Determining indigenous species to an area[edit | edit source]

Due to the rise of Biodiversity projects, it is now possible to find a list of species indigenous to any location on earth. This allows anyone to determine whether a fish is indigenous or not (and thus need to be removed). Examples of a popular catalogue available online is the Encyclopedia of Life, and the Global Biodiversity Information Facility.. Besides these international catalogues, local universities and governmental environment divisions also often have lists that may be used.

In practice, not all of the species that inhabit an area are not determined and thus it is not economically feasible nor recommended that all non-indigenous species are removed from the area you wish to repair. However, if certain species becomes a pest, and it is determined that they are non-inginious, it is advised that the species is eradicated fully. An aid in determining the species that has become a pest may be the DAISY, and the barcode of life[1]

Animal types[edit | edit source]

Several marine animals besides fish exist, algae, non-coral reef builders (oysters, kelp, mussels), ...

Soft Coral, and Non-Coral Reef Builders[edit | edit source]

Requirements of Soft Coral, and Non-Coral Reef Builders[edit | edit source]

If your goals include rehabilitation of both fish and soft corals, be sure to read the section regarding fish. This article deals with reef rehabilitation projects that do not intend to target hard corals, either due to budget, climate, or site conditions. This is a common goal in non-tropical or subtropical areas or in tropical areas with high sedimentation, variable salinities, low visibility, deep water or other conditions that prevent reef building hard coral growth on firm substrates. In these cases, it is still important to take into account water quality requirements of soft and hardy coral and/or other desirable reef building marine creatures (such as oysters, kelp, blue mussels etc.) that will inhabit the chosen substrate to create a reef ecosystem. This type of project can be used when a more natural reef is desired than a ‘fish-only’ project can provide. Perhaps divers will visit the reef or perhaps the reef is being built for habitat rehabilitation purposes. Possibly, the project orientation is ‘fish only’, but there might not be any extra cost to make the project more suitable for other benthic marine life.

To develop a good fouling community, it is best to make sure dissolved oxygen (DO) levels are not below species-specific requirements. Use a Dissolved Oxygen (DO) Test Kit if you are in a location where you suspect low oxygen levels. Test at times you believe the levels will be the lowest such as during calm, hot weather events, neap tides, or if the project is coastal, after heavy rains. Minimum DO levels vary widely by species. In general, benthic communities can tolerate lower oxygen levels than fish, so if your project targets both, be sure to use the threshold of the most sensitive species. As mentioned above, most organisms can survive as long as oxygen does not dip below 5mg/l (milligrams per liter), and only the hardiest can survive DO levels below 2mg/l. If your conditions are intermediate, or you are unsure, consult a local expert.

Salinity will also play a role, at different ranges for different fouling communities. Salinity is typically measured with a hydrometer (specific gravity meter) or refractometer. In general, as you move toward more sensitive soft corals and hardy hard corals; salinity levels must remain fairly constant over time. When working with fouling communities, the effect of currents, light and plankton levels play an important role. In general, the more current, light and plankton present, the faster the fouling community will grow. Oysters and other filter feeding communities do not directly require light, as long as current conditions are sufficient to provide enough plankton to feed them. Corals are divided into two classes, some are phototropic (requiring light), and in addition to filter feeding, these species photosynthesize to produce energy, with the help of symbiotic zooxanthellae (a brown algae which lives inside the coral tissue). Others are non-phototropic, and do not need light to grow. These corals are strictly filter feeders. Depending on the requirements of your target species, you may need to alter your site selection (see Step 4: Site Selection) to accommodate the needs of the species in question. If you are unsure of what conditions are required for your project, consult an expert.

Data for these parameters may be available in local scientific literature, or you may be able to ask a local expert for assistance. In a pinch, light penetration can be approximated using a secchi disk or calculated using a standard photographic light meter at the surface, a secchi disk, and Beer’s Law (see glossary for help with this calculation). Plankton levels can be approximated by measuring the level of chlorophyll in the water, which can be done by most basic science labs. Current is a bit more difficult, and here, it is best to seek out local knowledge from the fishing or diving community, or local scientists. In a pinch, surface current can be measured by dropping a floating object into the water, and timing how long it takes to move a known distance (make sure your boat is well anchored and is not moving). However, if you are doing this, it is important to measure currents at various periods of the tidal cycle, and during different types of weather.

If the project is species specific, its goals will be best served by selecting substrate materials that will encourage the growth of the specific target organism(s). This is because soft coral, oysters, mussels, kelp and most other non-coral reef producing creatures are fairly rapid growers. For this type of rehabilitation, check with your module manufacturer or local scientists to determine what module features complement the water quality in the area to achieve these goals. Items to consider when selecting modules are: material longevity, complexity, available surface area, stability, cost, surface textures, ability to create protective void space, and suitability to your project goals.

You may need to look at some very species-specific requirements. Oysters and kelp have tight site specific requirements. Many soft and hardy hard coral species need good water quality, but can tolerate temperature changes and higher levels of turbidity better than their tropical reef cousins. Again, talk with your module manufacturers or scientific specialists for your area specific requirements. Narrow down target fouling community types or non-coral reef building species to types that can be supported by the water quality at your selected site. If the communities supported by your site are not in line with your goals, go back to site selection.

If your goals include tropical coral re-stabilization or coral propagation and planting to speed up the development of a coral reef ecosystem, water quality will indeed be a very important variable. Before you invest a great deal of time and effort, however, remember from Step 1: Damage Assessment & organising the project that if you are rehabilitating a reef in its original location and only using brood stock from that location you may skip this process if there have been no changes to water quality, and move on to Permitting, because water quality has not changed from what you know to support the life on your site. Note: If you are building a new reef, you should ensure that the project goals included selecting a site with the best possible water quality available.

Once the best site has been determined, the next step is to determine which coral you will be able to successfully work with and plant. Coral cannot be planted in every desired location. Common sense will dictate that water quality, lighting conditions, and any other requirements of a coral species must be present before one can re-stabilize or propagate and plant that coral species with success. Often (but not always), if you can’t find a coral species growing naturally on hard substrates in an area, you will not be able to plant that species with success. However, there are soft bottom areas where coral species may not be present but could be if hard bottom was supplied.

Start by assuming that any coral that you can find within a reasonable distance (say 30 miles or an hour’s boating range) and of similar water quality as of your site has the possibility of being planted or stabilized on the selected site. Local coral identification books, often found at local dive shops can often provide an initial list. Next, narrow down the list of usable corals by eliminating corals not found growing naturally in areas which match your site in the following criteria:

  • Water Depth/ Lighting Level Range
  • Water Temperature Range
  • Saliently Range
  • Current/ Wave Climate Preferences
  • Biological Tide Line
  • Sedimentation Tolerance
  • Species not Amenable to Propagation, Transplant or Stabilize
  • Species not Cost Effective to Propagate, Transplant or Stabilize
Water Depth and Lighting Level Range[edit | edit source]

The first variable, water depth range, should already have been recorded in your survey. By looking at the natural reefs in these depth ranges, you will get an idea of which coral species you might be able to propagate and plant. A first point of reference might be coral reference guides as they contain species reported depth ranges. Note: Scientific coral reference guides tend to be broader in scope and contain more details than the local coral reference guide mentioned in above for obtaining an initial species list. In coral reference guides, reported ranges are the maximum reported ranges for the species so it is always better to try to get corals into the mid range of their depth tolerance. Depth ranges are usually based on light availability, which is critical for most tropical coral species. In optimal light ranges coral can thrive, in sub-optimal light they can survive, but may not grow as fast, or at all. Below or above the acceptable range they will slowly die. Conversely, if too much light (or a rapid change from darker to lighter conditions happen) they will sunburn or overheat which is usually fatal. Treat coral just like you would a plant…learn what lighting levels are correct for the individual coral or ‘plant’. If you must change those conditions do so slowly, just as you would acclimate a plant to changes in light levels. You would not put a houseplant in the full sun nor try to grow tomatoes in dim lighting. Use the same techniques with coral. If your team has a good coral expert, this person will give you advice about what lighting levels are appropriate for individual species. Knowing the local depth range of a species can give your team good clues as well. If you really want to be sure, you can buy a light meter that measures lux, lumen or candlepower and have an underwater case built for it, or use the light meter in conjunction with a secchi disk to calculate light penetration using Beer’s Law. There are several underwater light meters for underwater photographers that can be adapted for this purpose. Simply take a reading from where you are sourcing your broodstock, and be sure that you are moving the corals to areas with similar conditions. Take all readings at the same time of day under clear skies and make sure to adjust for changes in surface lighting by calculating the fraction of surface light which reaches a coral. Simply divide surface reading by reading at the bottom at the same time, and multiply the result by 100 to get percent surface light penetration: (Surface light/Bottom light).100=available surface light

Narrow down the species by eliminating those for which you cannot provide appropriate water depths or lighting ranges.

Water Temperature Range[edit | edit source]

Water temperature range is critical. If you have an open water site the temperature range is probably similar to other open water sites at the same depth but this is not always true. Upwelling, oceanic currents and other factors can affect a particular site’s temperature range. There are many websites that can help you determine the Sea Surface Temperature (SST) range but it is much harder to find ranges at depth were your coral would be planted. Sometimes the easiest way is to simply use a direct temperature measurement, but be aware that many factors including tidal cycle, time of day, and prevailing weather conditions can affect the temperature at a site, so be sure that your measurements are comparable.

If you are close to shore or in a lagoon or bay with restricted or tidal flushing, your site may be subject to higher temperatures that might limit the coral species to those that can survive in those conditions. Some coral reference guides give temperature ranges for specific species. Typically, tropical corals flourish in temperature ranges of 19-30oC (66oF-86oF). The highest normal range we have seen for a coral is 33.9°C or 93°F., (in the case of corals in Kuwait). Corals that can tolerate temperatures ranges below 10oC or 50oF are generally termed Hardy Corals for purposes of this manual. But tropical corals can often tolerate slightly lower or higher temperatures for very brief periods. There has been research in American Samoa that indicates that corals can tolerate temperatures above their normal ranges when water movement is high (Mike King, American Samoa, 2005-2007) but this is not to surprising because the real danger of high water temperature is low oxygen content which can exacerbate bleaching. Narrow down the species that you do not have appropriate temperature ranges for.

Salinity Range[edit | edit source]

If your project is in the open ocean, salinity is most likely not a serious concern, but projects near large sources of freshwater may have a limited number of coral species available. Occasionally salinity can play a localized role in open water sites. For example, off the coast of the Riviera Maya in Mexico, there are numerous cenotes (or underground springs) and many coral species cannot be placed within the influence range of these springs. These situations demand extra caution because the influenced area may grow exponentially in size during the wet season the same is true for large rivers. Projects on islands that have mountains or high relief must be especially cautious in this regard. It is also important to consider that fresh water can impact the availability of oxygen (by intensifying stratification), and increase turbidity, both factors which can be detrimental to corals. Eliminate species that you cannot provide appropriate salinity ranges for.

Current/Wave Climate Preferences[edit | edit source]

Many coral species prefer certain currents or wave climates. Elkhorn coral (Acropora palmata) prefers the highly oxygenated waters near breaking waves, whereas delicate Distichopora spp. and other solitary corals prefer the confines of a calm cave. Most coral can adapt to a range of wave climates if they are started as small fragments and allowed to grow into a form (morphology) adapted for the conditions (within the limits of the species). But adult coral colonies cannot adapt as easily to changes and can respond negatively to changes in any and/or all parameters. This may be one reason why planted fragments have higher success rates than transplanted adult colonies. Eliminate the species for which you cannot provide appropriate Current/Wave Climate. (Note: this may restrict transplant of adult colonies but not fragments for some species.)

Biological Tide Line[edit | edit source]

If you are planting in shallow water, especially in areas with very high tide ranges, then you must be mindful of the biological tide line, the highest point where hard corals can grow without being overly exposed to air during low tide. The biological tide line can be different for different species, depending upon their tolerance to light and dessication; but for most shallow water species it is a fairly well defined depth. It is not advisable to calculate this from tide charts, rather, it is much more effective to look for obvious signs of the maximum natural reef crest and use that as your benchmark to adjust minimum depths for planting. Keep in mind that corals will grow upward. So you may need to plant well below the biological tide line to allow for upward growth. Note that the biological tide line can vary due to tidal cycles that are longer than a month; so when in doubt, plant a little bit deeper if resources permit. Note: In addition to monthly and annual tides, their can be tidal variations over multiple years. For example, there is month or two of extreme tides in the Caribbean about every 17 years. (Source:Dr. Lee Harris) Eliminate the species that you cannot plant below their biological tide line while still allowing for normal growth.

Sedimentation Tolerance[edit | edit source]

Suspended sediment in the water poses a number of health hazards to corals, and must be carefully monitored. Different coral species often have a strict range of acceptable prey size. Sediment particles of the same size that a coral normally preys upon can therefore interfere with feeding. Additionally, sedimentation can cause a coral to produce excessive mucus to clear its polyps that requires energy expenditure. Finally, sediment can block sunlight from getting to a coral’s zooxanthellae, reducing its ability to photosynthesize energy. Extreme sediment can completely cover a coral colony and this will kill most colonies within a few days or weeks.

File:Repairing damaged reefs terminology image 35
Results of a sediment grain size analysis. A sample of sand is passed through stacked sieves with decreasing sized mesh. The proportion of the sample retained in each sieve can be used to approximate the distribution of grain sizes in the sediment at the site.

If you are concerned about higher sedimentation rates, you may want to start by analyzing the grain size distribution, sand composition, or amount of sediments transporting through your site. For example, sediment or sand sieve analysis can be performed to see what size particles are present. This is not a serious concern if you are moving corals from an area of more sedimentation to an area of less sedimentation presuming particle sizes are similar in distribution, but be extremely wary of moving a coral species into an area with increased sedimentation rates.

File:Repairing damaged reefs terminology image 37
Construction of a basic sediment trap to estimate sedimentation rates at a project site. Sediment accumulates in the PVC tubes, and can be retrieved and measured (by weight or volume) by removing the caps at the bottom of the PVC tubes and collecting the sediment within. Note: This method only provides a relative estimate of the amount of sediment at a specific depth, and not an exact value because it measures the vertical settling of sediment, and not horizontal transport.

It is also very important to know how much sediment is traveling at a particular height off the bottom at your site. This is critical, because it is an essential component in determining how high a particular coral species must be planted above the sea floor to avoid sedimentation stress. A simple sediment trap (Figure 9, also available in sketch-up) can be made to determine what level of sediment a particular coral can tolerate in its natural habitat, and then these data can be applied to your planting strategy. The length of time the trap must be in place depends on the volume of sediment in the area, but the duration should be the same in all your samples so sediment volume or weight is comparable. If it is impossible to use identical duration, be sure to calculate sedimentation rate relative to time (e.g. milligrams per day) in order to correct for variations in deployment time. Note the design allows for adjustable heights and easy retrieval of the sediment trap collection tubes.Eliminate species for which you cannot provide a location with low enough sedimentation rate.

“Non-Worthy” Corals[edit | edit source]

Many coral species simply are not worth the effort involved in propagating and planting them. This depends greatly on the goals of your project. Non-reef building corals that don’t add complexity or contribute to usable protective void space might not be worth the effort for projects that have goals emphasizing fish production, but if the goal of your project is to maximize coral diversity, or to replicate natural coral assemblages as much as possible, the extra effort may be justified. In addition, some coral species may already be prevalent at the site, or may naturally re-establish themselves so rapidly that it is inefficient to devote resources to their propagation or transplant. The latter is often the case for many common soft coral species. Propagation is typically the most time consuming and expensive portion of a project, so it is very important to make sure that propagation efforts directly support the project goals. Remember, most properly selected, sited and designed base materials will eventually turn into a natural reef without any assistance at all, propagation and transplant just speeds the process along. Eliminate species that are not worth the effort.

“Impractical” Corals[edit | edit source]

In almost all cases, insufficient resources are available to transplant every coral species desirable for your project. Economics is a common reason to do a genetic coral rescue instead of a re-stabilization. When resources are limited, is your project better served by rescuing one adult colony or by preserving the genetics of a hundred colonies? On one hand, you have one large beautiful colony and on the other hand planting fragments saves more but may take decades or even centuries to reach the size of that one re-stabilized colony. This is a tough question, and it depends on your answers from your project goals. Similarly, there are many coral species that are just not economically suitable for propagation, either because survival rates are low, or costs are too high. Eliminate species that consume more project resources than the benefits they provide.

“Impossible” Corals[edit | edit source]

Sometimes, you will have to accept the fact that a coral species (or at least some individual colonies) cannot be saved. Some corals cannot be propagated, transplanted or re-stabilized by professionals, much less grassroots organizations. Perhaps there is no stock left after a disaster, or the remaining stock is so diseased or injured that rescue efforts would not be effective. Perhaps the damage is in a place that is too remote or deep to facilitate safe access. In these cases, it is best to devote resources to re-stabilizing, propagating, and rehabilitating colonies that have a higher success rate without posing safety hazards to your team. Eliminate species that are impractical or impossible to save and note whether this applies to individual coral colonies or all colonies of a certain species.

Hard Coral Species Only[edit | edit source]

Occasionally, your project may be concerned only with tropical hard coral. This is a common goal for research projects, coral farming, or coral breeding. Most of these projects have a temporary rather than long term focus because the corals are ultimately used in another location. This manual is focused around long term rehabilitation projects, but can be adapted for projects with both short and long term goals by simply adding any short term objectives to your goals. If your project goals are short term only, you probably won’t need to take as much care in substrate selection or in long term coral basing needs. Often, steel and wire frames, such as those used to create temporary disaster nurseries are sufficient. There are several emerging technologies aimed to accelerate coral growth. These include captive breeding techniques,ocean based feeding, calcium supplementation, “accretion” or electricity based calcium supplementation. Temporary projects such as these are outside the scope of this manual, but there are resources out there to assist your team. A good place to start your search might be the Geothermal Aquaculture Research Foundation (GARF) website at , or, both popular sustainable reef-keeping forums. For electricity based calcium supplementation, which has an added benefit of creating substrate, check into the Global Coral Reef Alliance (GCRA).

Specific target species[edit | edit source]

Specific target species include eg lobster, grouper, ...

Requirements of specific Target Species[edit | edit source]

In addition to the fish and coral species addressed earlier in this step, your project may have some very specific target species. These may include the rehabilitation of commercially or recreationally important species such as lobster, abalone, octopus, grouper, snapper, or any of the hundreds of species heavily exploited by humans. Most species that have high human value also have a great deal of information regarding their needs available in the scientific literature. If your project has targeted interest in the rehabilitation of a specific species, it is advisable to seek out experts in that particular species. There are often very specific things you can do to better accommodate a particular species. This may be a combination of multiple factors including base design, layout, height, or specific habitat requirements. Your target species may also have specific water quality needs that must be considered in your [Original_environment_rehabilitation_manual_3.363|site selection]]. Make notes to investigate specific species requirements if these species are an important part of your goals.

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