Appendix A. A table showing simulation results to determine analysis methods for small data sets.

A table showing simulation results to determine analysis methods for small data sets

<i>Symbiodinium</i> Community Composition in Scleractinian Corals Is Not Affected by Life-Long Exposure to Elevated Carbon Dioxide

<div><p>Ocean acidification (OA) is expected to negatively affect coral reefs, however little is known about how OA will change the coral-algal symbiosis on which reefs ultimately depend. This study investigated whether there would be differences in coral <i>Symbiodinium</i> types in response to OA, potentially improving coral performance. We used denaturing gradient gel electrophoresis (DGGE) of the internal transcribed spacer 2 (ITS2) region of ribosomal DNA to investigate the dominant types of <i>Symbiodinium</i> associating with six species of scleractinian coral that were exposed to elevated partial pressures of carbon dioxide (pCO₂) <i>in situ</i> from settlement and throughout their lives. The study was conducted at three naturally occurring volcanic CO₂ seeps (pCO₂ ∼500 to 900 ppm, pH_Total 7.8 – 7.9) and adjacent control areas (pCO₂ ∼390 ppm, pH_Total ∼8.0 – 8.05) in Papua New Guinea. The <i>Symbiodinium</i> associated with corals living in an extreme seep site (pCO₂ >1000 ppm) were also examined. Ten clade C types and three clade D types dominated the 443 coral samples. <i>Symbiodinium</i> types strongly contrasted between coral species, however, no differences were observed due to CO₂ exposure. Within five species, 85 – 95% of samples exhibited the same <i>Symbiodinium</i> type across all sites, with remaining rare types having no patterns attributable to CO₂ exposure. The sixth species of coral displayed site specific differences in <i>Symbiodinium</i> types, unrelated to CO₂ exposure. Symbiodinium types from the coral inhabiting the extreme CO₂ seep site were found commonly throughout the moderate seeps and control areas. Our finding that symbiotic associations did not change in response to CO₂ exposure suggest that, within the six coral hosts, none of the investigated 13 clade C and D <i>Symbiodinium</i> types had a selective advantage at high pCO₂. Acclimatisation through changing symbiotic association therefore does not seem to be an option for Indo-Pacific corals to deal with future OA.</p></div

Diagram of the portable NDIR CO₂ equilibrator.

<p>The portable CO₂ equilibrator consists of a commercially available non-dispersive infrared (NDIR) CO₂ gas analyser and data logger display interface, in-line air pump, impermeable-walled tubing and a section of gas-permeable membrane that is submerged in water. Air is pumped in a closed loop around the system and equilibrates with CO₂ in seawater.</p

Relationship of seawater <i>p</i>CO₂ and aragonite saturation state (Ω_ar) determined by four different methods: 1) C_T and A_T (n = 25), 2) spectrophotometric pH_T and A_T (n = 45), 3) electrode pH_NBS and A_T (n = 49), and 4) the direct measurement of seawater CO₂ with a NDIR CO₂ equilibrator (n = 46).

<p>Relationship of seawater <i>p</i>CO₂ and aragonite saturation state (Ω_ar) determined by four different methods: 1) C_T and A_T (n = 25), 2) spectrophotometric pH_T and A_T (n = 45), 3) electrode pH_NBS and A_T (n = 49), and 4) the direct measurement of seawater CO₂ with a NDIR CO₂ equilibrator (n = 46).</p

Metabolic rates from benthic communities on settlement tiles across the seawater carbon chemistry gradients.

<p>Rates of gross photosynthesis (a), respiration (b) and net daily production (c) in 13 month old communities are plotted against the median pH_T from the tiles. Gross photosynthesis and respiration are displayed in μg O₂ cm^-2 hr^-1, and daily net production in μg O₂ cm^-2 day^-1. Rates of light (d), dark (e) and net daily calcification (f) are plotted against tile median aragonite saturation state (Ω_Ar) from the tiles. Light and dark calcification rates are displayed in μg CaCO₃ cm^-2 hr^-1, and daily net calcification in μg CaCO₃ cm^-2 day^-1. White points are from Upa-Upasina and grey are from Dobu. The black lines represent the modelled mean, while the grey lines are confidence intervals.</p

Ocean acidification alters early successional coral reef communities and their rates of community metabolism

<div><p>Ocean acidification is expected to alter community composition on coral reefs, but its effects on reef community metabolism are poorly understood. Here we document how early successional benthic coral reef communities change <i>in situ</i> along gradients of carbon dioxide (CO₂), and the consequences of these changes on rates of community photosynthesis, respiration, and light and dark calcification. Ninety standardised benthic communities were grown on PVC tiles deployed at two shallow-water volcanic CO₂ seeps and two adjacent control sites in Papua New Guinea. Along the CO₂ gradient, both the upward facing phototrophic and the downward facing cryptic communities changed in their composition. Under ambient CO₂, both communities were dominated by calcifying algae, but with increasing CO₂ they were gradually replaced by non-calcifying algae (predominantly green filamentous algae, cyanobacteria and macroalgae, which increased from ~30% to ~80% cover). Responses were weaker in the invertebrate communities, however ascidians and tube-forming polychaetes declined with increasing CO₂. Differences in the carbonate chemistry explained a far greater amount of change in communities than differences between the two reefs and successional changes from five to 13 months, suggesting community successions are established early and are under strong chemical control. As pH declined from 8.0 to 7.8, rates of gross photosynthesis and dark respiration of the 13-month old reef communities (upper and cryptic surfaces combined) significantly increased by 10% and 20%, respectively, in response to altered community composition. As a consequence, net production remained constant. Light and dark calcification rates both gradually declined by 20%, and low or negative daily net calcification rates were observed at an aragonite saturation state of <2.3. The study demonstrates that ocean acidification as predicted for the end of this century will strongly alter reef communities, and will significantly change rates of community metabolism.</p></div

Physical and chemical conditions underneath and above macroalgal assemblages in the field on inshore coral reefs.

<p>Physical and chemical conditions underneath and 0.3 m above mat- (N = 8) and canopy-forming (N = 11) macroalgal assemblages on inshore coral reefs of the Great Barrier Reef, and results of paired t-tests. Abbreviations and units: pH, dissolved oxygen (DO, mg L⁻¹), alkalinity (ALK, µEq/kg), dissolved inorganic carbon (DIC, µM) dissolved organic carbon (DOC, mg L⁻¹), silicic acid (Si, µM), soluble reactive phosphorus (SRP, µM) and Irradiance (µmol photons m⁻² s⁻¹).</p

Median pH_T and saturation state of aragonite (Ω_Ar) from the 88 settlement tiles.

<p>Median n = 8 pH and 5 Ω_Ar measures per tile. White points are from Upa-Upasina, grey are from Dobu. Error bars are standard errors.</p

Shifts in settlement tile community composition along the pH gradients.

<p>Percent cover of non-calcifying algae on the upper (a) and lower (b) settlement tile sides, <i>Peyssonnelia</i> spp. from the upper (c) and lower (d) sides, and crustose coralline algae (CCA) from the upper (e) and lower (f) sides in relation to pH_T. Left and right panels per plot represent the five and 13 month old communities, respectively. White points are tiles from Upa-Upasina and grey are from Dobu. The black lines represent the modelled means, while the grey lines are confidence intervals.</p

Changes in community metabolism in response to median pH (gross photosynthesis; respiration) or the saturation state of aragonite (Ω_Ar: Calcification) and Reef (contrasting Dobu against Upa-Upasina).

<p>Changes in community metabolism in response to median pH (gross photosynthesis; respiration) or the saturation state of aragonite (Ω_Ar: Calcification) and Reef (contrasting Dobu against Upa-Upasina).</p