candidatus N. gargensisSS15
| | `--N. viennensisIN20
| `--+--Cenarchaeum Preston et al. 1996SS15, C-S02 [Cenarchaeales]
| | `--C. symbiosumSS15
| `--+--Nitrosopumilus maritimusSS15
| `--NitrosoarchaeumSS15
| |--N. koreensisSS15
| `--N. limniaSS15
`--Bacteria (see below for synonymy)SS15
| i. s.: Albidovulum Albuquerque, Santos et al. 2003VP IJSEM03
| `--*A. inexpectatum Albuquerque, Santos et al. 2003VP IJSEM03
| Oceanobacillus Lu, Nogi & Takami 2002VP IJSEM02
| `--*O. iheyensis Lu, Nogi & Takami 2002VP IJSEM02
| Sneathia Collins, Hoyles et al. 2002VP IJSEM02
| `--*S. sanguinegens Collins, Hoyles et al. 2002VP IJSEM02
| GeobacillusJC08
| |--G. kaustophilus (Priest et al. 1989) Nazina et al. 2001JC08
| |--G. stearothermophilus (Donk 1920) Nazina et al. 2001JC08
| |--G. thermodenitrificans (Manachini et al. 2000) Nazina et al. 2001JC08
| |--G. thermoglucosidasius (Suzuki et al. 1984) Nazina et al. 2001JC08
| `--G. thermoleovorans (Zarilla & Perry 1988) Nazina et al. 2001JC08
| ReitlingerellidaeX04
| Salome hubeiensis Zhang 1986X04
| Polytrichoides Hermann 1974X04
| `--P. lineatusX04
| Nannococcus vulgarisX04
| Nitrocystis oceanusPHK96
| Beneckea natriegensPHK96
| SiderocapsaceaePHK96
| |--SiderocapsaPHK96
| |--NaumanniellaPHK96
| |--SiderococcusPHK96
| `--OchrobiumPHK96
| PelonemataceaePHK96
| |--PelonemaPHK96
| |--AchroonemaPHK96
| |--PeloplocaPHK96
| `--DesmanthosPHK96
| Schismatispaeridium kumauniT84
| Bryantella Wolin, Miller et al. 2004VP non Britton 1957 (ICZN)IJSEM04
| `--*B. formatexigens Wolin, Miller et al. 2004VP IJSEM04
| Parapandorina raphospissaBJ07, G02
| Trichlorobacter thiogenes De Wever et al. 2001JC08
| AnaerococcusJC08
| |--A. octavius (Murdoch et al. 1997) Ezaki et al. 2001JC08
| `--A. prevotii (Foubert & Douglas 1948) Ezaki et al. 2001JC08
| Carboxydibrachium pacificumJC08
| Desulfotignum balticum Kuever et al. 2001JC08
| Dorea formicigenerans (Holdeman & Moore 1974) Taras et al. 2002JC08
| Gallicola barnesae (Schiefer-Ullrich & Andreesen 1986) Ezaki et al. 2001JC08
| Marinibacillus marinus (Rüger & Richter 1979) Yoon et al. 2001JC08
| PeptoniphilusJC08
| |--P. asaccharolyticus (Distaso 1912) Ezaki et al. 2001JC08
| |--P. harei (Murdoch et al. 1997) Ezaki et al. 2001JC08
| |--P. indolicus (Christiansen 1934) Ezaki et al. 2001JC08
| `--P. ivorii (Murdoch et al. 1997) Ezaki et al. 2001JC08
| Nitrosolobus multiformisPHK96
| Candidatus Saccharobacterium [Saccharobacteria]RS13
| `--S. alaburgensisRS13
| Liberobacter asiaticumBJ02
| Candidatus Hodgkinia cicadicolaVLM14
| Candidatus Sulcia muelleriVLM14
| Thermanaerovibrio acidaminovoransWK13
| CarboxydobrachiumC-S02
| Megamonas hypermegas [=Bacteroides hypermegas]LHA02
| Arthromitus Leidy 1849 (n. d.) [incl. Microeccrina Maessen 1955, Microtrichella Maessen 1955]KC01
| Mylitta Fr. 1825 (n. d.)KC01
| Nigrococcus Castell. & Chalm. 1919KC01
| Schizotorulopsis Cif. 1930 (n. d.) [=Schizotorula (l. c.)]KC01
| Betabacterium vermiformeKC01
| Longibacillus elektroniP92
`--+--Synergistes Allison, Mayberry et al. 1993VP GH01 (see below for synonymy)
| `--S. jonesii Allison, Mayberry et al. 1993VP GH01
`--+--Candidatus Caldatribacterium [Atribacteria]RS13
| `--C. californienseRS13
`--+--+--Candidatus Fervidibacter [Fervidibacteria]RS13
| | `--F. sacchariRS13
| `--+--CaldisericaRS13
| `--Dictyoglomus [Dictyoglomaceae, Dictyoglomales, Dictyoglomi]WK13
| |--D. thermophilumRS13
| `--D. turgidumWK13
`--+--Kosmotoga oleariaWK13
|--Candidatus Acetothermum [Acetothermia]RS13
| `--A. autotrophicumRS13
`--Thermotogae [Thermotogota]CD21
`--Mesoaciditoga [Mesoaciditogaceae, Mesoaciditogales]CD21
`--M. lauensisCD21

Life incertae sedis:
Animikiea Barghoorn 1965G79
`--*A. septata Barghoorn 1965G79
Antigus Butin 1959G79
`--*A. cusarandicus Butin 1959G79
Archaeogloeocapsa Reitlinger 1956G79
`--*A. povarovkensis Reitlinger 1956G79
Archaeonema Schopf 1968G79
`--*A. longicellularis Schopf 1968G79
Archaeorestis Barghoorn 1965G79
`--*A. schreiberensis Barghoorn 1965G79
Archaeosphaeroides Schopf & Barghoorn 1967G79
`--*A. barbertonensis Schopf & Barghoorn 1967G79
Archaeotrichion Schopf 1968G79
`--*A. contortum Schopf 1968G79
Calyptothrix Schopf 1968G79
`--*C. annulata Schopf 1968G79
‘Catinella’ Pflug 1966 nec Pease 1870 (ICZN) nec Stache 1877 (ICZN) nec Boud. 1907 nec Kirschst. 1924G79
`--*C. polymorpha Pflug 1966G79
Cephalophytarion Schopf 1968G79
`--*C. grande Schopf 1968G79
Chlamydomonopsis Edhorn 1973G79
`--*C. primordialis Edhorn 1973G79
Contortothrix Schopf 1968G79
`--*C. vermiformis Schopf 1968G79
Cumulosphaera Edhorn 1973G79
`--*C. lamellosa Edhorn 1973G79
Cyanonema Schopf 1968G79
`--*C. attenuata Schopf 1968G79
Entosphaeroides Barghoorn 1965G79
`--*E. amplus Barghoorn 1965G79
Eoastrion Barghoorn 1965G79
`--*E. simplex Barghoorn 1965G79
Eobacterium Barghoorn & Schopf 1966G79
`--*E. isolatum Barghoorn & Schopf 1966G79
Eoepiphyton Butin 1959G79
`--*E. jalgamicum Butin 1959G79
Eosphaera Barghoorn 1965G79
`--*E. tyleri Barghoorn 1965G79
Fibularix Pflug 1965G79
`--*F. funicula Pflug 1965G79
Filamentella Pflug 1965G79
`--*F. plurima Pflug 1965G79
Filiconstrictosus Schopf & Blacic 1971G79
`--*F. majusculus Schopf & Blacic 1971G79
Halythrix Schopf 1968G79
`--*H. nodosa Schopf 1968G79
Heliconema Schopf 1968G79
`--*H. australiensis Schopf 1968G79
Millaria Pflug 1966G79
`--*M. implexa Pflug 1966G79
Montanella Pflug 1965G79
`--*M. beltensis Pflug 1965G79
Obconiphycus Schopf & Blacic 1971G79
`--*O. amadeus Schopf & Blacic 1971G79
Palaeoanacystis Schopf 1968G79
`--*P. vulgaris Schopf 1968G79
Palaeolyngbya Schopf 1968G79
`--*P. barghoorniana Schopf 1968G79
Palaeomicrocoleus Korde in Vologdin & Korde 1965G79
`--*P. gruneri Korde in Vologdin & Korde 1965G79
Palaeorivularia Korde 1965G79
`--*P. ontarica Korde 1965G79
Palaeoscytonema Edhorn 1973G79
`--*P. moorhousei Edhorn 1973G79
Palaeospiralis Edhorn 1973G79
`--*P. canadensis Edhorn 1973G79
Palaeospirulina Edhorn 1973G79
`--*P. arcuata Edhorn 1973G79
Partitiofilum Schopf & Blacic 1971G79
`--*P. gongyloides Schopf & Blacic 1971G79
Petraphera Nagy 1974G79
`--*P. vivescenticula Nagy 1974G79
Phanerosphaerops Schopf & Blacic 1971G79
`--*P. capitaneus Schopf & Blacic 1971G79
Primorivularia Edhorn 1973G79
`--*P. thunderbayensis Edhorn 1973G79
Protorivularia Butin 1959G79
`--*P. onega Butin 1959G79
Scintilla Pflug 1966 non Deshayes 1855 (ICZN)G79
`--*S. perforata Pflug 1966G79
Tenuofilum Schopf 1968G79
`--*T. septatum Schopf 1968G79
Tricellaria Pflug 1965G79
`--*T. deylensis Pflug 1965G79
Veteronostocale Schopf & Blacic 1971G79
`--*V. amoenum Schopf & Blacic 1971G79
Zosterosphaera Schopf 1968G79
`--*Z. tripunctata Schopf 1968G79
Agamus Vologdin 1970G79
`--*A. shungiticus Vologdin 1970G79
Aseptalia Vologdin in Vologdin & Strygin 1969G79
`--*A. ukrainica Vologdin in Vologdin & Strygin 1969G79
Asterosphaeroides Reitlinger 1959G79
Conferta Klinger 1968G79
`--*C. rara Klinger 1968G79
Crenulata Bertrand-Sarfati 1972G79
`--*C. gigantea Bertrand-Sarfati 1972G79
Foninia Korde 1973G79
`--*F. fasciculata Korde 1973G79
Globoidella Milstein 1970G79
`--*G. jusmastachica Milstein 1970G79
Gonamophyton Vologdin & Drozdova 1964G79
`--*G. ovale Vologdin & Drozdova 1964G79
Gorlovella Vologdin 1970G79
`--*G. obvoluta Vologdin 1970G79
Ladogaella Vologdin 1967G79
`--*L. variabilis Vologdin 1967G79
Marenita Korde 1973G79
`--*M. kundatica Korde 1973G79
Medullarites Narozhnykh in Narozhnykh & Rabotnov 1965G79
Nelcanella Vologdin & Drozdova 1964G79
`--*N. stellata Vologdin & Drozdova 1964G79
Protospira Vologdin in Vologdin & Strygin 1969 non Ruedemann 1916 (ICZN)G79
`--*P. strygini Vologdin in Vologdin & Strygin 1969G79
Ptilophyton Vologdin 1967G79
`--*P. makarovae Vologdin 1967G79
‘Vermiculites’ Reitlinger 1959 nec Bronn 1848 nec Rouault 1850G79
Vermiculus Bertrand-Sarfati 1972G79
`--*V. contortus Bertrand-Sarfati 1972G79
Vesicophyton Vologdin in Vologdin & Drozdova 1969G79
`--*V. punctatum Vologdin in Vologdin & Drozdova 1969G79
Idasola washingtoniaRK92
Caldocellum saccharolyticumCM92
Butyribacterium methylotrophicumD92
Propionispira arborisE92
|--A. proterozoicusAP68
`--A. stratusAP68
Alternia altaicaAP68
Palaeomicrocystis uzasensisAP68
Glebosites gentilisAP68
Archaeospongia radiataAP68
|--C. pristinaEB93
`--C. tetrasEB93
Latisphaera wrightii Licari 1978EB93
Palaeosiphonella cloudii Licari 1978EB93
Agonium Oerst. 1844KC01
Algacites Schloth. 1825KC01
Amphiconium Nees 1816 (n. d.)KC01
Capillaria Roussel 1806KC01
Centrospora Trevis. 1845KC01
Cerasterias Reinsch 1867 (n. d.)KC01
Chaetopeltis Berthold 1878KC01
Chionaster Wille 1903 (n. d.)KC01
Chlamydotomus Trevis. 1879 (n. d.)KC01
Chondrostroma Gürich 1906KC01
Ciliaria Stackh. 1809KC01
Eomyces Ludw. 1894 (n. d.)KC01
Granulocystis Hindák 1977KC01
Protonema [incl. Herpotrichum]KC01
Hyalinia Stackh. 1809KC01
Hyalochlorella Poyton 1970 (n. d.)KC01
Lemania Bory 1824KC01
Lepocolla Eklund 1883 (n. d.)KC01
Libellus Cleve 1873KC01
Marssoniella Lemmerm. 1900KC01
Micropyxis Duby 1930KC01
Moelleria Scop. 1777KC01
Myxonema Fr. 1825KC01
Naegeliella Correns 1892KC01
Nematonostoc Nyl. ex Elenkin 1934KC01
Neoplectana glaseriKC01
Pericystis Agardh 1847KC01
Phaeococcus Borzí 1892KC01
Phyllocardium Korshikov 1927KC01
Pila Bertrand & Renault 1892 nec Klein 1758 (ICZN) nec Röding 1798 (ICZN)KC01
Plocaria Nees 1820 (nom. rej.)KC01
Porodiscus Grev. 1863KC01
Pringsheimiella Höhn. 1920KC01
Pseudospora Schiffn. 1931 non Cienkowski 1865 (ICZN)KC01
Ramulina Thurm. 1863KC01
Rhabdium Wallr. 1833KC01
Schizospora Reinsch 1875KC01
Sirosiphon Kütz. 1843KC01
Sphaerella Sommerf. 1824KC01
Spiralia Toula 1900KC01
Syncoelium Wallr. 1833KC01
Torulopsidosira Geitler 1955KC01
Trichocladia Harv. 1836KC01
Trichodiscus Welsford 1912 non Strebel 1880 (ICZN)KC01
Tubularia Roussel 1806 non Linnaeus 1758 (ICZN)KC01
Vesicularia Micheli ex Targ. Tozz. 1826KC01
Woronichina Elenkin 1933KC01
Wrightiella Schmitz 1893KC01
Pelotomaculum schinkiiIN20
Leucophora conflictorG20
|--T. cometaG20
`--T. solG20
Kerone haustellumG20
Ovulites margaritulaG20
Orbulites complanataG20
Rubribacterium Boldareva et al. 2010VP IJSEM10b
`--*R. polymorphum Boldareva et al. 2010VP IJSEM10b
Ameyamaea Yukphan et al. 2010VP IJSEM10a
`--*A. chiangmaiensis Yukphan et al. 2010VP IJSEM10a
Desulfurispirillum Sorokin et al. 2010VP IJSEM10a
`--*D. alkaliphilum Sorokin et al. 2010VP IJSEM10a

Bacteria [Anoxyphotobacteria, Didermata, Endobacteria, Eubacteria, Eubacteriales, Eurybacteria, Exoflagellata, Ferrobacteria, Firmibacteria, Geobacteria, Geovibriales, Glycobacteria, Lipobacteria, Mastigomonera, Myxomonera, Negibacteria, Nitrobacteraceae, Photobacteria, Photomonera, Pimelobacteria, Posibacteria, Protobacteria, Schizomycetes, Schyzomycophyta, Togobacteria]SS15

LIFE [Algae, Chlorospermeae, Cryptogamia, Microsporae, Monades, Monera, Monodermata, Monophytes, Mychota, Procaryotae, Prokarya, Prokaryota, Prokaryotae, Scotobacteria, Thallophyta, Unibacteria]

Neomura [Archaea, Archaebacteria, Archaeobacteria, Eurytherma, Eurythermea, Mendosicutes, Metabacteria, Sulfobacteria]C-S02

Synergistes Allison, Mayberry et al. 1993VP GH01 [Synergistales, SynergistetesRS13, Synergistia, Synergistota]

*Type species of generic name indicated


[AP68] Afonin, A. I., & A. G. Pospelov. 1968. Novye dannye po stratigraphii verhnego Proterozoâ v severnoj časti Gornogo Altaâ (Katunskij Gorst). In: Selâtickij, G. A., I. P. Maksimov, Û. K. Mironov, I. M. Mârkov, N. G. Rožok, M. G. Rusakov, Û. D. Skobelev, L. D. Staroverov & A. N. Suharina (eds) Novye Dannye po Geologii i Poleznym Iskopaemym Zapadnoj Sibiri vol. 3 pp.70–76 . Izdatel’stvo Tomskogo Universiteta: Tomsk.

[BJ07] Bailey, J. V., S. B. Joye, K. M. Kalanetra, B. E. Flood & F. A. Corsetti. 2007. Evidence of giant sulphur bacteria in Neoproterozoic phosphorites. Nature 445: 198–201.

[BJ02] Becnel, J. J., A. Jeyaprakash, M. A. Hoy & A. Shapiro. 2002. Morphological and molecular characterization of a new microsporidian species from the predatory mite Metaseiulus occidentalis (Nesbitt) (Acari, Phytoseiidae). Journal of Invertebrate Pathology 79: 163–172.

Brochier, C., S. Gribaldo, Y. Zivanovic, F. Confalonieri & P. Forterre. 2005. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biology 6: R42.

[C-S02] Cavalier-Smith, T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. International Journal of Systematic and Evolutionary Microbiology 52: 7–76.

[CD21] Coleman, G. A., A. A. Davín, T. A. Mahendrarajah, L. L. Szánthó, A. Spang, P. Hugenholtz, G. J. Szöllősi & T. A. Williams. 2021. A rooted phylogeny resolves early bacterial evolution. Science 372: 588.

[CM92] Coughlan, M. P., & F. Mayer. 1992. The cellulose-decomposing bacteria and their enzyme systems. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 460–516. Springer-Verlag: New York.

[D92] Diekert, G. 1992. The acetogenic bacteria. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 517–533. Springer-Verlag: New York.

[E92] Eady, R. R. 1992. The dinitrogen-fixing bacteria. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 534–553. Springer-Verlag: New York.

[EB93] Edwards, D., J. G. Baldauf, P. R. Brown, K. J. Dorning, M. Feist, L. T. Gallagher, N. Grambast-Fessard, M. B. Hart, A. J. Powell & R. Riding. 1993. ‘Algae’. In: Benton, M. J. (ed.) The Fossil Record 2 pp. 15–40. Chapman & Hall: London.

Forterre, P., C. Brochier & H. Philippe. 2002. Evolution of the Archaea. Theoretical Population Biology 61 (4): 409–422.

[GH01] Garrity, G. M., & J. G. Holt. 2001. Phylum BVIII. Nitrospirae phy. nov. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 451–464. Springer.

[G02] Giribet, G. 2002. Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion? Molecular Phylogenetics and Evolution 24: 345–357.

[G79] Glaessner, M. F. 1979. Precambrian. In: Robison, R. A., & C. Teichert (eds) Treatise on Invertebrate Paleontology pt A. Introduction. Fossilisation (Taphonomy), Biogeography and Biostratigraphy pp. A79–A118. The Geological Society of America, Inc.: Boulder (Colorado), and The University of Kansas: Lawrence (Kansas).

[G20] Goldfuss, G. A. 1820. Handbuch der Naturgeschichte vol. 3. Handbuch der Zoologie pt 1. Johann Leonhard Schrag: Nürnberg.

[HH02] Huber, H., M. J. Hohn, R. Rachel, T. Fuchs, V. C. Wimmer & K. O. Stetter. 2002. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417: 63–67.

[IJSEM02] IJSEM. 2002. Validation list no. 85. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. International Journal of Systematic and Evolutionary Microbiology 52: 685–690.

[IJSEM03] IJSEM. 2003. Validation list no. 89. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. International Journal of Systematic and Evolutionary Microbiology 53: 1–2.

[IJSEM04] IJSEM. 2004. Validation list no. 95. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. International Journal of Systematic and Evolutionary Microbiology 54: 1–2.

[IJSEM10a] IJSEM. 2010a. Validation list no. 131. List of new names and new combinations previously effectively, but not validly, published. International Journal of Systematic and Evolutionary Microbiology 60 (1): 1–2.

[IJSEM10b] IJSEM. 2010b. Validation list no. 132. List of new names and new combinations previously effectively, but not validly, published. International Journal of Systematic and Evolutionary Microbiology 60: 469–472.

[IN20] Imachi, H., M. K. Nobu, N. Nakahara, Y. Morono, M. Ogawara, Y. Takaki, Y. Takano, K. Uematsu, T. Ikuta, M. Ito, Y. Matsui, M. Miyazaki, K. Murata, Y. Saito, S. Sakai, C. Song, E. Tasumi, Y. Yamanaka, T. Yamaguchi, Y. Kamagata, H. Tamaki & K. Takai. 2020. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 577: 519–525.

[JC08] Judicial Commission of the International Committee on Systematics of Prokaryotes. 2008. Status of strains that contravene Rules 27 (3) and 30 of the International Code of Nomenclature of Bacteria. Opinion 81. International Journal of Systematic and Evolutionary Microbiology 58: 1755–1763.

[KC01] Kirk, P. M., P. F. Cannon, J. C. David & J. A. Stalpers. 2001. Ainsworth & Bisby’s Dictionary of the Fungi 9th ed. CAB International: Wallingford (UK).

[LHA02] Lan, G. Q., Y. W. Ho & N. Abdullah. 2002. Mitsuokella jalaludinii sp. nov., from the rumens of cattle in Malaysia. International Journal of Systematic and Evolutionary Microbiology 52: 713-718.

Lienau, E. K., R. DeSalle, M. Allard, E. W. Brown, D. Swofford, J. A. Rosenfeld, I. N. Sarkar & P. J. Planet. 2010. The mega-matrix tree of life: using genome-scale horizontal gene transfer and sequence evolution data as information about the vertical history of life. Cladistics 26 (1): 1–11.

[P92] Poinar, G. O., Jr. 1992. Life in Amber. Stanford University Press: Stanford.

[PHK96] Prescott, L. M., J. P. Harley & D. A. Klein. 1996. Microbiology 3rd ed. Wm. C. Brown Publishers: Dubuque (Iowa).

[RS13] Rinke, C., P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson, J.-F. Cheng, A. Darling, S. Malfatti, B. K. Swan, E. A. Gies, J. A. Dodsworth, B. P. Hedlund, G. Tsiamis, S. M. Sievert, W.-T. Liu, J. A. H. Eisen, S. J., N. Kyrpides, C., R. Stepanauskas, E. M. Rubin, P. Hugenholtz & T. Woyke. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431–437.

[RK92] Robertson, L. A., & J. G. Kuenen. 1992. The colorless sulfur bacteria. In: Balows, A., H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer (eds) The Prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications 2nd ed. vol. 1 pp. 385–413. Springer-Verlag: New York.

[SS15] Spang, A., J. H. Saw, S. L. Jørgensen, K. Zaremba-Niedzwiedzka, J. Martijn, A. E. Lind, R. van Eijk, C. Schleper, L. Guy & T. J. G. Ettema. 2015. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521: 173–179.

[T84] Tewari, V. C. 1984. Stromatolites and Precambrian–Lower Cambrian biostratigraphy of the Lesser Himalaya. Proc. Vth India Geophytol. Conf., Lucknow (1983), Spec. Publ. 1984: 71–97.

[VLM14] Van Leuven, J. T., R. C. Meister, C. Simon & J. P. McCutcheon. 2014. Sympatric speciation in a bacterial endosymbiont results in two genomes with the functionality of one. Cell 158: 1270–1280.

[WK13] Williams, K. P., & D. P. Kelly. 2013. Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. International Journal of Systematic and Evolutionary Microbiology 63 (8): 2901–2906.

[X04] Xiao, S. 2004. New multicellular algal fossils and acritarchs in Doushantuo chert nodules (Neoproterozoic; Yangtze Gorges, south China). Journal of Paleontology 78 (2): 393–401.

[Z-NC17] Zaremba-Niedzwiedzka, K., E. F. Caceres, J. H. Saw, D. Bäckström, L. Juzokaite, E. Vancaester, K. W. Seitz, K. Anantharaman, P. Starnawski, K. U. Kjeldsen, M. B. Stott, T. Nunoura, J. F. Banfield, A. Schramm, B. J. Baker, A. Spang & T. J. G. Ettema. 2017. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541: 353–358.

Leave a comment

Your email address will not be published. Required fields are marked *