# Ideas and perspectives: the fluctuating nature of oxygen shapes the ecology of aquatic habitats and their biogeochemical cycles – the aquatic oxyscape

Marco Fusi, Sylvain Rigaud, Giovanna Guadagnin, Alberto Barausse, Ramona Marasco, Daniele Daffonchio, Julie Régis, Louison Huchet, Capucine Camin, Laura Pettit, et al.

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Marco Fusi, Sylvain Rigaud, Giovanna Guadagnin, Alberto Barausse, Ramona Marasco, et al. Ideas and perspectives: the fluctuating nature of oxygen shapes the ecology of aquatic habitats and their bio-geochemical cycles – the aquatic oxyscape. Biogeosciences, 2023, 20 (16), pp.3509-3521. 10.5194/bg-20-3509-2023.16.hal-04397286

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# Ideas and perspectives: The fluctuating nature of oxygen shapes the ecology of aquatic habitats and their biogeochemical cycles – the aquatic oxyscape

Marco Fusi<fnref n="1" />,*, Sylvain Rigaud<fnref n="2" />, Giovanna Guadagnin<fnref n="3" />, Alberto Barausse<fnref n="3" />, Ramona Marasco<fnref n="4" />, Daniele Daffonchio<fnref n="4" />, Julie Régis<fnref n="2" />, Louison Huchet<fnref n="2" />, Capucine Camin<fnref n="2" />, Laura Pettit<fnref n="1" />, Cristina Vina-Herbon<fnref n="1" />, and Folco Giomi<fnref n="5" />,★

**Correspondence:** Marco Fusi (marco.fusi@kaust.edu.sa) and Folco Giomi (folcog@gmail.com)

Received: 24 February 2023 – Discussion started: 3 March 2023

Revised: 5 July 2023 – Accepted: 11 July 2023 – Published: 23 August 2023

**Abstract.** Oxygen availability is a pivotal factor for ecosystem functioning and the resistance of organisms to the effect of climate change in aquatic habitats. Although extensive work has been done to assess the effect of oxygen on marine and freshwater biota, many studies have not captured the ecological importance of oxygen variations. Overlooking the fluctuating nature of oxygen may cause potential biases in the design and implementation of management policies for aquatic habitats. Conceptual perspectives on the dynamic nature of oxygen fluctuations have been raised in the scientific community in order to enhance the understanding of the effect of oxygen on the physiology and the ecology of aquatic species as well as the biogeochemical functioning of their ecosystems. A growing number of empirical work has been outlining a novel conceptual framework that considers the magnitude of oxygen fluctuation as a key variable that explains adaptation to stress conditions. Oxygen in productive aquatic habitats shows large fluctuations at the diel scale, exposing aquatic species to conditions ranging from extreme supersaturation to anoxia. Recent research has indicated that such a fluctuation tunes the physiological plasticity of the animal in response to thermal stresses. In this paper, we provide compelling evidence based on current research that the fluctuating oxygen landscape, here defined as “oxyscape”, has

an important role in aquatic animal physiology and adaptation as well as the ecosystem biogeochemistry. We propose that the oxyscape should be considered in the modelling and managing policies of aquatic ecosystems.

## 1 Introduction to environmental dissolved oxygen variability and its ecological relevance

The actual assembly of organism communities in a given habitat is determined by the specific environmental conditions that select specific sets of species. Climate anomalies and changes raise concerns over ecosystem stability and habitat preservation, with consequences ranging from species substitution to species extinction (Antão et al., 2020). To model and predict such effects on community composition and stability, it is necessary to learn about the limits of the environmental conditions that challenge the different species (Bennett et al., 2021). However, in many cases, such conditions are resumed into averaged parameters that do not capture the whole range to which organisms are exposed to (Bernhardt et al., 2020).

In aquatic environments, chemical and physical parameters vary greatly at different timescales and spatial scales,

<footnote n="1">¹Joint Nature Conservation Committee, Quay House, 2 East Station Road, Fletton Quays, Peterborough, PE2 8YY, UK</footnote>

<footnote n="2">²Univ. Nîmes, EA 7352 CHROME, Rue Du Dr Georges Salan, 30021 Nîmes, France</footnote>

<footnote n="3">³Department of Biology, University of Padova, Padua, Italy</footnote>

<footnote n="4">⁴Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia</footnote>

<footnote n="5">⁵Independent researcher, Padua, Italy</footnote>

<footnote>★These authors contributed equally to this work.</footnote>
following cyclical fluctuation or stochastic variations (Shaw et al., 2013; Kerrison et al., 2011; Vargas et al., 2017, 2022; Manzello, 2010; Challener et al., 2016; Duarte et al., 2013). The lack of details on such variations in time and space challenges our understanding of how the species adapt their physiology, limiting our estimation of their resilience to ongoing environmental changes (Booth et al., 2023a). The perception of such a knowledge gap is progressively moving the research interest on species' eco-physiological response to chemical and physical parameters, such as temperature, salinity, or pH, and the associated biogeochemical cycles toward more accurate assessments of their natural variability (Antão et al., 2020; Bernhardt et al., 2020). Increasing efforts are now devoted to upgrading eco-physiological approaches to integrate the relevant environmental background (Giomi et al., 2019; Marasco et al., 2023; Bitter et al., 2018, 2021; Pörtner et al., 2023).

Oxygen variability exerts a great effect on aquatic life yet remains underestimated. Most studies dealing with oxygen variation have addressed the decline of mean oxygen availability in oceans (Breitburg et al., 2018) and the occurrence and repercussions of events of environmental hypoxia (Diaz and Rosenberg, 2008; Bickler and Buck, 2007). How short-term (i.e. daily) oxygen variations shape aquatic life and biogeochemical processes remains largely overlooked. These variations are generally of greater amplitudes and more regular than seasonal ones (Limburg et al., 2020; Bates et al., 2018). We refer to deviation from the saturation of oxygen concentrations as the ratio between the actual concentration and the saturation concentration of oxygen that would be observed in water under equilibrium conditions between air and water. The fine measure of the range of variation in aquatic oxygen and its effect on organisms and biogeochemical cycles has the potential to elucidate unpredicted mechanisms of resilience and tolerance to ongoing climate change.

## 2 Oxygen trends and stochastic variations

A gradual decline in the total oxygen content of about 2% since the second half of the 20th century has recently been reported, with a further reduction of up to 7% predicted for the following century (Schmidtko et al., 2017; Breitburg et al., 2018). In parallel, open-ocean oxygen minimum zones (OMZs) have largely expanded (Stramma et al., 2010) together with the increasing occurrence of severe hypoxia events whose predictability has decreased as their occurrence spreads across all oceans (Diaz and Rosenberg, 2008). The main cause of deoxygenation is attributed to global warming, and deoxygenation is exacerbated by the discharge of nutrients and pollutants (Ito et al., 2016). The topography of water basins also affects the incidence of hypoxia events, thereby influencing the rate of mixing of oxygenated layers and the resident time of water bodies (Breitburg and Grégoire, 2018; Laffoley and Baxter, 2019). For example, in the Baltic Sea,

the geomorphology of the coastline can explain up to 80% of the hypoxic phenomena (Virtanen et al., 2019).

The gradual decrease in total oxygen in oceans has been reported in several studies that analyse long temporal trends (Keeling et al., 2010; Schmidtko et al., 2017; Breitburg et al., 2018) and in reports at the global geographical scale (Laffoley and Baxter, 2016). However, unexpected oxygen profiles have also been reported in several specific habitats and at different timescales, suggesting that different abiotic and biotic drivers modulate oxygen dynamics (Craig and Hayward, 1983). For instance, the alternation of oxygen biological production and consumption determines a massive fluctuation in oxygen availability in highly productive aquatic habitats, such as mangrove forests, salt marshes, coral reefs (Giomi et al., 2019; Fusi et al., 2021; Booth et al., 2021), kelp forests (Krause-Jensen et al., 2016), plankton blooms in pelagic systems (Riser and Johnson, 2008; Benoiston et al., 2017), freshwater lakes (Andersen et al., 2017), or even agricultural drainage channels (Booth et al., 2023a). The seasonal variation in diel oxygen fluctuations is increasingly reported at all latitudes and habitats, and it occurs in a vast range of water bodies independently of the scale, the hydrological features, and the local biotic components (Fig. 1). For example, fluctuations of 150% in spring and 30% in winter occur in the Venice lagoon (Fig. 1, Location 5), and even more pronounced fluctuations occur in mangroves, corals, and seagrasses (Fig. 1, Locations 10–12; Giomi et al., 2019). The magnitude of oxygen fluctuations is site-specific and depends, among other factors, on the solar radiation and water temperature and their effect on primary producers' photosynthetic and respiration activity, the cycles of water column stratification and mixing, and the nutrient loads. Spatial differences in oxygen saturation also occur between surface and bottom water masses because of isolation driven by water stratification, the decrease in light penetration and the coupling with increased oxygen demand close to the sediments at the bottom of the water column (Fig. 2). In summer, enhanced benthic respiration is determined by a higher water temperature, which decreases oxygen solubility and enhances oxygen demand. Lower vertical mixing, higher water residence time and higher turbidity due to a higher concentration of organic matter further decrease oxygen concentrations, causing hypoxia in the deep water layers (Fig. 2; Talke et al., 2009; Schmidt et al., 2019). Conversely, dissolved oxygen increases in the euphotic part of the water column because of the enrichment of photosynthetic communities (Spietz et al., 2015).

### 2.1 The oxygen variation in the daily lives of aquatic organisms

Marked oxygen variations occur at a diel scale, driven by temperature and light diel cycles as well as the balance between photosynthesis and respiration (Winter et al., 2019). The amplitude of diel oxygen variation can exceed the av-
<figure><img src="image_3.png" /><figcaption>**Figure 1.** Range of oxygen saturations in several productive aquatic habitats. The dashed line represents 100% oxygen saturation. The violin plots report the densities of the frequencies of oxygen saturation measured at each ecosystem across different seasons (based on data availability). The data source is specified for each environment in the supplementary dataset for Figs. 1 and 2.</figcaption></figure>

erage seasonal variation, thus being variable with a higher
explanatory power for the physiology of aquatic life (Giomi
et al., 2019). While water temperature is only linked to
meteorological changes, the oxygen concentration in pro-
ductive aquatic environments is also regulated by the biota
component (Chapman, 2021). The community composition
of primary producers (Power and Cardinale, 2009), rainfall
level (Mallin et al., 1993), nutrients' runoff (Kinney and Ro-
man, 1998), biotic networks (Graham et al., 2018; Breen and
Mann, 1976) and bacterial community dynamics (Guo et al.,
2022) govern, at a small scale, high spatial and temporal
changes in the concentrations of dissolved oxygen. The inter-
action of all these factors strongly affects dissolved oxygen
fluctuations beyond the levels that can be predicted from just
the meteorological trends.

Oxygen availability plays an important role in the phys-
iology of aquatic species (Pörtner, 2010; Hochachka, 1991;
Stillman and Somero, 2000). In the design of experiments
on the physiology of aquatic animals, oxygen is frequently
treated as a fixed factor and maintained around the water
saturation. However, organisms inhabiting aquatic environ-
ments experience ample diel oxygen fluctuations and are
adapted to endure or respond to the experienced variation
(Blewett et al., 2022; Morash et al., 2018). Oxygen may be

systematically depleted at night and fully recovered during
the day, changes that certainly have consequences for the
tolerance to acute stressors such as hypoxia and warming.
Depending on the intensity of the photosynthetic activity,
dissolved oxygen concentrations can reach levels far above
the physical saturation (Giomi et al., 2019; McArley et al.,
2020). Under such hyperoxic conditions, aquatic organisms
experience oxygen availability well beyond their physiologi-
cal needs, but the effects on their physiology and life history
are largely unknown.

Hyperoxia benefits the metabolic performance of fishes
and invertebrates, especially under acute warming that may
be very intense in tidal ponds or shallow coastal habitats
(Fusi et al., 2021; Booth et al., 2021; Giomi et al., 2019;
McArley et al., 2020; Booth et al., 2023a). It extends the up-
per thermal tolerance of aquatic animals during acute events
of daily warming and their survival of anomalous heat waves
(McArley et al., 2022). Within the current trend of climate
change, the beneficial effect of hyperoxia against extreme
heating events can have underestimated positive results on
the survival of the animals. For instance, an important con-
sequence of exposure to the hyperoxic conditions experi-
enced during the daytime under high heating regimes is the
enhanced capability to extract oxygen from the poorly oxy-
<figure><img src="image_4.png" /><figcaption>**Figure 2.** Fluctuations in oxygen saturation measured at the bottom (4 m) and surface (30 cm) oxygen saturation of the Rove canal in France highlight the contrast between the two depths of the eutrophicated coastal environment from the winter to summer.</figcaption></figure>

genated water during the night and endure hypoxic or even anoxic periods (Giomi et al., 2019; Booth et al., 2021).

Oxygen fluctuations are also appreciated as a factor con-
tributing to the structuring of organismal networks and to the
synchronisation of life history dynamics such as spawning or
larval recruitment (Garzke et al., 2019; Viaroli and Christian,
2004).

3 The role of oxygen fluctuation in coastal
biogeochemical cycles

3.1 Biogeochemical cycles in the pelagic compartment in relation to oxygen fluctuation at the daily scale

In productive coastal ecosystems, the biogeochemical cy-
cles of key chemical elements are strongly interconnected
with oxygen dynamics. Nitrogen and phosphorus are typi-
cally key elements which limit primary production in shal-
low coastal marine ecosystems, whose emissions from river
basins (or other sources, such as previously enriched sedi-
ments) can lead to eutrophication with detrimental effects
on biodiversity and human welfare (Palmeri et al., 2013).
The biogeochemical cycles of nitrogen and phosphorus are
composed of multiple physical, chemical, and biological pro-
cesses, of which some are accelerated by oxygen availability,
such as nitrification and mineralisation, while others are en-
hanced by its absence, such as denitrification and P release
from sediments. The regular daily alternation in contrasting
conditions of below- and above-saturation dissolved oxygen
concentrations in the water column, particularly in the eu-
photic zone, promotes changes in the relative abundance of
different nutrient forms (Fig. 3). This becomes clear when
looking, for example, at the nitrogen cycle in the water col-

umn and its complex relationship with oxygen availability:
the presence of dissolved oxygen speeds up the minerali-
sation of organic nitrogen to ammonium as well as nitrifi-
cation, i.e. the microbial oxidation of ammonium into ni-
trites and then nitrates. The absence of oxygen makes den-
itrification possible; i.e. the reduction of nitrates into inert
gaseous nitrogen is promoted by facultative aerobic bacte-
ria that, in the absence of anoxia, will prefer oxygen to ni-
trates as an electron acceptor (Palmeri et al., 2013). Am-
monium, nitrites, and nitrates are important nitrogen forms
that are bioavailable to primary producers, and the oscillat-
ing oxygen conditions in the water column at the diel scales
can promote their removal via the nitrification–denitrification
chain. High oxygen concentrations are also associated with
high photosynthetic activity (e.g. planktonic) and, therefore,
with the fast removal of dissolved inorganic nutrients from
water through uptake by primary producers (Caron, 1994).
The picture is made more complex by the typically non-
linear dependence of biogeochemical reactions on oxygen
concentration (e.g. nitrification and denitrification) and on
temperature (in the case of most biogeochemical processes),
which can both change enormously throughout the day, es-
pecially in shallow productive ecosystems, altering reaction
rates at sub-daily scales in a way which cannot be appreci-
ated if only the daily mean in dissolved oxygen is consid-
ered, but which needs to be quantified if we are to predict
future biogeochemical cycling mechanistically under climate
change (Caballero-Alfonso et al., 2015). A further source of
complexity is given by the feedback between abiotic and bi-
otic components of pelagic ecosystems. The growth of pri-
mary producers, both microscopic and macroscopic, is on
the one hand affected by the presence of bioavailable nutrient
forms, and on the other hand their biomass can reduce light
<figure><img src="image_5.png" /><figcaption>**Figure 3.** Nutrient concentration, dissolved oxygen, and water temperature measurements in the water of a salt marsh of the northern Venice Lagoon (Italy) on 13 August 2015. (a) The concentration of different nitrogen forms in the marsh water (notice the two different vertical axes) over time in the middle of the day. Measurements are made in the water entering the marsh (flood phase, left of the vertical grey line, which indicates the tidal peak) and in the water exiting from the salt marsh (ebb phase, right of the vertical grey line). After some time spent in the marsh, which is flooded by tides twice per day, water becomes depleted in inorganic nutrients, presumably due to the uptake by primary producers, exchanges with the sediments, and (in the case of ammonium) nitrification. Concurrently, water is enriched with dissolved organic nitrogen related to the intense biological activity within the marsh. (b) Dissolved oxygen and the temperature of the water entering the marsh (flood phase, left of the vertical grey line, which indicates the tidal peak) and the water exiting from the salt marsh (ebb phase, right of the vertical grey line) over time in the middle of the day. Notably, in the biologically productive habitat of the marsh, the increase in dissolved oxygen in the water is paralleled by an increase in water temperature.</figcaption></figure>

availability by increasing shading or turbidity and limiting light penetration and, so, oxygen production and warming in deeper waters. These examples highlight the importance of higher-frequency measurements of oxygen fluctuations; nutrient concentrations; and microbial community abundance, composition, and activity in the water column at sub-daily scales to get a better, more quantitative grasp of biogeochemical cycling in coastal water bodies (Meire et al., 2013). A general framework to assess the short-term (hourly) oxygen fluctuations in relation to the movement and related physical properties of water masses, i.e. of processes such as stratification, residence time, and thermohaline flows, in addition to other processes (photosynthesis, respiration, solubility changes, etc.) is important to future oxygen modelling.

## 3.2 Biogeochemical cycles in the benthic compartment in relation to oxygen fluctuation at the daily scale

The intertwined oxygen and nutrient dynamics in the water column cannot be understood, at least in relatively shallow

aquatic ecosystems, without looking at the interactions between the pelagic and the benthic compartment. This takes place through the vertical transport of matter (settling, resuspension, convection, upwelling currents, etc.) and is also affected by stratification, gradient-driven diffusive fluxes, and organism movements and vertical migrations.

When temperature and oxygen concentration in the water column fluctuate at short daily timescales, yet with a very large amplitude (from anoxia/hypoxia to hyperoxia), the impact on biogeochemical cycles and chemical transfers is mostly unknown. Based on the trends observed at seasonal “steady-state” conditions, a conceptual model on the location of the major benthic processes in the sediment and the resulting fluxes at the sediment-water interface within the diurnal temporal scale can be drawn (Fig. 4).

As oxygen penetration depth and concentration in sediment are known to evolve rapidly in response to the oxygen concentration in the overlying water (Glud, 2008), the importance of the aerobic process in surface sediment is also
<figure><img src="image_6.png" /><figcaption>**Figure 4.** Scheme of the benthic biogeochemical cycle in relation to diel oxygen fluctuation. Relative evolution of the bottom water chemical composition and evolution of the location of the most important biogeochemical processes in the benthic compartment. Relative influence of external drivers on benthic processes. Relative evolution of resulting flux direction and intensity. Note that the graphs are not drawn to scale. Although concentrations of PO₄³⁻ and NH₄⁺ and of Mn and Fe may behave differently, they are represented as similar in this figure for simplification.</figcaption></figure>

expected to fluctuate at the diurnal timescale, with a higher
contribution during the day than during the night. The fast ki-
netics of the reductive dissolution/oxidative precipitation of
Mn and Fe oxyhydroxides and the redox cycle of S chemical
species (i.e. H₂S/SO₄²⁻) suggests that those chemical species
should evolve with a similar trend over daily timescales,
with a reasonable short-term (minutes–hours) delay (Rigaud
et al., 2018). Consequently, we expect a vertical fluctuation
of those biogeochemical redox processes in the sediment and
related fluxes under diel oxygen fluctuation (Fig. 4). The low
oxygen concentration at night should induce a lower oxygen
penetration depth and an upward distribution of NO₃⁻, Mn

and Fe oxyhydroxides, and SO₄²⁻ reductions. If the oxygen
concentration is low enough, the reductive dissolution of Mn
and Fe oxyhydroxides may occur directly at the sediment–
water interface, inducing their release into the water column
with other chemical species associated with these phases
(i.e. PO₄³⁻ and most trace elements). In the specific case of
anoxia, the sulfate-reduction process may occur at the sedi-
ment surface, releasing H₂S into the water column. It is ex-
pected that in such a condition, the release of dissolved met-
als (Fe, Mn, and trace elements), which also present a rapid
kinetic for metal sulfide formation in the presence of S(−II),
can be reduced and likely reverted (Fig. 4). In contrast, the
increase in oxygen concentration during the day promotes oxygen penetration into the sediment and the oxidation of reduced species accumulated during the night, such as dissolved Mn, Fe, $NH_4^+$, and eventually $H_2S$, preventing their release from the sediment. The reconstitution of the Mn/Fe oxyhydroxide reservoir in surface sediment favours the trapping of $PO_4^{3-}$ and trace elements associated with Fe and Mn cycles. The oxidation of $NH_4^+$ induces the formation of $NO_2^-$ and $NO_3^-$ that may be released from the sediment.

In shallow coastal areas, the light radiation may also reach the sediment surface, allowing the photosynthetic activity of the microphytobenthos to occur in surface sediment (Fig. 4). The local source of oxygen at the sediment surface occurs because photosynthesis strongly enhances the biogeochemical processes described above (Denis et al., 2012; Rigaud et al., 2018). The oxygen released into the water column enhances the water hyperoxia and consumes nutrients and $CO_2$ during photosynthesis. This creates a very peculiar situation that modifies the direction and intensity of chemical fluxes at the sediment-water interface and the chemical composition of water and surface sediment in coastal areas at the diurnal scale. For those rapid redox-sensitive chemical species, processes and fluxes are thus expected to evolve, between such extreme night-day fluctuations, with a transient response related to the reaction kinetics and transport within the sediment surface.

For organic matter (OM) mineralisation processes, the effects of short-term oxygen fluctuation are more challenging to predict. It will also be dependent on the capacity of heterotrophs to react/adapt to the changing oxygen concentrations and eventually shift between different metabolic processes (for microorganisms where variable metabolic pathways coexist) or to activate/cease the process in relation to physicochemical conditions and oxidant availability (for microorganisms with specialised metabolisms). Consequently, the dynamic response of the microbial community to short-term oxygen and chemical fluctuations needs to be investigated in more detail in relation to microbial communities' resilience and adaptation capacity (see Sect. 5).

In productive coastal areas, the benthic organisms, including macro- and meiofaunal species, adapt to wide and rapid daily oxygen variation by modifying their behaviour. The bioturbating activity may be favoured during conditions of high oxygen concentration and lowered during conditions of low oxygen availability. We expect that during the night when oxygen is deficient, the benthic organism activity is reduced, inducing a decrease in the sediment reworking intensity. This is accompanied by a reduction in the biologically mediated solute fluxes at the sediment-water interface and oxygen penetration depth in the sediment. In contrast, during oxygen supersaturation occurring in the day, bioturbation is intensified and may induce a short-term change in the contribution of biologically mediated reactions and transfers. Here too, a delay between the oxygen fluctuation in the water column and the biogeochemical response of the sediment,

related to the biological activity, would depend on site characteristics (oxygen concentration, a range of fluctuation, bioturbating species). For instance, in areas where anoxia events are recurrent, the absence of macrofauna prevents bioturbation and its influence on the benthic biogeochemistry (Nilsson and Rosenberg, 1997).

In response to a large amplitude and diel oxygen fluctuations, the sediment's biogeochemical cycles are also expected to fluctuate (Fig. 4). However, as the resulting benthic biogeochemistry cycles are associated with the dynamics of three interdependent compartments (i.e. geochemical composition, microbial communities, bioturbating-faunal communities), each presenting its kinetics and responses to oxygen fluctuations, we expect the sediment to be permanently maintained under unsteady-state conditions. This makes it difficult to quantitatively predict the resulting OM mineralisation rates, the proportion of involved processes, and the chemical transfers at the sediment-water interface.

The recent development of tools which can measure the chemical composition and sediment-water fluxes over the short-term scale (i.e. microsensors, eddy covariance technic, gradient-flux method), in addition to benthic microbial and macrofaunal activity (e.g. improved sediment profile imaging), may be beneficial to producing experimental data that will help to fill these gaps in understanding. At the same time, specific efforts should be focused on assessing the isolated response to those three different compartments. Those data should then be implemented to appropriately calibrate non-steady-state coupled pelagic-benthic biogeochemical models, which can predict the resulting biogeochemical functioning of productive coastal ecosystems and, thus, predict their fate under climatic changes.

## 4 The interrelationship of oxygen fluctuation and aquatic microbial communities

Oxygen is a two-faced element that acts as the terminal electron acceptor in aerobic respiration (by far the most efficient energy metabolism) and as an element of toxicity because the reduction in $O_2$ molecules partly results in reactive oxygen species. For this reason, oxygen remains a strong evolutionary force dominating functional interactions and the spatial structure of many microbial communities (Fenchel and Finlay, 2008). Oxygen availability determines microbial metabolism, and many studies have been carried out to elucidate the different kinds of communities and metabolisms occurring under anaerobic or aerobic conditions (Sandrin et al., 2009). Marine microorganisms in productive coastal environments also experience wide oxygen diel fluctuations, especially at the boundary layer between sediment/primary producers and water (Pacherres et al., 2022).

Assessing the full environmental oxygen variability in aquatic habitats using high-resolution temporal and spatial scales relevant to microorganisms can reveal in detail the
<figure><img src="image_7.png" /><figcaption>**Figure 5.** Daily bacterial community cycle scheme in relation to diel oxygen fluctuation. Relative shift in the microbial community controlled by the oxygen availability that controls the ratio between aerobic and anaerobic taxa and their relative function. Oxygen fluctuation is important in order to determine the diel cycling of the bacterial communities that, in turn, affect the biogeochemistry and the overall functioning of the aquatic ecosystems. Note that the graphs are not drawn to scale.</figcaption></figure>

complexity of the patterns of community dynamics and diversity in such oxygen-variable environments (Berg et al., 2022). For example, oxygen largely varies during the day in tropical clear shallow waters because of the photosynthetic activity of seagrasses, corals, and mangroves (Giomi et al., 2019). Therefore, the microbial communities in these ecosystems can experience environmental conditions ranging from hyperoxia to anoxia (see the oxygen profile in Fig. 2). These fluctuations imply that the microbial communities have to shift their composition and function according to the oxygen availability (Fenchel and Finlay, 2008; Booth et al., 2023b, 2019). Microorganisms generally have a short generation time (and high turnover) that favour timely adaptation to new conditions in a changing environment (Steiner et al., 2019). During low oxygen availability at nighttime, bacterial communities will shift their composition and function toward anaerobic function (Fig. 5). End products of anaero-

bic metabolisms such as ammonium, sulfur, and methane are consumed when oxygen becomes available again during the daylight and photosynthesis recovery, re-establishing aerobic respiration as the central metabolism of the microbial communities (Fenchel and Finlay, 2008). For example, in the Bohai Sea (China), under an oxygen concentration lower than 4.2 mg L⁻¹, the microbial communities were dominated by bacteria belonging to the group of the Anaerolineaceae (Guo et al., 2022). In Chilean coast ecosystems, the composition of the bacterial communities is regulated by the seasonality of the upwelling waters, with the partitioning of community composition driven by dissolved oxygen. Bacteroidetes, SAR11, SAR86, and Alphaproteobacteria dominated in waters containing dissolved oxygen concentrations higher than 70 µM. In contrast, taxonomic groups such as Arctic96BD-19, SUP05, SAR324, and Desulfobacterales were observed at dissolved oxygen concentrations below 70 µM to unde-
tectable levels (Aldunate et al., 2018). The continuous vari-
ation in oxygen concentration enhances the diel cycling of
nutrients in productive coastal environments, highlighting
the importance of assessing the ecologically relevant oxy-
gen fluctuations in order to determine the effective microbial
functionality of the marine coastal ecosystem (Trowbridge
et al., 2017).

Incorporating methods to assess the ecologically relevant variability in oxygen availability, intensity, and synchronicity in future experimental designs will generate a more accurate prediction of the response of bacterial communities, and therefore their potential for biogeochemical cycling, to climate change, better informing the development of management strategies to mitigate detrimental stressor impacts on ecosystems effectively. The current challenge in microbial ecology is to understand the widespread temporal and spatial environmental oxygen variability and to switch from the “mean condition paradigm” often used for investigations of microbial ecological processes to a dynamic model able to capture the microbial changing and functional potential under oxygen-fluctuating conditions (Fusi et al., 2022).

**5 Implications for marine assessment and management**

Oxygen production is considered an ecosystem service (https://cices.eu/, last access: 2 June 2023) because of the benefits humans receive, but, to date, there has been limited inclusion of the impacts of deoxygenation or oxygen fluctuation in marine environmental policies. There are only a few areas whose oxygen dynamics have been extensively monitored, like North America (i.e. Chesapeake Bay, Gulf of Mexico, Long Island Sound), and have been included in management plans for environmental protections (e.g. https://coastalscience.noaa.gov/project/operational-gulf-of-mexico-hypoxia-monitoring/, last access: 2 June 2023). However, globally, there has been a lack of oxygen dynamics' integration into the computation of biodiversity indicators that assess aquatic communities (Breitburg et al., 2019; Chen et al., 2022), and in particular the oxygen dynamic at a daily scale remains largely neglected in marine assessment and management. Policies on pollution or nutrient control have had a positive effect on the oxygen level in ocean water; however, there is still a clear missing link on specific policies to monitor and manage daily oxygen variability. While attention has been given to ocean warming and acidification, daily oxygen dynamics have been overlooked in assessing marine habitat or species' sensitivity to climate changes and anthropogenic disturbances. Including ecologically relevant variations in oxygen availability into aquatic biodiversity indicators, in addition to continuous and high-temporal-resolution oxygen and chemical concentration measurements in the sediment and water column, offers a great opportunity to refine and produce more robust predictors that will be able to better disentangle the response

of aquatic ecosystems to climate change and anthropogenic
disturbances (Dafforn et al., 2012).

Current hypoxic thresholds for aquatic ecosystem management are generally calculated on averages and minimum oxygen concentrations in water with the risk of overlooking the effect of the oxygen fluctuation, which is more relevant for communities' physiology (Tomasetti and Gobler, 2020). Enhancing monitoring programmes by capturing the daily oxygen fluctuation will allow for the detection of when nighttime low-oxygen content is followed by a daytime recovery period, often reaching oxygen supersaturation. This alternation allows the aquatic communities to sustain their homeostasis in a fluctuating environment. Therefore, proper monitoring can inform correct management to conserve, protect, and restore coastal water mosaic patterns of primary producers to ensure the ecologically relevant fluctuations of dissolved oxygen.

In this paper, based on recent research, we provide evidence that fluctuating oxygen creates a spatial and temporal heterogeneous aquatic oxygen landscape that we define here as oxyscape. The oxyscape – having an important role in aquatic animal physiology and adaptation as well as the ecosystem biogeochemistry – should be considered in the modelling and managing policies of aquatic ecosystems in order to capture the ecologically relevant oxygen fluctuation. Understanding the oxyscape can help us to reconsider the dynamics of many productive aquatic ecosystems, and we, therefore, call on ecologists to rethink their models and experiments in light of this. This would increase the understanding of variations in and resilience of communities to changes in environmental conditions at the scales of space and time relevant to individual components.

*Data availability.* All the data are available as supplementary material.

*Supplement.* The supplement related to this article is available on-line at: https://doi.org/10.5194/bg-20-3509-2023-supplement.

*Author contributions.* MF and FG conceived the study and wrote Sects. 1 to 3. AB, GG, SR, and FG wrote Sect. 4.1 and 4.2 and provided data for the Mediterranean sites. MF, RM, and DD wrote Sect. 5 and provided data for the Red Sea. MF, LP, and CVH wrote Sect. 6. All the authors discussed and reviewed the final version of the paper.

***Competing interests.*** The contact author has declared that none of the authors has any competing interests.
*Disclaimer.* Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

*Special issue statement.* This article is part of the special issue "Low-oxygen environments and deoxygenation in open and coastal marine waters". It is a result of the 53rd International Colloquium on Ocean Dynamics (3rd GO2NE Oxygen Conference), Liége, Belgium, 16-20 May 2022.

*Acknowledgements.* We are very grateful to the LabEx DRIIHM French programme Investissements d'Avenir (ANR-11-LABX-0010), which is managed by the French ANR, under the Human-Environment Observatory Mediterranean coast (OHM Littoral Meéditerranéen), for its funding that allowed us to collect data from the Prevost lagoon. We also thank the Excellence Initiative of Aix-Marseille University - A*MIDEX, a French Investissements d'Avenir programme (reference number ANR-11-IDEX-0001-02); the PACA region and the CNRS-INSU-EC2CO programme (PREDHYP-O₂ programme) for its funding that allowed us to collect data from the Berre lagoon; and the Occitanie region and the University of Nîmes for the funding of Julie Réigis' PhD thesis. We also thank all the members who allowed us to collect data from the coastal Mediterranean lagoons in France (syndicat mixte GIPREB, Mairie de Chateauneuf-les-Martigues, Compagnons de Maguelone). The PREDHYPO programme has received funding from the Excellence Initiative of Aix-Marseille University - A*MIDEX, a French Investissements d'Avenir programme (reference number ANR-11-IDEX-0001-02), the PACA region, and the CNRS-INSU-EC2CO programme (PREDHYP-O₂ programme).

*Financial support.* This research has been supported by the King Abdullah University of Science and Technology (grant nos. REI/1/4483-01-01 and CRG-7-3739). Daniele Daffonchio was financially supported by the King Abdullah University of Science and Technology (KAUST) through the Circular Carbon Economy initiative (grant no. REI/1/4483-01-01). Daniele Daffonchio was also supported by a Competitive Research Grant for "the role of the bacterial symbiome at the gill-water (air) interface in the evolution toward territorialisation (microlanding)" (no. CRG-7-3739; 1 April 2019 to 31 March 2022).

*Review statement.* This paper was edited by Kenneth Rose and reviewed by two anonymous referees.

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