Side note: many nudibranchs eat cnidarians, and some aeolid nudibranchs (most notably the species Hermissenda crassicornis) are known to remove the nematocysts from the cnidarian remains in their digestive tract and, through a network of interconnected tubules, deposit them in a "cnidosac" at the tips of the the cerata, where the toxic harpoons can be used to defend against predators. They absorb the strength and toxicity of the cnidarians; they grow stronger on their enemies, the anemones. We still don't know how the nematocysts pass into and through the body of the nudibranch without being discharged.
What I find really interesting about alarm signaling in N. inermis and A. elegantissima is that neither species is really known for its altruism. Bristle-covered "sensory mounds" on each side of N. inermis's mouth can pick up the trail of almost any undersea critter, including the mucopolysaccharides in the slime trails of conspecifics. If it's hungry enough, N. inermis won't hesitate to follow down a member of its own species and engage in some cannibalism (the slime trails are also a convenient way for males to track down mates). E. elegantissima lives in clonal aggregations, meaning that it's surrounded by asexually-produced clones of itself, and members of the aggregation are friendly enough to each other. But when another aggregation's growth leads to the two groups bumping up against each other, the invaders receive a stinging rebuke. Using their acrorhagi (pale-colored tentacles specialized for repelling rival aggregations), the anemones sting their enemies and leave behind an ectodermic "peel" of skin and stinging nematocysts that kills the invader's tissue.
When it comes finding a mate, pheromones and signaling molecules really are everything to some ocean invertebrates. Mating behavior in many male brachyuran biramous-limbed arthropods (crabs) is initiated by a release of male attractant pheromone. In the case of the Blood-Spotted Swimming Crab, pre-molt females release attractant pheromones through their urine, an NH3 (ammonia) solution produced in the Malphigian tubules. Males spend their time buried in sand and sediment in waters about 10 meters shallower than where the females live, and will not exhibit search behavior unless exposed to the pheromone. Once the male find the female, she stops releasing pheromones, and the male carries her until ecdysis (shedding of the exoskeleton). Males appear to be more aggressive and territorial in colder waters, perhaps explaining why they are kept in the warm, shallow water until needed for egg-fertilizing.
We mentioned the mantis shrimp (stomatopods) above as an example of a marine invertebrate with keen eyesight, but it also has highly developed chemosensory abilities, and signaling chemicals factor into dominance hierarchies associated with mantis shrimp mating. Mantis shrimps are aggressive, and the males engage in ritualized combat over mates. Once one of the males have triumphed, the losers will stay away from the territory he has scented. Mantis shrimp, like many marine crustaceans, capture odorant molecules with chemosensory aesthetsacs on their antennules, which they flick around in the water.
Many species exhibit associational chemical defenses, where one species is sheltered by the toxicity of a partner. Chlorodesmis fastigiata is an algae on the Caribbean reef that provides shelter to amphipods, sacoglossans and crabs. These species depend entirely on C. fastigiata for their survival, protected by the algae's chlorodesmin (a highly toxic diterpene). Some carnivorous nudibranchs have also centered their niche around living in the C. fastigia; they feed on the sacoglossans. Tritonia hamnerorum, a Caribbean nudibranch that hangs out around sea fan colonies, sequesters the sea fans' defensive juliannafuran (a type of terpene), rendering the slug unpalatable to fishes.
Barnacles, sessile creatures with only the simplest of photosensory capabilities, are truly lost without chemical signaling. Their interactions with conspecifics are entirely mediated by chemical cues. A good example is barnacles' release of an a2-macroglobulin-like cuticular protein that draws in cyprids (barnacles in the second nektonic larval stage, after they pass through the five instars of the napulius stage), encouraging the young barnacles to settle close by. For barnacles, living in gregarious (physically clustered) communities is vital to future reproductive success, as these sessile creatures can only mate with neighbors.
Whale barnacles carpet the skin of massive cetaceans, as many as half a ton to a single whale (remember, baleen whales generally weigh in excess of 35 tons; the barnacles are like shorts and a T-shirt to them). The barnacles are referred to as obligate commensalists because 1) the barnacles are highly specialized to whales (in the case of Coronula diadema, Humpbacks specifically) and 2) the relationship is commensal, beneficial to the barnacles but with no net negative loss or gain for the whale. The tiny hangers-on don't harm their massive host in any way, and share in the whale's love of plankton-rich waters (despite the enormous size discrepancy, baleen whales and barnacles are curiously similar from a nutritional perspective: both are filter-feeders with a taste for plankton).
Living on a whale is a highly specialized ecological niche, and it's really very surprising that barnacles ever evolved to live on whales; barnacles were around a hundred million years before cetaceans arose. The whale-hosted lifestyle is confounding for a number of reasons, the first and most obvious being: how do cyprids find a whale in the first place? The answer, as you've probably guessed, is the recognition of chemical cues released from whale skin. In 2006, Yasuyuki Nogata and Kiyotaka Matsumura used a couple of petri dishes and a piece of Humpback skin tissue to prove that cyprid recognition of whales had a chemosensory basis, but we still have no clue what the chemical is that the cyprids are picking up on.
Internally brooding corals, which internally fertilize their eggs, generally receive symbionts through maternal inheritance. Once the oocyte is fertilized, it travels to an endodermic pouch and develops into an embryo. The soft mesoglea cloaking the embryo transfers algae from mother to child. But in many corals (including most hermatypic species), fertilization is external, and the planulae (coral larvae) need to find their own symbionts.
Both corals and algae secrete chemicals that function in initial recognition. A study of hydrozoans showed that symbiotic algae that secrete high levels of maltose (the photosynthate polyps feed on) were more likely to be identified and absorbed than algae that could not release maltose. Cnidarians also use pattern-recognitions receptors (PPRs) like lectins to pick up on microbe-associated molecular patterns in algae. C-type lectins are embedded in cellular membranes, and when they bind to passing glycoproteins (like the glycoconjugates released by Symbiodinium) a series of signaling serine proteases are triggered within the coral cell. Coral also secrete lectins (such as the millectin released by Acropora corals and the PdC lectin released by Pocillopora corals) that trigger morphological changes in free-swimming Symbiodinium, preparing them for life as a symbiont. Just like Mycobacterium tuberculosis, Symbiodinium stops the process of phagosomal maturation (being killed as a pathogen and destroyed by lysosomic enzymes) by manipulating endosomal trafficking.
But corals need to keep their algae under control, or the algae will overstay their welcome and become parasites. Corals use signaling peptides termed host-release factors (HRFs) to control the carbon metabolism of their symbionts. HRFs prompt the algae to release glycogen (a form of glucose) and several amino acids. This gives sustenance to the corals while at the same time depriving the algae of nutrients.
(interesting fact: while, like all hydrophilic biological compounds, HRF peptides are very hard to isolate, research indicates that they may be present in many plants and animals and play a role in their carbon metabolism.)