Halofolliculina ciliate and your reef: Aquarium guide

What is it?

Halofolliculina is a single-celled ciliate (a protist) that forms a dark, bottle-like lorica (a firm tube or shell) attached to the substrate. The lorica has a rounded base embedded in the coral’s skeleton and a narrow cylindrical neck. The best known species is Halofolliculina corallasia, identified as the causative agent of the coral syndrome 'Skeletal Eroding Band' (SEB). 

On corals it looks like fine black pepper sprinkled on fresh white skeleton right behind the edge of living tissue. It creates a slow, dark “band” that advances across the colony.

You may also see tiny free-swimming “swarmers” (larvae) if you scrape a few dots and look under a microscope. They don’t live long without settling on a host or substrate.

Below you can see examples of wild infections on two coral species.

Where does it show up & what does it target?

It is commonly found across the Indo-Pacific (e.g., Great Barrier Reef, Red Sea, SE Asia) but has also been reported in the Caribbean. It has an exceptionally broad host range, infecting at least 82 species of scleractinian (hard) corals in the Indo-Pacific and Red Sea. Acropora, Montipora, Pocillopora and Seriatopora are the most vulnerable, with Acropora species often suffering high mortality.

Halofolliculina can colonize any exposed skeleton (even on massive/encrusting corals) and hard surfaces in tanks: frag plugs, tiles, dried skeleton, snail shells, etc. We've even seen them on hardened superglue.

Halofolliculina  seems to act as an opportunistic pathogen: it can persist as a benign organism on substrate or minor lesions, but given the right conditions (host stress or wounds, high ciliate density, warm/high nutrient water) it forms pathogenic aggregations that overwhelm coral tissue.

The image below shows an electron microscope close-up of loricae (Lor) embedded in coral skeleton. Each image depicts Halofolliculina in infected coral from various regions (Montano et al. 2020).

How does it damage corals?

The ciliate bores into corals' skeleton to anchor its tube and feeds at the moving front, leaving white, peppered skeleton behind. They slowly move into the nearby living coral tissue, leading to tissue death. 

In aquariums, Halofolliculina can cause localized losses and even whole-colony mortality if left unchecked. Susceptible corals may experience chronic tissue recession. Frag plugs or colony bases often get encrusted by loricae, which can then spread onto the living tissue. Weaker specimens or recent shipments under stress are often the first to succumb. However, well-established corals with robust health might coexist with a few ciliate on dead spots without the infection actively advancing. In mixed-species tanks, SEB can hop from one coral to another, especially if corals are in direct contact or if swarmers circulate in the water.

Halofolliculina ciliates don’t directly eat coral tissue. They feed by filtering tiny particles from the water using hair-like structures called cilia. Instead, they might cause damage by releasing toxic metabolites to help clear the coral tissue for new Halofolliculina to settle, or by allowing other pathogenic infections to take hold.

Speed: usually millimeters per day. Slow enough to catch, relentless if ignored.

What makes it worse:

• Recent injuries (frag cuts, pest bites, stings).
• Low flow and nutrients imbalance (detritus feeds the ciliates).
• Thermal stress or generally stressed corals.

Wild vs tank: In the wild, storms, coralivorous snails, and starfish create injuries that SEB follows. In tanks, we create similar opportunities (fragging/handling), stress-induced tissue recession, and tissue necrosis. Their abundance can build up in closed aquarium systems unless we intervene.

How to recognise Halofolliculina in aquaria?

Typical signs

• Narrow gray-black band right where tissue meets bare skeleton.
• “Pepper dots” (hard, gritty tubes) embedded in the white skeleton.
• Steady recession (mm/day), not a sudden meltdown.

These frags show visible signs of infection 

Pocillopora frag that showed signs of infection within a week of tissue loss 

How to treat the corals and the system?

There are anecdotal reports of hobbyists controlling minor Halofolliculina outbreaks by physically removing affected areas and improving tank conditions, thereby saving most corals. Halofolliculina is an emerging pathogen in the hobby, and awareness is vital: early detection and prompt action can prevent a few black specks from turning into a tank-wide plague. 

Because this pathogen is a eukaryotic ciliate, typical antibiotic therapies (effective for bacterial diseases) are generally ineffective. In fact, early aquarium observations noted that adding broad-spectrum antibiotics “failed to halt the progression” of SEB lesions.

You’ll get best results by combining direct coral treatment and system measures.

Treat the coral 

1. Cut it out (mechanical removal).

• Remove the entire infected segment (using bone cutters/dremel) plus 5–10 mm of apparently healthy tissue ahead of it since swarmers may have already colonised beyond the visible band.
• Superglue the freshly cut area to seal potential entry points. 
• Discard the infected piece. Save clean frags and glue on a new plug.
  

2. Dip to kill remaining ciliates. 

Arguably the most effective approach in aquariums has been dipping infected corals in disinfectant solutions. Research in recent years has produced promising protocols:

Potassium chloride (KCl) dip: strong, simple osmotic shock

A concentrated potassium dip can quickly eliminate or dislodge Halofolliculina ciliates without causing lasting harm to corals (Cheng et al. 2021).

• Dip the whole colony for 5–10 minutes (after removing infected segments)
• Good for robust SPS/LPS; observe polyps closely and rinse well.

Iodine antiseptic dips 

Iodine is a common broad disinfectant used for corals. It likely has some effect against ciliates. Dip in iodine at the correct dose for 10–15 minutes. This can help disinfect lesions and possibly kill exposed swarmers, but efficacy against deeply embedded cysts is uncertain. 

• Gentler, useful adjunct after cutting; use as a supporting disinfectant.

Botanical extracts -Clove oil (eugenol) dip 

Recent peer-reviewed studies have explored reef-safe plant extracts to treat ciliate infections. Clove oil (eugenol) is a natural anesthetic and has shown good efficacy. Chu et al. (2022) determined that a 1500 ppm clove extract (approx. 0.15% or 1,500 mg/L) causes 100% mortality of Halofolliculina ciliates within 10 minutes, while causing minimal stress to the coral host. In experiments with Goniopora corals, a 10-min dip at 1500 ppm completely cleared the ciliates, with no significant change in the coral's health markers. Higher concentrations (≥5000 ppm) killed ciliates faster (within 60 seconds) but began to harm the corals.

• Dose: 1,500 ppm (≈ 0.15%) for 10 minutes.

How to mix (1 liter bath):

-Add 1.5 mL clove oil to a small cup with a bit of tank water + a drop of aquarium safe surfactant (to emulsify), then whisk this into 1,000 mL tank water.

-Gently baste the lesion with a pipette during the dip.

• Rinse in clean saltwater before returning.

BioScrub

Combines both potassium and iodine and is a good dipping solution against ciliates.

• Use the recommended dose and dip for 10 min with agitation.

3. Repeat a week later.

• A second dip picks up any late settlers missed the first time.

Control the system (stop re-seeding)

These aim to reduce the presence of swarmers and lorica in the entire environment, preventing re-infection after treating corals.

• Quarantine & dip all new corals. Visual check bases with a magnifying glass.
• UV steriliser (proper wattage/flow): deals with free-swimming stages.
• Good random flow: reduce biofilms and “dead” zones.
• Clean gear between tanks; don’t move water from suspect systems.
• Pest control: remove and treat corallivores pests (e.g., Drupella, AEFW) that create wounds.

In summary, integrated pest management is the strategy: combine mechanical, chemical, and environmental controls to combat Halofolliculina on all fronts. Recent evidence shows that some coral dips on the market can be used against Halofolliculina that is both ciliate-lethal and coral-safe. By applying these measures diligently, even entrenched ciliate infestations can be significantly reduced or eliminated in captive reef systems.