Coral Reef Science:  Development Highlights

Eric Borneman

Phylogeny of the order Zoantharia (Anthozoa, Hexacorallia) based on the mitochondrial ribosomal genes. Sinniger, F., Montoya-Burgos, J. I., Chevaldonné, P. and Pawlowski, J. 2005, Marine Biology 147: 1121 - 1128.


Zoantharia (or Zoanthidea) is the third largest order of Hexacorallia, characterized by two rows of tentacles, one siphonoglyph and a colonial way of life. Current systematics of Zoantharia is based exclusively on morphology and follows the traditional division of the group into the two suborders Brachycnemina and Macrocnemina, each comprising several poorly defined genera and species. To resolve the phylogenetic relationships among Zoantharia, we have analyzed the sequences of mitochondrial 16S and 12S rRNA genes obtained from 24 specimens, representing two suborders and eight genera. In view of our data, Brachycnemina appears as a monophyletic group diverging within the paraphyletic Macrocnemina. The macrocnemic genus Epizoanthus branches as the sister group to all other Zoantharia that are sampled. All examined genera are monophyletic, except Parazoanthus, which comprises several independently branching clades and individual sequences. Among Parazoanthus, some groups of species can be defined by particular insertion/deletion patterns in the DNA sequences. All these clades show specificity to a particular type of substrate such as sponges or hydrozoans. Substrate specificity is also observed in zoantharians living on gorgonians or anthipatharians, as in the genus Savalia (Gerardia). If confirmed by further studies, the substrate specificity could be used as reliable character for taxonomic identification of some Macrocnemina.

Molecular evidence suggesting species in the zoanthid genera Palythoa and Protopalythoa (AnthozoaL Hexacorallia) are congeneric. Reimer, J.D., Ono, S., Takashita, K., Tsukahara, J., and Maruyama, T. 2006. Zool Sci 23: 87-94.


Taxonomic status of the zoanthid genera Palythoa and Protopalythoa has been in question for almost a century. Separation of the two genera has been based on traditional morphological methods (colony and polyp form, nematocyst size and form, and number of septa), with Palythoa polyps embedded in a well developed coenenchyme and Protopalythoa polyps standing free and clear of the coenenchyme. Here we sequenced two mitochondrial regions, the cytochrome oxidase I (COI) gene and 16S ribosomal DNA (16SrDNA) genes from Palythoa and Protopalythoa samples from various parts of the world and performed phylogenetic analyses of the sequence data. The phylogenetic trees for both COI and 16SrDNA from Palythoa and Protopalythoa show four monophyletic groups (designated Palythoa tuberculosa, Palythoa heliodiscus, Palythoa mutuki 1 and Palythoa mutuki 2), with levels of sequence divergence (COI and 16SrDNA divergence approximately 0.0-1.1%) similar to or lower than previously found among congeneric species within the closely related genus Zoanthus. Surprisingly, sequence differences among Palythoa tuberculosa, Palythoa mutuki 1 and Palythoa mutuki 2 were negligible (0.0-0.2% for both COI and 16SrDNA), potentially indicating relationships below the species level. Our sequences align well with the few Palythoa and Protopalythoa sequences reported to date. These findings strongly indicate that our samples represent a minimum of two and possibly up to four species (the Palythoa tuberculosa-P. mutuki 1-P. mutuki 2 group, and P. heliodiscus) within the genus Palythoa and that the genus Protopalythoa is erroneous nomenclature.


The state of zoanthid taxonomy has long been questionable and in need of revision. These two papers bring some new information to the systematics of these popular aquarium inhabitants. The findings of Palythoa and Protopalythoa being congeneric and nearly conspecific, especially given the samples' geographic range, is surprising. I would like to see a larger number of types and samples and a replication of this study, for it almost seems implausible. It might be possible that the primers used were too conservative and did not allow for the determination of enough genomic variation of key alleles in this phylogenetic group.

Habib Sekha

The effects of waves and morphology on mass transfer within branched reef corals. Reidenbach, M. A., Koseff, J.R., Monismith, S.G., Steinbuck, J.V. and Genin, A. Limnol. Oceanogr., 51(2), 2006, 1134-1141.


Rates of mass transfer in coral reefs are governed both by the physical flow environment and the morphology of the coral. Laboratory experiments were conducted to estimate mass transfer in unidirectional and oscillatory flows by measuring the rate of dissolution of gypsum cylinders (clods) placed within the branching structure of three morphologically distinct coral species. Unidirectional flows were varied between 2.9 and 14.1 cm s-1 and, as expected, mass transfer rates increased with increasing flow and a more open branch spacing. Depending on morphology and flow, mass transfer rates within the interior of the branching structure were 50 to 75% of that measured outside the coral in free-stream conditions. Oscillatory conditions showed relative mass transfer rates 1.6 to 2.9 times greater than equivalent unidirectional currents. This ratio increased with increasing wave frequency, likely due to the corresponding decrease in the diffusive boundary layer thickness. The ratio also increased with a greater compactness in branch spacing, with mass transfer rates within the coral structure up to 130% of free-stream conditions. We used planar laser-induced fluorescence imaging to study the instantaneous structure of mass advection through the coral. Oscillatory flow acts as a dominant forcing mechanism to generate water motion within the coral structure at levels not attainable with comparable unidirectional currents.


Uptake and release rates (mass transfer rates) of nutrients and waste products, for example, is determined to a large extent by the boundary layer's thickness. This is a thin, stagnant layer of water touching the coral. The thinner this layer is, the faster the exchange rates will be. Usually, a higher water flow rate reduces the boundary layer's thickness; thus a flow is required that's strong enough to keep a coral alive. Within the coral's branches the flow is far lower than on the outside of the colony, and that flow is further reduced with increasing branch density. In the above study, the researchers found that an oscillating flow increased mass transfer rates, likely by reducing the boundary layer's thickness. The increase in mass transfer rates was sometimes severalfold and increased with increasing oscillation frequency. The authors suggest that oscillatory flow acts as the dominant mechanism forcing water motion within the coral colony at a level higher than would be attainable using a comparable unidirectional flow.

Alkaline phosphatase activity in the phytoplankton communities of Monterey Bay and San Francisco Bay. Nicholson, D., Dyhrman, S., Chavez, F. and Paytan, A. Limnol. Oceanogr., 51(2), 2006, 874-883.


Enzyme-labeled fluorescence (ELF) and bulk alkaline phosphatase (AP) activity enzyme assays were used to evaluate the phosphorus (P) status of phytoplankton communities in San Francisco and Monterey bays. Both regions exhibit spatial and temporal variability in bulk AP activity with maximum activities during the early spring and summer periods of high biological productivity. ELF analysis revealed pronounced differences in the makeup of organisms responsible for AP activity in these two environments. In Monterey Bay dinoflagellates are responsible for the bulk of the AP activity. Diatoms infrequently exhibited AP activity. Dinoflagellates that comprised only 14% of all cells counted in Monterey Bay accounted for 78% of AP-producing cells examined. The presence of AP activity in this group suggests that changes in P sources, concentrations, and bioavailability could disproportionably influence this group relative to diatoms in Monterey Bay. In San Francisco Bay, AP production, indicated by ELF, was associated primarily with bacteria attached to suspended particles, potentially used to hydrolyze organic compounds for carbon, rather than to satisfy P requirements. Our results highlight the importance of organic P as a bioavailable nutrient source in marine ecosystems and as a component of the marine P cycle.


From the above abstract the following part is, in my opinion, the most interesting for aquarists:

"In San Francisco Bay, AP production, indicated by ELF, was associated primarily with bacteria attached to suspended particles, potentially used to hydrolyze organic compounds for carbon, rather than to satisfy P requirements. Our results highlight the importance of organic P as a bioavailable nutrient source in marine ecosystems…"

Phosphate, if chemically bound to organics, usually can't be taken up by bacteria. Bacteria excrete an enzyme called alkaline phosphatase for that purpose, which splits the phosphate from the rest of the organic molecule. This allows the phosphate to be taken up by bacteria as a source of phosphor. Bacteria usually do this (excrete the enzyme) if the free inorganic phosphate concentration is very low. The most striking part of the study is that bacteria used the enzyme not to make the phosphate part, but to make the organic part bioavailable. The bacteria (in that particular environment) were apparently not phosphor-limited but organic carbon-limited. That is, it appears as if enough inorganic phosphate (the type of phosphate measurable by hobby test kits) was present in the water, but simple organic carbon compounds were not.

If something like that occurred in an aquarium not limited in inorganic phosphate but limited in simple bioavailable organics, then it would have implications. The organic phosphate compounds would be split by bacteria to obtain the carbon part before most of them could be skimmed out. This would result in an increase in phosphate's concentration because the bacteria would not care about the extra phosphate released. That is, the bacteria would not take the phosphate up and would leave it in the water.

This could be prevented if sufficient simple, non-phosphate containing, organic carbon compounds were present so that bacteria would not be limited by them, reducing their need to split the phosphate-containing organic compounds just to use the organic part and not the released phosphate part. I would speculate that this might be one of the mechanisms for reducing, at least partly, the phosphate concentration by the addition of certain simple organic carbon compounds, e.g., ethanol.

A different mechanism proposed elsewhere is that organic carbon fuels bacteria's growth and multiplication. This growth and multiplication requires phosphor and nitrogen, thus reducing the phosphate and nitrate/nitrite/ammonia concentration.

The mechanism which I proposed (based on the above abstract) is, therefore, different. If organic carbon (but not phosphate), is limited, and if it is dosed, it may reduce the bacteria-driven breakdown of organic phosphate compounds. This would keep them intact for longer periods and might increase the likelihood of their removal by skimming.

Results for phosphate and nitrate concentrations over time during an ethanol (Vodka) dosing experiment, published by Michael Mrutzek and Jörg Kokott in 2004, if measured accurately, support the mechanism I suggested by the initial decrease in phosphate concentration only, and not by the nitrate concentration. This mechanism is probably followed (after a few weeks of dosing) by the bacteria growth/multiplication fueling mechanism. This "fueling mechanism" results in a decrease in both phosphate and nitrate concentrations as opposed to a reduction of only phosphate in the initial part. Note the initial drop in phosphate only, followed by a "steady-state" period and then a drop in both nitrate and phosphate, from a graph of their results:

If you have any questions about this article or suggestions for future topics, please visit the respective author's forum on Reef Central (Eric Borneman's or Habib Sekha's).

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