Guidelines for the reporting of methods for estimating metabolic rates using aquatic intermittent closed respirometry

Author(s):  
Shaun Killen ◽  
Emil Christensen ◽  
Daphne Cortese ◽  
Libor Zavorka ◽  
Lucy Cotgrove ◽  
...  

Interest in the measurement of metabolic rates is growing rapidly, due to the relevance of metabolism in understanding organismal physiology, behaviour, evolution, and responses to environmental change. The study of metabolism in aquatic organisms is experiencing an especially pronounced expansion, with more researchers utilizing intermittent-closed respirometry as a research tool than ever before. Despite this, there remain no published guidelines on the reporting of methodological details when using intermittent-closed respirometry. Using a survey of the existing literature, we show that this lack of recommendations has led to incomplete and inconsistent reporting of methods for intermittent-closed respirometry over the last several decades. We also provide the first guidelines for reporting such methods, in the form of a checklist of details that are the minimum required for the interpretation, evaluation, and replication of experiments using intermittent-closed respirometry. This should increase consistency of the reporting of methods for studies that use this research technique. With the steep increase in studies using intermittent-closed respirometry over the last several years, now is the ideal time to standardise the reporting of methods so that data can be properly assessed by other scientists and conservationists.

2021 ◽  
Vol 224 (18) ◽  
Author(s):  
Shaun S. Killen ◽  
Emil A. F. Christensen ◽  
Daphne Cortese ◽  
Libor Závorka ◽  
Tommy Norin ◽  
...  

ABSTRACT Interest in the measurement of metabolic rates is growing rapidly, because of the importance of metabolism in advancing our understanding of organismal physiology, behaviour, evolution and responses to environmental change. The study of metabolism in aquatic animals is undergoing an especially pronounced expansion, with more researchers utilising intermittent-flow respirometry as a research tool than ever before. Aquatic respirometry measures the rate of oxygen uptake as a proxy for metabolic rate, and the intermittent-flow technique has numerous strengths for use with aquatic animals, allowing metabolic rate to be repeatedly estimated on individual animals over several hours or days and during exposure to various conditions or stimuli. There are, however, no published guidelines for the reporting of methodological details when using this method. Here, we provide the first guidelines for reporting intermittent-flow respirometry methods, in the form of a checklist of criteria that we consider to be the minimum required for the interpretation, evaluation and replication of experiments using intermittent-flow respirometry. Furthermore, using a survey of the existing literature, we show that there has been incomplete and inconsistent reporting of methods for intermittent-flow respirometry over the past few decades. Use of the provided checklist of required criteria by researchers when publishing their work should increase consistency of the reporting of methods for studies that use intermittent-flow respirometry. With the steep increase in studies using intermittent-flow respirometry, now is the ideal time to standardise reporting of methods, so that – in the future – data can be properly assessed by other scientists and conservationists.


2015 ◽  
Vol 12 (15) ◽  
pp. 4665-4692 ◽  
Author(s):  
G. Aloisi

Abstract. Coccolithophores are sensitive recorders of environmental change. The size of their coccosphere varies in the ocean along gradients of environmental conditions and provides a key for understanding the fate of this important phytoplankton group in the future ocean. But interpreting field changes in coccosphere size in terms of laboratory observations is hard, mainly because the marine signal reflects the response of multiple morphotypes to changes in a combination of environmental variables. In this paper I examine the large corpus of published laboratory experiments with coccolithophores looking for relations between environmental conditions, metabolic rates and cell size (a proxy for coccosphere size). I show that growth, photosynthesis and, to a lesser extent, calcification covary with cell size when pCO2, irradiance, temperature, nitrate, phosphate and iron conditions change. With the exception of phosphate and temperature, a change from limiting to non-limiting conditions always results in an increase in cell size. An increase in phosphate or temperature (below the optimum temperature for growth) produces the opposite effect. The magnitude of the coccosphere-size changes observed in the laboratory is comparable to that observed in the ocean. If the biological reasons behind the environment–metabolism–size link are understood, it will be possible to use coccosphere-size changes in the modern ocean and in marine sediments to investigate the fate of coccolithophores in the future ocean. This reasoning can be extended to the size of coccoliths if, as recent experiments are starting to show, coccolith size reacts to environmental change proportionally to coccosphere size. The coccolithophore database is strongly biased in favour of experiments with the coccolithophore Emiliania huxleyi (E. huxleyi; 82 % of database entries), and more experiments with other species are needed to understand whether these observations can be extended to coccolithophores in general. I introduce a simple model that simulates the growth rate and the size of cells forced by nitrate and phosphate concentrations. By considering a simple rule that allocates the energy flow from nutrient acquisition to cell structure (biomass) and cell maturity (biological complexity, eventually leading to cell division), the model is able to reproduce the covariation of growth rate and cell size observed in laboratory experiments with E. huxleyi when these nutrients become limiting. These results support ongoing efforts to interpret coccosphere and coccolith size measurements in the context of climate change.


2008 ◽  
Vol 16 (NA) ◽  
pp. 19-44 ◽  
Author(s):  
Catherine M. Couillard ◽  
Simon C. Courtenay ◽  
Robie W. Macdonald

Environmental change can increase the vulnerability of aquatic species to toxic chemicals by challenging an organism’s aptitude to respond to chemicals or to repair toxic injury or by modifying animal behaviours like migration or predation. On the other hand, xenobiotics may affect the capacity of aquatic species to adapt to environmental challenges that come with change (e.g., pathogens, temperature). Across Canada we have identified a number of circumstances where chemicals and environmental variability have likely worked together to affect vulnerability of aquatic organisms. For example in the Maritimes, exposure to municipal wastewater or bleached kraft pulp mill effluent altered immune function in bivalves and increased their risk of developing haemocytic neoplasia, a disease known to cause high mortality. Northwest Atlantic cod stocks have experienced large-scale changes in environment and exhibit marked seasonal cycles in energy reserves. The risk associated with subsequent redistribution of persistent chemicals in the body together with nutritional deficiency is presently under evaluation since it could affect the recovery of these endangered stocks. In the Great Lakes, the introduction of an invasive fish species, the alewife, modified the diet of salmonids, which led to a deficiency of the vitamin thiamine in eggs causing early mortality. Contaminants may interact with thiamine deficiency and thus critically impair recruitment of salmonids. Viewing the risks presented by toxic chemicals from the point of view of species vulnerability, offers managers opportunities to mitigate such risks, for example, through habitat, ocean and fisheries management. Further research is needed to develop biomarkers of vulnerability, identify most vulnerable life stages and populations, to understand the interactions between global environmental changes, nutritional status, pathogens and toxic chemicals, and to develop integrated approaches to manage vulnerability of aquatic ecosystems to toxic chemicals.


Sensors ◽  
2021 ◽  
Vol 21 (15) ◽  
pp. 4966
Author(s):  
Rich C. Lee ◽  
Ing-Yi Chen

Public aquariums and similar institutions often use video as a method to monitor the behavior, health, and status of aquatic organisms in their environments. These video footages take up a sizeable amount of space and require the use of autoencoders to reduce their file size for efficient storage. The autoencoder neural network is an emerging technique which uses the extracted latent space from an input source to reduce the image size for storage, and then reconstructs the source within an acceptable loss range for use. To meet an aquarium’s practical needs, the autoencoder must have easily maintainable codes, low power consumption, be easily adoptable, and not require a substantial amount of memory use or processing power. Conventional configurations of autoencoders often provide results that perform beyond an aquarium’s needs at the cost of being too complex for their architecture to handle, while few take low-contrast sources into consideration. Thus, in this instance, “keeping it simple” would be the ideal approach to the autoencoder’s model design. This paper proposes a practical approach catered to an aquarium’s specific needs through the configuration of autoencoder parameters. It first explores the differences between the two of the most widely applied autoencoder approaches, Multilayer Perceptron (MLP) and Convolution Neural Networks (CNN), to identify the most appropriate approach. The paper concludes that while both approaches (with proper configurations and image preprocessing) can reduce the dimensionality and reduce visual noise of the low-contrast images gathered from aquatic video footage, the CNN approach is more suitable for an aquarium’s architecture. As an unexpected finding of the experiments conducted, the paper also discovered that by manipulating the formula for the MLP approach, the autoencoder could generate a denoised differential image that contains sharper and more desirable visual information to an aquarium’s operation. Lastly, the paper has found that proper image preprocessing prior to the application of the autoencoder led to better model convergence and prediction results, as demonstrated both visually and numerically in the experiment. The paper concludes that by combining the denoising effect of MLP, CNN’s ability to manage memory consumption, and proper image preprocessing, the specific practical needs of an aquarium can be adeptly fulfilled.


2020 ◽  
Vol 16 (4) ◽  
pp. 20190825
Author(s):  
Yan Huang ◽  
Shijian Fu ◽  
Steven J. Cooke ◽  
Jigang Xia

Metabolic rates are typically thought to have important influences on fitness and more broadly be relevant to the ecology and evolution of animals. Previous studies demonstrate that metabolic rates are repeatable to a certain extent under constant conditions, but how social conditions influence the repeatability of metabolic rate remains largely unknown. In this study, we investigated the repeatability of resting metabolic rate (RMR) in the highly social crucian carp ( Carassius auratus ) after being socially separated for different time periods relative to control fish that were not socially separated. We found that RMR was repeatable in fish in the control group, while the repeatability of RMR disappeared quickly (even within 7 days) when fish were exposed to social separation. This study is the first to our knowledge to examine the role of social separation for different time periods on the repeatability of intra-individual physiological variation in fish. We highlight that the inter-individual repeatability of metabolic rate can be substantial over time but was eliminated by social separation. The findings indicate that the repeatability of metabolic rate in fish is condition dependent, and that the change in repeatability of metabolic rate should not be overlooked when considering the ecological and evolutionary effects of environmental change.


2021 ◽  
Vol 77 (01) ◽  
pp. 6482-2021
Author(s):  
Księżarczyk M. ◽  
Leśniak P. ◽  
Arciszewski M. B. ◽  
Valverde Piedra J. L.

The comet assay method is a research technique for detecting damage to cellular DNA due to active physical or chemical agents. The comet assay is based on electrophoretic migration of genetic material contained in the cell’s nucleus. This research method is commonly used in many different fields, such as toxicology, environmental protection, and pharmacology. In recent years, the comet assay has attracted considerable attention from scientists studying the effects of harmful substances on the genetic material in the cell’s nucleus. The presence of pesticides in the environment is a threat to animals, because of the negative effects of pesticides on cells and their genetic material. Therefore, the aim of this paper, based on the available literature, was to describe the use of the comet assay in assessing the genotoxicity of pesticides to cells of aquatic organisms, as well as to describe the methodology and potential complications of this procedure.


2015 ◽  
Vol 12 (8) ◽  
pp. 6215-6284 ◽  
Author(s):  
G. Aloisi

Abstract. Coccolithophores are sensitive recorders of environmental change. The size of their coccosphere varies in the ocean along gradients of environmental conditions and provides a key for understanding the fate of this important phytoplankton group in the future ocean. But interpreting field changes in coccosphere size in terms of laboratory observations is hard, mainly because the marine signal reflects the response of multiple morphotypes to changes in a combination of environmental variables. In this paper I examine the large corpus of published laboratory experiments with coccolithophores looking for relations between environmental conditions, metabolic rates and cell size (a proxy for coccosphere size). I show that growth, photosynthesis, and to a lesser extent calcification, co-vary with cell size when pCO2, irradiance, temperature, nitrate, phosphate and iron conditions change. With the exception of phosphate and temperature, a change from limiting to non-limiting conditions always results in an increase in cell size. An increase in phosphate or temperature produces the opposite effect. The magnitude of the coccosphere size changes observed in the laboratory is comparable to that observed in the ocean. If the biological reasons behind the environment-metabolism-size link are understood, it will be possible to use coccosphere size changes in the modern ocean and in marine sediments to investigate the fate of coccolithophores in the future ocean. This reasoning can be extended to the size of coccoliths if, as recent experiments are starting to show, coccolith size reacts to environmental change proportionally to coccosphere size. I introduce a simple model that simulates the growth rate and the size of cells forced by nitrate and phosphate concentrations. By considering a simple rule that allocates the energy flow from nutrient acquisition to cell structure (biomass) and cell maturity (biological complexity, eventually leading to cell division), the model is able to reproduce the co-variation of growth rate and cell size observed in the laboratory when these nutrients become limiting. These results support ongoing efforts to interpret coccosphere and coccolith size measurements in the context of climate change.


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