Pollution, fishing, and outbreaks of predators can heavily impact coastal coral reef ecosystems, leading to decreased water quality and benthic community shifts. To determine the main environmental drivers of coral reef status in the Spermonde Archipelago, Indonesia, we monitored environmental variables and coral reef benthic community structure along an on-to-offshore gradient annually from 2012 to 2014. Findings revealed that concentrations of phosphate, chlorophyll a-like fluorescence, suspended particulate matter, and light attenuation significantly decreased from on-to-offshore, while concentrations of dissolved O₂ and values of water pH significantly increased on-to-offshore. Nitrogen stable isotope signatures of sediment and an exemplary common brown alga were significantly enriched nearshore, identifying wastewater input from the city of Makassar as primary N source. In contrast to the high temporal variability in water quality, coral reef benthic community cover did not show strong temporal, but rather, spatial patterns. Turf algae was the dominant group next to live coral, and was negatively correlated to live coral, crustose coralline algae (CCA), rubble and hard substrate. Variation in benthic cover along the gradient was explained by water quality variables linked to trophic status and physico-chemical variables. As an integrated measure of reef status and structural complexity, the benthic index, based on the ratio of relative cover of live coral and CCA to other coral reef organisms, and reef rugosity were determined. The benthic index was consistently low nearshore and increased offshore, with high variability in the midshelf sites across years. Reef rugosity was also lowest nearshore and increased further offshore. Both indices dropped in 2013, increasing again in 2014, indicating a period of acute disturbance and recovery within the study and suggesting that the mid-shelf reefs are more resilient to disturbance than nearshore reefs. We thus recommend using these two indices with a selected number of environmental variables as an integral part of future reef monitoring.

Farming of Eucheuma denticulatum is a major activity in Zanzibar affecting seagrass ecosystems primarily through shading and trampling. The aim of this study was to test the impacts of shading and trampling during seaweed farming on seagrass meadows composed by Halophila stipulacea and Thalassia hemprichii and their associated benthic macroalgae. Areas covered by these species were selected for the building of seaweed farms in three treatments: seaweed farm plots (with shading and trampling effects), trampling plots (with trampling effects only), and control plots (with no shading or trampling effects). Reduction of light within the plots was recorded over 9 weeks. Percentage cover of seagrasses and macroalgae and shoot density of seagrasses were measured over 12 weeks to assess the impact of shading and trampling by seaweed farming activities. Light was significantly reduced in the seaweed farm plots by 75 to 90% by the end of a seaweed growth cycle. H. stipulacea, despite its capacity for rapid growth, was significantly affected by the combination of shading and trampling under the seaweed farm treatment, while the climax seagrass species T. hemprichii was unaffected. Due to the decline in H. stipulacea, benthic macroalgae cover increased in the seaweed farm treatment, suggesting a change in seagrass community dynamics. In contrast, trampling had a negative effect on the benthic macroalgae as an isolated disturbance, which suggests that seagrasses are more resistant to trampling than macroalgae and would likely dominate the benthic macrophyte community under these conditions.

Increasing temperature and CO₂ concentration are among the most important factors affecting marine ecosystems under climate change. We investigated the morphological, biochemical, and physiological trait responses of seedlings of the tropical seagrass Enhalus acoroides under experimental conditions. Trait responses were greater under temperature effects than increasing CO₂ concentration. Seedlings under rising temperatures showed enhanced leaf growth, lower leaf nutrient content, and stimulated down-regulating mechanisms in terms of photo-physiology. Increasing CO₂ concentrations did not show any significant effects independently. There was a significant interaction for some of the trait responses considered, such as leaf number and carbon content in the roots, and trends of higher starch concentrations in the leaves and lower rETR_max under combined enriched CO₂ and high temperature, even though none of these interactions were synergistic. Understanding the single and interactive trait responses of seagrass seedlings to increasing temperature and CO₂ concentration is of importance to determine the relative responses of early life stages of seagrasses, which may differ from adult plants, in order to form a more holistic view of seagrass ecosystem health under climate change.

Ocean acidification studies in the past decade have greatly improved our knowledge of how calcifying organisms respond to increased surface ocean CO2 levels. It has become evident that, for many organisms, nutrient availability is an important factor that influences their physiological responses and competitive interactions with other species. Therefore, we tested how simulated ocean acidification and eutrophication (nitrate and phosphate enrichment) interact to affect the physiology and ecology of a calcifying chlorophyte macroalga (Halimeda opuntia (L.) J.V. Lamouroux) and its common noncalcifying epiphyte (Dictyota sp.) in a 4-week fully crossed multifactorial experiment. Inorganic nutrient enrichment (+NP) had a strong influence on all responses measured with the exception of net calcification. Elevated CO2 alone significantly decreased electron transport rates of the photosynthetic apparatus and resulted in phosphorus limitation in both species, but had no effect on oxygen production or respiration. The combination of CO2 and +NP significantly increased electron transport rates in both species. While +NP alone stimulated H. opuntia growth rates, Dictyota growth was significantly stimulated by nutrient enrichment only at elevated CO2, which led to the highest biomass ratios of Dictyota to Halimeda. Our results suggest that inorganic nutrient enrichment alone stimulates several aspects of H. opuntia physiology, but nutrient enrichment at a CO2 concentration predicted for the end of the century benefits Dictyota sp. and hinders its calcifying basibiont H. opuntia.