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Cyanobacteria have dominated marine environments and have been reef builders on Earth for more than three million years (myr). Cyanobacteria still play an essential role in modern coral reef ecosystems by forming a major component of epiphytic, epilithic, and endolithic communities as well as of microbial mats. Cyanobacteria are grazed by reef organisms and also provide nitrogen to the coral reef ecosystems through nitrogen fixation. Recently, new unicellular cyanobacteria that express nitrogenase were found in the open ocean and in coral reef lagoons. Furthermore, cyanobacteria are important in calcification and decalcification. All limestone surfaces have a layer of boring algae in which cyanobacteria often play a dominant role. Cyanobacterial symbioses are abundant in coral reefs; the most common hosts are sponges and ascidians. Cyanobacteria use tactics beyond space occupation to inhibit coral recruitment. Cyanobacteria can also form pathogenic microbial consortia in association with other microbes on living coral tissues, causing coral tissue lysis and death, and considerable declines in coral reefs. In deep lagoons, coccoid cyanobacteria are abundant and are grazed by ciliates, heteroflagellates, and the benthic coral reef community. Cyanobacteria produce metabolites that act as attractants for some species and deterrents for some grazers of the reef communities.

Dinitrogen-fixing organisms in cyanobacterial mats were studied in two shallow coral reef ecosystems: La Reunion Island, southwestern Indian Ocean, Sesoko (Okinawa) Island, and northwestern Pacific Ocean. Rapidly expanding benthic miniblooms, frequently dominated by a single cyanobacterial taxon, were identified by microscopy and molecular tools. In addition, nitrogenase activity by these blooms was measured in situ. Dinitrogen fixation and its contribution to mat primary production were calculated using 15N2 and 13C methods. Dinitrogen-fixing cyanobacteria from mats in La Reunion and Sesoko showed few differences in taxonomic composition. Anabaena sp. among heterocystous and Hydrocoleum majus and Symploca hydnoides among nonheterocystous cyanobacteria occurred in microbial mats of both sites. Oscillatoria bonnemaisonii and Leptolyngbya spp. occurred only in La Reunion, whereas Hydrocoleum coccineum dominated in Sesoko. Other mats dominated by Hydrocoleum lyngbyaceum, Phormidium laysanense, and Trichocoleus tenerrimus occurred at lower frequencies. The 24-h nitrogenase activity, as measured by acetylene reduction, varied between 11 and 324 nmoles C2H2 reduced µg−1 Chl a. The highest values were achieved by heterocystous Anabaena sp. performed mostly during the day. Highest values for nonheterocystous cyanobacteria were achieved by H. coccineum mostly during the night. Daily nitrogen fixation varied from nine (Leptolyngbya) to 238 nmoles N2 µg−1 Chl day−1 (H. coccineum). Primary production rates ranged from 1,321 (S. hydnoides) to 9,933 nmoles C µg−1 Chl day−1 (H. coccineum). Dinitrogen fixation satisfied between 5% and 21% of the nitrogen required for primary production.

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Corals evolved by establishing symbiotic relationships with various microorganisms (the zooxanthellae, filamentous algae, cyanobacteria, bacteria, archaea, fungi and viruses), forming the ‘coral holobiont'. Among them, the endolithic community is the least studied. Its main function was considered to be translocation of photo-assimilates to the coral host, particularly during bleaching. Here, we hypothesize that (i) endolithic algae may show similar primary production rates in healthy or bleached corals by changing their pigment ratios, and therefore that similar production and translocation of organic matter may occur at both conditions and (ii) diazotrophs are components of the endolithic community; therefore, N2 fixation and translocation of organic nitrogen may occur. We tested these hypotheses in incubation of Porites lutea with 13C and 15N tracers to measure primary production and N2 fixation in coral tissues and endoliths. Assimilation of the 13C atom (%) was observed in healthy and bleached corals when the tracer was injected in the endolithic band, showing translocation in both conditions. N2 fixation was found in coral tissues and endolithic communities with translocation of organic nitrogen. Thus, the endolithic community plays an important role in supporting the C and N metabolism of the holobiont, which may be crucial under changing environmental conditions.