Respirometry is a ubiquitous practice in experimental biology, but there is a lack of standard practices when analysing the resulting data, limiting transparency and reproducibility. As respirometry datasets become increasingly large and analytical approaches more complex, manipulating the data remains a challenge and often intractable with existing tools. Here we describe the respR R package, a collection of functions that implement a workflow‐based approach to automate the analysis and visualisation of respirometry data. The package can be used for closed, intermittent flow, flow‐through and open‐tank respirometry and uses well‐defined sets of rules to reliably and rapidly generate reproducible results. We demonstrate how respR uses novel computing methods such as rolling regressions and kernel density estimates to reliably detect maximum, minimum and most linear sections of the data, and critical oxygen tension, . Although designed specifically with aquatic respirometry in mind, the object‐oriented approach of the package and the unit‐less nature of its analytical functions mean that parts of the package can easily be used to estimate linear relationships from a range of applications in many research disciplines.

Body size and temperature are the major factors explaining metabolic rate, and the additional factor of pH is a major driver at the biochemical level. These three factors have frequently been found to interact, complicating the formulation of broad models predicting metabolic rates and hence ecological functioning. In this first study of the effects of warming and ocean acidification, and their potential interaction, on metabolic rate across a broad range in body size (two to three orders of magnitude difference in body mass), we addressed the impact of climate change on the sea urchin Heliocidaris erythrogramma in context with climate projections for southeast Australia, an ocean warming hotspot. Urchins were gradually introduced to two temperatures (18 and 23°C) and two pH levels (7.5 and 8.0), at which they were maintained for 2 months. Identical experimental trials separated by several weeks validated the fact that a new physiological steady state had been reached, otherwise known as acclimation. The relationship between body size, temperature and acidification on the metabolic rate of H. erythrogramma was strikingly stable. Both stressors caused increases in metabolic rate: 20% for temperature and 19% for pH. Combined effects were additive: a 44% increase in metabolism. Body size had a highly stable relationship with metabolic rate regardless of temperature or pH. None of these diverse drivers of metabolism interacted or modulated the effects of the others, highlighting the partitioned nature of how each influences metabolic rate, and the importance of achieving a full acclimation state. Despite these increases in energetic demand there was very limited capacity for compensatory modulating of feeding rate; food consumption increased only in the very smallest specimens, and only in response to temperature, and not pH. Our data show that warming, acidification and body size all substantially affect metabolism and are highly consistent and partitioned in their effects, and for H. erythrogramma, near-future climate change will incur a substantial energetic cost.

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Climate-induced ocean warming and acidification may render marine organisms more vulnerable to infectious diseases. We investigated the effects of warming and acidification on the immune response of the sea urchin Heliocidaris erythrogramma Sea urchins were gradually introduced to four combinations of temperature and pHNIST (17°C/pH 8.15, 17°C/pH 7.6, 23°C/pH 8.15 and 23°C/pH 7.6) and then held in temperature-pH treatments for 1, 15 or 30 days to determine if the immune response would adjust to stressors over time. Coelomocyte concentration and type, phagocytic capacity and bactericidal activity were measured on day 1, 15 and 30 with different sea urchins used each time. At each time point, the coelomic fluid of individuals exposed to increased temperature and acidification had the lowest coelomocyte concentrations, exhibited lower phagocytic capacities and was least effective at inhibiting bacterial growth of the pathogen Vibrio anguillarum Over time, increased temperature alleviated the negative effects of acidification on phagocytic activity. Our results demonstrate the importance of incorporating acclimation time to multiple stressors when assessing potential responses to future ocean conditions and indicate that the immune response of H. erythrogramma may be compromised under near-future ocean warming and acidification.

Concurrent anthropogenic global climate change and ocean acidification are expected to have a negative impact on calcifying marine organisms. While knowledge of biological responses of organisms to oceanic stress has emerged from single‐species experiments, these do not capture ecologically relevant scenarios where the potential for multi‐organism physiological interactions is assessed. Marine algae provide an interesting case study, as their photosynthetic activity elevates pH in the surrounding microenvironment, potentially buffering more acidic conditions for associated epiphytes. We present findings that indicate increased tolerance of an important epiphytic foraminifera, Marginopora vertebralis , to the effects of increased temperature (±3°C) and p CO 2 (~1,000 µatm) when associated with its common algal host, Laurencia intricata . Specimens of M. vertebralis were incubated for 15 days in flow‐through aquaria simulating current and end‐of‐century temperature and pH conditions. Physiological measures of growth (change in wet weight), calcification (measured change in total alkalinity in closed bottles), photochemical efficiency ( Fv/Fm ), total chlorophyll, photosynthesis (oxygen flux), and respiration were determined. When incubated in isolation, M. vertebralis exhibited reduced growth in end‐of‐century projections of ocean acidification conditions, while calcification rates were lowest in the high‐temperature, low‐pH treatment. Interestingly, association with L. intricata ameliorated these stress effects with the growth and calcification rates of M. vertebralis being similar to those observed in ambient conditions. Total chlorophyll levels in M. vertebralis decreased when in association with L. intricata , while maximum photochemical efficiency increased in ambient conditions. Net production estimates remained similar between M. vertebralis in isolation and in association with L. intricata , although both production and respiration rates of M. vertebralis were significantly higher when associated with L. intricata . These results indicate that the association with L. intricata increases the resilience of M. vertebralis to climate change stress, providing one of the first examples of physiological buffering by a marine alga that can ameliorate the negative effects of changing ocean conditions.

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The composition of local ecological communities is determined by the members of the regional community that are able to survive the abiotic and biotic conditions of a local ecosystem. Anthropogenic activities since the industrial revolution have increased atmospheric CO 2 concentrations, which have in turn decreased ocean pH and altered carbonate ion concentrations: so called ocean acidification (OA). Single-species experiments have shown how OA can dramatically affect zooplankton development, physiology and skeletal mineralization status, potentially reducing their defensive function and altering their predatory and antipredatory behaviors. This means that increased OA may indirectly alter the biotic conditions by modifying trophic interactions. We investigated how OA affects the impact of a cubozoan predator on their zooplankton prey, predominantly Copepoda, Pleocyemata, Dendrobranchiata, and Amphipoda.Experimental conditions were set at either current (pCO 2 370 latm) or end-of-thecentury OA (pCO 2 1,100 latm) scenarios, crossed in an orthogonal experimental design with the presence/absence of the cubozoan predator Carybdea rastoni. The combined effects of exposure to OA and predation by C. rastoni caused greater shifts in community structure, and greater reductions in the abundance of key taxa than would be predicted from combining the effect of each stressor in isolation. Specifically, we show that in the combined presence of OA and a cubozoan predator, populations of the most abundant member of the zooplankton community (calanoid copepods) were reduced 27% more than it would be predicted based on the effects of these stressors in isolation, suggesting that OA increases the susceptibility of plankton to predation. Our results indicate that the ecological consequences of OA may be greater than predicted from single-species experiments, and highlight the need to understand future marine global change from a community perspective.

Ocean warming (OW) and acidification (OA) affects nearly all aspects of marine organism physiology and it is important to consider both stressors when predicting responses to climate change. We investigated the effects of long-term exposure to OW and OA on the physiology of adults of the sea urchin, Heliocidaris erythrogramma, a species resident in the southeast Australia warming hotspot. The urchins were slowly introduced to stressor conditions in the laboratory over a 7-week adjustment period to three temperature (ambient, +2°C, +3°C) and two pH (ambient: pHT 8.0; −0.4 units: pHT 7.6) treatments. They were then maintained in a natural pattern of seasonal temperature and photoperiod change, and fixed pH, for 22 weeks. Survival was monitored through week 22 and metabolic rate was measured at 4 and 12 weeks of acclimation, feeding rate and ammonia excretion rate at 12 weeks and assimilation efficiency at 13 weeks. Acclimation to +3°C was deleterious regardless of pH. Mortality from week 6 indicated that recent marine heatwaves are likely to have been deleterious to this species. Acclimation to +2°C did not affect survival. Increased temperature decreased feeding and increased excretion rates, with no effect of acidification. While metabolic rate increased additively with temperature and low pH at week 4, there was no difference between treatments at week 12, indicating physiological acclimation in surviving urchins to stressful conditions. Regardless of treatment, H. erythrogramma had a net positive energy budget indicating that the responses were not due to energy limitation. To test for the effect of parental acclimation on offspring responses, the offspring of acclimated urchins were reared to the juvenile stage in OW and OA conditions. Parental acclimation to warming, but not acidification altered juvenile physiology with an increase in metabolic rate. Our results show that incorporation of gradual seasonal environmental change in long-term acclimation can influence outcomes, an important consideration in predicting the consequences of changing climate for marine species.