Tropical coral reefs provide important ecosystem goods and services that are supported by one or more ecosystem functions (e.g., recruitment, primary production, calcification, and nutrient recycling). Scleractinian corals drive most of these functions, but a combination of global and local anthropogenic stressors has caused persistent shifts from coral- to algae-dominated benthic reef communities globally. Such phase shifts likely have major consequences for ecosystem functions; yet, related knowledge is scarce in general, but particularly at the community level, under ‘in situ’ conditions, and under the influence of changing environmental variables. Thus, we conducted a series of interconnected in situ experiments in coral- and algae-dominated reef communities in the central Red Sea, combining traditional community ecology approaches with novel metabolic and biogeochemical assessments from December 2016 to January 2018. Specifically, we (i) examined the influence of coral-algal phase shifts on recruitment and succession patterns, (ii) assessed the role of benthic pioneer communities in reef carbon and nitrogen dynamics, (iii) developed a novel approach to measure functions of structurally complex reef communities in situ, and (iv) quantified biogeochemical functions of mature coral- and algae-dominated reef communities. The findings suggest that coral-algal phase shifts fundamentally modify critical reef functions at different levels of biological organization, namely from pioneer to mature reef communities. For example, community shifts, through a lower habitat complexity and grazing pressure, decreased the number of coral recruits by >50 %, thereby inhibiting the replenishment of adult coral populations. At the same time, a 30 % higher productivity (annual mean) and increased organic carbon retention in algae-dominated communities supported a fast biomass accumulation and community growth, altering the habitat-specific community metabolism and reef biogeochemistry. Seasonal warming amplified these functional differences between coral- and algae-dominated communities, likely promoting a positive feedback loop of reef degradation under predicted ocean warming. Overall, this dissertation provides quantitative data on critical functions of classical and phase shifted novel reef communities, on tipping points for the collapse of community functions, and potential future winners and losers. The knowledge gained with this thesis helps, thereby, to understand how phase-shifted reef ecosystems function and which services will be generated in comparison to coral-dominated reefs under near-future stress scenarios.

Rates of primary production and community metabolism were monitored over a one year period using the diurnal oxygen method. Certain physico-chemical parameters were also measured, and autotrophic standing crops were estimated. An in-depth study was made of the phytoplankton community and various diversity indicies were calculated. Simple correlations were run between all parameters measured (biotic and abiotic), and their inter-relationships examined. Multiple linear regression analyses were used to develop equations predictive of production and community metabolism. Bluegreen algae were the dominant phytoplankters with blooms occurring in late summer and fall. Yearly mean production was approximately 21 kcal per meter square per day with a mean photosynthetic efficiency of 1.2 per cent. Of the various parameters measured turbidity and water temperature were most important in determining rates of primary production.

Aquatic eutrophication is a serious global problem, associated with phytoplankton blooms, hypoxia, and loss of species. The objective of this thesis was to advance understanding of stream and lake eutrophication within Canterbury (South Island, New Zealand). I investigated three key questions: 1) How do riparian characteristics control stream trophic state, 2) how does stream trophic state in the Canterbury region compare to stream trophic state nationally and internationally, and 3) what factors control trophic state in Te Wairewa/Lake Forsyth. I measured rates of stream community metabolism in 21 Canterbury streams over a gradient of riparian canopy cover, and conducted a literature review of national and international studies of stream metabolism. I also examined the occurrence of cyanobacterial blooms in Te Wairewa in relation to water quality and weather from 17 years of measurements, and performed series of nutrient addition assays on the lake to assess nutrient limitation. I found that riparian characteristics strongly controlled stream trophic state by shading, thereby reducing photosynthetic productivity. This overwhelmed the effects of high nitrate concentrations, which increased primary production. Compared to national and international rates of stream metabolism, Canterbury streams were strongly heterotrophic, with low rates of autotrophic production. Catchment streams draining into Te Wairewa were unlikely to be the main source of nutrients supporting large cyanobacterial blooms. Instead, internal lake nutrient loading mechanisms associated with calm weather were likely to supply blooms. My results emphasize the importance of light limitation, nitrogen and heterotrophy in controlling stream trophic state, and nutrient supply and weather in controlling lake trophic state.

Simultaneous size fractionation of plankton populations associated with NaH^14CO_3 and ^3H-glucose uptake was employed in eutrophic Lake Texoma (Texas and Oklahoma) and oligotrophic Flathead Lake (Montana). Autoradiography was utilized to determine the role of specific microorganisms in community metabolism. Ultraplankton (0.45-10 μm) dominated plankton numbers and metabolic activity in both aquatic systems. Many of the most abundant species were not the most productive, in terms of inorganic C fixation. Rates of heterotrophic uptake of ^3H-glucose were small in comparison to photolithotrophic uptake in both lakes, Photoheterotrophy was more extensive in Flathead Lake, Autoradiographs indicated that bacteria were responsible for observed photoheterotrophy. Oscillatoria sp. exhibited. mixotrophy in Lake Texoma,