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  <front>
    <journal-meta><journal-id journal-id-type="publisher">OS</journal-id><journal-title-group>
    <journal-title>Ocean Science</journal-title>
    <abbrev-journal-title abbrev-type="publisher">OS</abbrev-journal-title><abbrev-journal-title abbrev-type="nlm-ta">Ocean Sci.</abbrev-journal-title>
  </journal-title-group><issn pub-type="epub">1812-0792</issn><publisher>
    <publisher-name>Copernicus Publications</publisher-name>
    <publisher-loc>Göttingen, Germany</publisher-loc>
  </publisher></journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.5194/os-19-101-2023</article-id><title-group><article-title>Unifying biological field observations to detect and compare ocean
acidification impacts across marine species and ecosystems: <?xmltex \hack{\break}?>what to monitor
and why</article-title><alt-title>Unifying biological field observations</alt-title>
      </title-group><?xmltex \runningtitle{Unifying biological field observations}?><?xmltex \runningauthor{S.~Widdicombe et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Widdicombe</surname><given-names>Steve</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Isensee</surname><given-names>Kirsten</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Artioli</surname><given-names>Yuri</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff3">
          <name><surname>Gaitán-Espitia</surname><given-names>Juan Diego</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-8781-5736</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff4">
          <name><surname>Hauri</surname><given-names>Claudine</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-5048-0028</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff5">
          <name><surname>Newton</surname><given-names>Janet A.</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff6 aff7">
          <name><surname>Wells</surname><given-names>Mark</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="yes" rid="aff8 aff9">
          <name><surname>Dupont</surname><given-names>Sam</given-names></name>
          <email>sam.dupont@bioenv.gu.se</email>
        </contrib>
        <aff id="aff1"><label>1</label><institution>Plymouth Marine Laboratory (PML), Plymouth, PL1 3DH, UK</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>Intergovernmental Oceanographic Commission of the United Nations
Educational, <?xmltex \hack{\break}?>Scientific and Cultural Organization, Paris, 75732, France</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>The Swire Institute of Marine Science, School of Biological Sciences,
The Hong Kong University, Hong Kong, China</institution>
        </aff>
        <aff id="aff4"><label>4</label><institution>International Arctic Research Center, University of Alaska Fairbanks,
Fairbanks, AK 99775-0100, USA</institution>
        </aff>
        <aff id="aff5"><label>5</label><institution>Applied Physics Laboratory and College of the Environment, University
of Washington, Seattle, WA 98105-6698, USA</institution>
        </aff>
        <aff id="aff6"><label>6</label><institution>School of Marine Sciences, The University of Maine, Orono, ME
04469-5706, USA</institution>
        </aff>
        <aff id="aff7"><label>7</label><institution>State Key Laboratory of Satellite Ocean Environment Dynamics, Second
Institute of Oceanography, <?xmltex \hack{\break}?>Ministry of Natural Resources, Hangzhou, China</institution>
        </aff>
        <aff id="aff8"><label>8</label><institution>Department of Biological and Environmental Sciences, University of
Gothenburg, Fiskebäckskil, 45178, Sweden</institution>
        </aff>
        <aff id="aff9"><label>9</label><institution>Radioecology Laboratory International Atomic Energy Agency (IAEA),
Marine Laboratories, <?xmltex \hack{\break}?>98000, Principality of Monaco</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Sam Dupont (sam.dupont@bioenv.gu.se)</corresp></author-notes><pub-date><day>25</day><month>January</month><year>2023</year></pub-date>
      
      <volume>19</volume>
      <issue>1</issue>
      <fpage>101</fpage><lpage>119</lpage>
      <history>
        <date date-type="received"><day>10</day><month>September</month><year>2022</year></date>
           <date date-type="rev-request"><day>26</day><month>September</month><year>2022</year></date>
           <date date-type="rev-recd"><day>15</day><month>December</month><year>2022</year></date>
           <date date-type="accepted"><day>26</day><month>December</month><year>2022</year></date>
      </history>
      <permissions>
        <copyright-statement>Copyright: © 2023 Steve Widdicombe et al.</copyright-statement>
        <copyright-year>2023</copyright-year>
      <license license-type="open-access"><license-p>This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this licence, visit <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">https://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><self-uri xlink:href="https://os.copernicus.org/articles/19/101/2023/os-19-101-2023.html">This article is available from https://os.copernicus.org/articles/19/101/2023/os-19-101-2023.html</self-uri><self-uri xlink:href="https://os.copernicus.org/articles/19/101/2023/os-19-101-2023.pdf">The full text article is available as a PDF file from https://os.copernicus.org/articles/19/101/2023/os-19-101-2023.pdf</self-uri>
      <abstract><title>Abstract</title>

      <p id="d1e210">Approximately one-quarter of the CO<inline-formula><mml:math id="M1" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> emitted to the
atmosphere annually from human activities is absorbed by the ocean,
resulting in a reduction of seawater pH and shifts in seawater carbonate
chemistry. This multi-decadal process, termed “anthropogenic ocean
acidification” (OA), has been shown to have detrimental impacts on marine
ecosystems. Recent years have seen a globally coordinated effort to measure
the changes in seawater chemistry caused by OA, with best practices now
available for these measurements. In contrast to these substantial advances
in observing physicochemical changes due to OA, quantifying their
biological consequences remains challenging, especially from in situ
observations under real-world conditions. Results from  2 decades of
controlled laboratory experiments on OA have given insight into the likely
processes and mechanisms by which elevated CO<inline-formula><mml:math id="M2" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> levels affect biological
process, but the manifestation of these process across a plethora of natural
situations has yet to be fully explored. This challenge requires us to
identify a set of fundamental biological and ecological indicators that are
(i) relevant across all marine ecosystems, (ii) have a strongly demonstrated
link to OA, and (iii) have implications for ocean health and the provision of
ecosystem services with impacts on local marine management strategies and
economies. This paper draws on the understanding of biological impacts
provided by the wealth of previous experiments, as well as the findings of
recent meta-analyses, to propose five broad classes of biological indicators
that, when coupled with environmental observations including carbonate
chemistry, would allow the rate and severity of biological change in
response to OA to be observed and compared. These broad indicators are
applicable to different ecological systems, and the methods for data
analysis suggested here would allow researchers to combine biological
response data across regional and global scales by correlating rates of
biological change with the rate of change in carbonate chemistry parameters.
Moreover, a method using laboratory observation to design an optimal
observing strategy (frequency and duration) and observe meaningful
biological rates of change highlights the factors that need to be considered
when applying our proposed observation strategy. This innovative observing
methodology allows inclusion of a wide diversity of marine ecosystems in
regional and global assessments and has the potential to increase the
contribution of OA observations from countries with developing OA science
capacity.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <label>1</label><title>Introduction</title>
      <p id="d1e240">Anthropogenic perturbations to the Earth system directly impact the health
of the world's ocean, its biochemical dynamics, its ecological properties
and natural resources, and consequently the provision of ecosystem services.
Ocean change includes so-called “slow onset events”, such as ocean warming,
acidification, deoxygenation, sea level rise, and glacial retreat, as well
as an increase in extreme weather and biogeochemical anomalous conditions,
such as marine heat waves (Hobday et al., 2016), storms, and extreme
acidification and deoxygenation events (Gruber et al., 2021).</p>
      <p id="d1e243">Today, the ocean absorbs about one-quarter of the CO<inline-formula><mml:math id="M3" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> emitted to the
atmosphere annually by human activities, resulting in a reduction of
seawater pH (Friedlingstein et al., 2019, 2020). This multi-decadal process,
termed “anthropogenic ocean acidification”, causes additional chemical
changes, including altering the speciation of dissolved inorganic carbon.
Other regional and local changes also affect carbonate chemistry, such as
enhanced upwelling, sea ice melt, riverine inputs, or increased temperature.
Marine species and ecosystems respond to changes in carbonate chemistry
regardless of the driving mechanism, so we use the term ocean acidification
(OA) here more broadly to refer to all acidification whether
anthropogenically derived global, regional, or local processes.</p>
      <p id="d1e255">Although there is an accepted recognition of OA as a threat to ocean health
and its detrimental and nonlinear impacts on marine species and ecosystems,
the initial focus of international networks, projects, and organizations was
to adequately describe, quantify, and understand the chemical changes
associated with OA (Newton et al., 2015). Substantial progress in this
direction has been made (Tilbrook et al., 2019), notwithstanding the fact that many
geographical regions still lack sufficient capability, information, and data
to determine local OA conditions. Best practices and standard operating
mechanisms are now available to the global scientific community to assess
spatial and temporal patterns in pH and carbonate chemistry, to quantify
trends and rates of change, and to identify areas with strong signals of OA
chemical impacts (IOC-UNESCO, 2019, and references therein).</p>
      <p id="d1e258">The second, even more challenging goal for the scientific community is to
identify the impacts of OA on marine life, as they occur in real-world
situations, over timescales that are appropriately matched to the rate at
which the chemical changes are occurring and over spatial scales that are
appropriate for the biological processes being impacted. Currently less than
10 % of the published literature addressing the impacts of OA on species
and ecosystems has included biological field observations.
The majority of scientific publications that have focused on field
observations are discrete studies in areas of unusually high CO<inline-formula><mml:math id="M4" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> levels
(OA-ICC source, February 2022). For example, in their pioneer studies,
Hall-Spencer et al. (2008) showed significant changes in community
structures along CO<inline-formula><mml:math id="M5" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> gradients at the vent site in Ischia. Typical
rocky shore communities with abundant calcareous organisms shifted to
communities lacking corals and other calcifying organisms. Scaling up the
knowledge gained from 2 decades of experimental results from both
laboratories and natural high-CO<inline-formula><mml:math id="M6" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> environments, such as CO<inline-formula><mml:math id="M7" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>
seeps and upwelling regions, to appreciate the chronic impacts of OA across
a variety of marine ecosystems will inevitably require a significant
increase in the in situ biological monitoring that is specifically relevant to
OA.</p>
      <p id="d1e298">Marine environmental in situ observations are a prerequisite for
ecosystem-based management and are essential to ensure that sustainable
management targets are met. Traditionally, monitoring and observations
provide the context to marine science and have allowed development of a
critical scientific understanding of the marine environment and the impacts
that humans are having on it (Bean et al., 2017). Biological observations
are also an important complement to experimental studies as they set the
boundary conditions within which to measure the rate of change (speed at
which a given process changes over a specific period of time) in any given
biological parameter (e.g., biodiversity; see Luypart et al., 2020). Whilst
traditional biological observations programs focus on identifying and
quantifying (counting and weighing) a wide range of taxa and communities
(Muller-Karger et al., 2018a), such programs are rarely linked to direct OA
field observations. This means that presently, applied biological
observation strategies have difficulties in attributing the change, or a
proportion of it, to OA as there is little specific focus on those
biological parameters most affected by carbonate chemistry, as well as a
lack of supporting carbonate chemistry data. Long-term studies that
appropriately consider the biological changes driven by OA are still
missing, which limits the development of appropriate marine management
strategies to either mitigate stress or adapt to OA impacts.</p>
      <p id="d1e301">The biggest obstacle to increasing the overall effectiveness of biological
observations for OA is currently a lack of clear guidance on what biological
parameters to measure and, importantly, how such observations can be
compared with others to generate greater understanding of the trends,
hotspots, and patterns occurring over local, regional, and global scales. To
address this challenge, we need to identify a clear subset of biological
variables and indicators that provide quantitative information across all
ecosystems, as well as a method to not only understanding the rate and
severity of the local impact, but also compare multiple datasets to deliver
a greater holistic understanding of OA's biological impacts regionally and
globally. Such methods will rely on biological observations being coupled
with a suite of environmental observations including, but not limited to,
measures of carbonate chemistry, in integrated observing activities.</p>
      <p id="d1e304">Here, we present an innovative approach that stems from considering five
fundamental ecosystem traits that span across marine ecosystems and which
have been identified as potentially sensitive to OA by a significant body of
previously published studies. Firstly, we introduce our approach and
describe why such a trait-based approach is appropriate. Secondly, we
illustrate why these five specific traits have been identified and provide
examples of what parameters and processes can be measured in each of the
traits (e.g., Kroeker et al., 2013). Thirdly, we present an example of how
biological observing data can be coupled with environmental data to compare
the results from multiple studies or observations in order to better
understand the biological impacts of OA, identify trends and hotspots,
appreciate the generality of response, and identify the extent to which OA is
driving the changes observed in relation to other environmental stresses. We
recognize that there could be several different methods that would be appropriate
for such data analyses and encourage researchers to employ those methods
most suitable to address their specific research question. Finally, we will
use a combination of conceptual and real data examples to illustrate the key
factors and assumptions that need to be considered when applying the
monitoring approaches proposed here.</p>
      <p id="d1e307">If widely adopted, the approaches proposed in this paper would promote much
greater co-location of biological and ocean acidification monitoring to help researchers
better understand the biological consequences of ocean acidification in the
real world. This outcome aligns with previous recommendations (Muller-Karger
et al., 2018b), which call for greater global connectivity between the
collection of essential ocean variables (EOVs) through the Global Ocean
Observing System (GOOS) and essential biodiversity variables (EBVs) from
the Group on Earth Observations Biodiversity Observation Network (GEO BON).
However, our inclusive approach encourages the collection of carbonate
chemistry and biological data that go beyond the defined set of
observations that are recognized as either EOVs or EBVs. It should be noted
that several biological EOVs remain to be fully defined, and their
observation alongside physical and biogeochemical variables has yet to be
implemented (Miloslavich et al., 2018). Our paper supports the ambitions
outlined by Muller-Karger et al. (2018b) by proposing a practical way to
detail the biotic impacts of ocean acidification by embracing a huge variety
of biological observations. Such an approach would not only facilitate the
creation of completely new observing activities that include both biological
and biogeochemical observations from the start, but would also provide
guidance on how existing biogeochemical ocean acidification monitoring can
add relevant biological observations to their suite of observations, and
vice versa, to better appreciate the biological consequences of OA across
regional and global scales.</p>
</sec>
<sec id="Ch1.S2">
  <label>2</label><title>Biological field observations using traits as indicators of OA</title>
      <p id="d1e318">Quantifying rates of change in carbonate chemistry due to anthropogenic
inputs at a suite of globally distributed locations is one of the main goals
of the observing community (Newton et al., 2015) and is included in the
indicator for Sustainable Development Goal (SDG) target 14.3. In principle,
using a similar approach to evaluate biological sensitivity to OA would
allow direct comparability between the growing availability of carbonate
chemistry data and biological observations. However, while the measurement
of carbonate chemistry is largely limited to a small number of parameters
(pH, dissolved inorganic carbon – DIC, partial pressure of carbon dioxide
– <inline-formula><mml:math id="M8" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula>CO<inline-formula><mml:math id="M9" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>, total alkalinity – TA), all of which can be calculated with
different degrees of uncertainty from direct measurements of any two of
these parameters, measurement of biological impacts encompasses a much wider
range of parameters, each with different scales and units. Thus, while
standardizing the observation of carbonate chemistry changes is relatively
straightforward, standardizing the measurement of biological impacts in a
way that would allow broad-scale comparisons among regions and ecosystems is
considerably more challenging.</p>
      <p id="d1e337">The first challenge for delivering a truly global assessment of OA impacts
is to identify a set of fundamental biological parameters that (a) are not
linked to any model organism, (b) are relevant across different biological
systems, (c) have a strongly demonstrated link to OA, (d) have implications
for the overall function of ecosystems and the provision of ecosystem
services, and (e) should be easily measurable. OA alters multiple properties
of the seawater carbonate system, including pH, speciation of DIC, and
carbonate saturation state, that individually or in combination affect
marine organisms. Consideration of only one of these parameters may then
obscure the mechanistic origin of any observed OA-driven change in
biological attributes. While other drivers, such as temperature, nutrients, and
oxygen, may exert proximate control over changes in many marine
ecosystems, it is important to recognize that OA may have a major role in
modulating these consequences in most marine waters, while being the
dominant driver for ecosystem change in others (e.g., Kroeker et al., 2013;
Vargas et al., 2017, 2022).</p>
      <p id="d1e340">In addition to the influence of other climate drivers, it should be noted
that biological impacts can be heavily moderated by other environmental and
ecological factors such as energy supply as well as other drivers and stressors
such as nutrient and food content. In regions experiencing multiple elevated
environmental stressors (e.g., increased sedimentation, organic or inorganic
contaminants) it will be more difficult to disentangle the longer-term OA
effects from those potential confounding effects. However, while
complicating factors do not negate the importance of collecting OA impact
data from these areas, it does emphasize the importance of collecting
additional relevant environmental data to aid interpretation of the observed
biological responses. In addition, for indicators measured at the species
level, different life stages may also show different responses (e.g., Kroeker
et al., 2013; Bednarsek et al., 2019, 2021a, b). These measures for adults
can give regional insights into how ecosystems have responded to OA pressures,
while measuring these aspects on juvenile stages may help to presage the
future changes in these ecosystems. So again, the importance of collecting
environmental, ecological, and physiological contextual data cannot be overemphasized.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1" specific-use="star"><?xmltex \currentcnt{1}?><?xmltex \def\figurename{Figure}?><label>Figure 1</label><caption><p id="d1e346">Five fundamental ecosystem traits identified as potentially
sensitive to ocean acidification and their observable indicators.</p></caption>
        <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://os.copernicus.org/articles/19/101/2023/os-19-101-2023-f01.png"/>

      </fig>

</sec>
<sec id="Ch1.S3">
  <label>3</label><title>Five traits that are influenced by OA</title>
      <p id="d1e363">Based on previously published meta-analysis and reviews (e.g., Doney et al.,
2020; Figuerola et al., 2021; Hancock et al., 2020; Kroeker et al., 2013;
Turley and Gattuso, 2012), we delineate five fundamental ecosystem traits
and their suite of observable indicators (Fig. 1): (1) calcified organisms
and calcification, (2) autotrophs and primary production, (3) heterotrophs and
secondary production, (4) biodiversity and community structure, and (5) genetic adaptation. The specific choice of indicator at different sites will
depend on the questions or concerns of the investigator but should relate
to fitness of species and the health of marine populations and communities;
if relevant, it should also be associated with key ecosystem services. The
feasibility of obtaining these observations over the long term must also be
considered. Detection of OA-induced change in these indicators hinges upon
the variability of the data, so a first step is to apply recognized best
practices for biological measurements (Katsanevakis et al., 2012; Bean et
al., 2017). Even so, natural “noise” of the system, in terms of short-term
environmental changes (weather) and organismal plasticity, must also be
taken into account when selecting indicators because it strongly influences
the time of emergence of long-term trends (Vargas et al., 2017, 2022).</p>
      <p id="d1e366">The specific biological observations listed in this section are
examples of potential parameters to measure and are not exhaustive. They
provide a suitable framework on which to build both intensive and pragmatic
field observation programs that are best suited for local capacities and
funding. These methodological inventories will undoubtedly evolve as future
technologies emerge and become more widely available over the coming decades
(Bean et al., 2017), but the central ecosystem traits they manifest,
combined with high-quality carbonate system data, will enable quantification
of OA-driven changes in marine ecosystems. The goal is to determine the
relationship between rates of chemical and biological changes, enabling
comparisons of those relationships across diverse and
geographically distributed ecosystems.</p>
<sec id="Ch1.S3.SS1">
  <label>3.1</label><title>Calcified organisms and calcification</title>
<sec id="Ch1.S3.SS1.SSS1">
  <label>3.1.1</label><title>Rationale</title>
      <p id="d1e383">The use of calcium carbonate (CaCO<inline-formula><mml:math id="M10" display="inline"><mml:mrow><mml:msub><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msub><mml:mo>)</mml:mo></mml:mrow></mml:math></inline-formula> structures
for structural support and protection is widespread amongst marine organisms
(e.g., Monteiro et al., 2016; Fitzer et al., 2019; Clark et al., 2020). As
changes in seawater chemistry have been demonstrated to affect calcium
carbonate structures and biomineralization rates (see references in Fitzer et al.,
2019), analysis of effects from acidification on calcifiers is perhaps the
most documented of OA biological impact studies (e.g., Hofmann et al., 2008;
Vézina and Hoegh-Guldberg, 2008; Wittmann and Pörtner, 2013;
Bednaršek et al., 2014, 2017, 2021a; Osborne et al., 2020). OA can
affect the ratio of calcifiers to non-calcifiers in an ecosystem, aspects of
calcified structures, and measured rates involving calcium carbonate,
including both the deposition and dissolution of calcium carbonate (Fitzer
et al., 2019).</p>
</sec>
<sec id="Ch1.S3.SS1.SSS2">
  <label>3.1.2</label><title>Indicator categories and observations</title>
</sec>
<sec id="Ch1.S3.SS1.SSSx1" specific-use="unnumbered">
  <title>Biomass, abundance, and percent cover of calcifying organisms within an
ecosystem</title>
      <p id="d1e412">Changes in biomass, abundance, and percent cover of biocalcifying
species, compared to non-calcifying species, measured across either fine
scales (meters) or broad scales (kilometers) can be used as a primary
indicator of OA stress once other known factors are ruled out (e.g.,
eutrophication). Inorganic to organic biomass ratios (PIC <inline-formula><mml:math id="M11" display="inline"><mml:mo>:</mml:mo></mml:math></inline-formula> POC) of individual
organisms, populations, or whole assemblages can also provide a sensitive
measure of relative changes in the presence of biocalcifying organisms
within an ecosystem (Thomsen et al., 2010).</p>
</sec>
<sec id="Ch1.S3.SS1.SSSx2" specific-use="unnumbered">
  <title>Skeletal morphology and composition</title>
      <p id="d1e428">The state, structure, and mineral
composition of calcified biostructures yield information about the ability
of organisms to maintain the balance of calcification over dissolution and are thus indicators of biological stress. Calcified structure morphology or
function can be assessed through measures such as weight, density, damage,
porosity, abnormality, dissolution severity, or strength (e.g., Bednarsek
et al., 2017, 2021a; Osborne et al., 2020).</p>
</sec>
<sec id="Ch1.S3.SS1.SSSx3" specific-use="unnumbered">
  <title>Rates of calcification</title>
      <p id="d1e438">Calcifying conditions in benthic habitats can
undergo large shifts over short (hourly, diurnal) timescales related to
physical forcing (e.g., tides, light levels). Measured rates of
calcification or dissolution on organismal to ecosystem scales help to
discern short-term (semi-instantaneous) responses of biocalcifying organisms
to present conditions (e.g., Goreau, 1959; Cohen et al., 2017; Schoepf et
al., 2017). These can be accomplished at larger scales with water-mass
tracking of observed changes in TA and DIC (along with <inline-formula><mml:math id="M12" display="inline"><mml:mi>T</mml:mi></mml:math></inline-formula>, <inline-formula><mml:math id="M13" display="inline"><mml:mi>S</mml:mi></mml:math></inline-formula>) to estimate net
community calcification (Fitzer et al., 2019), but also at organismal scales
with in situ approaches (Melzner et al., 2010; Dellisanti et al., 2020).</p>
</sec>
</sec>
<sec id="Ch1.S3.SS2">
  <label>3.2</label><title>Autotrophs and primary production</title>
<sec id="Ch1.S3.SS2.SSS1">
  <label>3.2.1</label><title>Rationale</title>
      <p id="d1e471">Primary production, in all of its myriad forms,
serves as the foundation for marine ecosystems. Quantifying its
susceptibility to OA is crucial because primary production ultimately
provides the energy for all trophic levels to adjust to OA-induced stress.
Increasing CO<inline-formula><mml:math id="M14" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> can modulate primary production in confounding ways. OA
shifts the carbonate system to yield higher <inline-formula><mml:math id="M15" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula>CO<inline-formula><mml:math id="M16" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>(aq), which is a
fundamental fuel for photosynthesis that often becomes limiting in high-productivity systems (Beardall et al., 2009). Many primary producers (but
not all) initiate metabolically costly carbon-concentrating mechanisms that
divert energy from growth and reproduction. So, increases in <inline-formula><mml:math id="M17" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula>CO<inline-formula><mml:math id="M18" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>(aq)
then have the potential to stimulate carbon fixation rates in pelagic and
benthic primary producers (Raven et al., 2014), including in marine
animal–algal symbioses (Dupont et al., 2012). However, decreasing external
and cytosolic pH can disrupt a broad suite of physiological and biochemical
factors, including proton pumps, cellular membrane potential, enzyme
activity, and energy partitioning (Beardall and Raven, 2004; Giordano et
al., 2005). OA may also influence the chemical availability of essential
micronutrients (e.g., trace metals, Gledhill et al., 2015), thereby
potentially affecting the nutritional support of primary production in some
coastal and offshore waters (Hutchins and Boyd, 2016). Another mode of
potential impact is that transmembrane proton gradients regulate flagellar
motion and thus cell motility (Manson et al., 1977), so OA may reduce the
access of vertically migrating flagellated phylogenetic groups to nutrients
while simultaneously increasing their susceptibility to predation
(Hallegraeff et al., 2012). Despite the likely complexity of potential OA
effects on autotrophs and primary production, the responses will be
underlain by three chief indicators.</p>
</sec>
<sec id="Ch1.S3.SS2.SSS2">
  <label>3.2.2</label><title>Indicator categories and observations</title>
</sec>
<sec id="Ch1.S3.SS2.SSSx1" specific-use="unnumbered">
  <title>Biomass and abundance</title>
      <p id="d1e529">The total biomass of primary producers in pelagic
and benthic environments is often  used to signal the energy available for
transfer to higher trophic levels (Pauly and Christensen, 1995; Brown et
al., 2010). Although methods for quantifying biomass or standing stock vary
depending on the environment or organism of interest, they can include
measures of total chlorophyll <inline-formula><mml:math id="M19" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> (chl <inline-formula><mml:math id="M20" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>) concentrations, phytoplankton cell
abundance, microphytobenthos biomass (e.g., chl <inline-formula><mml:math id="M21" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> per area of surficial
sediments), and the biomass of macroalgae and seagrasses. A central
benefit of this metric is that it is less susceptible to interannual
variability and thus gives more time-integrated insight into the status
of communities and regions.</p>
</sec>
<sec id="Ch1.S3.SS2.SSSx2" specific-use="unnumbered">
  <title>Productivity</title>
      <p id="d1e559">Lower levels of biomass at times can mask high carbon
turnover rates, so measuring carbon fixation rates or planktonic, macroalgal,
or seagrass growth rates can provide more sensitive and comprehensive
insight into energy flows in the system (Eddy et al., 2021). In some cases,
whole community production rates can be estimated by measuring net carbon
and oxygen dynamics (e.g., Juranek and Quay, 2005). However, such estimates
are prone to variability at hourly, weekly, and seasonal intervals.
Establishing trends associated with OA will require longer time series.</p>
</sec>
<sec id="Ch1.S3.SS2.SSSx3" specific-use="unnumbered">
  <title>Phenology</title>
      <p id="d1e569">Any change in the rates of primary production will alter
nutrient dynamics, so it will be important to measure the timing of
blooms or other rapid growth periods. If these shifts in phenology become
significant, they can lead to temporal disconnect between the timing of high
primary producer biomass and sensitive (e.g., larval) life cycle stages of
secondary producers that depend upon this energy source (Yamaguchi et al.,
2022).</p>
</sec>
</sec>
<sec id="Ch1.S3.SS3">
  <label>3.3</label><title>Heterotrophs and secondary production</title>
<sec id="Ch1.S3.SS3.SSS1">
  <label>3.3.1</label><title>Rationale</title>
      <p id="d1e589">There is good evidence that long-term exposure to
elevated <inline-formula><mml:math id="M22" display="inline"><mml:mi>p</mml:mi></mml:math></inline-formula>CO<inline-formula><mml:math id="M23" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula> levels increases metabolic energy demand in many marine
organisms (e.g., Stumpp et al., 2011; Pan et al., 2015; Jager et al., 2016).
This additional energy is needed to support increased acid–base balance
activities (e.g., increased cellular proton pump activity to counter acidosis
of intracellular fluids) (e.g., Stumpp et al., 2012), increased calcification
to counter increased calcium carbonate dissolution (e.g., Ventura et al.,
2016), and increased physical activities (e.g., increased burrow ventilation)
(Donohue et al., 2012). These additional energy expenditures leave less
energy available to invest in other key processes, including protein
synthesis and growth. Conversely, any increase in energy demands may be
alleviated in part or wholly by increased food supply from CO<inline-formula><mml:math id="M24" display="inline"><mml:msub><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msub></mml:math></inline-formula>-enhanced
primary production, leading to overall increases in heterotroph populations
and productivity and thereby changes in ecosystem function. For humans,
reductions in marine secondary production may have profound implications for
fisheries and aquaculture.</p>
</sec>
<sec id="Ch1.S3.SS3.SSS2">
  <label>3.3.2</label><title>Indicator categories and observations</title>
</sec>
<sec id="Ch1.S3.SS3.SSSx1" specific-use="unnumbered">
  <title>Biomass, abundance, and percent cover</title>
      <p id="d1e631">The total biomass or standing stock
of secondary producers in pelagic and benthic environments is not only a
sentinel of the available energy transfer upwards into food webs, but also
serves as a top-down integrated measure of effective primary production,
i.e., autotrophic growth utilized by grazing versus that produced by
noxious, toxic, or unpalatable autotrophs. The total heterotrophic community
abundance, ideally quantified as biomass per individual but also as numbers
of individuals, average body sizes, or percent cover (e.g., sponges,
colonial organisms), should be quantified to estimate total heterotrophic
biomass on appropriate seasonal or annual timescales. Splitting the
quantification of abundance and biomass into major functional or species
groups can provide greater detail and resolution for identifying those
aspects of the community or ecosystem that are most affected.</p>
</sec>
<sec id="Ch1.S3.SS3.SSSx2" specific-use="unnumbered">
  <title>Productivity</title>
      <p id="d1e640">As with primary producers, the observed biomass or standing
stock of secondary producers can be the consequence of rapid or more
sluggish growth and predation cycling, so quantifying the rates of secondary
production at either community or species scales provides important
additional insights into change within environments. There is a wide range
of methodologies to calculate gross estimates of pelagic and benthic
secondary production from in situ techniques to algorithms (Brey, 2012). It
may be useful to emphasize the observation of selected heterotrophic taxa
that play a strong structuring role within the local ecosystem or that have
high cultural or commercial value. Through its integrative nature, the
estimates of secondary productivity are likely to exhibit less temporal
variability than that of primary productivity, although the metrics of
biomass or standing stock are still the preferable indicator for
establishing OA-induced effects on heterotrophs and secondary production.</p>
</sec>
<sec id="Ch1.S3.SS3.SSSx3" specific-use="unnumbered">
  <title>Phenology</title>
      <p id="d1e650">Most marine secondary producers have planktonic life stages
that are coupled to environmental cues which signal food abundance (e.g.,
temperature, light), but this pairing may fail if OA-driven shifts in
primary production become substantial. The same may be true for other
segments of the food web (e.g., migration patterns of higher organisms). As
with primary producers then, quantifying any changes in the phenology of
secondary producers will be important for assessing the potential influence
of OA on marine ecosystems (Calbet et al., 2014).</p>
</sec>
</sec>
<sec id="Ch1.S3.SS4">
  <label>3.4</label><title>Biodiversity and community structure</title>
<sec id="Ch1.S3.SS4.SSS1">
  <label>3.4.1</label><title>Rationale</title>
      <p id="d1e669">Many of the processes mentioned in the previous
paragraphs result in changes in biodiversity and community structure. There
is compelling evidence that the sensitivity of marine organisms to all
aspects of OA varies enormously among species (Wittmann and Pörtner,
2013; Vargas et al., 2017, 2022). This variability is created via the
combination of different physiological and ecological traits exhibited by
the different taxa. Such interspecific variability could allow OA to act
directly as a strong selective pressure (Kroeker et al., 2010, 2013; Hancock
et al., 2020; Figuerola et al., 2021), decreasing biodiversity directly
through species loss (Hall-Spencer et al., 2008; Enochs et al., 2015) or
indirectly through a host of processes, such as disrupting competition (e.g.,
space occupation or resource allocation) or trophic interactions (e.g.,
predation and grazing; Kroeker et al., 2013b; Vizzini et al., 2017),
decreasing energy generation and flow, degrading critical biogenic habitats,
or increasing susceptibility to pathogens and diseases (Bibby et al., 2008;
Widdicombe and Spicer, 2008; Sunday et al., 2017). Evidence from the
paleontological record supports this assumption, with large species
extinctions and biodiversity losses being associated with periods of extreme
climate change events (Twichett, 2007).</p>
</sec>
<sec id="Ch1.S3.SS4.SSS2">
  <label>3.4.2</label><title>Indicator categories and observations</title>
</sec>
<sec id="Ch1.S3.SS4.SSSx1" specific-use="unnumbered">
  <title>Taxonomic diversity and community composition</title>
      <p id="d1e686">This represents the
manifestation of all the direct and indirect impacts acting upon all of the
individuals within a community. It is an established metric used in many
existing marine monitoring programs and impact assessments. The essential
observations to be made are to identify and quantify (number or biomass) the
species present within a community or assemblage at any given time. From
abundance and biomass data on these species, it is possible to calculate a wide
variety of indices, each focusing on specific aspects of community structure
and biodiversity (e.g., community abundance and biomass, species richness,
evenness, taxonomic relatedness; Gaston and Spicer, 2004). This approach is
applicable to all types of communities, including microbial assemblages.
Whilst identification of individuals to the species level is desirable, this
is not always possible; however, identification at lower taxonomic
resolution still allows the relative effects of OA to be assessed on
specific taxonomic or functional groups.</p>
</sec>
<sec id="Ch1.S3.SS4.SSSx2" specific-use="unnumbered">
  <title>Functional or trait diversity</title>
      <p id="d1e695">Similar to taxonomic biodiversity metrics
described in the previous section, metrics of functional or trait diversity
again require the collection of species abundance and biomass data as detailed
above. However, in this instance individual organisms are grouped, not by
their taxonomic relationships, but by their shared functional, ecological, or
behavioral traits. The same biodiversity metrics as used for describing
taxonomic diversity can then also be applied to these aggregated data to
generate estimates of functional or trait diversity. The benefit of this
approach is that it provides information on the potential function and
performance of ecosystems and is particularly employed in the study of
microbial biodiversity (Krause et al., 2014).</p>
</sec>
</sec>
<sec id="Ch1.S3.SS5">
  <label>3.5</label><title>Genetic diversity</title>
<sec id="Ch1.S3.SS5.SSS1">
  <label>3.5.1</label><title>Rationale</title>
      <p id="d1e714">Understanding the impact of OA on marine
biodiversity requires not only characterizing how these changes will affect
ecosystems, but also how populations will respond via acclimation and
adaptive evolution (Sunday et al., 2014). OA is an important driver of
phenotypic (e.g., morphology, physiology, life history, and even behavior)
(Kroeker et al., 2013) and genetic change (functional and structural) (e.g.,
de Wit et al., 2016; Lloyd et al., 2016). OA is therefore an important
component of natural selection. The selective effects of OA can influence
micro-evolutionary dynamics by altering demographic parameters (Bramanti et
al., 2015), genetic diversity (Lloyd et al., 2016), and the molecular
regulation of functional pathways (de Wit et al., 2016; Runcie et al., 2016)
in marine organisms. Every species and population has an adaptation
potential to OA that is mostly dependent on genetic diversity (Sunday et
al., 2014). Characterizing the present level and rate of changes in relevant
aspects of genetic diversity is key to understanding the future of marine
ecosystems. While this signature can be specific to OA, the signal can vary
in strength and direction across temporal and spatial scales depending on
the particular genetic and environmental backgrounds of natural populations
(Pespeni et al., 2013; Calosi et al., 2017; Gaitan-Espitia et al., 2017).</p>
      <p id="d1e717">Progress in high-throughput sequencing technologies allows rapid,
cost-effective, and informative measurements of molecular genetic variation
(functional and neutral) in natural populations. These techniques have the
potential to track, assess, and disentangle the specific OA signature at the
molecular level and estimate the rate of micro-evolution in response to OA
across population and species.</p>
</sec>
<sec id="Ch1.S3.SS5.SSS2">
  <label>3.5.2</label><title>Indicator categories and observations</title>
</sec>
<sec id="Ch1.S3.SS5.SSSx1" specific-use="unnumbered">
  <title>Neutral genetic variation</title>
      <p id="d1e734">OA can negatively impact nonfunctional genetic
variation in marine organisms (Lloyd et al., 2016; Bitter et al., 2019).
Indicators of these effects can be estimated from population genetic
parameters such as the number of alleles, heterozygosity, effective
population size, inbreeding, and population divergence (Schwartz et al.,
2007). This assessment can be achieved using classic molecular markers
(e.g., allozymes, microsatellites, or mtDNA) or through high-throughput
sequencing approaches (e.g., Lloyd et al., 2016; Bitter et al., 2019).</p>
</sec>
<sec id="Ch1.S3.SS5.SSSx2" specific-use="unnumbered">
  <title>Functional genetic variation</title>
      <p id="d1e743">Identifying and monitoring variation in
ecologically important and heritable phenotypes traditionally involves the
assessment of quantitative, functional genetic variation (Charmantier et
al., 2014). For this, different approaches can be used, including
quantitative trait locus (QTL) analysis, genome-wide association studies
(GWAS), genome scan via restriction-site-associated DNA taqs (RAD-seq), and
RNA sequencing (RNA-seq). Linkage and association mapping approaches (QTL
and GWAS) allow the identification of regions of the genome that contribute
to phenotypic variation and divergence among populations (Savolainen et al.,
2013). Similarly, RAD genome scans can affordably and efficiently identify
(i) candidate loci underlying local adaptation, (ii) signals of selection
across the genomes and species range, and (iii) neutral and non-neutral genetic
variation (Lowry et al., 2017). It is important to highlight here that
functional genetic variation is not only related to structural differences
in protein-coding loci but also in regulatory sequences that influence gene
expression (Whitehead and Crawford, 2006). Therefore, approaches such as
RNA-seq can help to identify candidate loci and regulatory pathways involved
in phenotypic responses to OA across spatiotemporal scales, as well as the
mechanisms underlying phenotypic divergence, local adaptation, and phenotypic
plasticity in natural populations.</p>
</sec>
<sec id="Ch1.S3.SS5.SSSx3" specific-use="unnumbered">
  <title>Mutation rates</title>
      <p id="d1e753">Mutations are fundamental to evolution as they provide the
ultimate source of novel and heritable variation on which selection can act.
Thus, assessing mutation rates in natural populations allows us to infer
ecological (e.g., population dynamics) and evolutionary (e.g., adaptation)
responses of marine organisms to climate change factors such as OA (Collins
et al., 2020). In short-living organisms, drastic changes in environmental
conditions can induce strong selection, driving rapid evolutionary change
(sometimes as few as two generations) as a result of increases in the
frequency of rare existing beneficial genetic variants or the generation of
new beneficial mutations (Schaum et al., 2018). Estimates of mutation rates
can be obtained from few loci (including genes of particular interest) or
from whole genomes using high-throughput sequencing technologies. In both
cases, molecular variants can be screened among individuals and populations
in order to identify candidate genetic changes (de novo mutations and/or
existing mutations) that might contribute to the ecological and evolutionary
responses to particular environmental conditions such as OA (Schaum et al.,
2018; Krasovec et al., 2020). This association between molecular variants
such as single-point mutations and the fitness of the organisms can be
tested experimentally (e.g., Schaum et al., 2018; Waldvogel and Pfenninger,
2021), linking geno- and phenotypes in evolving populations. This linkage
could be achieved using traditional physiological experiments or by
measuring the effects of the mutations on gene expression. Finally,
mutations can be placed into a functional context by annotation of the
protein sequences that host molecular variants using public databases such
as the National Center for Biotechnology Information (NCBI) GenBank and the
European Nucleotide Archive (ENA) (e.g., Mock et al., 2017).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2" specific-use="star"><?xmltex \currentcnt{2}?><?xmltex \def\figurename{Figure}?><label>Figure 2</label><caption><p id="d1e758">Within each of the five proposed biological impact indicator
categories (calcification, primary production, heterotrophic production,
biodiversity, adaptation), it is possible to combine the data from numerous
individual time series stations in order to compare the rates of chemical
change  with the rate of biological change across different geographical
locations and between different biological contexts. Each individual data
point on the graph represents the summary information from a single time
series that has coupled biological impact and carbonate chemistry
observation data. With enough observations, it is possible to generate a
generic relationship (blue line). Using the relative positions of data
points on this plot it is possible to derive site-specific information about
the relative importance of OA in driving biological change at the individual
time series stations. In scenario 1, the biological impact is largely
caused by other environmental drivers, or the biological parameter that was
measured is highly sensitive to OA. In scenario 2, the measured biological
impact parameter is not sensitive to OA, or the biological impact is being
mitigated by other environmental drivers or biological processes.</p></caption>
            <?xmltex \igopts{width=398.338583pt}?><graphic xlink:href="https://os.copernicus.org/articles/19/101/2023/os-19-101-2023-f02.png"/>

          </fig>

</sec>
</sec>
</sec>
<sec id="Ch1.S4">
  <label>4</label><title>Using “rates of change” to compare in situ observations of biological
impact and OA trends to allow regional and global comparisons</title>
      <p id="d1e777">Monitoring any one of the parameters described above, over a period of time
and in combination with coupled environmental data that include at least
two carbonate chemistry parameters, will allow the observer to better
describe how their specific measured biological trait is changing in
response to ocean acidification. In essence, by calculating and then
comparing the rate at which the biological parameter is changing with the
rate at which ocean acidification is occurring will identify how closely
correlated they are with each other. Such information will augment
experimental studies that identify mechanisms by which OA would act upon a
biological process to generate a better conceptual understanding of how
biological responses to OA will manifest themselves in the field. By the
inclusion of other potentially important environmental parameters, such as
hypoxia, temperature, and pollution, it will also be possible to see how
important OA is in driving biological response compared to the other
environmental stressors for that particular biological trait. However, the
overall purpose, and greater benefit, of increasing the volume of OA
biological monitoring is to collectively use these data together in order to
scale up site-specific observations and to thereby understand OA impacts
within and across species and populations, geographical locations, and
complex environments. For example, analyses could bring together multiple
time series datasets to understanding which specific elements of a trait are
most affected, whether there is spatial and/or geographical variability in the
responses observed, and what the key confounding drivers or processes are
that influence the biological response of organisms to OA. Below we outline
just one simple methodology for combining data gathered from different
parameters and indices within a trait in order to achieve such a holistic
overview of trait response. We appreciate that there are other more
sophisticated data analysis techniques available, and undoubtedly new ones
will evolve in the future. For now, we present this simple method to
illustrate a way in which the data we are advocating should be
collected and can easily be used to support greater understanding of OA's
biological impacts.</p>
      <p id="d1e780">As the volume of information on the biological impact of OA has grown, there
have been various efforts to synthesize this available knowledge and provide
tools for meaningful comparisons among ecosystems and locations. For
example, several approaches have been used to synthesize the literature on
experimental biological studies including meta-analyses (e.g., Kroeker et
al., 2013; Busch and McElhaney, 2016; Bednarsek et al., 2019) and
semi-quantitative reviews (e.g., Wittmann and Pörtner, 2013). These
approaches largely compare measurements of “effect size”, whereby all
observed responses are represented as the relative change from a defined
baseline or control condition specific to that observation (e.g., Kroeker et
al., 2013). Whilst this approach overcomes the initial problem of data
comparability, it still relies on assumptions that effect sizes are roughly
representative of biological or ecological consequence. Whilst we
acknowledge that further work will undoubtedly be needed to fully understand
the ecological consequences associated with different scales of effect size
and how this will change depending on the biological process being
considered, the basic principle of using effect sizes to compare across
different indices remains useful.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3" specific-use="star"><?xmltex \currentcnt{3}?><?xmltex \def\figurename{Figure}?><label>Figure 3</label><caption><p id="d1e785"><bold>(a)</bold> Conceptual relationship between the rate of chemical change
(e.g., pH units per year) and the rate of biological change (e.g., percent of
change per year) under three different scenarios of rates of chemical change
(low, medium, and high). Rates of chemical and biological changes are
positively correlated. The rates of biological change calculated by 2100 are
compared with rates calculated after 10, 30, and 50 years of observation.
After 10 years, the rate of biological change is dramatically
underestimated compared to the rate observed by 2100. Under a low rate of
chemical change, the rate of biological change is still underestimated
after 50 years of observation. Under high chemical rates of change, similar
biological rates of change can be calculated after 30, 50, and 80 years of
observations. <bold>(b)</bold> Relationship between pH and larval abnormality (%) in three
hypothetical organisms with different sensitivity: low, medium, and high,
with tipping points reached at pH 7.6, 7.75, and 7.9, respectively. The
medium scenario is based on the mussel <italic>Mytilus edulis</italic> (from Ventura et al., 2016).</p></caption>
        <?xmltex \igopts{width=455.244094pt}?><graphic xlink:href="https://os.copernicus.org/articles/19/101/2023/os-19-101-2023-f03.png"/>

      </fig>

      <p id="d1e803">At any given location, we propose that biological observations can be
transformed into an effect size (e.g., in percent) relative to a given reference
time, and modeling the evolution of this effect size through time allows the
calculation of a rate of biological change as the total percent change in the
biological process divided by the time over which that change happened.
We propose that quantifying the relationship between these rates of
biological change and the rates of chemical change associated with OA is an
effective way to assess the influence of that OA on the biological change
observed. At any given location, this approach would thereby provide
information on the risks and vulnerabilities associated with OA. A
comparison of rates of change of specific chemical and biological indicators
will also help in building a mechanistic understanding of the relationship
between changes in relevant carbonate parameters and biological processes
(e.g., Osborne et al., 2019). More importantly, it would allow comparison
among overall biological responses across a wide range of locations.</p>
      <p id="d1e806">As a general principle, in situations in which OA is the primary driver of a
biological response, the rate of that biological change is expected to be
closely correlated with the rate of chemical change. The precise nature of
this relationship (i.e., the direction and slope magnitude) will also depend
on the sensitivity of the process, organism, or ecosystem: at a given rate of
chemical change, a sensitive organism is expected to show a stronger
biological response than a less sensitive one. The rate of biological change
is then the product of the interaction between biological sensitivity and
rate of chemical change. By plotting together data from various long-term
studies, with each time series of biological and chemical observations
represented on a plot by a single point (defined by the rate of biological
change on the <inline-formula><mml:math id="M25" display="inline"><mml:mi>x</mml:mi></mml:math></inline-formula> axis and the rate of chemical change on the <inline-formula><mml:math id="M26" display="inline"><mml:mi>y</mml:mi></mml:math></inline-formula> axis), it is
possible to compare across different studies to define a generic
relationship between OA and a specific biological trait (Fig. 2). While we
use a linear relationship between the chemical and biological rates of
change as an illustration in the Fig. 2, the precise nature of this
relationship may follow other patterns such as a nonlinear tipping point
response (e.g., Wunderlink et al., 2021).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4" specific-use="star"><?xmltex \currentcnt{4}?><?xmltex \def\figurename{Figure}?><label>Figure 4</label><caption><p id="d1e825"><bold>(a)</bold> Projection of larval abnormality under different scenarios
of rate of chemical change. The rate of biological change was estimated for
each scenario as the coefficient of the significant regression between time
and abnormality (%) over the linear phase of the curve. <bold>(b)</bold> Relationship
between the chemical and the biological rates of change.</p></caption>
        <?xmltex \igopts{width=455.244094pt}?><graphic xlink:href="https://os.copernicus.org/articles/19/101/2023/os-19-101-2023-f04.png"/>

      </fig>

      <p id="d1e839">It is important to remember that OA will not be the dominant driver at all
locations. For example, a sensitive species exposed to a low rate of chemical
change may lead to a lower rate of biological change than a more tolerant
species exposed to a high rate of chemical change. Such deviations from the
generic relationship would therefore identify locations where other
biological drivers play a more important role or amplify (scenario 1 in Fig. 2) or mitigate the effect of OA that is being investigated (scenario 2 in
Fig. 2). Furthermore, those deviations could highlight situations in which the
specific biological parameter measured was more or less sensitive to OA than
others: for example, observations of calcification rate may all appear above
the generic relationship line, while observations of shell mass may all
appear below the line. Both of these parameters (calcification rate and
shell mass) provide information on the calcification process, but their
relative positions on the plot would indicate differences in the mechanisms
by which OA impacts those particular biological indices.</p>
</sec>
<sec id="Ch1.S5">
  <label>5</label><title>Points to consider when comparing the impacts of OA on biological traits
derived from different observations and different places</title>
      <p id="d1e851">To be meaningful and useful in the analysis proposed above, observed rates
of biological change must be robust. If calculated with too few data, these
rates can severely underestimate the real impacts. One of the key questions
when evaluating an OA biological observation time series is how long
that time series needs to be to ensure that rates of change have been accurately
quantified. The minimum duration of observation is largely dependent on both
the specific sensitivity of the organism or ecosystem being observed and the
underlying rate of chemical change. This concept is described theoretically
in Fig. 3a, which shows that the longer the data are collected for, the more
likely they are to provide an accurate estimate of the rate of change over
that time period. However, under higher rates of chemical changes, robust
estimates of the rate of biological change can be obtained over a shorter
period of time. This illustrates the importance of backing up monitoring
observations with targeted studies that can approximate the likely
sensitivity of biological processes and parameters to OA stress. For
example, generating a performance curve can provide an illustration of the
effect of a given parameter (e.g., pH) on a biological response.
Relationships between a stress and a biological response are often not
linear and can be measured under laboratory conditions for a given species
and location (e.g., Ventura et al., 2016). These curves can then be used to
provide estimates of the minimum duration of a biology monitoring program
under different rates of chemical changes to properly quantify the rate of
biological change.</p>
      <p id="d1e854">Here we use real data to illustrate the point. The performance curve between
pH and larval abnormality was experimentally measured for the blue mussel
<italic>Mytilus edulis</italic> population from the Gullmarsfjord in Sweden (Ventura et al., 2016; medium
sensitivity on Fig. 3b). The present average pH in surface seawater in the
Gullmarsfjord is 8.1 (Dorey et al., 2013). Rates of pH change ranging from
0.001 (slow change corresponding to a decrease by 0.08 pH units by 2100) to
0.006 pH units of decrease per year (fast change corresponding to a decrease by
0.48 pH units by 2100) were compared. These rates were used to estimate the
pH at any given time, and the associated abnormality was calculated using the
performance curve adapted from Ventura et al. (2016) (Fig. 4a). For each
scenario of rate of chemical change, the rate of biological change was
calculated as the slope of the significant linear regression between time
and abnormality (%) over the linear phase of the curve. Ideally, the rate
of biological change should be calculated using a nonlinear model following
the shape of the nonlinear performance curve between pH and the tested
parameter (e.g., Fig. 3b for percent of abnormality). These performance curves
can take many forms depending on the measured parameter and species. For
example, common shapes of physiological performance curves include U shape,
sigmoidal, logarithmic, exponential, and inverted U shape (Little and
Seebacher, 2021). However, in practice the shape of these curves is often
unknown and it would not be possible to derive relevant rates of change from
biological observations over a relatively short period of time. Under these
circumstances, using a linear regression is a good alternative. From the
projections using the blue mussel data, we observe a linear relationship
between rates of chemical and biological change. In other words, for a given
organism at a given location, the rate of biological change increases with
the rate of chemical change (Fig. 4b).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5" specific-use="star"><?xmltex \currentcnt{5}?><?xmltex \def\figurename{Figure}?><label>Figure 5</label><caption><p id="d1e862"><bold>(a)</bold> Evaluation of the rate of biological change as the
coefficient of the significant regression between time and abnormality over
time (after collecting 10 years of data, 20 years of data, etc.). <bold>(b)</bold> Relationship between the number of years of data for the biological
monitoring and the calculated rate of biological change.</p></caption>
        <?xmltex \igopts{width=441.017717pt}?><graphic xlink:href="https://os.copernicus.org/articles/19/101/2023/os-19-101-2023-f05.png"/>

      </fig>

      <p id="d1e877">It is then possible to use these data to estimate the number of years of
observations to detect a negative impact. In the region where the mussels
were collected, the current rate of chemical change in surface water is
estimated as a decrease of 0.0044 pH units per year, corresponding to a
decrease of 0.35 pH units by 2100 (Andersson et al., 2008). Based on our
model, this would lead to an observed rate of biological change of 0.8861 % of abnormality per year by 2100 (Fig. 4). Using this model, it is
possible to quantify the evolution of the rate of biological change over
time (Fig. 5a) and then estimate how many years of observations are needed
to calculate a good estimate. The rate of biological change increases with
increasing years of observations (Fig. 5b). As a consequence, biological
monitoring over a short period of time leads to an underestimation of the
rate of biological change. For the mussel <italic>M. edulis</italic> in the Gullmarsfjord and under a
realistic rate of chemical change, we can then estimate that at least 70
years of biological monitoring would be needed to calculate an accurate rate
of biological change.</p>
      <p id="d1e883">It is worth noting that in the example presented above, the subject species
was considered to be relatively insensitive to OA, resulting in a need for
many decades of monitoring. For more sensitive biological subjects and
processes in areas of more rapid chemical change, the required length of
observations will be much shorter. It is also important to note that other
parameters or stressors, short-term variability, ecology, and evolution can
modulate the biological response and then influence the rate of biological
change. As an example, we compared rates of biological changes in three
“hypothetical model” organisms with different levels of sensitivity to pH
(Fig. 3b). This scenario could represent different populations of the same
species adapted to different levels of pH variability (e.g., Vargas et al.,
2017, 2022) or with different modulating factors (e.g., temperature or food
concentration) or evolution of the performance curve within one population
through time as a consequence of transgenerational adaptation or evolution
(Parker et al., 2015; Thor and Dupont, 2015; De Wit et al., 2016). Assuming
a rate of chemical change of 0.0044 pH units per year (Andersson et al.,
2008), the rate of biological change observed by 2100 would be dependent on
the species sensitivity (Fig. 6a).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6"><?xmltex \currentcnt{6}?><?xmltex \def\figurename{Figure}?><label>Figure 6</label><caption><p id="d1e888"><bold>(a)</bold> Projection of larval abnormality under a rate of chemical
change of 0.0044 pH units per year (Andersson et al., 2008) for organisms
with three different levels of sensitivity to pH (low, medium, high). The rate
of biological change was estimated for each scenario as the slope of the
significant regression between time and abnormality (%) over the linear
phase of the curve. For the species with low sensitivity, the linear phase
was not reached, and it was not possible to calculate the rate of biological
change. <bold>(b)</bold> Relationship between the number of years of data for the
biological monitoring and the calculated rate of biological change for three
organisms with different levels of sensitivity to pH (low, medium, high). Sufficient years of data were considered to have been collected when the
observed rate of biological change was above the 0.86 threshold (5 % from
the maximum rate of change of 0.91 % of abnormality per year).</p></caption>
        <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://os.copernicus.org/articles/19/101/2023/os-19-101-2023-f06.png"/>

      </fig>

      <p id="d1e902">For each level of sensitivity, it is possible to estimate the minimum number
of years of observation needed to calculate an accurate rate of biological
change (with a 5 % error; Fig. 6b). As expected, biological monitoring can
be shorter for organisms with higher sensitivity to pH. An accurate rate of
biological change can be estimated after only 40 years for an organism with
high sensitivity compared to 70 years for those with  medium
sensitivity. For organisms with low sensitivity, the rate of biological
change is dramatically underestimated after 80 years. As a consequence, if
the purpose of a time series is to calculate a meaningful rate of biological
change in as short a time as possible, it is recommended to focus on
environments with a high rate of chemical changes and biological indicators
that are highly sensitive to OA. However, other sites and processes of high
ecological and socioeconomic importance should not be neglected, even if it
is likely to take many years for a truly accurate relationship between
biological response and OA to appear. It is essential to acknowledge that
identifying trends in regions with low rates of chemical change or in
organisms with high tolerances to OA may require more time, but that does
not mean those impacts do not exist or are of low importance.</p>
      <p id="d1e905">Species and population sensitivities are key parameters to
consider in the design of a new biological program aiming to document the
biological impact of OA. Working with low-sensitivity organisms would lead
to a severe underestimation or unrealistically long data collection periods
for an accurate estimation of the rate of biological change. As sensitivity
can be modulated by several parameters (e.g., evolution) within a population,
it is recommended to regularly calculate the rate of biological change and
plot it over time. The rate of biological change is expected to increase
with time until saturation is reached (Figs. 5 and 6b). At saturation, the
rate of biological change can then be considered robust.</p>
      <p id="d1e909">Finally, when comparing chemical and biological rates of change, it is also
critical to ensure that the spatiotemporal resolution of the carbonate
chemistry data is directly relevant for the given species or ecosystem being
observed. For example, chemistry data collected in the surface water may not
be relevant for a tidal organism experiencing much more variability than
that detected by the chemical observations. Similarly, it is important to
remember that the carbonate chemistry experienced by a given species is also
dependent on its biology. For example, some species migrate over large
distances and through very different bodies of water or have different
life-history stages living in different environments. Alternatively, some
species, mainly sessile, can alter temporal dynamics in the surrounding
carbon chemistry through physiological processes such as respiration,
photosynthesis, and calcification (e.g., seagrasses, kelp) (Pfister et al.,
2019; Unsworth et al., 2012).</p><?xmltex \hack{\newpage}?>
</sec>
<sec id="Ch1.S6" sec-type="conclusions">
  <label>6</label><title>Conclusions</title>
      <p id="d1e921">Assessing the vulnerabilities and adaptive capacity of marine ecosystems and
coastal communities towards OA requires a broad range of data. Measurements
and calculations related to SDG indicator 14.3.1 (“average marine acidity
– pH – measured at agreed suite of representative sampling stations”) provide
the chemical information required for such analyses. However, achieving
SDG target 14.3 (“minimize and address the impacts of ocean acidification,
including through enhanced scientific cooperation at all levels”) will also
require correlating those observed chemical changes with the biological
response. This immense task can only be accomplished with a combination of
approaches including laboratory and field experimentation, modeling, and biological observations. While the body of experimental evidence on OA
impacts is growing rapidly, in situ monitoring conducted specifically for
identifying and quantifying biological responses to OA is far less common.</p>
      <p id="d1e924">Our innovative approach goes beyond the simple monitoring of specified
biological traits. We propose a strategy that aims to compare the
relationships between rates of chemical and biological change under
different circumstances, allowing comparison across regional and global
scales. We have shown that identifying robust rates of biological changes
over a reasonable time (within a few decades) depends on local species,
ecosystem sensitivities, and rates of chemical change and that the
interpretation of observed biological responses needs to be mindful of this.
We show that it is possible to use performance curves from experimental
studies and data from chemical monitoring programs as a first-order step to
identify the sites for biological monitoring that will give the most rapid
indication of OA impacts, as well as the minimum duration to measure robust
rates of biological change. We also propose five fundamental ecosystem
traits that optimize the probability of identifying OA impacts: (1) calcified
organisms and calcification, (2) autotrophs and primary production, (3) heterotrophs and secondary production, (4) biodiversity and community
structure, and (5) genetic adaptation. These traits span all marine
ecosystems, are anticipated to be sensitive to OA, and can be quantified
using “standardized” biological observations that in many cases are already
collected alongside chemical observations. It needs to be highlighted that
the specific choice of trait and respective parameters at different sites
will depend on local practicalities, specific scientific questions, and
envisaged outcomes related to fitness of species and the health of marine
populations and communities. The feasibility of obtaining these observations
over the long term must also be considered, e.g., access to the marine
ecosystem, as well as technical and human scientific capacity.</p>
      <p id="d1e927">Selection of sites for biological observations should be based on answering
a scientific question or to fit a specific stakeholder need. For example,
sites can be selected for a practical reason (e.g., co-location with a
long-term chemical observing site or at a marine station facilitating data
collection), at a site of particular socioeconomic or cultural value, or
scientific interest (e.g., predicted low or high sensitivity to OA). We
propose a conceptual framework that would allow bridging chemical and
biological monitoring as well as identifying the issues to consider when
interpreting the collected data and evaluating the relevance of observed
trends. We also argue that meaningful trends can be more rapidly identified
at sites combining a high rate of chemical change with high biological
sensitivity to changes in the carbonate chemistry. However, this is only one
of the many valid reasons to identify a monitoring site, and as OA is only
one of the many environmental parameters driving biological changes, other
sites should not be neglected.</p>
      <p id="d1e930">No single approach can explain the complexity of the biological consequences
of OA. Monitoring is the ultimate tool to observe the impact of OA in the
ocean, but understanding and addressing the issue will require a combined
approach with paleo-investigations, field and laboratory experimentation, and modeling (Dupont et al., 2021). Each of these approaches is
associated with its own set of strengths and limitations. Monitoring is
realistic but often requires decades of data; experimentation can provide a
mechanistic understanding over shorter periods of time but leads to
practical limitations in terms of the realism (e.g., single stressors, lack
of ecological relevance, short term; Riebesell and Gattuso, 2015). The real
strength comes from a combination of approaches. For example, we show that
laboratory-based performance curves combined with data from observations of
the carbonate system can be used to estimate the duration of a biological
observing program to detect meaningful trends. Similarly, data from chemical
and biological observations could be combined to evaluate the performance curve of a given species in
its natural environment (realized niche) and compare with the curves from
the laboratory (fundamental niche).</p>
      <p id="d1e934">New data and information obtained when measuring biological indicators
alongside chemical changes due to OA will allow the scientific community to
contribute to the achievement of the vision of the UN Decade of Ocean
Science for Sustainable Development, which involves “the science we need for the ocean we
want” (IOC-UNESCO, 2020), as well as its outcomes and objectives. Biological
observations assessing the impacts of OA will support several Ocean Decade
challenges, in particular Challenge 2, which is to “understand the effects of multiple
stressors on ocean ecosystems, and develop solutions to monitor, protect,
manage and restore ecosystems and their biodiversity under changing
environmental, social and climate conditions”. Furthermore, the
implementation and related initiatives of this proposed strategy will be an
integral part of delivering the Ocean Decade program “Ocean Acidification
Research for Sustainability (OARS) – Providing society with the
observational and scientific evidence needed to sustainably identify,
monitor, mitigate and adapt to ocean acidification; from local to global
scales”. The strategies for biological observing and data analysis
presented here offer a vision towards achieving OARS Outcome 4: increase
understanding of ocean acidification impacts to protect marine life by 2030.
Specifically, by supporting the implementation of an established framework
for biological observation set within the existing ocean acidification
monitoring framework,  the possibility to improve
predictions of vulnerability and resilience to ocean acidification at all
temporal and spatial scales can be provided. This paper presents a way to unify
biological field observations and thereby detect and compare ocean acidification
impacts across marine species and ecosystems, thus improving our
understanding and knowledge about OA and actively contributing to
human well-being (Falkenberg et al., 2020). In doing so, our approach
to coupled biological and environmental observations will facilitate
greater global connectivity between the collection of physical, biogeochemical,
and biological essential ocean variables (EOVs) through the Global Ocean
Observing System (GOOS) and essential biodiversity variables (EBVs) from
the Group on Earth Observations Biodiversity Observation Network (GEO BON).</p>
</sec>

      
      </body>
    <back><notes notes-type="dataavailability"><title>Data availability</title>

      <p id="d1e941">No datasets were used in this article.</p>
  </notes><notes notes-type="authorcontribution"><title>Author contributions</title>

      <p id="d1e947">This article is a product of the work of the Biology Working Group of the Global Ocean Acidification Observing Network (GOA-ON, <uri>http://www.goa-on.org/</uri>, last access: 24 January 2023). All authors are members of this working group and significantly contributed to the development of the proposed framework, identification of indicators, and methodologies for the design of relevant biological monitoring strategies for ocean acidification. The first draft was written collectively, with all authors contributing to the revisions.</p>
  </notes><notes notes-type="competinginterests"><title>Competing interests</title>

      <p id="d1e956">The contact author has declared that neither of the authors has any competing interests.</p>
  </notes><notes notes-type="disclaimer"><title>Disclaimer</title>

      <p id="d1e962">Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.</p>
  </notes><ack><title>Acknowledgements</title><p id="d1e968">Authors would like to thank the Ocean Acidification International Coordination Centre (OA-ICC), the Global Ocean Acidification Observing Network (GOA-ON), the Intergovernmental Oceanographic Commission (IOC-UNESCO), and the University of Gothenburg for hosting and supporting two workshops of the GOA-ON Biology Working group during which the ideas presented in this paper were discussed and developed.</p></ack><notes notes-type="financialsupport"><title>Financial support</title>

      <p id="d1e973">The article processing charges for this <?xmltex \notforhtml{\newline}?>open-access publication were covered by the <?xmltex \notforhtml{\newline}?>Gothenburg University Library.</p>
  </notes><notes notes-type="reviewstatement"><title>Review statement</title>

      <p id="d1e983">This paper was edited by Mario Hoppema and reviewed by two anonymous referees.</p>
  </notes><ref-list>
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