This study examined patterns of coral reproduction and recruitment on lagoonal reefs adjacent to Mombasa in Kenya, at latitude 4ºS. Very little detailed research has been done on the reproductive patterns of scleractinian corals on equatorial reefs, where it has been suggested that seasonality and spawning synchrony may break down due to the weak environmental cues that are thought to govern the onset and timing of reproduction. Gametogenic data were collected for three faviid (Echinopora gemmacea, Platygyra daedalea and Leptoria phrygia) and three Acropora species (A. tenuis, A. valida and Acropora sp.1) in the Mombasa Marine National Park and Reserve between April 2003 – May 2005. A further 20 species of Acropora were identified (9 species represented range extensions) and marked to examine intra- and inter-specific spawning synchrony within this genus. In comparison to other regions, the overall pattern of coral reproduction in Kenya was found to be asynchronous, with spawning occurring over 9 months of the year from August – April, with some level of ‘temporal reproductive isolation’ occurring between species in relation to the main lunar month and lunar quarter when spawning occurred. Proximate cues governing the timing of reproduction could not be clearly discerned in Kenya with spawning occurring during both rising and maximum temperatures, during both neap and spring tides and across all lunar phases. Acropora species spawned over a 7-month period between October – April and faviid species over a 5-month period from December - April. The timing of reproduction in Acropora varied both within and among species, with the main release of gametes occurring from January – March when sea surface temperatures were at their summer maximum. Individual species released gametes over 2-5 months. The greatest overlap in spawning Acropora species occurred in February, which coincided with the spawning months of P. daedalea and E. gemmacea and suggests that some degree of multispecific spawning is a characteristic of Kenyan reefs. Within the main spawning period individual Acropora species had their main spawning in different lunar months. Acropora species released gametes in all lunar quarters, with the highest number of colonies and species spawning in the 3rd lunar quarter (i.e. in the 7 nights after full moon). Spawning in the faviids was more synchronised than Acropora species with the majority of faviid corals spawning in the 3rd lunar quarter. Single annual cycles of gametogenesis were recorded in E. gemmacea, A. tenuis, L.phrygia, most colonies of A. valida and Acropora sp.1, and in 84% of P. daedalea colonies. Biannual cycles of gametogenesis were recorded in 16% of P.daedalea colonies, which included two morphotypes identified in the Mombasa lagoon through morphometric and genetic studies. The presence of different oocyte sizes in L.phrygia during gametogenesis suggested that in some colonies there were two slightly overlapping oogenic cycles, which terminated in spawning within 1-2 months of each other. Overlapping oogenic cycles have not previously been recorded in hermaphroditic broadcast spawning corals in the tropics. The findings from Kenya support the hypothesis of protracted breeding seasons and a breakdown of spawning synchrony nearer the equator. It is hypothesised that the high fecundities recorded in faviid and Acropora species in Kenya compared to other regions, may allow reef corals to stagger their reproduction over 2-5 months, without incurring a significant reduction in fertilisation rates. Spat from the Family Pocilloporidae dominated settlement tiles in the Marine National Park and Reserve comprising 93.7% of spat, which contrasts with other tropical reefs where Acroporidae spat dominate. Patterns of settlement of Acroporidae spat generally coincided with the timing and extended spawning season in Acropora species in Kenya. The density and relative composition of coral recruits and juvenile corals on natural substrata recorded during this study were similar to those recorded before the 1997-98 bleaching event. There is no evidence to suggest that Kenya’s reefs have undergone a phase-shift in community structure, and reef recovery is occurring post-bleaching with mean percent hard coral cover currently at 25%. The slow rate of recovery of Kenya’s reefs is likely to reflect the scale of the mortality, source and availability of coral larvae as well as post-settlement processes operating at individual sites. In the medium-term, the recovery of Kenya’s reefs appears to be more strongly dependent on larvae from local reefs.

<p>Discoveries in recent years have disclosed the importance of marine cyano-bacteria in the context of primary production and global nitrogen cycling. It is hypothesized here that microbial mats in tropical coastal habitats harbour a rich diversity of previously uncharacterized cyanobacteria and that benthic marine nitrogen fixation in coastal zones is substantial.</p><p>A polyphasic approach was used to investigate cyanobacterial diversity in three tropical benthic marine habitats of different characters; an intertidal sand flat and a mangrove forest floor in the Indian Ocean, and a beach rock in the Pacific Ocean. In addition, nitrogenase activity was measured over diel cycles at all sites. The results revealed high cyanobacterial diversity, both morphologically and genetically. Substantial nitrogenase activity was observed, with highest rates at daytime where heterocystous species were present. However, the three habitats were dominated by non-heterocystous and unicellular genera such as <i>Microcoleus</i>, <i>Lyngbya</i>, <i>Cyanothece</i> and a large group of thin filamentous species, identified as members of the Pseudanabaenaceae family. In these consortia nocturnal nitrogenase activities were highest and <i>nifH</i> sequencing also revealed presence of non-cyanobacterial potential diazotrophs. A conclusive phylogenetic analysis of partial nifH sequences from the three sites and sequences from geographi-cally distant microbial mats revealed new clusters of benthic potentially ni-trogen-fixing cyanobacteria. Further, the non-heterocystous cyanobacterium <i>Lyngbya majuscula</i> was subjected to a physiological characterization to gain insights into regulatory aspects of its nitrogen fixation. The data demon-strated that nitrogenase activity is restricted to darkness, which called upon a re-evaluation of its diazotrophic behaviour.</p>

Discoveries in recent years have disclosed the importance of marine cyano-bacteria in the context of primary production and global nitrogen cycling. It is hypothesized here that microbial mats in tropical coastal habitats harbour a rich diversity of previously uncharacterized cyanobacteria and that benthic marine nitrogen fixation in coastal zones is substantial. A polyphasic approach was used to investigate cyanobacterial diversity in three tropical benthic marine habitats of different characters; an intertidal sand flat and a mangrove forest floor in the Indian Ocean, and a beach rock in the Pacific Ocean. In addition, nitrogenase activity was measured over diel cycles at all sites. The results revealed high cyanobacterial diversity, both morphologically and genetically. Substantial nitrogenase activity was observed, with highest rates at daytime where heterocystous species were present. However, the three habitats were dominated by non-heterocystous and unicellular genera such as Microcoleus, Lyngbya, Cyanothece and a large group of thin filamentous species, identified as members of the Pseudanabaenaceae family. In these consortia nocturnal nitrogenase activities were highest and nifH sequencing also revealed presence of non-cyanobacterial potential diazotrophs. A conclusive phylogenetic analysis of partial nifH sequences from the three sites and sequences from geographi-cally distant microbial mats revealed new clusters of benthic potentially ni-trogen-fixing cyanobacteria. Further, the non-heterocystous cyanobacterium Lyngbya majuscula was subjected to a physiological characterization to gain insights into regulatory aspects of its nitrogen fixation. The data demon-strated that nitrogenase activity is restricted to darkness, which called upon a re-evaluation of its diazotrophic behaviour.

Tropical seagrass ecosystems are highly productive and important for sustaining marine life and associated coastal societies. In this study, the diversity and role of nitrogen-fixing cyanobacteria associated with five common seagrass genera in coastal regions of the western Indian Ocean (WIO; Tanzania) were examined, as well as the impact of anthropogenic activities. Cyanobacteria were characterized morphologically and genetically (16S rRNA and nifH gene phylogeny), as were diel variations in nifH gene expression, NifH protein levels and nitrogenase activity. The results revealed that WIO seagrass beds supported rich cyanobacterial diversity and that these represented approx. 83% of total clones obtained (DNA and RNA nifH clone libraries). Non-heterocystous genera, such as Oscillatoria, Lyngbya, Leptolyngbya, Phormidium and Microcoleus dominated, while heterocystous morphotypes such as Calothrix were less frequent and unicellular morphotypes (e.g. Gloeocapsa, Chroococcus and Chroococcidiopsis) were few. Additionally, the phylogenetic analysis revealed several novel uncharacterized cyanobacterial clades. Cyanobacterial composition and nitrogenase activity varied over seasons and between the seagrass species. Day time nitrogenase activity originated primarily from heterocystous phylotypes, while non-heterocystous filamentous phylotypes fixed nitrogen at night. The highest activity in the diel cycle was 358 ± 232 nmol C2H4 g-1 h-1at 09.00 associated with epiphytes of the seagrass Cymodocea. Nitrogenase activity was consistently lower in anthropogenically disturbed (eutrophication) seagrass sites. Such data suggest that diazotrophic cyanobacteria may be a significant source of ‘new’ nitrogen in the often oligotrophic coastal regions of tropical oceans. It is also proposed that the rapid shifts in the cyanobacterial population and function found may also be used as early disturbance indicator in coastal management practices. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript. / SIDA SAREC Bilateral Marine Sciences Project / The Swedish Foundation for International Cooperation in Research and Higher Education

This study examined patterns of coral reproduction and recruitment on lagoonal reefs adjacent to Mombasa in Kenya, at latitude 4ºS. Very little detailed research has been done on the reproductive patterns of scleractinian corals on equatorial reefs, where it has been suggested that seasonality and spawning synchrony may break down due to the weak environmental cues that are thought to govern the onset and timing of reproduction. Gametogenic data were collected for three faviid (Echinopora gemmacea, Platygyra daedalea and Leptoria phrygia) and three Acropora species (A. tenuis, A. valida and Acropora sp.1) in the Mombasa Marine National Park and Reserve between April 2003 – May 2005. A further 20 species of Acropora were identified (9 species represented range extensions) and marked to examine intra- and inter-specific spawning synchrony within this genus. In comparison to other regions, the overall pattern of coral reproduction in Kenya was found to be asynchronous, with spawning occurring over 9 months of the year from August – April, with some level of ‘temporal reproductive isolation’ occurring between species in relation to the main lunar month and lunar quarter when spawning occurred. Proximate cues governing the timing of reproduction could not be clearly discerned in Kenya with spawning occurring during both rising and maximum temperatures, during both neap and spring tides and across all lunar phases. Acropora species spawned over a 7-month period between October – April and faviid species over a 5-month period from December - April. The timing of reproduction in Acropora varied both within and among species, with the main release of gametes occurring from January – March when sea surface temperatures were at their summer maximum. Individual species released gametes over 2-5 months. The greatest overlap in spawning Acropora species occurred in February, which coincided with the spawning months of P. daedalea and E. gemmacea and suggests that some degree of multispecific spawning is a characteristic of Kenyan reefs. Within the main spawning period individual Acropora species had their main spawning in different lunar months. Acropora species released gametes in all lunar quarters, with the highest number of colonies and species spawning in the 3rd lunar quarter (i.e. in the 7 nights after full moon). Spawning in the faviids was more synchronised than Acropora species with the majority of faviid corals spawning in the 3rd lunar quarter. Single annual cycles of gametogenesis were recorded in E. gemmacea, A. tenuis, L.phrygia, most colonies of A. valida and Acropora sp.1, and in 84% of P. daedalea colonies. Biannual cycles of gametogenesis were recorded in 16% of P.daedalea colonies, which included two morphotypes identified in the Mombasa lagoon through morphometric and genetic studies. The presence of different oocyte sizes in L.phrygia during gametogenesis suggested that in some colonies there were two slightly overlapping oogenic cycles, which terminated in spawning within 1-2 months of each other. Overlapping oogenic cycles have not previously been recorded in hermaphroditic broadcast spawning corals in the tropics. The findings from Kenya support the hypothesis of protracted breeding seasons and a breakdown of spawning synchrony nearer the equator. It is hypothesised that the high fecundities recorded in faviid and Acropora species in Kenya compared to other regions, may allow reef corals to stagger their reproduction over 2-5 months, without incurring a significant reduction in fertilisation rates. Spat from the Family Pocilloporidae dominated settlement tiles in the Marine National Park and Reserve comprising 93.7% of spat, which contrasts with other tropical reefs where Acroporidae spat dominate. Patterns of settlement of Acroporidae spat generally coincided with the timing and extended spawning season in Acropora species in Kenya. The density and relative composition of coral recruits and juvenile corals on natural substrata recorded during this study were similar to those recorded before the 1997-98 bleaching event. There is no evidence to suggest that Kenya’s reefs have undergone a phase-shift in community structure, and reef recovery is occurring post-bleaching with mean percent hard coral cover currently at 25%. The slow rate of recovery of Kenya’s reefs is likely to reflect the scale of the mortality, source and availability of coral larvae as well as post-settlement processes operating at individual sites. In the medium-term, the recovery of Kenya’s reefs appears to be more strongly dependent on larvae from local reefs.

This study examined patterns of coral reproduction and recruitment on lagoonal reefs adjacent to Mombasa in Kenya, at latitude 4ºS. Very little detailed research has been done on the reproductive patterns of scleractinian corals on equatorial reefs, where it has been suggested that seasonality and spawning synchrony may break down due to the weak environmental cues that are thought to govern the onset and timing of reproduction. Gametogenic data were collected for three faviid (Echinopora gemmacea, Platygyra daedalea and Leptoria phrygia) and three Acropora species (A. tenuis, A. valida and Acropora sp.1) in the Mombasa Marine National Park and Reserve between April 2003 – May 2005. A further 20 species of Acropora were identified (9 species represented range extensions) and marked to examine intra- and inter-specific spawning synchrony within this genus. In comparison to other regions, the overall pattern of coral reproduction in Kenya was found to be asynchronous, with spawning occurring over 9 months of the year from August – April, with some level of ‘temporal reproductive isolation’ occurring between species in relation to the main lunar month and lunar quarter when spawning occurred. Proximate cues governing the timing of reproduction could not be clearly discerned in Kenya with spawning occurring during both rising and maximum temperatures, during both neap and spring tides and across all lunar phases. Acropora species spawned over a 7-month period between October – April and faviid species over a 5-month period from December - April. The timing of reproduction in Acropora varied both within and among species, with the main release of gametes occurring from January – March when sea surface temperatures were at their summer maximum. Individual species released gametes over 2-5 months. The greatest overlap in spawning Acropora species occurred in February, which coincided with the spawning months of P. daedalea and E. gemmacea and suggests that some degree of multispecific spawning is a characteristic of Kenyan reefs. Within the main spawning period individual Acropora species had their main spawning in different lunar months. Acropora species released gametes in all lunar quarters, with the highest number of colonies and species spawning in the 3rd lunar quarter (i.e. in the 7 nights after full moon). Spawning in the faviids was more synchronised than Acropora species with the majority of faviid corals spawning in the 3rd lunar quarter. Single annual cycles of gametogenesis were recorded in E. gemmacea, A. tenuis, L.phrygia, most colonies of A. valida and Acropora sp.1, and in 84% of P. daedalea colonies. Biannual cycles of gametogenesis were recorded in 16% of P.daedalea colonies, which included two morphotypes identified in the Mombasa lagoon through morphometric and genetic studies. The presence of different oocyte sizes in L.phrygia during gametogenesis suggested that in some colonies there were two slightly overlapping oogenic cycles, which terminated in spawning within 1-2 months of each other. Overlapping oogenic cycles have not previously been recorded in hermaphroditic broadcast spawning corals in the tropics. The findings from Kenya support the hypothesis of protracted breeding seasons and a breakdown of spawning synchrony nearer the equator. It is hypothesised that the high fecundities recorded in faviid and Acropora species in Kenya compared to other regions, may allow reef corals to stagger their reproduction over 2-5 months, without incurring a significant reduction in fertilisation rates. Spat from the Family Pocilloporidae dominated settlement tiles in the Marine National Park and Reserve comprising 93.7% of spat, which contrasts with other tropical reefs where Acroporidae spat dominate. Patterns of settlement of Acroporidae spat generally coincided with the timing and extended spawning season in Acropora species in Kenya. The density and relative composition of coral recruits and juvenile corals on natural substrata recorded during this study were similar to those recorded before the 1997-98 bleaching event. There is no evidence to suggest that Kenya’s reefs have undergone a phase-shift in community structure, and reef recovery is occurring post-bleaching with mean percent hard coral cover currently at 25%. The slow rate of recovery of Kenya’s reefs is likely to reflect the scale of the mortality, source and availability of coral larvae as well as post-settlement processes operating at individual sites. In the medium-term, the recovery of Kenya’s reefs appears to be more strongly dependent on larvae from local reefs.

Collecting sea cucumbers to supply the high value Chinese dried seafood market is a livelihood activity available to many people in the Western Indian Ocean (WIO), making it an important part of local economies. These fisheries are generally not successfully managed and tropical sea cucumber fisheries show continuing signs of decline. This thesis takes a social-ecological systems approach to guide better management of sea cucumber fisheries and aquaculture in the WIO. Papers 1 and 2 analyse the fishery situation in Zanzibar and find that in the absence of effective management institutions and income alternatives among fishers, leading to dependence, there are unsustainable expanding processes. Paper 3 compares the unmanaged fishery in Zanzibar to the highly controlled situation in Mayotte. In Mayotte, a protection effect is evident and the commercial value of stocks is significantly higher than in Zanzibar. The analysis of the situation in Mayotte demonstrates the importance of matching the fishery – management temporal scales through prepared and adaptive management to avoid processes that reinforce unsustainable expansion. Paper 4 analyses sea cucumber community spatial distribution patterns at a coastal seascape-scale in Mayotte establishing baseline patterns of habitat utilization and abundance, which can be used as reference in management. Paper 5 reviews the potential for sea cucumber aquaculture in the WIO. The review illustrates that this activity, which is currently gaining momentum, does so based on inflated promises and with significant social-ecological risks. Emphasis for improvements is, in this thesis, placed on the importance of prepared and adaptive institutions to govern and control expanding processes of the fishery. These institutional features may be achieved by increasing the level of knowledge and participation in governance and by integration of sea cucumber resources management into higher-level policy initiatives. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.</p>

<p>The present study is one of the first attempts to analyze the societal importance of seagrasses (marine flowering plants) from a Natural Resource Management perspective, using a social-ecological systems (SES) approach. The interdisciplinary study takes place in East Africa (Western Indian Ocean, WIO) and includes in-depth studies in Chwaka Bay, Zanzibar, Tanzania. Natural and social sciences methods were used. The results are presented in six articles, showing that seagrass ecosystems are rich in seagrass species (13) and form an important part of the SES within the tropical seascape of the WIO. Seagrasses provide livelihoods opportunities and basic animal protein, in from of seagrass associated fish e.g. Siganidae and Scaridae. Research, management and education initiatives are, however, nearly non-existent. In Chwaka Bay, the goods and ecosystem services associated with the meadows and also appreciated by locals were fishing and collection grounds as well as substrate for seaweed cultivation. Seagrasses are used as medicines and fertilizers and associated with different beliefs and values. Dema (basket trap) fishery showed clear links to seagrass beds and provided the highest gross income per capita of all economic activities. All showing that the meadows provide social-ecological resilience. Drag-net fishery seems to damage the meadows. Two ecological studies show that artisanal seaweed farming of red algae, mainly done by women and pictured as sustainable in the WIO, has a thinning effect on seagrass beds, reduces associated macrofauna, affects sediments, changes fish catch composition and reduces diversity. Furthermore, it has a negative effect on i.a. women’s health. The two last papers are institutional analyses of the human-seagrass relationship. A broad approach was used to analyze regulative, normative and cultural-cognitive institutions. Cooperation and conflict take place between different institutions, interacting with their slow or fast moving characteristics, and are thus fundamental in directing the system into sustainable/unsustainable paths. Ecological knowledge was heterogeneous and situated. Due to the abundance of resources and high internal control, the SES seems to be entangled in a rigidity trap with the risk of falling into a poverty trap. Regulations were found insufficient to understand SES dynamics. “Well” designed organizational structures for management were found insufficient for “good” institutional performance. The dynamics between individuals embedded in different social and cultural structures showed to be crucial. Bwana Dikos, monitoring officials, placed in villages or landing sites in Zanzibar experienced four dilemmas – kinship, loyalty, poverty and control – which decrease efficiency and affect resilience. Mismatches between institutions themselves, and between institutions and cognitive capacities were identified. Some important practical implications are the need to include seagrass meadows in management and educational plans, addressing a seascape perspective, livelihood diversification, subsistence value, impacts, social-ecological resilience, and a broad institutional approach.</p>

The present study is one of the first attempts to analyze the societal importance of seagrasses (marine flowering plants) from a Natural Resource Management perspective, using a social-ecological systems (SES) approach. The interdisciplinary study takes place in East Africa (Western Indian Ocean, WIO) and includes in-depth studies in Chwaka Bay, Zanzibar, Tanzania. Natural and social sciences methods were used. The results are presented in six articles, showing that seagrass ecosystems are rich in seagrass species (13) and form an important part of the SES within the tropical seascape of the WIO. Seagrasses provide livelihoods opportunities and basic animal protein, in from of seagrass associated fish e.g. Siganidae and Scaridae. Research, management and education initiatives are, however, nearly non-existent. In Chwaka Bay, the goods and ecosystem services associated with the meadows and also appreciated by locals were fishing and collection grounds as well as substrate for seaweed cultivation. Seagrasses are used as medicines and fertilizers and associated with different beliefs and values. Dema (basket trap) fishery showed clear links to seagrass beds and provided the highest gross income per capita of all economic activities. All showing that the meadows provide social-ecological resilience. Drag-net fishery seems to damage the meadows. Two ecological studies show that artisanal seaweed farming of red algae, mainly done by women and pictured as sustainable in the WIO, has a thinning effect on seagrass beds, reduces associated macrofauna, affects sediments, changes fish catch composition and reduces diversity. Furthermore, it has a negative effect on i.a. women’s health. The two last papers are institutional analyses of the human-seagrass relationship. A broad approach was used to analyze regulative, normative and cultural-cognitive institutions. Cooperation and conflict take place between different institutions, interacting with their slow or fast moving characteristics, and are thus fundamental in directing the system into sustainable/unsustainable paths. Ecological knowledge was heterogeneous and situated. Due to the abundance of resources and high internal control, the SES seems to be entangled in a rigidity trap with the risk of falling into a poverty trap. Regulations were found insufficient to understand SES dynamics. “Well” designed organizational structures for management were found insufficient for “good” institutional performance. The dynamics between individuals embedded in different social and cultural structures showed to be crucial. Bwana Dikos, monitoring officials, placed in villages or landing sites in Zanzibar experienced four dilemmas – kinship, loyalty, poverty and control – which decrease efficiency and affect resilience. Mismatches between institutions themselves, and between institutions and cognitive capacities were identified. Some important practical implications are the need to include seagrass meadows in management and educational plans, addressing a seascape perspective, livelihood diversification, subsistence value, impacts, social-ecological resilience, and a broad institutional approach.

Cette étude a pour but d'identifier les principales maladies coralliennes, de quantifier leurs prévalences sur les récifs de la Réunion, d'Afrique du Sud et de Mayotte et de déterminer leurs variations spatiales et saisonnières. Les résultats ont révélé la présence de six grands types de maladies coralliennes. Les prévalences totales moyennes des maladies ont été plus élevées à la Réunion (7.5 ± 2.2%) qu'en Afrique du Sud (3.9 ± 0.8%) et qu'à Mayotte (2.7 ± 0.3%). Les genres coralliens Acropora et Porites ont été les plus vulnérables aux maladies dans les trois régions étudiées. Des variations spatiales et saisonnières ont été détectées pour la maladie de la bande noire (BBD) et les syndromes blancs (WS) à la fois à la Réunion et en Afrique du Sud avec des prévalences plus élevées sur les récifs peu profonds et pendant la saison chaude. Ce travail a également pour but de caractériser deux maladies non décrites à ce jour : le syndrome des patches blancs (PWPS) et le syndrome du patch noir (PBPS) chez Porites. PWPS, observé à fois à la Réunion, en Afrique du Sud et à Mayotte est caractérisé par d'importantes fragmentations tissulaires généralement associées à des corps ovoïdes basophiles ressemblant à des agrégats bactériens. L'analyse bactérienne a révélé une grande variabilité entre les tissus infectés et sains. L'identification des pathogènes responsables de PWPS a également été réalisée en laboratoire. Sur les 14 souches bactériennes sélectionnées et testées, seule la P180R, génétiquement proche de Vibrio tubiashii a généré des signes de PWPS. Pour finir, PBPS, une forme atypique de BBD a été observée sur les récifs de la Réunion. Les suivis réalisés ont montré des variations spatiales et saisonnières avec des prévalences plus élevées sur le platier et pendant l'été. L'histologie a mis en évidence la présence de cyanobactéries et de corps basophiles dans les tissus infectés du corail. L'analyse génétique a révélé la présence d'une plus grande diversité de taxons dans les tissus infectés par PBPS que dans les tissus sains représentés par le genre Vibrio. / During the past two decades, the emergence and spread of infectious diseases have caused substantial declines in the biodiversity and abundance of reef-building corals. Despite their increased global prevalence and virulence, little is known about coral diseases on Indian Ocean coral reefs. This study aims to fill this gap in knowledge by identifying the main coral diseases and quantify their prevalence at three localities Reunion, South Africa and Mayotte, determining their spatial distribution and seasonal variation. Principal findings of this study demonstrated the presence of six main coral diseases including black band disease (BBD), white syndromes (WS), pink line syndrome (PLS), growth anomalies (GA), skeleton eroding band (SEB) and Porites white patch syndrome (PWPS). The overall disease prevalence was higher in Reunion (7.5 ± 2.2%; mean ± SE) compared to South Africa (3.9 ± 0.8%; mean ± SE) and Mayotte (2.7 ± 0.3%; mean ± SE). Acropora and Porites were the genera most vulnerable to disease. Spatial variability was detected in both Reunion and South Africa with BBD and WS more prevalent on shallow than deep reefs. There was also evidence of seasonality in two diseases: BBD and WS, their prevalence being higher in summer than winter. Corals exhibiting signs of PWPS revealed extensive tissue fragmentation, generally associated with ovoid basophilic bodies resembling bacterial aggregates within the mesoglea of the body wall. Other organisms, including Cyanobacteria, Nematoda, Ciliata and endophytic algae, were also observed on diseased tissues and were generally associated with the dead epidermis and cell debris. Results of 16S rRNA sequence analysis revealed a high variability between bacterial communities associated with PWPS-infected and healthy tissues in Porites lutea. Several bacterial ribotypes affiliated to potential putative pathogens notably Shimia marina and Vibrio hepatarius were consistently found among the 16S rRNA sequences derived from the PWPS lesions, and absent and/or poorly represented in HT. Primary pathogens involved in the PWPS were also investigated in this study using traditional culturing techniques and laboratory infection trials. Of the 14 isolates selected for the inoculation trials, only the bacterial strain P180R mostly phylogenetically closely related8 to Vibrio tubiashii with its closest known sister taxon, V. hepatarius, was shown to cause signs resembling those of PWPS and satisfied the four Henle-Koch’s postulates. P180R displayed focalised and progressive tissue paling 12 h after inoculation and visible lesions of PWPS were observed 12 h thereafter. Signs of PWPS appeared on 90% of the exposed coral fragments (27 of 30) under controlled environmental conditions. Moreover, the virulence of this marine pathogen was tested and seemed to be strongly dependent on seawater temperature, resulting in significantly higher tissue loss at 30°C than 28°C and 26°C. Finally, a multidisciplinary approach involving field surveys, gross lesion monitoring, histopathology and 454-pyrosequencing was investigated to characterize an atypical form of BBD named PBPS. Histology revealed cyanobacterial penetration of the compromised tissue as well as the presence of basophilic bodies resembling bacterial aggregates in the living tissue, adjacent to the bacterial mat. Bacterial 16S rRNA sequences yielded a broader diversity of bacterial taxa in PBPS-infected tissues than in healthy tissue, represented by the genus Vibrio (24.9%), followed by sulfate-reducers or sulfide-oxidizers such as Desulfovibrio (20%), Clostridium (12.9%) and Arcobacter (9.9%). PBPS appears to be a multi-stage disease triggered by cyanobacterial invasion and resulting in secondary infections by environmental bacteria that grow in mucus-like decomposing tissue.