Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes

Abstract

Almost all eukaryote life forms have now been placed within one of five to eight supra-kingdom-level groups using molecular phylogenetics1–4. The ‘phylum’ Hemimastigophora is probably the most distinctive morphologically defined lineage that still awaits such a phylogenetic assignment. First observed in the nineteenth century, hemimastigotes are free-living predatory protists with two rows of flagella and a unique cell architecture5–7; to our knowledge, no molecular sequence data or cultures are currently available for this group. Here we report phylogenomic analyses based on high-coverage, cultivation-independent transcriptomics that place Hemimastigophora outside of all established eukaryote supergroups. They instead comprise an independent supra-kingdom-level lineage that most likely forms a sister clade to the ‘Diaphoretickes’ half of eukaryote diversity (that is, the ‘stramenopiles, alveolates and Rhizaria’ supergroup (Sar), Archaeplastida and Cryptista, as well as other major groups). The previous ranking of Hemimastigophora as a phylum understates the evolutionary distinctiveness of this group, which has considerable importance for investigations into the deep-level evolutionary history of eukaryotic life—ranging from understanding the origins of fundamental cell systems to placing the root of the tree. We have also established the first culture of a hemimastigote (Hemimastix kukwesjijk sp. nov.), which will facilitate future genomic and cell-biological investigations into eukaryote evolution and the last eukaryotic common ancestor. Phylogenetic analyses based on single-cell transcriptomic data from two hemimastigotes, a Spironema species and the newly described Hemimastix kukwesjijk, indicate that Hemimastigophora is a supra-kingdom-level lineage of eukaryotes.

Full text

LETTER https://doi.org/10.1038/s41586-018-0708-8
Hemimastigophora is a novel supra-kingdom-level
lineage of eukaryotes
Gordon Lax1,4, Yana Eglit1,4, Laura Eme2,3,4, Erin M. Bertrand1, Andrew J. Roger2 & Alastair G. B. Simpson1*
Almost all eukaryote life forms have now been placed within
one of five to eight supra-kingdom-level groups using molecular
phylogenetics1–4. The ‘phylum’ Hemimastigophora is probably
the most distinctive morphologically defined lineage that still
awaits such a phylogenetic assignment. First observed in the
nineteenth century, hemimastigotes are free-living predatory
protists with two rows of flagella and a unique cell architecture
5–7
;
to our knowledge, no molecular sequence data or cultures are
currently available for this group. Here we report phylogenomic
analyses based on high-coverage, cultivation-independent
transcriptomics that place Hemimastigophora outside of all
established eukaryote supergroups. They instead comprise an
independent supra-kingdom-level lineage that most likely forms a
sister clade to the ‘Diaphoretickes’ half of eukaryote diversity (that
is, the ‘stramenopiles, alveolates and Rhizaria’ supergroup (Sar),
Archaeplastida and Cryptista, as well as other major groups). The
previous ranking of Hemimastigophora as a phylum understates the
evolutionary distinctiveness of this group, which has considerable
importance for investigations into the deep-level evolutionary
history of eukaryotic life—ranging from understanding the origins
of fundamental cell systems to placing the root of the tree. We have
also established the first culture of a hemimastigote (Hemimastix
kukwesjijk sp. nov.), which will facilitate future genomic and cell-
biological investigations into eukaryote evolution and the last
eukaryotic common ancestor.
We identified two previously undescribed species of the rarely
observed protist group Hemimastigophora (one Spironema and one
Hemimastix) in enrichments from soil. Here we formally describe the
newly identified Hemimastix species.
Hemimastix Foissner, Blatterer & Foissner 1988
Hemimastix kukwesjijk Eglit and Simpson, sp. nov.
Etymology. Kukwesjijk (approximate pronunciation, ‘ku–ga–wes–jij–
k’). ‘Kukwes-’ (Mi’kmaq), a rapacious, hairy ogre from the traditions
of the Mi’kmaq First Nation of Nova Scotia; ‘-jijk’, a diminutive
plural suffix. ‘Little ogres’ reflects the predatory and hairy nature of
this microorganism, and the use of Mi’kmaq language and tradition
acknowledges the region in which the species was isolated.
Type material. The name-bearing hapantotype consists of trophic cells
and dividing cells of strain BW2H that are osmium-fixed, sputter-coated
and mounted for scanning electron microscopy. This material is deposited
with the American Museum of Natural History (New York) with accession
code AMNH_IZC 00267132. This material also contains prey Spumella
sp. (Stramenopiles) and uncharacterized prokaryotes, both of which are
explicitly excluded from the hapantotype.
Description. Hemimastix species, 16.5–20.5-μm long with 17–19
flagella per row.
Type locality. Bluff Wilderness Trail, Nova Scotia, Canada
(44.6610154°N, 63.7674669°W); soil from mixed-species woodland.
Gene sequence. The partial small subunit ribosomal RNA (SSU
rRNA) gene sequence of strain BW2H has been deposited in GenBank,
accession code MF682191.
Comments. Cells are larger and have several more flagella than
Hemimastix amphikineta, the only previously described species
(14-μm by 7-μm cell body, 12 flagella per row6).
Cells of H. kukwesjijk are oval in profile with a blunt anterior
projection (the capitulum) and two rows of flagella along their
whole length (Fig.1b, Extended Data Fig.1). In cultivation as
strain BW2H, live cells were 16.5–20.5-μm long by 7–12.5-μm wide
(18.3 ± 1μm × 9.9 ± 1.2μm; n = 61), with a sub-central, rounded
nucleus and posterior contractile vacuole (Fig.1c). Each row of 17–19
flagella (mean 18.4; n = 25) lay in a channel between the two thick
thecal plates. The anteriormost 9 or 10 flagella were closely spaced,
and the rest emerged from separate notches in the underlying plate
(Fig.1b, e). The capitulum was bordered by the overlapping anterior
1Department of Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada. 2Centre for Comparative Genomics and
Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada. 3Present address: Department of Cell and Molecular Biology,
Science for Life Laboratory, Uppsala University, Uppsala, Sweden. 4These authors contributed equally: Gordon Lax, Yana Eglit, Laura Eme. *e-mail: alastair.simpson@dal.ca
cap.
ef
ab
cd
Fig. 1 | Micrographs of studied hemimastigotes. a, Spironema cf.
multiciliatum, cell 1 (of 4) isolated for transcriptomics. b–f, H. kukwesjijk,
cell 1 (of 2) isolated for transcriptomics (b); note the presence of the
capitulum (cap.). c, d, Cells from culture (strain BW2H); note the nucleus
and the contractile vacuole at the posterior (c), and feeding on prey
with the capitulum (d). e, General view of cell (strain BW2H), anterior
with the capitulum to right. f, Detail of the capitulum, showing caps
of undischarged extrusomes (arrowheads) and close-spaced flagella in
anterior part of flagellar rows. a–d, Differential interference contrast light
microscopy. e, f, Scanning electron microscopy. Scale bars, 10μm (a), 5μm
(b–e; scale bar in b applies to images b–d), 1μm (f).
410 | NATURE | VOL 564 | 20/27 DECEMBER 2018
© 2018 Springer Nature Limited. All rights reserved.