Pawlowski BMC Biology 2013, 11:40

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10th anniversary

A N N I V E R S A R Y U P D AT E Open Access

The new micro-kingdoms of eukaryotes

Early metagenetic surveys of micro-eukaryotic diversity left as incertae sedis in the recently revised eukaryote
revealed numerous phylotypes that seemed unrelated to classification [2].
any described eukaryotic taxa. It has been proposed that What are these hypothetical novel eukaryotic micro-
some of them may represent novel kingdom-level kingdoms? First of all, many of them are not really new.
taxonomic diversity in eukaryotes. However, detailed For example, the genus Collodictyon was described 150
analysis of DNA sequences retrieved from environmental years ago but the diversity and evolutionary importance
samples and assigned to these putative new kingdoms of Collodictyonidae have been investigated only recently
showed that most of them were undetected chimeras or [3]. The unclassified eukaryotic lineages represent a large
incorrectly placed fast-evolving phylotypes [1]. Since variety of forms and modes of life, from free-swimming
then, the number of new eukaryotic lineages revealed by or gliding biflagellated cells to amoeboflagellates or
environmental surveys grew exponentially, but the filopodia-bearing amoeboid cells. Some lineages have
question of how many of them deserve the highest cells covered with mineralized scales or spicules (Hapto­
taxonomic level has remained. phyta, Centrohelida) or organic thecae (Apusomona­di­
Over the past few years, reconstruction of deep dae, Rigidifilida). Few lineages are phototrophs and
eukaryote phylogeny focused on grouping various possess chloroplasts acquired as a result of the secondary
eukaryotic lineages into large monophyletic assemblages. symbiosis (Cryptophyta, some Haptophyta). Most of
Advances in phylogenomic studies led to the formation them are mixotrophs or heterotrophs, often bacteri­vor­
of four to seven supergroups (Figure 1). The classical ous, living in marine or freshwater environments. Only
multicellular kingdoms of animals and fungi are placed in one lineage (Breviatea) is amitochondriate and lives in
the supergroup Opisthokonta, while green plants together anaerobic conditions, but interestingly no group com­
with red algae form a supergroup of Archaeplastida. All prises parasitic species. With the exception of Hapto­
other supergroups are composed of typically unicellular phytes and Cryptophytes, all other lineages are repre­
eukaryotes: Amoebozoa comprise the lobose amoebae sented by very few described species, although their
and slime molds, Stramenopiles include among others environmental diversity may be quite large. For example,
diatoms, kelps, and oomycetes (previously classified as the genus Telonema, represented by only two described
fungi), Alveolata are composed of ciliates, dinoflagellates morphospecies, has seen its diversity explode with more
and parasitic apicomplexans (among which the causative than 20 phylotypes revealed by environmental study [4].
agents of malaria and toxoplasmosis), Rhizaria are Metagenetic studies played a key role in discovery and
dominated by amoeboid protists, such as foraminifera, assessment of the diversity of these putative micro-
radiolarians or filose amoebae, and heterotrophic flagel­ kingdoms. Two lineages (Picobiliphytes, Rappemonads)
lates with filose pseudopodia, and Excavata group are known exclusively from environmental sequence data
together euglenozoans, heterolobosean amoebae and [5,6]. Very little is known about their morphology and
some amitochondriate parasitic phyla (such as diplo­ cell characteristics and in some cases even the features
monads and parabasalids). However, with an increasing that seemed to be well established, like the presence of
amount of phylogenetic and metagenetic data available chloroplasts in Picobiliphytes, have been questioned based
for larger taxon sampling of eukaryote diversity, there on a single-cell genomic study [7]. Compared to some
was growing evidence that not all lineages could be other planktonic groups revealed by metagenetics, such as
placed inside the established supergroups. More than ten marine stramenopiles (MAST) or marine alveo­ lates
lineages were considered as of uncertain placement and (MALV) [8], the environmental diversity of novel lineages
seems relatively modest, though some of them have been
found to be quite diverse when specifically targeted [9].
*Correspondence: Jan.Pawlowski@unige.ch
Department of Genetics and Evolution, University of Geneva, 30, Quai Ernest The phylogenetic position of these lineages remained
Ansermet, Sciences 3, CH-1211 Geneva, Switzerland an unresolved conundrum, in spite of genomic and/or
© 2013 Pawlowski; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly cited.
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Katablepharidae

Figure 1. Deep phylogeny of eukaryotes showing the position of small eukaryotic lineages that branch outside the seven supergroups
(modified after Burki et al. [12]; drawings S Chraiti).

transcriptomic data available for most of the groups that these groupings is usually weak and there is no general
include cultivable species. A new supergroup, called consensus about their classification.
Hacrobia or CCTH has been created for some of these One of the most striking characteristics of these
orphan lineages [10,11], but later analyses did not support orphan lineages and the reason why it is so difficult to
this hypothetical grouping [12]. An up-to-date phylo­ place them in the eukaryotic tree is their extreme
genomic tree (Figure 1) shows 13 independent lineages genetic divergence. High genetic distances separating
branching in three paraphyletic assemblages placed at them from other supergroups suggest that they
the base of SAR assemblage grouping Stra­ meno­piles, represent the deepest eukaryotic lineages. Identifying
Alveolata and Rhizaria (Telonema, Hapto­phytes, Rappe­ and characterizing these deep lineages is essential for
mo­nads, Centrohelids), next to Archae­plastida (Glauco­ understanding the early evo­ lu­
tion of eukaryotes.
phytes, Picobiliphytes, Cryptophytes, Katablepharids), However, their number and diversity is difficult to
and close to Amoebozoa (Breviatea, Collodictyon, assess. It has been assumed that many new deep
Rigidifilida, Apusomonads, and Ancyro­monads). Phylo­ lineages will be revealed by next-generation sequencing
genetic relations between these lineages and the adjacent surveys of environmental diversity but their identifi­
supergroups are not well established. Some of them, like cation using short and standardized sequence tags [13]
Breviatea and Glaucophyta are included in Amoebozoa might not be straightforward. The single-cell genomic
and Archaeplastida, respectively. However, support for approach [7] may represent a much more efficient way
Pawlowski BMC Biology 2013, 11:40 Page 3 of 3
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multiple marine-freshwater colonizations. BMC Microbiol 2010, 10:168.

foundly changed as a result of phylogenetic and meta­ 6. Kim E, Harrison JW, Sudek S, Jones MD, Wilcox HM, Richards TA, Worden AZ,
genetic studies. The traditional oversimplified classifica­ Archibald JM: Newly identified and diverse plastid-bearing branch on the
eukaryotic tree of life. Proc Natl Acad Sci U S A 2011, 108:1496-1500.
tion of unicellular eukaryotes based on their mode of 7. Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, Wilson WH, Yang
locomotion or capacity to photosynthesize has been EC, Duffy S, Bhattacharya D: Single-cell genomics reveals organismal
replaced by a phylogenetically robust system of large, interactions in uncultivated marine protists. Science 2011, 332:714-717.
8. Logares R, Audic S, Santini S, Pernice MC, de Vargas C, Massana R: Diversity
monophyletic eukaryotic supergroups that originated patterns and activity of uncultured marine heterotrophic flagellates
more than 1 billion years ago. Still, relatively little is known unveiled with pyrosequencing. ISME J 2012, 6:1823-1833.
about the radiation of numerous small lineages that 9. Liu H, Probert I, Uitz J, Claustre H, Aris-Brosou S, Frada M, Not F, de Vargas C:
Extreme diversity in noncalcifying haptophytes explains a major pigment
preceded the divergence of these supergroups. The paradox in open oceans. Proc Natl Acad Sci U S A 2009, 106:12803-12808.
challenge of future eukaryotic research is to describe the 10. Okamoto N, Chantangsi C, Horák A, Leander BS, Keeling PJ: Molecular
vastness of this radiation and to determine the ecological phylogeny and description of the novel katablepharid Roombia truncata
gen. et sp. nov., and establishment of the Hacrobia taxon nov. PLoS One
and evolutionary importance of the new micro-kingdoms. 2009, 4:e7080.
11. Burki F, Inagaki Y, Brate J, Archibald JM, Keeling PJ, Cavalier-Smith T, Horak A,
Sakaguchi M, Hashimoto T, Klaveness D, Jakobsen KS, Pawlowski J, Shalchian-
This article is part of the BMC Biology tenth anniversary series. Other
Tabrizi K: Early evolution of eukaryotes: two enigmatic heterotrophic
articles in this series can be found at http://www.biomedcentral.com/ groups are related to photosynthetic chromalveolates. Genome Biol Evol
bmcbiol/series/tenthanniversary. 2009, 1:231-238.
12. Burki F, Okamoto N, Pombert JF, Keeling PJ: The evolutionary history of
haptophytes and cryptophytes: phylogenomic evidence for separate
origins. Proc Biol Sci 2012, 279:2246-2254.
Published: 15 April 2013
13. Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, Bowser SS, Cepicka I,
Decelle J, Dunthorn M, Fiore-Donno AM, Gile GH, Holzmann M, Jahn R, Jirků
References
M, Keeling PJ, Kostka M, Kudryavtsev A, Lara E, Lukeš J, Mann DG, Mitchell EA,
1. Berney C, Fahrni J, Pawlowski J: How many novel eukaryotic “kingdoms”?
Nitsche F, Romeralo M, Saunders GW, Simpson AG, Smirnov AV, Spouge JL,
Pitfalls and limitations of environmental DNA surveys. BMC Biol 2004, 2:13.
Stern RF, Stoeck T, et al.: CBOL Protist Working Group: Barcoding Eukaryotic
2. Adl SM, Simpson AG, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F,
Richness beyond the Animal, Plant, and Fungal Kingdoms. PLoS Biol 2012,
Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, Le Gall L, Lynn DH,
10:e1001419.
McManus H, Mitchell EA, Mozley-Stanridge SE, Parfrey LW, Pawlowski J,
Rueckert S, Shadwick L, Schoch CL, Smirnov A, Spiegel FW: The revised
classification of eukaryotes. J Eukaryot Microbiol 2012, 59:429-493.
3. Zhao S, Burki F, Bråte J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K: doi:10.1186/1741-7007-11-40
Collodictyon--an ancient lineage in the tree of eukaryotes. Mol Biol Evol Cite this article as: Pawlowski J: The new micro-kingdoms of eukaryotes.
2012, 29:1557-1568. BMC Biology 2013, 11:40.
4. Bråte J, Klaveness D, Rygh T, Jakobsen KS, Shalchian-Tabrizi K: Telonemia-
specific environmental 18S rDNA PCR reveals unknown diversity and