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Methods matter: considering locomotory mode and respirometry technique when estimating metabolic rates of fishes.

ABSTRACT: Respirometry is frequently used to estimate metabolic rates and examine organismal responses to environmental change. Although a range of methodologies exists, it remains unclear whether differences in chamber design and exercise (type and duration) produce comparable results within individuals and whether the most appropriate method differs across taxa. We used a repeated-measures design to compare estimates of maximal and standard metabolic rates (MMR and SMR) in four coral reef fish species using the following three methods: (i) prolonged swimming in a traditional swimming respirometer; (ii) short-duration exhaustive chase with air exposure followed by resting respirometry; and (iii) short-duration exhaustive swimming in a circular chamber. We chose species that are steady/prolonged swimmers, using either a body-caudal fin or a median-paired fin swimming mode during routine swimming. Individual MMR estimates differed significantly depending on the method used. Swimming respirometry consistently provided the best (i.e. highest) estimate of MMR in all four species irrespective of swimming mode. Both short-duration protocols (exhaustive chase and swimming in a circular chamber) produced similar MMR estimates, which were up to 38% lower than those obtained during prolonged swimming. Furthermore, underestimates were not consistent across swimming modes or species, indicating that a general correction factor cannot be used. However, SMR estimates (upon recovery from both of the exhausting swimming methods) were consistent across both short-duration methods. Given the increasing use of metabolic data to assess organismal responses to environmental stressors, we recommend carefully considering respirometry protocols before experimentation. Specifically, results should not readily be compared across methods; discrepancies could result in misinterpretation of MMR and aerobic scope.

SUBMITTER: Rummer JL

PROVIDER: S-EPMC4922262 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Methods matter: considering locomotory mode and respirometry technique when estimating metabolic rates of fishes.

Rummer Jodie L JL Binning Sandra A SA Roche Dominique G DG Johansen Jacob L JL

Conservation physiology 20160323 1

Respirometry is frequently used to estimate metabolic rates and examine organismal responses to environmental change. Although a range of methodologies exists, it remains unclear whether differences in chamber design and exercise (type and duration) produce comparable results within individuals and whether the most appropriate method differs across taxa. We used a repeated-measures design to compare estimates of maximal and standard metabolic rates (MMR and SMR) in four coral reef fish species u ...[more]

PMID: 27382471

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Project description:The difficulty involved in quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina, USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentrations consistent with the predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, which stands for "fraction of read abundance times cells"), to estimate the population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply branching uncultured groups, and ?98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from qPCR at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis, with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate-reducing bacteria, Desulfovibrio, Desulfobacter, and Desulfobacterium, increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions stimulates growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community.IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for "fraction of read abundance times cells," which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes.

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Methods matter: considering locomotory mode and respirometry technique when estimating metabolic rates of fishes.

Publications

Methods matter: considering locomotory mode and respirometry technique when estimating metabolic rates of fishes.

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