Cnidarians

Corals, and the symbiosis that makes a reef possible

A reef-building coral is not really one organism. It is a colony of genetically identical polyps sharing a skeleton, and every one of those polyps is packed with photosynthetic algae living inside its own cells. The animal contributes structure, nitrogen, and CO₂; the algae contribute most of the food. Nearly everything that stresses a coral stresses that partnership first.

1. Who they are

Phylum Cnidaria, class Anthozoa, order Scleractinia — the stony, reef-building corals. Cnidarians branched off before the split between protostomes and deuterostomes, making them the most distantly related of the lab’s study animals.

They are diploblastic: two tissue layers with a non-cellular mesoglea between them, not the three germ layers that bilaterians have. There is no brain, no heart, no blood, and no through-gut.

Species Why it appears
Stylophora pistillata The long-term ocean acidification and methylome work anchoring the foundational papers
Porites astreoides The reciprocal-transplant expression-plasticity work — the cleanest evidence that plasticity itself is the adaptive trait
Acropora spp. The first sequenced coral genus; fast-growing and thermally sensitive

2. Body plan

The polyp. A sac with a single opening ringed by tentacles. That opening is both mouth and anus, leading into the gastrovascular cavity, which is subdivided by sheets of tissue called mesenteries where digestion and gamete production occur.

Two layers. An outer epidermis and an inner gastrodermis, separated by mesoglea. The symbiotic algae live inside gastrodermal cells — intracellular, each in a host-derived membrane.

Coenosarc. The living tissue sheet connecting polyps across the colony surface. It is what makes a colony an integrated organism able to share resources, rather than a cluster of independent animals.

The skeleton and where it forms. Beneath the tissue sits the aragonite skeleton. Calcification happens at the calicoblastic epithelium, the tissue layer facing the skeleton, which secretes into a thin subcalicoblastic space between tissue and mineral. The coral is not calcifying in seawater — it is calcifying in a compartment whose chemistry it controls.

Corallite and calyx. Each polyp sits in a skeletal cup. Calyx dimensions, septal spacing, and skeletal porosity are all standard morphometric readouts in acidification experiments — they are how a chemical treatment becomes a measurable phenotype.

Nematocysts. The stinging organelles that name the phylum: pressurized capsules that fire on contact, used for prey capture and defense against neighbors.

TipWhy coral experiments have a design advantage

A colony can be cut into fragments that are all the same genet — genetically identical — and distributed across treatments. Genotype is held constant by construction, not by statistical adjustment.

This is why coral studies can make claims about environmental effects with a confidence that is hard to reach in oysters, where every individual is a different genotype. When you read “same-genet fragments distributed across pH treatments,” recognize it as a real strength of the design.

3. Life cycle

Corals reproduce sexually as broadcast spawners or brooders, and asexually by budding — which is how a colony grows and how fragmentation propagates a genet.

flowchart LR
  A["Spawning<br/>or brooding"] --> B["Planula larva"]
  B --> C["Settlement<br/>on cue"]
  C --> D["Primary polyp"]
  D --> E["Budding"]
  E --> F["Colony"]
  F -.-> A
  B -. "horizontal" .-> S["Symbiont<br/>acquisition"]
  A -. "vertical" .-> S
  S -.-> D

Many broadcast-spawning species release gametes in mass synchronized spawning events, with whole reefs spawning within a night or two, cued by lunar cycle, temperature, and sunset timing. Fertilization is external, producing a swimming planula larva.

Settlement is cue-driven — crustose coralline algae and specific bacterial biofilms are among the recognized signals. The settled larva becomes a primary polyp, and the colony grows from there by budding.

ImportantVertical vs. horizontal symbiont acquisition

Vertical: symbionts are passed directly into eggs or larvae, so offspring start life already partnered. Common in brooders.

Horizontal: larvae start symbiont-free and must acquire algae from the environment. Typical of broadcast spawners.

This matters for how fast a population’s symbiont community can shift. Horizontal acquisition means each generation re-samples what is locally available — a potential route to a more thermally tolerant partnership, and a reason not to treat host genotype as the only thing that determines a colony’s stress tolerance.

4. Physiology essentials

The symbiosis. Symbiodiniaceae — dinoflagellate algae, formerly all called Symbiodinium — live inside gastrodermal cells and translocate photosynthate to the host, often supplying the majority of its energy budget. This is what allows a reef to be spectacularly productive in nutrient-poor tropical water. The host reciprocates with CO₂, nitrogen, and a protected, well-lit position in the water column.

The partnership is established by phagocytosis — the host cell takes the alga up by the same mechanism it would use to engulf a microbe, and then does not digest it. Understanding why is one of the open questions in the field.

Heterotrophy. Corals also eat, capturing zooplankton with tentacles and nematocysts and taking up organic material via mucus. Photosynthate is not the whole story, and heterotrophic feeding capacity affects how well a colony survives bleaching.

Calcification. Aragonite is deposited at the calicoblastic layer. Calcification is typically light-enhanced — it runs faster when the symbionts are photosynthesizing, which couples skeletal growth to the health of the partnership. Ocean acidification does not simply dissolve corals; it raises the cost of maintaining the internal chemistry that calcification requires.

NoteBleaching, correctly stated

Under stress — most often elevated temperature with high light — the symbiosis breaks down and symbionts or their pigments are lost, leaving white skeleton visible through transparent tissue.

Three things newcomers routinely get wrong:

  1. A bleached coral is not dead. It has lost its energy supply and will die if the condition persists, but bleaching is recoverable.
  2. The skeleton was always white. The color comes from the symbionts and host pigments, not the mineral.
  3. It is not simple heat damage. A well-supported reading treats bleaching as a host innate immune response to a symbiont that has become damaging — reactive oxygen species from stressed photosynthetic machinery signal the problem, and the host expels the partner. That framing connects coral stress biology directly to invertebrate immunity.

5. Why the lab cares

Thermal stress and bleaching. Marine heatwaves have driven repeated mass bleaching events. The question of which colonies survive, and why, is exactly a question about environmental memory: does prior exposure to variable conditions leave a state that changes the response to the next event?

Expression plasticity as the adaptive trait. Reciprocal transplant work in Porites astreoides showed that corals from environmentally variable inshore sites have more flexible transcriptomes than those from stable offshore sites, and that this flexibility predicts bleaching outcome. It is the cornerstone empirical result for predictive phenotyping in the conceptual framework — the plasticity itself is the trait under selection, not any particular expression level.

Gene body methylation and acclimatization. Long-term ocean acidification work in Stylophora pistillata linked methylation state to sustained phenotypic acclimatization across molecular and morphometric scales, anchoring the lab’s reading of gene body methylation as a regulator of transcriptional noise.

The holobiont problem. A coral sample contains host, symbiont, and an associated microbial community. That is a methodological burden — reads have to be partitioned — but also an opportunity, because the unit that acclimatizes may be the partnership rather than the animal.

6. Genomic resources

Reference assemblies as listed by NCBI. Accessions verified against the NCBI Datasets API on 2026-07-30.

Species Assembly Accession Note
Stylophora pistillata Stylophora pistillata v1.1 GCF_002571385.2 RefSeq
Acropora digitifera Adig_1.1 GCF_000222465.1 RefSeq; the first coral genome
Porites astreoides — — No NCBI reference assembly
WarningPorites astreoides has no NCBI reference genome

This is worth knowing before you plan work on it. The species behind one of the lab’s anchor papers has no reference assembly in NCBI — which is precisely why that study used TagSeq with reference-free and host/symbiont-partitioned approaches rather than a standard genome-guided pipeline.

If a species you need is missing an assembly, that constrains your method choice from the start. Check first.

Symbiont genomes are separate. Symbiodiniaceae genomes are deposited independently of their hosts. Any coral RNA-seq dataset contains both, and you have to decide deliberately how to partition reads — mapping to a concatenated host+symbiont reference is the usual approach. Note also that the family was taxonomically revised in 2018, so genomes deposited under Symbiodinium may now sit in other genera.

8. Check yourself

  1. A coral polyp has one opening. What are the consequences for how it feeds and digests?
  2. Where does calcification physically happen, and why does it matter that this is not simply “in seawater”?
  3. Someone says a bleached coral is dead and its skeleton has turned white. Correct both halves.
  4. Two species, one brooding with vertical symbiont transmission and one broadcast spawning with horizontal acquisition. Which might shift to a more heat-tolerant symbiont community faster, and why?
  5. You have coral RNA-seq reads. Why can’t you just map them to the host genome and move on?