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1. Vertical structure of flows on a shallow reef flat: A coral reef surf zone

   https://doi.org/10.1016/j.coastaleng.2024.104499  

   Monismith, Stephen G.; Maticka, Samantha A.; Rogers, Justin S.; Hefner, Ben; Woodson, C. Brock (June 2024, Coastal Engineering)
2. Bottom Stress and Drag on a Shallow Coral Reef

   https://doi.org/10.1029/2024JC021528  

   Boles, Elisabeth; Khrizman, Alexandra; Hamilton, Jenny; Mucciarone, David; Dunbar, Robert; Koseff, Jeffrey; Monismith, Stephen (November 2024, Journal of Geophysical Research: Oceans)

   Abstract Coral reef roughness produces turbulent boundary layers and bottom stresses that are important for reef metabolism monitoring and reef circulation modeling. However, there is some uncertainty as to whether field methods for estimating bottom stress are applicable in shallow canopy environments as found on coral reefs. Friction velocities () and drag coefficients () were estimated using five independent methods and compared across 14 sites on a shallow forereef (2–9 m deep) in Palau with large and spatially variable coral roughness elements (0.4–1 m tall). The methods included the following: (a) momentum balance closure, (b) log‐fitting to velocity profiles, (c) Reynolds stresses, (d) turbulence dissipation, and (e) roughness characterization from digital elevation models (DEMs). Both velocity profiles and point turbulence measurements indicated good agreement with log‐layer scaling, suggesting that measurements were taken within a well‐developed turbulent boundary layer and that canopy effects were minimal. However, estimated from the DEMs, momentum budget and log‐profile fitting were consistently larger than those estimated from direct turbulence measurements. Near‐bed Reynolds stresses only contributed about 1/3 of the total bottom stress and drag produced by the reef. Thus, effects of topographical heterogeneity that induce mean velocity fluxes, dispersive stresses, and form drag are expected to be important. This decoupling of total drag and local turbulence implies that both rates of mass transfer as well as values of fluxes inferred from concentration measurements may be proportional to smaller, turbulence‐derived values of rather than to those based on larger‐scale flow structure. 

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3. Loss of reef roughness increases residence time on an idealized coral reef

   https://doi.org/10.1038/s41598-022-24045-4  

   Lindhart, M. (December 2022, Scientific Reports)

   Abstract Through idealized, numerical models this paper investigates flows on a reef geometry which has received significant attention in the literature; a shallow, fringing reef with deeper, shore-ward pools or lagoons. Given identical model geometries and varying only reef flat drag coefficients between model runs ( $$C_D = [0.001,0.005,0.01,0.05,0.1]$$ C D = [ 0.001 , 0.005 , 0.01 , 0.05 , 0.1 ] ), two distinct circulation patterns emerge. One is related to low reef water levels and high roughness, and efficiently flushes the entire reef system resulting in low residence times (an ‘open reef’). The other is related to high reef water levels and low roughness, and in spite of the development of an offshore undertow, this dynamic is inefficient at flushing the reef-pool system and facilitating exchange flow with offshore waters (a ‘closed reef’). This paper shows that even given indistinguishable geometry and offshore conditions, this information is insufficient to predict reef dynamics, and suggests that reef roughness (and thus reef health) plays a comparable role in determining circulation patterns and residence times. Furthermore, a transition from open to closed or vice versa caused by e.g., a loss of reef roughness or increase in mean sea level could have implications for transport and mixing of nutrients and water masses, as well as larval dispersal. 

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4. The coral ecosphere: A unique coral reef habitat that fosters coral-microbial interactions

   https://doi.org/10.1002/lno.11190  

   Weber, Laura; Gonzalez-Díaz, Patricia; Armenteros, Maickel; Apprill, Amy (January 2019, Limnology and Oceanography)

   Scleractinian corals are bathed in a sea of planktonic and particle-associated microorganisms. The metabolic products of corals influence the growth and composition of microorganisms, but interactions between corals and seawater microorganisms are underexplored. We conducted a field-based survey to compare the biomass, diversity, composition, and functional capacity of microorganisms in small-volume seawater samples collected adjacent to five coral species with seawater collected > 1 m away from the reef substrate on the same reefs. Seawater collected close to corals generally harbored copiotrophic-type bacteria and its bacterial and archaeal composition was influenced by coral species as well as the local reef environment. Trends in picoplankton abundances were variable and either increased or decreased away from coral colonies based on coral species and picoplankton functional group. Genes characteristic of surface-attached and potentially virulent microbial lifestyles were enriched in near coral seawater compared to reef seawater. There was a prominent association between the coral Porites astreoides and the coral symbiont Endozoicomonas, suggesting recruitment and/or shedding of these cells into the surrounding seawater. This evidence extends our understanding of potential species-specific and reef site-influenced microbial interactions that occur between corals and microorganisms within this near-coral seawater environment that we propose to call the “coral ecosphere.” Microbial interactions that occur within the coral ecosphere could influence recruitment of coral-associated microorganisms and facilitate the transfer of coral metabolites into the microbial food web, thus fostering reef biogeochemical cycling and a linkage between corals and the water column. 

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5. Influence of reef habitat on coral microbial associations

   https://doi.org/10.1111/1758-2229.70051  

   Gantt, Shelby_E; Kemp, Keri_M; Colin, Patrick_L; Hoadley, Kenneth_D; LaJeunesse, Todd_C; Warner, Mark_E; Kemp, Dustin_W (November 2024, Environmental Microbiology Reports)

   Abstract Corals have complex symbiotic associations that can be influenced by the environment. We compare symbiotic dinoflagellate (family: Symbiodiniaceae) associations and the microbiome of five scleractinian coral species from three different reef habitats in Palau, Micronesia. Although pH and temperature corresponded with specific host‐Symbiodiniaceae associations common to the nearshore and offshore habitats, bacterial community dissimilarity analyses indicated minimal influence of these factors on microbial community membership for the coralsCoelastrea aspera,Psammocora digitata, andPachyseris rugosa. However, coral colonies sampled close to human development exhibited greater differences in microbial community diversity compared to the nearshore habitat for the coral speciesCoelastrea aspera,Montipora foliosa, andPocillopora acuta, and the offshore habitat forCoelastrea aspera, while also showing less consistency in Symbiodiniaceae associations. These findings indicate the influence that habitat location has on the bacterial and Symbiodiniaceae communities comprising the coral holobiont and provide important considerations for the conservation of coral reef communities, especially for island nations with increasing human populations and development. 

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