Deep Sea Bonanza I: The Deep Sea as a Biome

A couple of notes before starting:

– The literature list at the end is for Part 1 through 4.

– Most pictures are taken from Google Image searches and I never note where I get them from. If you spot one that’s yours and want a citation or want it taken down, tell me.

From the extreme pressures at the bottom of trenches to the heavy metal pollution at hydrothermal vents, from methane seeps letting out toxic sulfides to anoxic zones, the deep ocean is where you find some of the harshest environments on Earth. However, it is now known that life flourishes in all of them – and that’s what this post is all about. There are charismatic parts, but in keeping with the serious tone of the blog, there are a lot of not-so-charming sections.

Let’s get the first one out of the way now: defining the deep ocean. There is no set, agreed-on boundary between the “deep sea” and the “shallow sea”, but 200 m is the one most often quoted: it represents the transition from the continental shelf to the continental slope. Also, sunlight does not penetrate strongly enough for plant life to survive at any depth greater than 200 m, even in the clearest waters. So, when I say deep sea, I mean anything beneath 200 m. The slope that goes from 200 m to 4000 m is called the continental slope.

That means that the deep sea is by far the largest biome on Earth – it covers slightly more than 70% of the Earth. Half of that is beneath 3000 m.

Divisions of the Ocean. Source: Wikipedia

The rest of the terminology is outlined in the picture above. When I refer to pelagic organisms, I mean those swimming around at the bathypelagic zone or deeper, unless I specify. I will mention seamounts: these are underwater plateaus or mountains that rise from the ocean floor, but don’t go over the bathyal zone (for this post anyway).

Some more miscellaneous terms: benthos is the ocean floor. Benthic organisms are those that live on or in the sediment. Sessile organisms are those that are anchored to the ground. I may also mention meiofauna: this is just a step between macrofauna and microfauna (no real definition: smaller than worms, larger than bacteria!) Anoxic means no oxygen present; dysoxic means very little oxygen present.

It’s hard to deny that the deep sea is a fascinating place. It’s the largest biome on Earth, yet we’re just beginning to realise how it really works. All the old ideas and theories we had about it, from it being lifeless to it being a place where everything happens very slowly, are constantly being toppled by new research showing just how dynamic it is. Not only that, new discoveries from the ocean floor are changing our thoughts about how life itself can function.

Take this find by Danovaro et al. earlier this year as an example. They found three new animals living in a ~3500 m deep basin in the Mediterranean – a basin that is hypersaline, polluted by extreme levels of sulfides and completely devoid of oxygen. In other words, the last place you’d expect to find life, much less multicellular animals! We can ask ourselves where else can life survive? Can these organisms tell us anything about the origin of life? Even more ambitious: are there any implications for exobiology?

Let’s not get carried away – questions like these are merely thought experiments, suitable for insomniac nights or bad sci-fi movies. The deep sea is not only exciting because of a few tiny animals found there. There are complete ecologies on the ocean floor, be it at shelf depth or abyssal. Every depth has its own characteristic sessile fauna, and that’s where we’ll start.


The shelf is a sandy and muddy area, strongly affected by tides, waves and the seasons. It’s in this area where deep-water coral reefs thrive. You find examples of them all around the world, notably off the coast of Norway, in the Mediterranean and off Florida. Associated with the corals are giant sponges, and the usual reef biodiversity – except instead of being in warm, shallow, tropical waters, they are in deep, not well-lit, cold waters. The reason I stress this is that the key to shallow-water reefs is sunlight: the corals there live in symbiosis with photosynthetic organisms (zooxanthellae) which act as the primary producers of the ecosystem. Without sunlight, the reef collapses. It may not sound very significant, but these cold-water reefs are currently a center of ecological research because of their intriguing ecosystem dynamics.


Next we come to the upper bathyal zone, which is more rugged, with small valleys and strong turbidity currents mixing things up (they have been measured at 15 cm/s). These combine to form a habitat suitable for all sorts of suspension feeder, like corals, sponges and giant protozoan colonies.


Going deeper to the lower slope, we notice a decrease in the diversity of the species. Sessile organisms get more important here and act as biological hotspots, since the rest of the environment is bland and featureless. Solitary corals, sea pens, crinoids and sponges are the permanent biological markers in this area.

Finally, we come to the deep-sea floor. Generally very slow currents, mud and no nutrients characterise this place. It’s far from the ideal environment for sessile organisms and this is reflected by their rarity: you may find some individual corals, glass sponges and sea pens, but they are rare. Where they do occur, though, they are hotspots and other organisms crowd around.


It’s important to remember these as guidelines. The sessile organisms are not just parts of an ecosystem, they also serve as a microhabitat, and nowhere is this as necessary as in the deep-sea. Amphipod crustaceans are especially associated with corals, both isolated and colonial. In deeper waters, echinoderms, especially brittlestars, are often found with the corals. In the coral reefs, it’s not uncommon to find very specialised behaviours. For example, the polychaete worm Eunice norvegica uses the calcium carbonate shed by the corals to build a shell around itself (like a house). This shell has several openings, each of which points at a polyp opening, where the food streams in – the worm can just pop out and take some.


It’s not just the living sessile fauna that’s important, especially when considering sponges. Their skeletons form another microhabitat, one where nematodes and copepods dominate as meiofauna. Again, this doesn’t sound amazing, until you realise that 60 years ago, we had no idea it was possible for life to survive here.

“There are no such things as mountains and valleys on the deep-sea bottom.”
Mosley, 1880.


Just like there are valleys on land, the continental slope is also very rugged, with canyons and other extreme topographies, and one of the most basic rules of ecology is that the more variable a habitat is, the higher the biodiversity is. This is especially true for the deep sea. The reason should be clear: more places to hide, different resources, more microhabitats and different types of ground.

These canyons are a very different environment compared to the regular benthos. There are regular flows of nutrients from the shallow sea (brought by underwater rivers, so to speak), so they can support much more life. They include everything from plant rests to carcasses – anything that’s deposited in the shallower waters.  Suspension feeders take advantage of the currents, while detritivores profit from the sediment brought by them, and fish can eat the high concentrations of zooplankton that travel along with the currents. At the same time, there is a high level of endemism within each canyon, with species not being able to migrate away from individual canyons.

Therefore, submarine canyons are critical habitats in the deep sea: they are a sort of island, where species can come to feed and reproduce. This also makes them interesting places to study speciation, isolation and gene flow. In fact, numerous studies have shown empirically that the fauna of submarine canyons is distinct from that of the slope.

Because Earth is a tectonically active planet, there are underwater mountains called seamounts – around 200000 of them around the world. Again, the ecosystems here are different and varied. Think of them like a regular mountain, with specific ecologies found at specific heights. Seamount faunas follow the same gradients as those on the continental slope: temperature, pressure, food availability and oxygen level, with depth being the defining factor. Seamounts come in all shapes and sizes and this can have drastic effects on their faunal compositions. For example, you will not find many corals (or other filter feeders) on plateau-like seamounts, since the currents are too slow there. Therefore, seamount ecologies are fragmented – but this doesn’t lead to endemism, nor does it make seamounts isolated islands, since animals can still spread out as they wish, as long as they find a suitable place to colonise.

Hydrography at Seamounts

Seamounts are of special interest for the deep sea because of their local hydrological system: water currents lead and trap nutrients on seamounts (see picture above), making them natural hotspots for life in the deep sea.

Fish schools are often found at seamounts and serve as the top consumers. Filter feeders are the major benthic organisms (sponges, corals, crinoids). But don’t think that food chains are simple in the deep sea: there are all sorts of evolutionary adaptations for feeding, like carnivorous sponges. There are also normal deposit feeders (sea cucumbers) and predators (brittlestars).

It used to be thought that seamounts were hotspots for endemism, but again, that view is now generally outdated. Species in the oceans are restricted in the range of depths they can tolerate, but generally not in their global distributions (to a point: I’m not talking of tropical organisms being able to survive completely in Antarctic water). The only thing that will stop an organism from spreading out to other suitable seamounts is ocean currents – and this is not a problem for the megafauna, only for the sessile organisms and the molluscs that can only spread via their larvae.

The proper question to ask now is: where does the primary energy come from? In shallow waters and terrestrial ecosystems, it’s from photosynthesis. In the deep sea, there is no sunlight – so all the primary production comes from whatever sinks from above. Besides extraordinary carcasses, this is just zooplankton which migrates down to the deeper ocean (the so-called marine snow, because they look like falling snow when light shines on them). Staying with the seamounts, they are the most important energy suppliers for the ecosystem. Fish are their major predators, and they can then be eaten by the deep-sea seamount fish (as well as the top predator megafauna, like squids or dolphins). Always keep such links in mind: they’re the basis for any ecology.

Having looked at the ecological basics of the deep sea, let’s look at the habitats where the really cool stuff is.

The first are underwater volcanic chains and mid-ocean ridges. These are geologically active areas and as such are not homogeneous. I may have summed them up together here, but they actually consist of many related habitats. You have volcanically active seamounts next to fractures and trenches over 4000 m deep. Instead of a soft, sandy benthos, you have rock, home to different kinds of sessile filter feeders.

Associated with these areas are hydrothermal vents and black smokers: here, the cold seawater reacts with the hot, newly-formed ocean crust to make very hot, chemically rich water. This habitat is very unique and fascinating, because here you have direct primary productivity powered not by the sun and photosynthesis, but by chemosynthetic bacteria fuelled by hydrogen sulphide and methane present in the hydrothermal water. Their metabolic pathway results in a net increase in organic carbon, so they essentially play the same role that plants do on land: generating organically viable molecules from abiotic sources.


These bacteria live in colonies, forming microbial mats around hydrothermal vents. There are also many symbiotic relationships between them and the macrofauna, which can get pretty extreme: the tubeworms pictured above, Riftia pachyptila, have no mouths or digestive tract, having replaced them with a special organ (called a trophosome) packed with chemosynthetic bacteria, in an arrangement somewhat similar to what you find in cows and the bacterial symbionts in their stomachs or corals with their zooxanthellan symbionts.

Needless to say, these bacteria are responsible for the success of the vent ecosystem – they’re what allow it to even survive. They’re also the reason why vent communities are so specialised, with over 70% of the species living there being endemic. You can think of hydrothermal vents as oases in the middle of a desert – but that simile falls apart when you realise that the overall diversity at a hydrothermal vent is lower than the abyssal benthos around it.

As for macrofaunal diversity, it is low. The shrimp, mussel and polychaete fauna is specialised and these animals are very typical at vents all around the world.

The hydrothermal ecosystem is unstable – a single eruption will kill it off. Even without such catastrophes, the temperatures and chemical nature of the water there (especially the hydrogen sulfide) are toxic to animals – leading to very strong selection towards very specific solutions (which I will get into later).

But a vent is nothing more than a crack in the abyssal plain, a continuous valley with a soft benthos made up of microscopic particles that come from rocks and planktonic organisms (the calcareous shells of foraminifera and coccoliths, the siliceous shells of diatoms and dinoflagellates). The benthos is thousands of metres thick, with only the top couple of meters containing any organic material. Not only that, it’s also quite uniform: with the exception of the Mediterranean and Red Seas, the temperature is always ~2°C and the salinity is constant. The oxygen level is at its maximum (barring anomalous oxygen minimum zones) and the pressure gradient is linear. And of course, there is no light. It’s no wonder it was thought that this is a stable environment uninfluenced by the surface world.

That view is not supportable anymore. There is a direct link to the shallow realms: energy. There is no sunlight for photosynthesis and no chemosynthesis. The only energy source comes from the top – so the productivity of the shallow waters has a direct effect on the ocean floor beneath. This is most spectacularly seen with whale falls. It is not uncommon to find brittlestars feeding on the marine snow that lands on the ground, and various crustaceans and fish will scavenge for food. The benthos itself can support a very high diversity of life.

Polychaete worms are found all over the abyssal plain, as are small crustaceans and gastropods. But by far the most successful animals living there are the nematodes. But they’re not the most successful organisms, as formaniniferans surpass them in terms of biomass. This is why I decided to write about the whole of the deep sea, not just the charismatic animals: they are the exception, not the rule, and writing only about them would give a very distorted view.

Now when we talk of the abyssal plain, we picture a sort of underwater desert landscape, more or less flat and covered in sand. But as we saw before, the ocean floor is not even, and the most striking features are trenches: very narrow (~40 km wide), V-shaped and extremely deep gorges: their depth goes from 4000 m (near Crete) to the 11000 m deep Mariana Trench. At their bottom, there is no calcium carbonate anymore, since it simply dissolves under the pressure. There are fast, turbulent currents swirling the sediment around, and the pressure ranges from 600 to 1100 atmospheres. These places are called Hadal systems, after Hades.

But despite such hellish conditions (I couldn’t come up with a better one, sorry), life still survives in the benthos here! Not only that, the biomass of bacteria and total amount of activity here is double that found at an abyssal plain of the same depth! The reason is what I’ve been saying the whole time: energy. The trenches are traps for organic matter. The currents carry them down here (it’s basic hydrography) – the abyssal plain depends on whatever sinks down, the trenches get a ‘regular input’, so to speak.

The deepest of these trenches is the Mariana Trench between Japan and Papua New Guinea, and is the site of a subduction zone: the Pacific Plate is subducting beneath the Mariana Plate. And yes, life survives down at 10916 meters. At least microbial life, from regulars to extremophiles. They include bacteria that like alkaline conditions (alkaliphiles), those that like warm condition (thermophiles) and even some fungi. Although a word of warning: only some of these are actually alive down there; to differentiate between living cells and dormant spores, they have to be grown in a lab, which is not as easy as it sounds.

Now that’s an extreme example at an extreme depth which can’t be compared with the regular abyssal plain. If one looks at regular trenches, for example in the Eastern Mediterranean Sea, it becomes obvious that they really do support more life than the abyssal plain.

But so far, all these ecologies are strikingly similar to terrestrial ones, seeing as how they’re tied to the ground. Before any particles land on the ocean floor, they have to sink through thousands of meters of water: the pelagic realm. In terms of biomes, this is the largest one, and also the most unique in terms of ecology, since it is three dimensional. On land, even birds have to come back to the ground to feed. In the bathypelagic realm, there is no dependance on the ground.

There are no constants in the pelagic. Temperature, salinity, nutrient availability are all functions of depth, surface productivity and ocean currents. The first two are obvious, so let’s look at what currents do. At higher latitudes, the oceans are cooler. The cold water sinks and flows towards the central latitudes, and this is the basis for all the circulation systems in the oceans. For example, North Atlantic waters will flow all the way down to South Africa, around the Cape and into the Indian and Pacific Oceans.

These systems are important: they are what control the distributions of animals in the oceans. Larvae can only colonise where the currents take them. Lack of circulation will create ‘islands’, where no gene flow will occur to the outside, as can be seen in the Arctic.

The Arctic Ocean is a special place. I’ve been parrotting the same line all this time abount energy sinking from above. But in the Arctic, there is no shallow water productivity, since it’s covered by ice. It is a typical oligotrophic system: one in which organisms can live without many nutrients. Life in the Arctic Ocean is not abundant or diverse as in other deep ocean areas, but it’s still there. The reason I’m spotlighting it is just to show that life really can survive anywhere, from places with extreme conditions to places where there is no food.

These biogeographic islands are also exciting from an evolutionary perspective – several trends have always been observed on terrestrial islands, and have always been explained as being due to isolation. Is there any sense in calling such isolated places in the deep sea ‘islands’ or is it a bad metaphor?


All the research so far shows that yes, the island rule is completely valid for the deep sea. Taking the example of snails, they show the most common of the trends: insular gigantism and dwarfism. Comparing shallow water and deep water snails, there are very clear trends in body size changes. Consider the sea spiders as an other example: they are normally quite small, yet deep-sea species get freakishly large legs and grow to immense sizes. Or just look at the isopod above – isopods includes animals like woodlice (you know, those tiny bugs you step on by accident).

I stress this because it shows that the deep sea is a regular biome, subject to the same restrictions and rules of any other one, and this is an important realisation: thinking of the deep sea as an exotic place is nice and poetic, but it doesn’t really apply. It functions differently from most other ecosystems, but it does not cheat the rules of evolution, ecology or biogeography.


For those without university access, there is this excellent book on the seep sea which I also used:

Ecosystems of the Deep Ocean (2003), edited by Tyler. Published by Elsevier (Netherlands).

Reference List: [Citation style not ideal because having to HTML this shit is torturous]

Collin, Lloyd, Wagner. 2000. Foveate vision in deep-sea teleosts: a comparison of primary visual and olfactory inputs. Philosophical Transactions of the Royal Society B.

Danovaro, Dell’anno, Pusceddu, Gambi, Heiner, Møbjerg Kristensen. 2010. The first metazoa living in permanently anoxic conditions. BMC Biology.

Dubilier, Bergin, Lott. 2008. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nature Reviews Microbiology.

Goffredi, Warén, Orphan, Van Dover, Vrijenhoek. 2004. Novel forms of structural integration between microbes and a hydrothermal vent gastropod from the Indian Ocean. Applied and Environmental Microbiology.

Hoegh-Guldberg, Mumby, Hooten, Steneck, Greenfield, Gomez, Harvell, Sale, Edwards, Caldeira, Knowlton, Eakin, Iglesias-Prieto, Muthiga, Bradbury, Dubi, Hatziolos. 2007. Coral reefs under rapid climate change and ocean acidification. Science.

Kenaley. 2010. Comparative innervation of cephalic photophores of the loosejaw dragonfishes (Teleostei: Stomiiformes: Stomiidae): evidence for parallel evolution of long-wave bioluminescence. Journal of Morphology.

Miyazaki, Martins, Fujita, Matsumoto, Fujiwara. 2010. Evolutionary Process of Deep-Sea Bathymodiolus Mussels. PLoS One.

Ramirez-Llodra, Brandt, Danovaro, Escobar, German, Levin, Martinez Arbizu, Meno, Buhl-Mortensen, Narayanaswamy, Smith, Tittensor, Tyler, Vanreusel, Vecchione. 2010. Deep, diverse and definitely different: unique attributes of the world’s largest ecosystem. Biogeosciences Discussions.

Raupach, Mayer, Malyutina, Wägele. 2009. Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data. Proceedings of the Royal Society B.

Smith, De Leo, Bernardino, Sweetman, Arbizu. 2008. Abyssal food limitation, ecosystem structure and climate change. Trends in Ecology & Evolution.

Wagner. 2002. Sensory brain areas in three families of deep-sea fish (slickheads, eels and grenadiers): comparison of mesopelagic and demersal species. Marine Biology.

Widder. 2010. Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity. Science.

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