A widespread coral-infecting apicomplexan with chlorophyll biosynthesis genes

Abstract

Apicomplexa is a group of obligate intracellular parasites that includes the causative agents of human diseases such as malaria and toxoplasmosis. Apicomplexans evolved from free-living phototrophic ancestors, but how this transition to parasitism occurred remains unknown. One potential clue lies in coral reefs, of which environmental DNA surveys have uncovered several lineages of uncharacterized basally branching apicomplexans1,2. Reef-building corals have a well-studied symbiotic relationship with photosynthetic Symbiodiniaceae dinoflagellates (for example, Symbiodinium³), but the identification of other key microbial symbionts of corals has proven to be challenging4,5. Here we use community surveys, genomics and microscopy analyses to identify an apicomplexan lineage—which we informally name ‘corallicolids’—that was found at a high prevalence (over 80% of samples, 70% of genera) across all major groups of corals. Corallicolids were the second most abundant coral-associated microeukaryotes after the Symbiodiniaceae, and are therefore core members of the coral microbiome. In situ fluorescence and electron microscopy confirmed that corallicolids live intracellularly within the tissues of the coral gastric cavity, and that they possess apicomplexan ultrastructural features. We sequenced the genome of the corallicolid plastid, which lacked all genes for photosystem proteins; this indicates that corallicolids probably contain a non-photosynthetic plastid (an apicoplast⁶). However, the corallicolid plastid differs from all other known apicoplasts because it retains the four ancestral genes that are involved in chlorophyll biosynthesis. Corallicolids thus share characteristics with both their parasitic and their free-living relatives, which suggests that they are evolutionary intermediates and implies the existence of a unique biochemistry during the transition from phototrophy to parasitism.

Full text

LETTER https://doi.org/10.1038/s41586-019-1072-z
A widespread coral-infecting apicomplexan with
chlorophyll biosynthesis genes
Waldan K. Kwong1*, Javier del Campo1, Varsha Mathur1, Mark J. A. Vermeij2,3 & Patrick J. Keeling1
Apicomplexa is a group of obligate intracellular parasites that
includes the causative agents of human diseases such as malaria
and toxoplasmosis. Apicomplexans evolved from free-living
phototrophic ancestors, but how this transition to parasitism
occurred remains unknown. One potential clue lies in coral reefs,
of which environmental DNA surveys have uncovered several
lineages of uncharacterized basally branching apicomplexans1,2.
Reef-building corals have a well-studied symbiotic relationship
with photosynthetic Symbiodiniaceae dinoflagellates (for example,
Symbiodinium3), but the identification of other key microbial
symbionts of corals has proven to be challenging4,5. Here we
use community surveys, genomics and microscopy analyses to
identify an apicomplexan lineage—which we informally name
‘corallicolids’—that was found at a high prevalence (over80%
of samples, 70% of genera) across all major groups of corals.
Corallicolids were the second most abundant coral-associated
microeukaryotes after the Symbiodiniaceae, and are therefore
core members of the coral microbiome. In situ fluorescence and
electron microscopy confirmed that corallicolids live intracellularly
within the tissues of the coral gastric cavity, and that they possess
apicomplexan ultrastructural features. We sequenced the genome
of the corallicolid plastid, which lacked all genes for photosystem
proteins; this indicates that corallicolids probably contain a non-
photosynthetic plastid (an apicoplast
6
). However, the corallicolid
plastid differs from all other known apicoplasts because it retains the
four ancestral genes that are involved in chlorophyll biosynthesis.
Corallicolids thus share characteristics with both their parasitic and
their free-living relatives, which suggests that they are evolutionary
intermediates and implies the existence of a unique biochemistry
during the transition from phototrophy to parasitism.
Apicomplexan parasites rely on highly specialized systems to infect
animal cells, live within those cells and evade host defences. Recently,
it has come to light that these parasites evolved from phototrophic
ancestors. Most apicomplexans have been found to retain relict plast-
ids6, and two photosynthetic ‘chromerids’ (Chromera velia and Vitrella
brassicaformis) isolated from coral reef environments have been found
to be the closest free-living relatives to the parasitic Apicomplexa
7–9
.
The finding that thephotosynthetic relatives of apicomplexans are
somehow linked to coral reefs has prompted a major re-evaluation of
the ecological conditions and symbiotic associations that drove the
evolution of parasitism in this clade2,10–12. Corals (class Anthozoa)
have not traditionally been considered a common host for apicompl-
exans: sporadic reports over the last 30 years include the morphological
description of a single coccidian (Gemmocystis cylindrus) from histo-
logical sections of eight Caribbean coral species
13
, and the detection
of 18S rRNA gene sequencesof apicomplexans (known as the ‘type-N’
apicomplexan) in Caribbean, Australian and Red Sea corals
14–16
. Plastid
16S rRNA gene surveys have also revealed that a number of uncharac-
terized apicomplexan-related lineages (notably, the ‘ARL-V’ lineage)
are closely associated with reefs worldwide
1,2
. These lineages appear
to occupy a phylogenetic position that is intermediate between the
obligate parasitic Apicomplexa and the free-living chromerids, which
makes them promising candidates for studying the transition between
these different lifestyles.
To address evolutionary questions surrounding the transitional
steps to parasitism, and to reconcile thecurrently incomparable data
on the extent of apicomplexan diversity in corals, we sampled diverse
anthozoan species from around the island of Curaçao in the south-
ern Caribbean and surveyed the composition of their eukaryotic and
prokaryotic microbial communities (Supplementary Table1). From a
total of 43 samples that represent 38 coral species, we recovered api-
complexan type-N 18S rRNA genes (putatively encoded by the nucleus)
and ARL-V 16S rRNA genes (putatively encoded by the plastid) from
62% and 84% of samples, respectively (Fig.1a, Supplementary Table2).
The type-N genes were only detected in corals that were also posi-
tive for ARL-V, which suggests that they come from the same organ-
ism; the high abundance of Symbiodiniaceae probably depressed our
detection of the type-N apicomplexan. Excluding Symbiodiniaceae,
type-N apicomplexanswere the most common microbial eukaryote
detected in corals, comprising 2.1% of the total sequence reads (56%
of all non-Symbiodiniaceae reads). No other apicomplexan-related lin-
eage was present, except for six reads of Vitrella 16S rRNA in a single
sample. We also searched 31 publically available coral metagenomic
and metatranscriptomic datasets that collectively amount to 15.8Gb
of assembled sequence (Supplementary Table3). Sequences that
correspond to rRNAs from type-N and ARL-V were present in 27 and
12 datasets, respectively (Fig.1b); the discrepancy probably reflects
the lower copy number of plastid rRNA genes. We further identified
a suite of organelle-derived protein-coding genes (see below), and
for each gene we found only a single apicomplexan sequence type
to be predominant (Fig.1b, Extended Data Fig.1). All of these data
are consistent with the presence of a single dominant apicomplexan
lineage in corals, for which we propose the name corallicolids (meaning
‘coral-dwellers’, from Latin corallium combined with the suffix –cola,
derived from the Latin incola). Our results indicate that this is the sec-
ond most abundant microeukaryote that lives in association with coral,
after the Symbiondiniaceae.
The high prevalence of corallicolids in wild corals is suggestive of
a tight symbiosis (defined as two organisms that engage in long-term
interactions), across a broad diversity of coral species. To test the host
range of this symbiosis, we analysed 102 commercial aquarium samples
that represented at least 61 species from across the major clades
of Anthozoa. We detected corallicolid 18S rRNA genes in 53% of
aquarium samples, including in soft-bodied octocorals, zoanthids,
anemones and corallimorphs (Fig.1c). Combined with existing
data from wild corals (Supplementary Table4), corallicolids were
found in 1,271 of 1,546 samples (82% prevalence) and in 43 outof
62 host genera (70%), from all parts of the anthozoan phylogeny
that we have examined thus far. Ecologically, the distribution of
corallicolids is highly restricted: we searched large-scale 18S rRNA
datasets from various terrestrial and marine ecosystems (1,014 sam-
ples, 837 million sequence reads), and found that type-N was almost
1Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada. 2Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam,
Amsterdam, The Netherlands. 3CARMABI Foundation, Willemstad, Curaçao, The Netherlands. *e-mail: waldankwong@gmail.com
4 APRIL 2019 | VOL 568 | NATURE | 103