In the five years since publication, respR has picked up
91
citations.
We are very happy to see the package being used to conduct quality, reproducible science, and excited to see what experiments and data users will put it towards in the future. It’s been especially encouraging to see it used for calculating the respiration rates of a wide range of species, as well as oxygen production rates of algae and corals.
If you use the package please cite the publication in Methods in Ecology and Evolution. If you use it for any other purpose (e.g. teaching, industry use, environmental reports and monitoring, etc.) we’d love to hear about it.
respR
The following publications (most recent first) have used and cited
respR. If we have missed any let
us know.
This preprint examines how biofouling on microplastics effects on
fish physiology using intermittent-flow respirometry. The authors used
auto_rate to obstain MMR and SMR from a kingfish. Looking
forward to seeing it officially in print.
This preprint on bioRxiv
examines the thermal tolerances of a coral symbiont. Yet another study
which used respR to get both respiration rates and net
photosynthesis. Great to see and looking forward to seeing it officially
in print.
Heather Leigh Sheffey’s MSc thesis done at the Old Dominion University looks at the effects on a coral of warming, bacterial disease, and microplastics. Ambitious! Congrats on the MSc! 🥳
Personality is not something you think of when you think of sea anemones, but they do come in types which might be described as ‘bold’ or ‘shy’. This study looked at the metabolic rates of these two types under a simulated heatwave event. Very different responses: shy anemones had highest metabolic rates at low temperatures, but bold anemones higher rates at high temperatures. Interesting stuff.
This study looked at how a chemical treatment for sea lice in Norwegian fish farming affects the physiology of sea pens. The contaminant did not have an apparent effect on mortality, behaviour or metabolism, though was present in tissues. Nice to see ‘null’ results being published by prominent journals. These are just as important as positive results!
Having done a lot of both, I love seeing studies that combine
metabolism and escape responses! This looked at how exposure to
petroleum products affects these parameters in a marine fish. Great
example of how auto_rate can be used to extract a rolling
rate, which can then be filtered to identify a maximum rate for a fixed
period. Great study that ticks all our boxes.
This study examines how metabolic rates (or ‘pace of life’) traits
may be passed on to zebrafish by their parents. respR was
used to extract rates from closed respirometry experiments.
This study used in-situ respirometry to examine the metabolic rates
of stream salmonids transferred between naturally variable thermal
regimes. They used auto_rate to identify the metabolic
rates from their respirometry data.
Who doesn’t like octopuses? This study examined the unusual behaviour of octopuses crawling on land, and the physiological consequences of that behaviour. They did respirometry experiments on specimens which had been exposed to air and also a chase protocol, showing the octopuses’ metabolic rate did not differ between exposure and having been chased. So it seems it is something they can handle quite well. Very cool study!
Maria Auxiliadora Sabando Plaza’s MSc thesis done at the University
of Delaware looks at the sublethal effects of methylmercury on spiny
dogfish, which include lower growth rates and food consumption. She used
respR to analyse the respirometry data which showed
increased SMR in response to doses. Congrats on the MSc! 🥳
This study examined if BPA exposure affects metabolic rates and behaviour in zebrafish. Turns out lots of disruption to regular behaviour, less so to physiological functioning.
Another study showing that respR can help anaylyse
respirometry data from really tiny organisms, in this case not just a
copepod, but its larvae. Here, they found metabolic rates increase in
response to ocean warming and acidification combined, but not
separately. Interesting!
Another nice urchin study, with some bonus gastropods thrown in. This study shows the links between food availability and heat resistance, and the role of metabolic depression.
This preprint on bioRxiv
examines how Chinook salmon thermal adaptation occurs, and the role of
mitochondrial function. The authors used respR to analyses
intermittent-flow respirometry experiments. Looking forward to seeing it
officially in print.
This study used intermittent-flow respirometry to examine thermal tolerance in largemouth bass. They show that enzyme activity associated with the electron transport system could be another tool to determine thermal tolerances in a way that is a non-lethal, rapid, and efficient alternative to traditional techniques. Nice!
This study looks at the responses of brook charr to thermal stress, with negative effects to aerobic scope and MMR. Nice example of using the package to extract metabolic rates using specific criteria (high r2, 10th percentile etc) to arrive at a final SMR.
This follows up on Nicolas Evensen’s 2021 study paper looking at physiological responses of Red Sea corals to thermal stress. Once again, it’s gratifying to see the package being used to extract not just respiration rates, but also photosynthesis rates.
Francisco Márquez Borrás’s PhD project used long-term mesocosm
experiments to examine how a New Zealand brittlestar species adapts or
acclimates to ocean warming and acidification. He examined a wide range
of responses, including physiological and behavioural, and used
respR for analysing respirometry data. Hope to see these as
papers soon and congrats on the PhD! 🥳
A timely and prominent paper examining how oxygen and body size modulate responses to warming in marine invertebrates. Very nicely done study.
Hannah Lowes has already published a chapter of her MSc thesis (see below) on sea cucumber responses to copper exposure, so massive congrats on the MSc! 🥳 Hopefully we see the rest published soon.
This study used respR to get metabolic rates of
microfragments of corals to examine the effects of antibiotics on the
holobiont community. Great to see the package being used to analyse
micro-respirometry data like this.
This MSc project looked at thermal microclimates amongst kelp
holdfasts, and used respR in getting metabolic rates of a
snail and an amphipod. These microclimates seem to provide some
buffering against external warming and may be something of a refuge for
invertebrates, which is really interesting. Congrats on the MSc Frances!
🥳
This study used respR to anaylse data from experiments
looking at the effects of extreme hypoxia on metabolic rate and
behaviour in a seahorse. Perhaps unsurprisingly, extreme hypoxia led to
a signicant reduction in metabolic rate and also signs of movement
lethargy.
We love seeing respR used on species we were never even
aware of. This study looked at the physiology and escape behaviour of
blind cavefish and their closely related sighted species. We were also
really happy to see the respR output plots are good enough
to be publication quality (Fig. 2).
Really happy to be involved in this publication detailing a new low-cost and relatively simple method for conducting micro-respirometry on corals. Respirometry on very small organisms has until now been costly and difficult and this makes it much more practical, and this should help extend our knowledge of the functioning of reefs. Thanks to Kate for inviting me to be a part of this exciting project.
Another nice study showing how respR can be used with
micro-respirometry data, this time on copepod nauplii. Here the authors
looked at if heatwaves have ongoing effects on metabolism and
development. Turns out they don’t! So these copepods might be quite
resilient to warming events.
Another interesting study by Noelle M. Lucey. This looked at the
effects of heatwaves and hypoxic events on tropical species in a reef
habitat, and how they can combine to reduce available habitat. Like her
earlier study
this used respR to determine \(P_{crit}\) of two species of brittle stars
under these stressors.
Abdisalan Hawadle’s summer undergrad project conducted at Friday Harbor Labs (beautiful place, did lots of respirometry there!) examines how temperature and water flow speed affect metabolic rate in two mussel species. Thermal performance curves differed between the two species in response to both temperature and water speed. Nice project, hope you publish it Abdisalan!
A study looking at the effects of copper exposure on how sea
cucumbers tolerate emersion during low tides. It used respR
to get RMR upon re-immersion after copper exposure, but found no
difference with specimens which had not been exposed. Looks like sea
cucumbers can tolerate emersion just fine, even after copper exposure.
Nice study!
This study looked at the effects of hypoxic conditions on corals from
the eastern Pacific and used respR to get MO2 and PCrit.
What’s really interesting about this study is that it also determined
the same metrics using the respirometry
package, and we were happy to see that results between the two packages
are largely equivalent. It is also good to see the authors varying the
width used in the PCrit analysis to see how it affects the results. The
width
over which a rolling rate is determined from the oxygen timeseries is a
really important parameter that is often unreported for PCrit results,
so good to see the authors taking account of it. Of course
respR makes this easy!
Ashleigh Hawke’s MSc project examines how polymers from microplastics affect the behaviour and physiology of marine fish, in the form of escape responses and metabolic rate. Interesting results in that both polymers examained affected escape performance, but only one affecting standard metabolic rate. Congrats on the MSc! 🥳
Derek Somo’s PhD project looked at a wide range of physiological
functioning in an intertidal fish under warming and hypoxia. He used the
oxycrit function to get the PCrit of his intertidal
sculpins. Congrats on the PhD! 🥳
Excellent work from Davide Thambithurai and collaborators. They found
parasite density affected capture probability in zebrafish, with
implications for vulnerability to capture in commercial fisheries. As
for metabolic rate, they showed parasites increased SMR, but not MMR or
AAS. Davide was one of our early beta testers. In fact the
zeb_intermittent.rd example data comes from this very
study!
This is an interesting study looking at the effects of effluents from
fish farms on cold water corals in Norway. It used the
auto_rate function to get the respiration rates of coral
fragments to establish the negative effects of effluent on metabolic
rates, and also showed it has negative effects on energy stores and
growth.
Another awesome sea urchin respirometry study! This looked at the
combined effects of heatwaves and deoxygenation events on a tropical sea
urchin, and used respR to determine both metabolic rates
and \(P_{crit}\) under these stressors.
The authors show that the compound effects of marine heatwaves and
hypoxic events, which usually occur together, are devastating to the
populations of this species.
Joëlle Guitard and colleagues examined how parasite load affected
metabolic rates and escape responses in a freshwater fish. They
discovered that parasites reduced metabolic rates and also adversely
affected escape responsiveness. They used respR to
calculate MO2 and the auto_rate function to do 60 second
rolling regressions from which MMR were calculated. Really nice write-up
of the methods. Lots of detail, just what we like to see! 👌
Jordan Grigor and collaborators used respR to compare
respiration and swimming activity from epi- and mesopelagic copepods and
how they may be indicators of the onset of diapause. They found
differences in size, activity and metabolism between epi- and
mesopelagic groups. Nice work, and another example of how the package is
being used to analyse micro-respirometry data.
We’ve always noted in our documentation that except for the final
conversion step, respR treats data as unitless, and it
could be used to identify and extract rates from other types of
experimental data, and here is the proof. It was used in this study,
specifically auto_rate, to quantify \(H_2O_2\) consumption rates as part of
development of a system to study biofilm activity. Really great to see
the package being used like this.
José Ricardo Paula et al. looked at the interactions between ocean acidification, access to cleaner species, and parasite infection and how they affect physiology (MMR, RMR and AS) in damselfish on beautiful Lizard Island on the GBR. Looks like increased parasite tolerance comes at the cost of responsiveness to other stressors such as OA. Nice work. Thanks for the citation!
This study by William Joyce et al. looked at heart rates in
larval zebrafish and conducted respirometry trials to determine if
altered heart rates were associated with changes in oxygen consumption
or \(P_{crit}\) (spoiler: they
weren’t). Great to see respR put to use on
microrespirometry data on such small specimens - 0.16 mg 😱.
More sea urchin respirometry in this study looking at differences in
physiology between green sea urchin populations from urchin barrens and
kelp forests. respR was used to determine the metabolic
rates of the urchins, and the authors found those from barrens to have
lower oxygen consumption rates and also that these populations were more
sensitive to temperature changes.
A really cool and extensive study by Rachael Morgan et al.
Zebrafish were acclimated to 15 (🤯) temperatures and then a host of
traits measured, including physiology, gene expression, and behaviour.
They found that physiological plasticity was lost from fish adapted to
stable temperatures. Incredible amount of work, and really clear results
with important implications for anyone doing experimental work on
animals in different temperatures. respR was used to get
SMR, MMR, and aerobic scope.
Dom Roche et al. review the status of open science and
reproducibility in experimental biology and their role in consensus
building and cross-discipline collaborations. Very interesting paper and
essential reading for anyone doing collaborative experimental biology
and sharing their results. They gave respR a quick
shout-out as an example of open-source software aiding
cross-disciplinary collaboration. Thanks for the citation!
This study on Sydney rock oysters and the buffering effects of
seagrasses on seawater pH used respR to examine the
metabolic rates of oysters under different pH. The authors showed
seagrasses boosted oyster growth at ambient pH, but did not do so at
elevated pH. So seagrasses may not be able to buffer out the negative
effects of ocean acidification. Cool study.
Halle Berger used respR in this MSc thesis, looking at
the response of the Dungeness crab to climate stressors in the context
of a regional vulnerability assessment. They found that respiration
rates of this species increased exponentially under higher temperatures.
We hope the package proved useful in establishing this from your
respirometry data. Congrats on the Masters! 🥳
In this study Nicholas Wu examined how an endocrine disruptor in the
environment exacerbated the effects of high temperatures on growth and
metabolism in zebrafish. He used respR to calculate the
resting MO2 of zebrafish under warming and exposure to plastic
pollution. Nice work Nic!
In this study Jenni Prokkola et al. examine the genetic
basis of how energy metabolism and life history interact in Atlantic
Salmon. This used the respR function
auto_rate() to calculate rates across one and two-minute
time windows to identify maximum metabolic rates. After seeing it as a
preprint we’re delighted to see it published in a top journal. Nice work
Jenni!
respR (and one of its developers) had a small role in
this huge and extensive study by Ben Burford as part of his PhD. Ben
used metabolic rate measurements to model the physiological sensitivity
in terms of temperature and dissolved oxygen of a squid which occurs
across a wide latitude range in the eastern Pacific, and how these may
allow for rapid range expansions. Incredibly impressive, wide-ranging
work.
Jennifer Mallon is another researcher who took advantage of our open
offer to help get users started with respR by sending us a
data file. Great to see the work published! They looked at both oxygen
uptake and production in corals and coralline algae to calculate net
photosynthesis. Really great to again see oxygen production being
calculated using the package, not just consumption.
Lewis Jone’s MSc thesis, in which he used respR to get
the Pcrit from a flounder acclimated to different temperatures. Congrats
on the Masters! 🥳
Ivar Optun Andersen’s MSc thesis, in which he used respR
to get the metabolic rate and Pcrit of a isopod exposed to aqueous
aluminium. Congrats on the Masters! 🥳
Christophe Jourdain Bonneau’s MSc thesis, which he later went on to publish in CJZ - see above. Congrats on the Masters! 🥳
Cuen Muller’s PhD thesis, which examined fisheries-induced evolution under ocean acidification. Congrats on the PhD! 🥳
Yangfan Zhang’s PhD thesis. He has gone on to publish much of it. Congrats on the PhD!
Alexandra Burns used respR in this MSc project, looking
at oxygen supply capacity under different temperatures in a species of
shrimp. Congrats on the Masters! 🥳
Excellent summary and guide to best practices in conducting, analysing and reporting intermittent-flow respirometry studies. Essential reading!
An excellent summary and guide to the best practices and tools
available to estimate maximum metabolic rates. Goes into a lot of detail
about rolling regressions, and the importance of the sampling window
used, something that was instrumental to the design of
respR, and is relevant to all metabolic rate calculations
not just MMR. Very much required reading if you are interested in
respirometry analyses in general.
This study looked at how physiological plasticity in invasive species
can potentially predict invasion success. respR was used to
calculate the Pcrit of native and invasive shrimp. Really nice results
showing the invader having a lower Pcrit at higher temperatures than the
native, potentially allowing it to tolerate hypoxic events better.
This study examines the effects of nitrate pollution on thermal and
hypoxia sensitivity in European grayling. respR was used to
calculate the Pcrit. They show (quite definitively, using three
different PCrit methods) that Pcrit significantly increases under
nitrate exposure, indicating a lower hypoxia tolerance. Nice work!
This study looked at the performance of the common carp when exposed
to heavy metals, and found metabolic rates increased after 3 days of
exposure. respR was used to process the respirometry data
and calculate both SMR and MMR. Marion Pillet was a researcher who took
advantage of our open offer to help get users started with
respR by sending us a data file, so we are happy to see the
work published!
This MSc project examined the effects of salinity on Nile tilapia
growth and physiology in aquaculture recirculation tanks, and used
respR to calculate the metabolic rates. It’s mostly in
Lithuanian, so we haven’t been able to figure out the details, but
congrats on the MSc!
Another study we were happy to see examining both oxygen production
rates as well as consumption rates. It used respR to
determine gross primary production by determining both oxygen production
and respiration rate in coralline algae. Take home message: lots of
salmon poop is bad for algae.
This review on methods in stress assessment studies mentions
respR as one of the analytical options for examining
respiration rates.
Here, the package was used to calculate mass-specific metabolic rates of sea urchins from intermittent-flow respirometry data, to examine the carryover effects of acclimation to different temperatures and ocean acidification conditions. Can’t say too much about this one, except it’s good to see a package author still using his own tools. 😉
This study is a great example of how respirometry is not all about
respiration, and exactly what we were thinking of when we designed
respR to handle oxygen production rates as well as
consumption. Here, it was used to calculate oxygen flux (net
photosynthesis and respiration) of Red Sea corals under simulated
heatwaves in large mesocosms.
This study used respR to calculate the aerobic scope of
juvenile brown trout to investigate the effects of egg incubation
temperature. We were very happy to see the auto_rate()
function being used to extract both most linear and maximum metabolic
rates to calculate the aerobic scope, one of the primary use cases we
designed it to handle.
This study looked at thermal tolerance and oxygen supply capacity in
newborn sharks. This shows a great use for respR outside of
the lab, in that it was used to determine oxygen decline from field
recordings of oxygen off the coast of Moorea. We were especially pleased
to see the auto_rate() function get a mention in the
manuscript for calculating maximum metabolic rates.
Joëlle Guitard’s MSc thesis, which she later published in JEB. Congrats on the Masters! 🥳
This study compared the results of different methods of determining
maximum metabolic rates. The authors point out minimum sampling window
is a very important factor in determining MMR. We always thought this
was pretty obvious, which is why respR has always allowed
rolling regressions of different window sizes to be performed, with
visualisations to see the results of how this affects rate calculations.
🤔
This is a really cool study looking at how warming may affect brain
size and cognition in minnows, as well as metabolic rate. Warm fish had
bigger brains, but weren’t as good at finding their way through a maze!
Awesome stuff. It used respR to determine SMR, MMR and
aerobic scope.
We have a special fondness for studies doing respirometry on sea urchins (we feel your pain, especially the spines under the fingernails). This study compared the physiology of urchins from kelp barrens and kelp forests, and found those in barrens have dramatically reduced resting metabolic rates, by up to 40%. Cool stuff!
This is another study that used respR to determine the
Pcrit, this time of an invasive bivalve, and the authors used it to show
that the lack of metabolic regulation may limit the spread of this
invader.
This study looked at the effects of ocean acidification on a larval
fish. The authors used respR to calculate SMR and MMR
rates, then filtered the rates according to various criteria (above 80%
oxygen, r2 above 0.85, etc.). This is a great idea, and exactly why we
introduce the function select_rate() in v2.0, which allows
for exactly this kind of application of easily reported rate selection
criteria.
Amazingly, this is the only study on zebrafish to cite
respR so far, which is surprising given how many groups are
working and doing respirometry on them. This study looked at the effects
of microplastics on oxygen consumption and gene expression in larval
zebrafish. They did not find any effects on metabolic rate, but did on
the fish microbiome, which could lead to higher susceptibility to
disease.
Anna M. Internicola used respR in this MSc project,
looking at the effects of microplastics on zooplankton in Delaware Bay.
She found, amongst other effects, chronic exposure increased metabolic
rates. Nice work, and congrats on the Masters! 🥳
Daniel F. Gomez Isaza used the calc_rate() function to
calculate mass-specific metabolic rates of juvenile silver perch to
examine the effects of nitrates on thermal sensitivity in Chapter 5 of
his PhD thesis and accompanying JEB paper. Thanks for the citations, and
congrats on the PhD! 🥳
Matthew Gilbert cited respR in his PhD thesis as an
example of how analytical tools in physiology are improving and
evolving. Thanks for the citation, and congrats on the PhD! 🥳
Another study that used respR to determine the Pcrit,
this time of an estuarine fish. This was an examination of methods of
determining Pcrit, both the analytical method of processing the
metabolic rate data, and the respirometry method used (closed
vs. intermittent-flow). There has been concern that closed respirometry
mis-estimates Pcrit, because of the build-up of toxic metabolic end
products, and intermittent-flow methods are preferable. The authors
showed here this is not the case, and results were the same with either
method. Really interesting stuff, and essential reading if you are
wanting to determine Pcrit via respirometry.
This study examined how diatoms dominate food webs under ocean
acidification conditions. Another study that uses respR to
examine both oxygen production as well as consumption rates. The authors
used the package to determine net oxygen production by determining both
production and respiration.
This paper looked for the first time at the effects of grouping on
metabolic rate in a social squid. The package was used here to calculate
metabolic rates of both individual and groups of squid in a swim tunnel,
and also their Pcrit. The very first paper to cite respR -
a co-author may have had some influence on that… 🤔