Reunion Island (21°S, 55°E) is located in the south-western Indian Ocean. Coral reefs are limited to small and discontinuous systems scattered along the western coast. This study was conducted in a wide range of environment at 4 reef flat stations and 4 back reef stations (Fig. 1) of La Saline fringing reef (500 m wide, 1 to 1.5 m deep), which is the most extensive reef of the island (9 km long). Tides are semidiurnal and the range varies from 0.1 m (neap) to 0.9 m (spring). We performed our measurements during the two main seasons: in summer from January to April and winter from July to October [22]. The summer season is characterised by high seawater temperature and high rainfall.

Three environmental parameters were analysed in the water column: temperature, pH and chlorophyll a (Chlo_SW); and three parameters in sediments: granulometry, organic matter (OM_SED) and chlorophyll a (Chlo_SED). Six water samples were collected simultaneously at each station over 3 days in summer 2004 (3 at 9 h and 3 at 15 h) and again in the same way in winter 2004. Water samples for chlorophyll a were filtered onto GF/F glass-fiber filters. After extraction (12 h at 4 °C) with acetone (90%), chlorophyll a was measured fluorimetrically (Turner 700), according to Welschmeyer [23]. Water samples for pH were collected and measured according to the method described in Section 2.3. Six sediment cores (2.9 cm diameter, 5 cm deep) were collected at each station concurrently to the flux measurements at the water–sediment interface (see Section 2.3). Three cores were used to determine total organic matter load, corresponding to the weight loss between sediment dried at 60 °C for 48 h and ashed at 550 °C for 3 h [24]. Three other samples were frozen at −80 °C and later used to measure chlorophyll a content of the sediments. Extraction was performed in 90% acetone for 12 h at 4 °C. After centrifugation, the optical density of the extracts was measured with a spectrophotometer (Kontron Uvikon 922) at 750 and 665 nm, and calculations made according to Lorenzen [25]. Granulometry was assessed on cores collected in triplicate at each station (4.3 cm diameter, 5 cm deep) in summer 2004. The sediment mean size was calculated in the φ value, according to Folk and Ward [26].

Fluxes of O₂ and DIC at the water–sediment interface were assessed using in situ benthic chambers [27]. During the experiments, the weather was calm; the swell was very low and no ripple formation was observed on the bottom. At each station and, in the course of the main two seasons (winter 2002 or 2003, summer 2001 or 2004), at least eight runs of triplicate incubations, lasting about 60 min, were performed over two or three diel cycles, in order to get the whole range of irradiance. Among these runs, two runs of triplicate incubations (generally one per day of sampling) were performed at night (around 20 h) to assess respiration. The benthic chambers were composed of a PVC ring pushed into the sediment to a depth of ca. 10 cm, covered with a transparent acrylic hemisphere. The volume of the enclosed water varied from 66 to 69 L. The water was continuously homogenised with adjustable submersible pumps at 2 L min⁻¹. Dissolved oxygen, temperature and salinity were recorded with multiparameter probes (YSI 6920). A quantum sensor (LI-1400) was deployed inside one of the benthic enclosures to measure irradiance, defined as the photosynthetically active radiation (PAR, 400 to 700 nm) available for microphytobenthos. Between incubations, enclosures were opened for 60 min to restore ambient conditions. Further details about the experimental device are given in Clavier et al. [28].

Seawater samples were collected inside the chamber at the beginning and at the end of each incubation. They were immediately poisoned with HgCl₂ (20 μL of saturated solution per 100 mL of sample) and stored in darkness at 5 °C pending subsequent potentiometric determination of pH and total alkalinity (TA). Samples intended for TA measurement were filtered through GF/C glass-fiber filters. DIC concentrations (mmol L⁻¹) were determined from pH, TA, temperature and salinity [29]. pH (±0.002) was measured on to the total hydrogen ion concentration (mol kg  SW⁻¹) pH scale, using a Ross combination electrode (Orion 81-03) calibrated against Tris/HCl and 2-aminopyridine/HCl buffers in synthetic seawater [30]. To measure TA, inflection point titrations (Radiometer TIM 865) were performed on 20 mL subsamples (4 replicates) maintained at 25 °C (±0.1°C), and slowly neutralized with saline (0.7 M NaCl) HCl 0.01 M solution. TA was obtained from the second inflection point of the curve. The mean standard deviation of replicate measurements was less than 0.003 mmol L⁻¹.

The DIC flux (F_DIC; mmolC m⁻² h⁻¹) was calculated as the difference in DIC concentrations between the end and the start of the incubation, corrected from half the TA variation, to account for the effects of carbonate dissolution and precipitation [17]. O₂ flux (F_O2; mmolO₂ m⁻² h⁻¹) was calculated as the difference in concentrations between the end and the start of the incubation.

The community respiratory quotient (CRQ) is defined as:

Temperature, pH and chlorophyll a content of seawater showed significant seasonal variability, with the highest values in summer (Table 1). The pH differences reflect seasonal variations, as sampling was undertaken at the same hour of the day in summer and winter. In sediments, the highest chlorophyll a content was found in summer. The organic matter load remained constant over the year. The mean grain size in φ value was 0.61 (SD 0.38) which corresponds to coarse sand on the Wentworth scale [33]. The underwater maximum mean irradiance at the sediment level, calculated from data measured during benthic incubations, was 1532 μmol m⁻² s⁻¹ at about 11 h in summer and 995 μmol m⁻² s⁻¹ at about 12h30 in winter (Fig. 2). In summer, the daily curve was not symmetrical, and the maximum was before midday as clouds often appear at the beginning of the afternoon. The mean irradiance varied significantly according to the season (U-test; p<0.001). In winter, bottom communities received 33% less of light than in summer (respectively 21 and 31 mol m⁻² d⁻¹).

CRQ were 1.01 (SD 0.11) in winter and 1.15 (SD 0.07) in summer (Fig. 3). These two values were not significantly different (Z-test; p>0.05). The common CRQ for the two seasons was 1.08 (SD 0.05) and did not significantly differ from 1 (Z-test; p>0.05). The intercepts of the regression line in winter and summer were not significantly different (Z-test; p>0.05) but they significantly differed from 0 (Z-test; p<0.001). The mean DIC release was 1.21 mmolC m⁻² h⁻¹ when the oxygen uptake was zero.

In winter CPQ was 1.06 (SD 0.05) and did not differ significantly from 1 (Z-test; p>0.05); the intercept of the regression line differed significantly from 0 (Z-test; p<0.001). We observed an oxygen uptake of 2.8 mmolO₂ m⁻² h⁻¹ when the DIC uptake was zero. In summer CPQ was 0.79 (SD 0.02) and differed significantly from winter and from 1 (both: Z-test; p<0.001). The intercept of the regression line was significantly lower than 0 and different from winter (both: Z-test; p<0.001). The oxygen uptake was 0.8 mmolO₂ m⁻² h⁻¹ when DIC uptake is zero.

A low CPQ may be caused by the effect of hydrodynamism [15,40]. Atkinson and Grigg [40] attributed the curvilinearity of their FO2/FDIC relationship to breaking waves. They hypothesised that waves could have converted dissolved O₂ into bubbles, resulting in an underestimation of the oxygen fluxes. Our measurements were carried out in benthic chambers where there exists a risk of bubble formation, due to the supersaturating of water in oxygen. However, we found no curvilinerarity in summer (or winter) FO2/FDIC relationship for La Saline sediments (Fig. 3 a and b) excluding the supersaturating seawater factor to explain our low CPQ.

Calcium carbonate precipitation or dissolution can affect DIC concentration and therefore CPQ [41]. The production of one mole of CaCO₃ is a CO₂-releasing process and requires the uptake of two moles of HCO₃⁻; therefore total alkalinity decreases by 2 equivalents and DIC decreases by 1 mole for precipitation or the reverse for dissolution [17]. Boucher et al. [42] showed a light-induced CaCO₃ precipitation in coral reef sediments, similar to that occurring in calcifying organisms. Anaerobic respiration is also a potential source of alkalinity for the water column [17]. However, the associated changes in total alkalinity during short-term incubation (60 min) are probably negligible [42] and nitrogen fluxes measured for La Saline sediments are low (see below). In our study, a relationship between irradiance and CaCO₃ fluxes was found [43]. Therefore, CPQ was calculated from F_DIC resulting from total DIC fluxes subtracted from calcification (1/2 of total alkalinity variation). The dissolution recorded by Oviatt et al. [41] contributed to 14% of DIC fluxes and had significant lowering effect on CPQ. The contribution of carbonate metabolism to DIC fluxes in our study reached 16% [43]. As calcification had been already integrated in our calculations, causes of low CPQ may be found in photosynthetic activity of primary producers.

Algal respiration includes both ‘dark respiration’ similar to heterotrophic respiration and photorespiration. The latter that decreases CPQ [44] occurs when RUBISCO (ribulose 1,5-biphosphate carboxylase/oxygenase) principal function as a carboxylase is substituted by oxygenase function [45]. The oxygenase function of RUBISCO is favoured under increasing oxygen levels, increasing temperatures, and high light [46]. No relationship was found between CPQ (either divided by Chlo_SED or OM_SED, or not) and seawater O₂ concentrations, DIC/O₂, light or temperature (results not shown) either in summer or in winter suggesting the absence of photorespiration for La Saline sediments. Some studies demonstrated the existence of photorespiration in marine algae [47,48] but the rate is generally low or insignificant due to the existence of a CO₂-concentrating mechanism [45,49] which preserves RUBISCO from high environmental O₂ concentrations. However, we cannot rule out photorespiration in this study because higher temperature and irradiance in summer compared to winter, in which CPQ = 1, could induce photorespiration.

Oxic respiration is generally considered to be the main pathway of organic matter degradation in coastal sediments [5]. However, other metabolic pathways, including sulphate reduction, denitrification, methanogenesis, and iron or manganese reduction, may have a more or less important contribution in some environments [5], especially in coral reef sediments where decomposition of detritus is essentially a microbially mediated process [50]. Aerobic metabolism appears to prevail at the beginning of the night in La Saline sediment (CRQ = 1). Nevertheless, the intercept of FO2/FDIC regression line in darkness indicates that DIC are produced (29 mmol m⁻² d⁻¹) without O₂ uptake (Fig. 3 c and d). This anaerobic respiration appears to be steady whatever the rate of aerobic respiration. This rate is in the range of literature values reported in Table 3 and close to the sulphate reduction rate which is the major anaerobic respiration process in coral reef sediments, although the rates are low compared to most over marine environments [50]. As DIC is produced without oxygen consumption, anaerobic sulphur metabolism in sediments can contribute to higher CPQ and therefore does not explain the low summer CPQ in La Saline.

Other metabolic processes producing a release of DIC without simultaneous oxygen uptake are iron or manganese reduction, methanogenesis and denitrification. Iron or manganese reduction and methanogenesis are minor contributors (Table 3), with less than 1% following Alongi et al. [20]. Several metabolic processes involving nitrogen can also affect metabolic quotients, including the nitrification/denitrification process [41]. CPQ is affected by nitrogen species taken up by primary producers [51]. CPQ is not modified by NH₄ uptake but is increased by NO₃ uptake [52] as shown by the equation:

Since sediments are heterotrophic [43] an other source of nitrogen is exogenous dissolved and particulate organic matter. Organic matter input needed to balance production and respiration is at most 53 mmolC  m⁻² d⁻¹ in summer. The C:N ratios of particulate and dissolved organic matter in seawater are respectively 10.06±2.69 (N=52) and 10.88±0.58 (N=50) [43]; therefore, 5 mmolN m⁻² d⁻¹ (high estimation calculated from the average C:N ratio) are brought by exogenous material and sustain gross production in the sediment. Assuming that this pool of nitrogen is ultimately denitrified through the nitrification/denitrification pathways:

Community respiration has generally been measured at the beginning of the night and the 24 h values are estimated assuming that respiration is constant [40,53]. However, the fact that community light respiration exceeds dark respiration seems unquestionable [5,54]. Several processes can produce daily variations in community respiration such as variations in microphytobenthic biomass [55] or in oxygen penetration into the sediments (for more details, see [28]). At La Saline reef, Clavier et al. [28] demonstrated a daily cycle of community respiration in sediments, with values at the end of the day 2.8 and 3.8 higher than the fluxes at the end of the night for oxygen and DIC, respectively. In order to test the influence of a daily respiration variation on CPQ, this pattern was included in our calculations, instead of assuming that respiration is constant. This was done for the back reef of Planch'Alizés station, the same studied by Clavier et al. [28] in summer 2003. Benthic parameters were relatively similar between the two studies: 4.32 (SD 0.51) and 4.32 (SD 0.32)% for OM content; 0.44 (SD 0.27) and 0.41 (diameter scale) for the main grain size; 82.3 (SD 30.5) and 47.4 (SD 18.1) mg m⁻² for chlorophyll a content for the present study and Clavier et al. [28], respectively. Community gross productions were calculated with community respiration values obtained from the third-order polynomial regression proposed by Clavier et al. [28] (Fig. 4) and reported in Table 4.

For the present study, the CPQ reached 0.82 (significantly inferior to unit: Z-test, p<0.001) in back reef of Planch'Alizés in summer. When taking the daily evolution of the respiration into account, the new CPQ equals to 0.91 and is not significantly different to 1 (Z-test, p>0.05), which is a value more commonly found for sediments (Table 3). The variation range of community respiration in terms of carbon is higher than in terms of oxygen, resulting in a daily evolution of the CRQ with a minimum at 6h00 and a maximum value at 18h00 (Fig. 5 in [28]). In other words, the amount of DIC release compared to oxygen uptake increases at daytime; at the end of the day CRQ is close to unity. Finally, more than the daily evolution of the respiration, it is the discrepancy in the daily evolution of respirations in terms of carbon and in oxygen that caused a mistake in CPQ calculations.