FishResp: R package and GUI application for analysis of aquatic respirometry data.

Sergey Morozov,Juha Merilä,R J Scott Mccairns,Steven Cooke

doi:10.1093/conphys/coz003

Sergey Morozov, Juha Merilä + Show 2 more

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https://doi.org/10.1093/conphys/coz003

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Abstract

Intermittent-flow respirometry is widely used to measure oxygen uptake rates and subsequently estimate aerobic metabolic rates of aquatic animals. However, the lack of a standard quality-control software to detect technical problems represents a potential impediment to comparisons across studies in the field of evolutionary and conservation physiology. Here, we introduce 'FishResp', a versatile R package and its graphical implementation for quality-control and filtering of raw respirometry data. Our goal is to provide a straightforward, cross-platform and free software to help improve the quality and comparability of metabolic rate estimates for reducing methodological fragmentation in the field of aquatic respirometry. FishResp accepts data from various respirometry systems, allows users to detect potential mechanical problems which can occur during oxygen uptake measurements (e.g. chamber leaking, poor water circulation), and offers six options to correct raw data for microbial oxygen consumption. The software performs filtering of raw data based on user criteria, and produces accurate and unbiased estimates of absolute and mass-specific metabolic rates. Using data from three-spined sticklebacks (Gasterosteus aculeatus) and Trinidadian guppies (Poecilia reticulata), we demonstrate the virtues of FishResp, highlighting the importance of detecting mechanical problems and correcting measurements for background respiration.

Highlights

Whole-body intermittent-flow respirometry represents the most reliable and widespread technique to estimate aerobic metabolic rate of aquatic animals (Steffensen, 1989; Clark et al, 2013; Svendsen et al, 2016b)
We demonstrate the utility of FishResp for detecting mechanical problems and correcting for background microbial oxygen consumption using raw data obtained from the three-spined stickleback (Gasterosteus aculeatus) and the Trinidadian guppy (Poecilia reticulata)
Our case studies demonstrate that neglecting mechanical problems and microbial growth in a respirometry system can lead to underestimation and/or overestimation of metabolic rate

Summary

Introduction

Whole-body intermittent-flow respirometry (i.e. measuring the oxygen uptake of an organism) represents the most reliable and widespread technique to estimate aerobic metabolic rate of aquatic animals (Steffensen, 1989; Clark et al, 2013; Svendsen et al, 2016b). It has been applied to the identification of ecological and environmental factors that cause metabolic rate variation (Ohlberger et al, 2007; Auer et al, 2015; Christensen et al, 2017) and for studying physiological plasticity and adaptation to novel Whilst inter-population comparisons of mean standard metabolic rate (SMR) estimates of Trinidadian guppy (Poecilia reticulata) have reported difference up to 1.7fold between populations (Handelsman et al, 2013; Auer et al, 2018), comparisons between independent studies conducted under similar temperature conditions show 5-fold differences (from 100 to 550 mg O2/kg/h; Svendsen et al, 2013; Ejbye-Ernst et al, 2016; Killen et al, 2016) Such a wide range of SMR estimates within a species are unlikely to be explained by biological factors, but more likely, reflect unstandardized measurement conditions and data post-processing procedures

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