Principles of marine degradation 4

physical, biological and ecological indicators of degradation

by Dr J Floor Anthoni (2004)
A long list of physical indicators showing what to look for, like reduced visibility, dense plankton blooms, slime, sedimentation, bottom fog and smell. Ecological indicators like unoccupied territory, missing organisms, patchines and symptoms of recent death.
Do indicator species have things in common? Which organisms are good indicators of which threats? The young of all species are good indicators of decay.
Many organisms have beneficial effects on their surroundings, mitigating or postponing the ill effects of degradation. When they die, their environment may go through a critical period of decline.
Many organisms display a kind of unhappiness or ill health before dying. These are important warnings as they are visible on organisms which have not yet disappeared and which may recover without surrendering their space.
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indicators of doom

Seldom are the causes of degradation directly visible. They also have to act over a period of time, usually when diving is unpleasant or impossible. But fortunately there are many indicators, which taken together, give a reasonable picture of the threat to the environment and the quality of that environment. 

Obvious indicators: Agents
The most common indicator agents (media) are:

Zone indicators
Everywhere in the world the rocky shore is zoned by three most important limiting factors: drying above low tide, wave action and reduction in light. Of these the bottom of the sunlit zone, is the most telling of degrading water quality. Thus the lower boundary of the kelp is an important measure. Note however, that the sandy bottom reflects so much light (almost 100%) that widely spaced plants can live much deeper.

Thus the amount of kelp cover is also important. Fortunately, the transition from full cover to sparse cover is rather sudden and this is what one looks for. The maximum amount of cover (including younger plants) is also a good indication.
When new recruits are not found under old kelp, this means that the lower boundary is shifting upward as a result of degradation. So the lower boundary of kelp recruits is an even stronger indicator of decay or health.

In general, the first indicators of degradation are found along habitat boundaries, of which the photic (= light) boundary is the most telling. This boundary runs roughly along a depth contour but climbs to the surface at the entrances of caves and archways, which are therefore treasure troves for investigation and monitoring. As this boundary shifts, space becomes available for new organisms. Often these organisms are new to the area or totally unknown or they may be foreign and introduced.
Traces left behind from recently disappeared organisms
Although some organisms will always be found missing due to normal mortality, one does get a feel for abnormal mortality rates. By calculating the ratio of traces over what was once there (= remaining organisms + traces), one gets an idea of the rate of decay.
  • kelp holdfasts: these disappear in 6 months after the plant dies
  • pink paint 'prints': when organisms attach to the underlying pink paint, they may shade it off sufficiently to deprive it from light such that it dies. The difference between dead pink paint (white) and live (pink) is very clearly visible as an imprint of the deceased organism. Pink paint prints can remain for up to two years, first showing as white, then as dark pink.

Prime real estate or hot spots
Before touching on missing species we need to introduce the concept of prime real estate, or the preferred places (hot spots) for certain organisms. This is particularly important for species that move around freely like schooling fish but it also applies to territorial species.

As individuals die, their space becomes available. If that space is more beneficial than that which is occupied by survivors, these will leave their territories to move in next door. Thus organisms diffuse towards hot spots. Because of this, the prime real estate is always fully occupied, even after severe mass mortalities (after a while). One has to learn to recognise the preferred places or hot spots but this is easy because they are so obvious. It is more difficult to find the reasons why hot spots are popular. Most hot spots are found in places that offer shelter against storms, but fish return here during the evening. Thus censusing (counting organisms) in sheltered places is best done by night.
The moment one finds fish missing from a hot spot, it almost certainly means that a mass mortality happened very recently. Frequent visits thereafter will see the hot spot fill up again by diffusion while their surroundings remain depleted.
  • archway: an archway is a cave with two openings and usually also has vertical walls. Often a current runs through an archway. Therefore archways combine the three hotspot qualities mentioned below.

Patchiness describes the randomness (=erratic) occurrence of individuals and species as a result of competition for space, rather than a single species dominating all. Even habitat zones of a single species can be patchy with regard to year classes. Stable, healthy environments look patchy. Patchiness is a good indicator of health.

Missing individuals/species
One cannot see missing individuals, but there are some clear indicators:
  • open empty space: space on the rocky shore is heavily competed for by both plants and animals and is therefore a strong indicator. Every part of the rock should be occupied, unless heavily grazed, but even then the grazers must be visible and densely spaced (some grazers appear only by night). Thus seeing empty rock, even when covered by pink paint, should cause suspicion. The amount of cover in old individuals is a strong indication of the quality of the environment.
f037722: example of a fully occupied two dimensions. Alas these species cannot grow outward. Jewel anemones in a Goat Island archway.
f021711:fierce competition for the third dimension. Callyspongia spp on Whangarei Harbour pier in the currents.
f048712: A fine example of fierce 3D-competition in a very healthy environment. Poor Knights under a deep ledge.

Missing year classes
It is not always possible to estimate the age of individuals but almost always one can distinguish this year's, last year's, mature and old species. By measuring sizes exactly, scientists can obtain size distributions which may indicate missing year classes. However, our simple method is very effective.
  • missing recruits: this year's recruits are easily visible, particularly during night dives, but some remain cryptic (= hidden) like sea urchins do. They can be found by turning a few stones or peering into cracks. Recruits may be missing because they may not have arrived yet (this year's). Missing recruits indicates a recruitment problem, usually in their planktonic stages when they are extremely sensitive to water quality. Missing recruits may suddenly appear as next year's yearlings.

Stunted growth and runts
The difference between a small individual because of age and one because of unfavourable growth conditions, is often difficult to see. Small anemones almost certainly indicate poor availability of food. Runts (= the smallest in a litter) may show unusual distorted shapes and growth on their skins. Ironically, runts often survive better than others, perhaps because they have  coped from birth.
Pink paint on the outsides of shells may serve as a growth marker, where recent growth is still free from the pink paint. The faster the shell grows, the wider this margin.

Weakness and disease may be the causes of runts, but they can also be a recent phenomenon. Signs of disease are very strong signals of degradation because the chance of observing them on long-lived organisms is small.
  • opportunistic species/ invasions: most species have defences against being invaded by opportunistic species, but less so when they weaken, giving opportunity to overgrowth. The invaders often kill themselves by killing their host, which then detaches from the rock. It is most observed on old individuals and is a strong indication of the beginning of degradation. Plants are cleaned firstly by exuding (= sweating out) slime and secondly by grazers such as parore and grazing snails. Note that some species such as some seasquirts promote organisms to grow on their skins. Ironically, some opportunistic species are beautiful in appearance (zoanthids, carpeting species, some nudibranchs). In the 1970s yellow zoanthid anemones were uncommon on the Poor Knights, but today they are very common.
Displacement by more robust species
Sometimes missing species are replaced by more robust species with the same functionality, although this is unfortunately uncommon. In general, when species disappear, the environment becomes less dense and less diverse.
  • maomao/ sweep: blue maomao prefers the warmer and clearer waters of NE New Zealand, whereas sweep thrives in less favourable coastal conditions. When sweep become more populous where they were not before, this is a sure sign of degradation.

Left-over species
The species that once grew everywhere in areas more exposed to degradation, can still be found in the best and most protected places on the reef. Look underneath overhangs or inclining walls to find the left-over species representing what once grew more profusely everywhere. Places rinsed by currents and moderate wave action, such as around promontories, also show left-over species. Often the left-over individuals grow larger than before due to reduced competition for space and food. Ironically, left-over species are profound indicators of degradation, as they enable one to look back in the past, to see what once lived here profusely. They are like the exceptions proving the rule. The rule being the omni-present result of degradation, whereas the exceptions those hard-to-find niches not yet affected.

Note that some plankton feeders do not live entirely from planktonic food but also from algal cells embedded in their tissues (zooxanthella). Various anemones are suspected of this as are several sponge species. For them the availability of light is important, and they cannot live well under overhangs and inside caves and archways. They are also affected by the water becoming more turbid (=muddy, thick, opaque). Note also that some species under overhangs cannot live on rock faces exposed to sunlight.

left-over Pterocella bryozoans growing unusually large
f036830: left-over Pterocella vesiculosa bryozoans growing unusually large. Arid Island.
disappeared stick bryozoa are found under overhangs
f029419: where stick bryozoa have disappeared from vertical walls, they can still be found under overhangs.
leftover sponges
f037717: leftover sponges under an overhang in the channel to Rogers Cave, show what once lived around Goat Island a long time ago.
leftover anemones
f037722: a gaudy carpet of leftover Corynactis jewel anemones and other species at the entrance to Rogers Cave are all that is left of an environment that began degrading a long time ago. But some of this can still be found under ledges elsewhere. Goat Island marine reserve.

Left-over dead species
Some species leave their hard shells behind which may remain for several years. By making a record of the number of dead shells over living ones, one can obtain a measure of decay. Sometimes one finds a shell trap with debris rained from above. By inspecting this debris, one can also obtain an impression of the recent past.
dead and alive hat urchin
f041628: the ratio of dead hat urchins over living ones gives an idea of recent mortality rates. Poor Knights. Left one dead and broken; right one well alive, covering itself.
broken kelp holdfasts disappear in six months
f042519: this stalked kelp may have been removed by storm, grazing or decay. It takes about 6 months for it to rot away. It is surrounded by organisms competing fiercely for space.

Increased species of decay
Sometimes decay is accompanied by species that are typical of decay. Such species adapt quickly in numbers by replicating profusely while living short.
  • sea lice: Sea lice attack all organisms but are successful only on weak or dying ones. An increase in sea lice, observed during a night dive may indicate acute decay.
drooping sponges in a badly degraded environment
f011003: drooping sponges and colonial seasquirts are a sure sign of serious decay. Houhora Harbour.
leafy bryozoa belong to degraded environments
f040020: fast growing leafy bryozoa belong to degraded environments. Whangaroa Harbour.
black velvet mushy sponges
f011302: intestinal compound seasquirts and black mushy sponges are sure signs of severe degradation. Houhora Harbour.
dark purple mushy sponges
f040020: dark purple mushy finger sponges and lumps are a sure sign of far advanced degradation. Port Fitzroy.

Indicator species
The holy grail of water quality assessment are species that have a narrow range of tolerance, such that they can be used as indicator species like the hand on a voltmeter. But finding these is not likely since most species tolerate a range of conditions such that their ranges overlap, which is an ecological requirement for resilience. See separate chapter below.

When organisms vanish suddenly, space becomes available which will be colonised. Often (but not always) recolonisation begins with short-lived fast-reproducing species (like barnacles) followed by longer living species and eventually replaced by a patchwork of long-lived species. Typical first wave colonisers are:
  • jellyfish polyps: the scyphistoma polyps of jellyfish quickly occupy vacant space under overhangs in degraded waters
Note that kelp recruits are also first-wave colonisers. Typical second-wave colonisers are:
  • encrusting sponges:
  • various bryozoa:
  • anemones:

Every event WILL have ecological consequences because everything is connected. Thus having observed the indicators of an event this year, one can expect to observe its consequences next year, such as:
  • larger nest sites: due to fewer breeders and fewer nest raiders: demoiselle, black angelfish, tripefins


Indicator species

As shown in the previous chapters, there are many indicators of health and decay. To focus on a few single species would only narrow one's vision. Yet some things can be said about indicator species. The idea behind it is that threats or changes in environmental conditions leave traces behind in the surviving organisms. Ideally, indicator species should be:
Indicators of decay should in addition be low in the food chain, such as filter feeders like sponges. It should be noted that juveniles of any species are good indicators by themselves since they appear more sensitive to unforeseen circumstances, and particularly to eutrophication by bacterial attack:
Missing species
Indicator species are typically not found in the laboratory but by observation in the environment. Species that suddenly disappear are the first candidates. Those that disappear more gradually next. A sudden disappearance may be correlated to a recently observed event such as an oil spill or an industrial spill or an unusual temperature. The disappearance may be correlated to the area affected by the spill, and further testing in the laboratory may confirm the species' sensitivity to the particular threat. The following species have disappeared suddenly from various places:
  • red actinia anemone (Isactinia tenebrosa): living in shaded places around the high tide mark, this species appears vulnerable to floating chemical pollution such as oil slicks.
The above list will be augmented (= made larger) with time. Do you have suggestions?

The cleaning gang

If left unchecked, small algae will smother all rocks and larger seaweeds. Planktonic scum will descend on all sandy sea bottoms. Dust will smother sponges and other filter feeders. Decay and rot will set in. Fortunately a large cleaning gang is omnipresent doing what they were designed to do, to keep the environment clean. This metaphor is of course poetic, as these various organisms just go about their business of finding food, not aware that they provide a cleaning service to others, in doing so.
parore grazing fine algae from seaweeds
f000832: Parore (Girella tricuspidata) seen stripping fine algae from the coarse brown featherweed (Carpophyllum plumosum) in a side-ways swipe. Parore are important environmental cleaners. Leigh marine reserve.
parore scrape marks on polluted rock
f991027: parore scrape-marks on heavily polluted rock where even the coralline algae known as pink paint, won't grow any longer. A serious sign of degradation. Long Bay marine reserve, Auckland.
grazing snails remove invasive species
f040013: grazing snails remove invasive species from various organisms. Here the top shell is no longer capable of removing the already established bryozoan mats from stalked kelp in this highly degraded Whangaroa Harbour.
Sea cucumber cleaning sponges
f004917: a sea cucumber (Stichopus mollis) seen cleaning heavily dusted yellow nipple sponges (Polymastia croceus). Other sponge species also benefit. The sea cucumber excretes a solid turd which confines decomposing bacteria. Near Mahurangi Harbour.
sea urchins prevent slimy algae Ostreopsis from establishing
f041916: sea urchins (Evechinus chloroticus) prevent slimy algae such as this poisonous dinoflagellate slime (Ostreopsis sp.) from establishing. Once established, it also kills the sea urchins. Little Barrier Island.
cushion stars are resistant to many natural poisons
f039221: cushion stars (Patiriella regularis) graze large surface areas and they tolerate many natural poisons, dinoflagellate slime and decomposing bacteria. Parengarenga Hr.(on snow-white sand)



Many organisms display what could be called unhappiness or a sense of not being well or ill health before dying. Such symptoms are important to recognise, as the organism may stay alive or recover completely, being available for next occurrence of the offending threat. I have been documenting such symptoms only recently and do not have enough illustrative photographs, but their number will undoubtedly grow.
Many gorgoneans, soft corals and anemones withdraw in case of adversity but they also have cycles of rest which are entirely normal. Thus care must be taken in explaining unhappiness from a temporary rest. However, in a single dive many hundreds or thousands of individuals can be observed, either corroborating or contradicting one another.
Unhappiness or ill-health can easily be seen in seaweeds as their fronds and branches droop, assuming a collapsed appearance. Healthy seaweeds feel slimy and bouncy while they hold their fronds up.
a sick sea urchin folding its spines
f042803: a sea urchin folding its spines is a sure sign of unhappiness. The more spines folded, the less happy it is. Eventually it dies. Poor Knights marine reserve.
Yellow nipple sponge about to die
f042719: this is a very unhappy yellow nipple sponge, (Polymastia croceus) which is about to die. When Polymastia sponges become hard, withdrawing their nipples, they are unhappy. This one is also grown over by invading red algae, a sure sign of severe stress. Poor Knights marine reserve.
happy sea rimu seaweeds
f042628: green sea rimu with all its branches held upward, is a sign of health, as also expressed by the red seaweeds. However, they are insufficiently grazed, as is also the drooping stalked kelp centre-right. Eventually this will lead to rot. Insufficient grazing points to a decline in grazing fish, a sign of degradation. Poor Knights marine reserve.
Decaying seaweeds drooping their branches
f041022: unhappy seaweeds droop their branches. Float bladders lack the gas to pull the branches up. These flexible weeds (Carpophyllum flexuosum) are normally able to shed dust but cannot resist bacterial attack. This photo shows the end of a habitat. Near Whangaroa Harbour.