<figure><img src="image_1.png" /></figure>

# Understanding the ecosystem quality of Mediterranean shallow rocky reefs: Insights from the application of ecosystem-based indices

Élodie Jacob<sup>a,b,*</sup>, Mélanie Cabral<sup>b</sup>, Thomas Schohn<sup>b</sup>, Bruno Belloni<sup>b</sup>, Charles-François Boudouresque<sup>a</sup>, Thierry Thibaut<sup>a</sup>, Sandrine Ruitton<sup>a</sup>, Patrick Astruch<sup>b,**</sup>

## ARTICLE INFO

**Keywords:**

Biological indicator

Mediterranean Sea

Ecological status

Ecosystem-based Quality Index

Infralittoral rocky reefs

Canopy-forming macroalgae

## ABSTRACT

* Infralittoral rocky reefs (IRR) are a coastal marine habitat subject to various anthropogenic pressures in the Mediterranean. An ecological assessment using an ecosystem-based approach appears essential to guide sustainable environmental management practices and meet the requirements of the European Union Marine Strategy and Habitats Directive. For this, the reef-EBQI has been developed at 96 sites along the French Mediterranean coast. We show an overall ‘good’ and ‘moderate’ IRR status based on the reef-EBQI. The status appears sensitive to the level of pressure, but more to local specificities. Management and geomorphology did not significantly impact the status. Comparing reef-EBQI scores with another ecosystem-based index, ECOfast, revealed a positive correlation but dissimilarities. Thus, the reef-EBQI is suitable for long-term monitoring in the Mediterranean but interpreting ecological status requires careful handling. Further work should include abiotic factors such as geomorphology and a suitable quantitative pressure index.

## 1. Introduction

Coastal marine ecosystems face substantial impact related to human use, especially in the Mediterranean Sea, where the coastal areas are densely populated. This has resulted in persistent anthropogenic pressures impacting the seabed (e.g. Lotze et al., 2006; Lejeusne et al., 2010; Coll et al., 2011; Holon et al., 2015a; Quemmerais-Amice et al., 2020; Boudouresque et al., 2023). Coastal development, anchoring and trawling, overfishing, sewage, biological invasions, and climate change pose threats in terms of habitat destruction, mechanical degradation, and a decline in water quality (Holon et al., 2015b; Tornero and Hanke, 2016; Korpinen et al., 2021; Pergent-Martini et al., 2022). The spread of Non-Indigenous Species (NIS) represents a specific pressure, particularly affecting the eastern and central Mediterranean Sea (Katsanevakis et al., 2014; Tsirintanis et al., 2022), as well as the Adriatic and western

Mediterranean coastal and lagoon habitats (Klein and Verlaque, 2008; Boudouresque et al., 2011; Sfriso et al., 2023; Borriglione et al., n.d.). These pressures can significantly impact the structure and function of the ecosystem. It is for this reason that coastal marine ecosystems require ecological assessments to monitor changes in response to these pressures (Halpern et al., 2008) for each different coastal marine habitat.

Coastal marine habitats in the Mediterranean Sea are predominantly represented by *Posidonia oceanica* seagrass meadows and infralittoral rocky reefs (IRR) (Holon et al., 2015a). The latter habitat, as defined by Pérès (1982), constitutes a shallow ecosystem (i.e. from 0 to 15–30 m depth depending on water clarity) structured by photophilous canopy-forming Multicellular Photosynthetic Organisms (MPOs, hereafter named ‘macrophytes’), including the Fucales *Cystoseira sensu lato* (e.g. Boudouresque, 1971a, 1971b; Verlaque, 1987; Ballesteros, 1988;

<footnote><sup>a</sup> Aix-Marseille University and Toulon University, Mediterranean Institute of Oceanography (MIO), CNRS, IRD, UM110, Marseille, France</footnote>

<footnote><sup>b</sup> GIS Posidonie, Marseille, France</footnote>

<footnote>* Correspondence to: E. Jacob, Aix-Marseille University and Toulon University, Mediterranean Institute of Oceanography (MIO), CNRS, IRD, UM110, Marseille, France.</footnote>

<footnote>** Corresponding author.</footnote>

<footnote>E-mail addresses: elodie.jacob@univ-amu.fr (É. Jacob), patrick.astruch@univ-amu.fr (P. Astruch).</footnote>
Ballesteros, 1990; Sales et al., 2012; Bevilacqua et al., 2021) and Sargassum spp. (Thibaut et al., 2005, 2015, 2016; Verlaque et al., 2019). Fucale forests can face high herbivore pressure, characterized by over-grazing by sea urchins (Paracentrotus lividus and Arbacia lixula) and the salema Sarpa salpa (Agnetta et al., 2015; Thibaut et al., 2016; Tsirintanis et al., 2018). This pressure is further intensified by fishing, leading to the overpopulation of herbivores (Sala et al., 1998). In addition, the invasive herbivorous teleosts Siganus luridus and S. rivulatus strongly impact this habitat in the eastern Mediterranean (Sala et al., 2011; Katsanevakis et al., 2023). These pressures result in a regime shift from perennial canopy-forming macroalgae towards turf-dominated or barren grounds, leading to the decline of specific functional and structural biodiversity (Cheminée et al., 2013; Thiriet, 2014; Cuadros, 2015; Thibaut et al., 2017; Bevilacqua et al., 2021). Hence, its ecological assessment is crucial for monitoring IRR potential shifts and preserving its seascapes.

An ecological assessment is essential for guiding management and mitigation strategies, especially within the frame of the European Directives (ED) which have been implemented to ensure the maintenance or attainment of a suitable status for the marine environment since the 1990s: (i) the Habitat Directive (HD: 92/43/EEC), which lists habitats and species of European interest needing protection through the Natura 2000 site network; (ii) the Water Framework Directive (WFD: 2000/60/CE), aiming at characterizing the quality of water body masses using physical-chemical parameters and biological indicators (Ecological Quality Ratio); and (iii) the Marine Strategy Framework Directive (MSFD: 2008/56/CE), which aims to achieve Good Environmental Status (GES) in marine ecosystems through an ecosystem-based management approach (Boero, 2016; Paramana et al., 2021; Fraschetti et al., 2022).

These EDs require proper tools to management strategies and their consequences for water body masses, habitats, and ecosystems. Monotypical indicators were thus widely developed to address the requirements of the HD and the WFD. Concerning IRR, macrophytes are the descriptors used to assess the ecological status (e.g. Ecological Evaluation Index continuous (EEI-c) by Orfanidis et al. (2011) or the cartography of littoral and upper-sublittoral rocky-shore communities (CARLIT) by Ballesteros et al., 2007). Embracing an ecosystem-based approach (Boudouresque et al., 2020a), the mainstay of the MSFD, Thibaut et al. (2017) have defined an Ecosystem-based Quality Index designed for IRR (hereafter reef-EBQI) in the northwestern Mediterranean context. Lately, the reef-EBQI has been implemented in other parts of the Mediterranean basin (Bevilacqua et al., 2020; Nikolaou et al., 2023; Savin et al., 2023). Reef-EBQI results in the assessment of different compartments with 11 distinct ecological functions (e.g. macrophytes, sea urchins, piscivorous teleosts). Recently, Kytinou et al. (2023) developed and applied the ECOfast index, aiming at assessing IRR quality in the Aegean Sea (northeastern Mediterranean) context with an ecosystem-based approach with a rapidly available outcome. The originality of the ECOfast index lies in the possibility of also taking into account the occurrence of NIS.

However, factors beyond just anthropogenic pressure can influence the ecosystem functioning. Macrophytes, invertebrates, and teleost assemblages vary strongly with regard to habitat structures, including vertical and horizontal substrate complexity (Benedetti-Cecchi, 2001; García-Charton and Pérez-Ruzafa, 1998, 2001; García-Charton et al., 2004) and the substratum slope (Whorff et al., 1995; Harmelin-Vivien et al., 1995). Furthermore, management levels correspond to areas with different regulations: unprotected zones with no regulation, and Marine Protected Areas (MPAs) aiming at safeguarding all or part of the ecosystems. These areas have regulations spanning from single to multiple zones and from no regulation to no-take zones (Rife et al., 2013; Boudouresque et al., 2019). Numerous studies have demonstrated the effect of management levels on biomass, size, and age of teleost assemblages (e.g. Claudet et al., 2006, 2008; Harmelin-Vivien et al., 2008; García-Charton et al., 2008; Sala and Giakoumi, 2018; Rojo et al., 2021) as well as on the resilience and recovery of benthic assemblages (Bevilacqua

et al., 2006; Micheli et al., 2014; Mellin et al., 2016). To distinguish properly the effect of anthropogenic pressures, the analysis of the effect of the local specificities, geomorphology (i.e. habitat structure and slope) and management level on reef-EBQI is required.

Between 2015 and 2023, reef-EBQI assessments were conducted at 96 sites along the French Mediterranean and Monaco coasts. The aims of this paper are thus to (i) establish an assessment framework for IRR of the French Mediterranean using the reef-EBQI; (ii) analyze the influence of local specificities, management practices, geomorphology and anthropogenic pressures on the ecological status, and (iii) discuss the relevance of the reef-EBQI compared to the ECOfast index.

## 2. Materials and methods

### 2.1. Study area

The study area corresponded to the French and Monaco Mediterranean coasts, between the Spanish and Italian borders, including Corsica. A total of 96 sampling sites were monitored across six sub-regions: French Catalonia (i.e. southern Gulf of Lions), northern Gulf of Lions, western Provence, eastern Provence, French Riviera (including Principality of Monaco) and Corsica (Fig. 1, Supplementary S1). These sites are subject to varying levels of management, categorized as in Thibaut et al. (2017): no regulation, Natura 2000 site, Marine Protected Area with Multi-Use Management area (MPA-MUM), and Marine Protected Area with No Take Zone (MPA-NTZ; Supplementary S1). Natura 2000 is classified as an environmentally significant zone under the EU Habitat Directive 1992. Management levels can overlap (e.g. Natura 2000 and MPA-NTZ). In such cases, the higher level was considered.

### 2.2. Ecosystem-based Quality Index (reef-EBQI)

#### 2.2.1. General description

The reef-EBQI (Thibaut et al., 2017) allows the determination of the status of IRR sites in the Mediterranean Sea, categorizing them as ‘high’, ‘good’, moderate, ‘poor’,’’ or ‘bad’. This classification is based on a score out of 10 by assigning a score (S) category from 0 to 4 for each functional compartment, determined in the Supplementary S2. Different weightings (W) are given to each compartment in the final score according to their importance in the functioning of the ecosystem (1 through 15, Supplementary S2). These compartments include macrophytes (MPOs), detritus-feeders, filter- and suspension-feeders, sea urchins, invertivorous invertebrates, herbivorous teleosts, omnivorous and invertivorous teleosts, piscivorous teleosts, planktivorous teleosts, sea birds. The final ecosystem score at a site was determined by summing the scores of all considered compartments and converted from 0 to 10:

$$ \text{reef-EBQI} = \frac{\sum_{i=1}^{10} (W_i \times S_i)}{\sum_{i=1}^{10} (W_i \times S_{\text{max}})} \times 10 $$

where: $W_i$ is the weight of compartment i, $S_i$ is the status of compartment i, $S_{\text{max}}$ is the maximum grade (= 4) for a compartment, and i represents the compartment number (1 to 10, compartments 7 and 8 are merged). Then, the ecological status is determined as follows: ‘bad’ (reef-EBQI < 3.5), ‘poor’ (3.5 ≤ reef-EBQI < 4.5), ‘moderate’ (4.5 ≤ reef-EBQI < 6), ‘good’ (6.0 ≤ reef-EBQI < 7.5) and ‘high’ (reef-EBQI ≥ 7.5). Additionally, a confidence index (CI) assesses the evaluation quality (0 to 4): 0 for no data and unsuitable expert judgment, 1 for no data with earlier expert judgment, 2 for no data with recent expert judgment, 3 for recent field data partially supplemented with expert judgment, and 4 for recent, suitable field data with recommended methods (for more details, see Thibaut et al., 2017; Ruitton et al., 2021; Boudouresque et al., 2020b).
<figure><img src="image_2.png" /><figcaption>**Fig. 1.** Sampling sites (n = 96) assessed with the reef-EBQI along the French Mediterranean and Monaco coast. The temporal variability is represented with a color gradient according to the year of the sampling (from 2015 to 2023). The numbers correspond to the sites listed in Supplementary S1.</figcaption></figure>

### 2.2.2. Data sampling

Between 2015 and 2023, the reef-EBQI was implemented across 96 IRR sites along the French and Monaco Mediterranean coast during late spring to late summer (i.e. between May and September; Fig. 1). The depth range falls between 3 and 15 m. Data collection followed the protocol established by Thibaut et al. (2017). The macrophyte cover type, including arborescent perennial, shrubby or turf, was determined at the site scale to ascertain the macrophyte compartment score. In addition, the identification and the abundance of invertebrate species were noted in 1 m² quadrats to score detritus-feeders, filter- and suspension-feeders and sea urchins. The abundance of *Hexaplex trunculus*, *Octopus vulgaris* and *Marthasterias glacialis* was assessed for evaluation as a proxy of the invertivorous invertebrate compartment. The abundance of the latter, as well as that of teleosts, was estimated through visual censuses conducted on replicates of 25 m long and 1 m wide linear transects (4 m wide for teleosts). Abundance and total length of each teleost individual were noted for each replicate and used to determine the wet biomass (WM) for the compartments: herbivorous, omnivorous and invertivorous, piscivorous, and planktivorous teleosts compartments. Sea birds scores were calculated based on the distance of the study site from the nearest nesting site of *Phalacrocorax* spp. and *Pandion haliaetus*. However, 31 sites were assessed on the basis of different protocols or expert' inputs (Supplementary S3).

## 2.3. ECOfast index

### 2.3.1. General description

The ECOfast index is another ecosystem-based index defined and implemented by Kytinou et al. (2023). It aims at facilitating the assessment of the environmental status (categorized as ‘high’, ‘good’, ‘moderate’, ‘poor’, or ‘bad’) based on a score on a scale 0 to 1. This score is derived as the mean of three sub-indexes standardized within this range. Specifically, these sub-indexes include ECOfast-m for ‘macroalgae’ (i.e. MPOs), ECOfast-f for ‘fish’ (i.e. teleosts), and ECOfast-i for ‘invertebrates’. ECOfast-m is based on the same criteria as the MPO’s compartment in the reef-EBQI (i.e. cover type). ECOfast-f and ECOfast-i are based on the presence or absence of a specific list of species. Fish species are classified into four trophic categories (herbivores/omnivores preferring phyto-benthos, omnivores, carnivores, large predators). If a category is absent across the transects of the site, a 15 % penalty is applied to the sub-index score. Invertebrates are grouped into five trophic categories (herbivores/omnivores with a preference for phyto-benthos, detritivores, filter feeders or suspension feeders, carnivores, large predators), with missing categories result in a 5 % penalty. The ECOfast-NIS is another version of the index, which adds penalties for

non-indigenous species (NIS). A negative value is applied for each presence of NIS in a transect or quadrat (for more details, see Kytinou et al., 2023).

### 2.3.2. Data acquisition

For this study, the ECOfast index was estimated using the dataset available for reef-EBQI assessment following the strategy of Kytinou et al. (2023). However, it is intended to be calculated through observations on six random-transects lasting 10 min each: three at 5 m and three others at 15 m. Species occurrences on each transect were summarised and additional points were assigned for key and commercially important species. Penalties are also applied to ECOfast-i and ECOfast-f if a trophic group is missing. Then, the mean sum between the six transects corresponds to the score of the sub-indexes.

Some adjustments were made to fit the dataset available for the reef-EBQI and the ECOfast protocol. The score of the ECOfast-m was determined using the cover type as in Kytinou et al. (2023) but directly at the site scale. For the ECOfast-fish, the visual census data of teleosts from reef-EBQI data were converted into presence/absence data in each size class (small and large) for the 30 species listed by Kytinou et al. (2023). The size limit between the small and large size class of fish has been adjusted to the western Mediterranean context based on our dataset (Supplementary S4). Estimating that one 10 min transect corresponds to two 25 m transects, reef-EBQI transects were paired according to their similar depth. If the number of reef-EBQI transects for a site was odd, a transect was randomly excluded. For the ECOfast-invertebrates, transects conducted to count *H. trunculus*, *O. vulgaris* and *M. glacialis* individuals were used and processed similarly to teleost data. In addition, the identification of invertebrates performed on 30 quadrats of 1 m² was used to estimate the score of the site directly and converted to presence/absence for the 33 species listed. The score of the ECOfast-i is simply the sum of each present taxa in these 30 quadrats, to which is added the mean score of *O. vulgaris* and *M. glacialis* transect. The ECOfast-NIS index was not considered here because no NIS were found among fish and invertebrates and data on the occurrence of NIS macroalgae (e.g. *Caulerpa cylindracea*) were not available.

## 2.4. Data analysis

Normal distribution was confirmed using a Shapiro test and comparisons between the reef-EBQI and ECOfast index were conducted using the Student test. Pearson correlations were used for normally distributed variables, while Spearman correlations were applied for non-normal data. Significant correlations were followed by linear regression. Statistical analyses were carried out using the R programming
environment with *FactoMineR*, *gtsummary*, *cartography* and *ggplot2* packages (R Core Team, 2023; Lè et al., 2008; Sjoberg et al., 2021; Giraud and Lambert, 2016; Wickham, 2016).

The assessment framework for IRR is based on the mapping of reef-EBQI status and the analysis of functional compartment scores. Spider-web graphics depicted the average scores of sites with the same status for each compartment. Principal Component Analysis (PCA) was used to visualize the combination of these scores, with supplementary variables including latitude, longitude, management level (0 for no regulation, 1 for Natura 2000 sites, 2 for MPA-MUM, and 3 for MPA-NTZ), level of pressure (ranging from 0 to 12, with 0 indicating no pressure and 12 indicating maximum pressure), and geomorphology level (ranging from 0 to 6, with 0 for sites lacking vertical and horizontal complexity in rocky reefs). The geomorphology level is the addition in the score for the heterogeneity of the substratum slope (0: subhorizontal homogenous slope; 1: low changes in slope; 2: heterogenous slope mostly between 0 and 45°; 3: numerous changes of the slope between 0 and 90°) and the one from the substrate rugosity scores, which correspond to the size and number of blocks (0: very low rugosity; 1: low rugosity; 2: moderate rugosity; 3: high rugosity). Level of pressure was determined as in Sar-toretto et al. (2017) by summing scores from four pressure categories (cover of marine litter, sedimentation/eutrophication, mechanical abrasion from scuba diving and anchoring, and mechanical abrasion/ sampling from fishing). Scores are defined following a semi-qualitative scale (0, 1, 2, 3) according to the level of each pressure category. The assessment was carried out based on the empiric knowledge of the au-thors at site scale during the sampling. Significant differences (i.e. at α = 0.05) between categories in the PCA were assessed using v-test absolute values (>1.96; Lè et al., 2008) and represented by the barycentre of site categories.

Furthermore, the ECOfast scores ranging from 0 to 1 have been rescaled to 0–10 to be comparable with reef-EBQI scores. The relevance of the reef-EBQI and ECOfast index was analysed comparing the different compartments of reef-EBQI and ECOfast sub-indexes (ECOfast-m, ECOfast-f, and ECOfast-i). Scores for all functional compartments in

the reef-EBQI, including those for teleosts (herbivorous, piscivorous, planktivorous, omnivorous, and invertivorous teleosts) and in-vertebrates (detritus-feeders, filter and suspension-feeders, sea urchins and invertivorous invertebrates), were aggregated, taking into account their weighting according to Thibaut et al. (2017) (Supplementary S2).

## 3. Results

### 3.1. Reef-EBQI status

The sampling strategy encompassed 96 sites along the French Med-iterranean coast, monitored between 2015 and 2023, offering a repre-sentative overview of IRR ecological status (Fig. 2, Supplementary S5). The site distribution displayed a relative geographical homogeneity, with the exception of the northern Gulf of Lions, represented by only eight sites, due to the scarcity of hard natural substrate. In addition, the French Catalonia sites were concentrated predominantly along the rocky Albères coast. Regarding the management level of sites, 12 presented no regulation, 42 were Natura 2000 sites, 20 were MPA-MUM and 22 MPA-NTZ. The CI ranged between 76 % (n°70 — Larvotto est) and 100 %. The reef-EBQI score ranged between 2.48 (n°18 — Les Esclops) and 8.92 (n°48 — Gabinière est). The health ecosystem status of 35 sites was ‘moderate’, 32 ‘good’, 13 ‘high’, 12 ‘poor’ and 4 ‘bad’ (Fig. 2). The distribution of the reef-EBQI differed from the monotypic macrophytes score which showed a score of 1 (i.e. ‘poor’) for 24 sites and a score of 2 (i.e. ‘moderate’) for 46 sites.

The reef-EBQI scores give a first broad overview of the ecological status of the ecosystem but also of each functional compartment (i.e. MPOs, detritus-feeders, filter- and suspension-feeders, sea urchins, invertivorous invertebrates, herbivorous teleosts, omnivorous and invertivorous teleosts, piscivorous teleosts, planktivorous teleosts, sea birds).

Overall, the ‘high’ sites had higher status for the functional com-partments than sites with lower status, as reflected on the macrophytes compartment (Fig. 3). However, the reef-EBQI status does not seem to

<figure><img src="image_3.png" /><figcaption>**Fig. 2.** Reef-EBQI status along the French and Monaco coast. Site status (n = 96) corresponds to ‘bad’ in red, ‘poor’ in orange, ‘moderate’ in yellow, ‘good’ in green and ‘high’ in blue). The numbers correspond to the sites listed in Supplementary S1. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)</figcaption></figure>
<figure><img src="image_4.png" /><figcaption>**Fig. 3.** Average profile of the ecological reef-EBQI status of the infralittoral rocky reefs along the French Mediterranean and Monegasque Monaco coasts. The spider-web graphic represents the average score for each functional compartment (from 0 to 4) according to the reef-EBQI status (i.e. 'bad' in red, 'poor' in orange, 'moderate' in yellow, 'good' in green and 'high' in blue). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)</figcaption></figure>

reflect the status of all compartments (Fig. 3). There was indeed a consistent trend of low scores (i.e. lower than 2, 'moderate') for sea birds and high scores (i.e. higher than 3, 'good') for detritus-feeders, sea urchins (e.g. 50 % of 'poor' sites were associated with a score of 4), and invertivorous invertebrates.

The site ordination, based on the scores for each compartment, displays the role of each functional compartment with regard to the reef-EBQI status. A gradient from 'poor' to 'high' scores follows the first axis of the PCA (Fig. 4A). The primary contributors to this component were planktivorous teleosts (28.8 %) followed by herbivorous teleosts (27.1 %), invertivorous invertebrates (19.4 %) and piscivorous teleosts (15.0 %). The weak contribution of MPOs and sea urchins, the most important functional compartments in terms of weighting, was notable. The second axis of the PCA was predominantly explained by herbivorous teleosts (49.7 %) and piscivorous teleosts (21 %), which appeared to differentiate the 'good' and 'high' status sites. 56 % of herbivorous teleosts scoring 'high' were linked with moderate scores in piscivorous teleosts, while 57 % of herbivorous teleosts scoring 'bad' were associated with high scores in piscivorous teleosts. Less notably, piscivorous, planktivorous teleosts, and macrophytes were opposed to those of herbivorous and omnivorous-invertivorous teleosts.

The variables latitude, longitude, management level, pressure level and geomorphology were included as S variables on the PCA in order to investigate their influence on the ecological status (Fig. 4A). Thus, the latitude and level of pressure were the S variables most closely correlated with the first axis of the PCA (0.396 and -0.293 respectively). With the second axis, longitude and latitude were the most correlated (-0.446 and 0.392) and the correlations with other variables were negligible (< 0.1).

<figure><img src="image_5.png" /><figcaption>**Fig. 4.** Ordination of infralittoral rocky reef sites along the French and Monaco Mediterranean coasts depicting the contribution of functional compartments to the reef-EBQI status and the role site characteristics. Variables of the Principal Analysis Component (PCA), which remains the same across the both ordinations, correspond to the score of the different ecological comportments. Reef-EBQI status is represented as follows: 'bad' with a small red circle, 'poor' with an orange rhombus, 'moderate' with a large yellow circle, 'good' with a green square, and 'high' with a blue triangle (A). Site characteristics is defined by local specificities, management, pressure and geomorphology and included as S variables (A) represented by the coordinates barycentre (B). MPA-NTZ: No-take Zone within a Marine Protected Area. MPA-MUM: Multi-Use Management Zone within a Marine Protected Area. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)</figcaption></figure>
Northern Gulf of Lions and western Provence, characterized by 'bad' and 'poor' sites, were significantly contrasted with eastern Provence and French Riviera which had none (v-test = -3.96 and -2.37 for the former, 2.44 and 2.38 for the latter; Fig. 4B). Otherwise, with 62 % of 'high' sites, Corsica was significantly distinguished from other categories along the second axis (v-test = 5.00; Fig. 4B). It also showed higher scores for the piscivorous teleosts compartment (mean ± error standard; 2.1 ± 0.3) than for herbivorous teleosts (1.3 ± 0.3).

The level of pressure followed the first axis from 'high' to 'bad' status (Fig. 4A), which significantly discriminates sites with a level of pressure of 10 and 0 (v-test = -3.20 and 2.00, Fig. 4B). Sites with a pressure level of 10 and classified as 'bad' or 'poor' were in the Gulf of Fos (western Provence), while those with no pressure were located in Corsica (Supplementary S5). Thus, a significant correlation between reef-EBQI scores and level of pressure was found (Spearman's rho, r = -0.646, p-value < 0.001).

Geomorphology and management level were not correlated with the first axis of the PCA (0.222; 0.209) indicating a slighter effect on the combination of the functional compartment scores (Fig. 4A). In fact, geomorphology was positively correlated with the reef-EBQI scores (Spearman's rho, r = 0.539). For the management level, only sites without regulations were significantly distinguished (v-test = -2.10) because all status were represented in all management levels. However, the gradient from 'bad' to 'high' was followed by the barycentres of sites with no regulation, Natura 2000, MPA-MUM and MPA-NTZ (Fig. 4B). For example, 50 % of 'bad' sites and 52 % of 'poor' sites were Natura 2000 sites, while 40 % of sites in MPA-MUM and 36 % sites in MPA-NTZ were 'good'.

## 3.2. Comparison between the reef-EBQI and the ECOfast index

The reef-EBQI was compared to the ECOfast index using 89 sites sorted from our dataset (Supplementary S1). It has been found that the two indices are strongly correlated (r = 0.748, p-value < 0.001), and according to the linear regression line, the ECOfast index and reef-EBQI described sites' ecosystem quality in a similar way (Fig. 5). However, only 37 sites out of 89 obtained the same status with the reef-EBQI and ECOfast index with 3 classified as 'good', 26 as 'moderate', 7 as 'poor', and 1 as 'bad'. Only the reef-EBQI exhibited 'high' scores. The

<figure><img src="image_6.png" /><figcaption>**Fig. 5.** Linear regression analysis of the ECOfast scores according to reef-EBQI scores for 89 sites. Reef-EBQI and ECOfast index status are displayed (i.e. 'bad' in red, 'poor' in orange, 'moderate' in yellow, 'good' in green and 'high' in blue). r is the correlation calculated with the Spearman rho. p is the p-value of the model resulting from Fisher statistics. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)</figcaption></figure>

differences in scores and in status were analysed (Fig. 6A), as well as the differences in intermediate scores used by the ECOfast index (i.e. macrophytes, teleosts and invertebrates; Fig. 6B), and reported in (Table 1).

# 4. Discussion

This work assessed the ecological status of the French Mediterranean IRR and examined how it varies according to anthropogenic and natural factors but also using two ecosystem-based indicators (i.e. reef-EBQI and ECOfast index). The majority of sites were classified as 'moderate' and 'good' (Figs. 2 & 6). Herbivorous, piscivorous, and planktivorous teleosts were the compartments which contributed the most to the differences in reef-EBQI scores (Figs. 3 & 4). The local specificities appear as a principal factor in variation between reef-EBQI scores before the level of pressure and thus discriminate 'high' Corsica sites. Geomorphology and management level also contributed, but less significantly (Fig. 4). 41 % of the sites had the same ecological status based on ECOfast index and reef-EBQI but differences in status distributions were established (Figs. 5 & 6; Supplementary S1).

## 4.1. What describes the ecological status of the rocky reef ecosystem?

An increasing number of studies have attempted to assess the ecological status of infralittoral rocky reefs, particularly in the framework of EU Directives (Ballesteros et al., 2007; D'Archino and Piazzi, 2021). Our results using reef-EBQI (Fig. 2; Supplementary S5) were consistent with the literature and underline the overall 'moderate' status of the IRR ecosystem in the Mediterranean Sea (Thibaut et al., 2017; Bevilacqua et al., 2020; Fraschetti et al., 2022). In addition, 'bad' and 'poor' status represented a minor proportion of sites, as found by Bevilacqua et al. (2020) at the Mediterranean scale. However, in the eastern Mediterranean, the ecological status of IRR appears to be mostly 'poor' or 'bad' (Fraschetti et al., 2022; Kytinou et al., 2023; Savin et al., 2023). Thus, possessing sites with a 'high' ecological status seems to be a characteristic of the northwestern Mediterranean (Bevilacqua et al., 2020). Before interpreting the final status, care is required for a proper assessment of the ecosystem quality. While it has proved to be a practical and essential tool for management, this general and discrete assessment of the ecosystem could lead to an inaccurate oversimplification of the final result. For this reason, it will always be necessary to consider not only the final score but also the scores of each compartment (Gatti et al., 2012, 2015; Thibaut et al., 2017; Oprandi et al., 2023; Fig. 3; Supplementary S5). Thus, the average picture of 'moderate' to 'good' sites highlighted a 'moderate' status of macrophytes, low status of piscivorous teleosts and high scores for detritus-, and filter- and suspension-feeders and sea urchins. This status represents a cover of shrubby macroalgae populated with a weak density of piscivorous teleosts, detritus-, and filter- and suspension-feeders and sea urchins. This general picture of the French and Monaco Mediterranean coasts is quite consistent with the literature describing the degradation of the macrophyte canopy by the extinction or strong regression of arborescent perennial macrophytes such as *Cystoseira sensu lato* and *Sargassum* spp. (Thibaut et al., 2005, 2015, 2016; Verlaque et al., 2019) and piscivorous teleost biomass (e.g. Lotze et al., 2011). The low density of detritus-, filter- and suspension-feeder and sea urchin compartments is dependent on the concentration of particulate organic matter (Massin and Jangoux, 1976; Delmas and Régis, 1985; Mezali et al., 2006) and a high density of these compartments would suggest eutrophic conditions. The water quality along the French and Monaco Mediterranean coasts has improved (Feuilloley et al., 2020), which might also have contributed to the regulation of these compartments since the 2000s.

High scores for piscivorous, planktivorous, and macrophytes appear to be associated with 'high' sites, whereas high scores for herbivorous and omnivorous and invertivorous teleosts were associated with 'good' sites (Fig. 3, 4A). Macrophytes play a crucial role in this ecosystem by structuring the habitat and providing shelter and food to other
<figure><img src="image_7.png" /><figcaption>**Fig. 6.** Site distribution according to the status attributed by the reef-EBQI and ECOfast index (A), macrophytes (B) invertebrates (C) and teleosts sub-indexes (D). The reef-EBQI is represented in purple and the ECOfast index in brown. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)</figcaption></figure>

<table><caption>**Table 1**
Notable differences between the reef-EBQI and the ECOfast index.</caption><thead><tr><th>Differences</th><th>reef-EBQI</th><th>ECOfast</th></tr></thead><tbody><tr><td>Average score***</td><td>5.8 ± 0.2</td><td>4.6 ± 0.1</td></tr><tr><td>Status</td><td>All status represented with a majority of 'moderate' and 'good'</td><td>64 % of sites as 'moderate' and none 'high' sites</td></tr><tr><td>Macrophyte</td><td>Mostly 'moderate' and 'poor'</td><td>Mostly 'good' and 'high'</td></tr><tr><td>Invertebrate</td><td>53 % were 'high' status</td><td>All status represented with a majority of 'moderate'</td></tr><tr><td>Teleost</td><td>All status represented with a majority of 'bad' and 'poor'</td><td>Mostly 'poor' and 'moderate' but none 'high'</td></tr></tbody></table>

compartments (Cheminée et al., 2013; Blanfuné et al., 2016), thereby enhancing its ecosystem quality. Because piscivorous teleosts (e.g. *Epi-nephelus marginatus*, *Pagrus pagrus*, *Dentex dentex*) occupy the highest trophic level, their high biomass is a good proxy of the quality of teleost assemblages, particularly when fishing is regulated or banned (Harmelin-Vivien et al., 2008; Rojo et al., 2021).

## 4.2. How do site characteristics influence the ecological status?

An ecological indicator should aim at being sensitive and able to address the influence of anthropogenic pressures and related management levels. The level of pressure influenced the combined reef-EBQI

scores component (Fig. 4). Anthropogenic pressure, as documented by Coll et al. (2010), plays a significant role in shaping the complexity of benthic communities. However, caution must be taken in interpreting these results because the level of pressure was estimated rather than calculated directly, following the method of Sartoretto et al. (2017). A standardized and more accurate method that considers the synergy between pressures and cumulative impacts is essential for improving our understanding of human threats to coastal ecosystems (Micheli et al., 2013; Halpern et al., 2019; Quemmerais-Amice et al., 2020). However, while global assessments, such as those by Halpern et al. (2019), provide valuable insights, applying these large-scale datasets at a local scale—particularly in coastal and shallow areas—requires careful consideration. Coastal ecosystems, including rocky reefs, are influenced by a specific set of pressures that differ from those affecting deeper or more open marine environments. As such, an approach that focuses on site-specific pressures would be more reliable for local-scale studies.

Local specificities appear to discriminate the most the site scores before the level of pressure, particularly through the latitude (Fig. 4). Sites to the south and east of Corsica are mainly characterized by a 'high' status. This could be explained by the persistent *Cystoseira sensu lato* arborescent perennial forest in contrast to the mainland subregions (Thibaut et al., 2005, 2015, 2016). Corsica was also associated with high scores in piscivorous teleost compartments, probably because of a lesser pressure from fishing and better settlement for coastal teleost species at the juvenile stage within perennial MPOs associations (Cheminée et al., 2013, 2021). This confirms the importance of considering the geographical differentiation between islands and the mainland

<footnote>*** Average scores (mean ± standard error) indicate a *p*-value < 0.0001 for the Student test.</footnote>
(Benedetti-Cecchi, 2003). However, this spatial variability was studied with sites sampled between 2015 and 2023 (Fig. 1), potentially hiding local or regional temporal changes.

Despite the majority of Mediterranean protected areas being situated along rocky coasts (Sala et al., 2012), the management level did not appear as the most discriminating factor (Fig. 4). The effectiveness of MPAs in promoting the recovery of macrophytes' canopy remains limited (Parravicini et al., 2013; Tamburello et al., 2022; Boudouresque et al., 2022). Even with a strong level of protection, the return of perennial canopy-forming macrophytes will not occur because of the low dissemination capacity of Fucales taxa (Thibaut et al., 2005, 2016). Management level seems to directly impact mostly teleost and assemblages of economic interest (e.g. Harmelin-Vivien et al., 2008; Claudet et al., 2006, 2008). This result could also underscore the 'paper park' phenomenon regarding some Marine Protected Areas (MPAs), particularly obvious in poorly-managed Natura 2000 sites, which have been shown to be ineffective (Meinesz and Blanfuné, 2015; Reker et al., 2015; Thibaut et al., 2017; Fraschetti et al., 2022; Boudouresque et al., 2022). However, in contrast with the results of Thibaut et al. (2017), Natura 2000 sites are closer to NTZ and MUM sites than to sites with no regulation (Fig. 4B). Additionally, it is important to recognize that certain pressures, such as nutrient inputs, climate change, and the spread of non-indigenous species (NIS), are beyond the control of MPA governance, even in highly protected areas. For example, in the Calanques National Park (Provence), nutrient inputs and the spread of NIS *Rugulopteryx okamurae*, along with mass mortality events associated with marine heatwaves, have been documented (Ourgaud et al., 2018; Ruitton et al., 2021; Estaque et al., 2023). Similarly, in Port-Cros National Park (Provence), the spread of the NIS *Lophocladia trichoclados* has been reported (Boudouresque et al., 2022).

The geomorphology was also a minor factor for the reef-EBQI scores component compared to the others (Fig. 4) but was correlated with reef-EBQI scores. The complexity of the abiotic habitat structure increases the abundance and the species richness of fish teleost assemblages (García-Charton and Pérez-Ruzafa, 1998, 2001; García-Charton et al., 2004; Monfort et al., 2021) and influences the settlement of fish juveniles (Harmelin-Vivien et al., 1995). This complexity means a more diverse habitat providing additional resources for teleosts (García-Charton and Pérez-Ruzafa, 1998) and probably also a refuge for the invertebrates, as shown for the biotic *Cystoseira sensu lato* algal complexity (Piazzi et al., 2018).

### 4.3. Relevance of the reef-EBQI compared to the ECOfast index

In this study, we compared two ecosystem-based indicators, the reef-EBQI and the ECOfast index, along the French and Monaco Mediterranean coast. The ECOfast index appeared applicable in the northwestern Mediterranean, as did the reef-EBQI for the eastern Mediterranean (Savin et al., 2023). These indicators were correlated (Fig. 5A) and 41% of the sites shared the same status. However, discrepancies emerged in the status assigned to sites: the reef-EBQI tended to provide a more discriminating assessment compared to the ECOfast index, which frequently categorized sites as 'moderate' or with lower scores (Fig. 6, Table 1). Further analysis of sub-indexes (i.e. MPOs, invertebrates and teleosts) indicated similarities in the description of teleosts between the two indicators, but notable differences in the treatment of invertebrates (Fig. 5B, C, Table 1). This could be explained by the penalties attributed to the invertebrate ECOfast sub-index for sites that do not present all trophic levels, and nearly all the sites were in this situation. Kytinou et al. (2023) revealed the absence of high trophic levels in carnivorous invertebrates in the Aegean Sea. The reef-EBQI, by accounting for the biomass, provides a nuanced understanding of teleosts status, revealing an overall low status.

Furthermore, differences in sampling relative to the recommendations of Kytinou et al. (2023) should be taken into account for a direct comparison between the ECOfast and reef-EBQI. If we assess the CI for

the ECOfast index, it reaches 83% for all sites (data not shown), which can be considered as suitable. Both indices offer cost-effective implementation, achievable in a single one-hour dive with 2 to 4 observers. The ECOfast index provides semi-qualitative data, while the reef-EBQI yields mainly quantitative data, valuable for detailed management analyses or assessing specific pressures, such as the impact of fishing activities on fish assemblages, as illustrated in the conceptual model of Thibaut et al. (2017). The fact that the score differs between indicators highlights a weakness in the management with regard to different indicators. However, looking at the fluctuation of the score over time seems to be more useful than the absolute score (Ferrario et al., 2021).

### 4.4. Suitability of the reef-EBQI for the long-term monitoring of infralittoral rocky reefs for the purposes of European Directives

Ecological indicators have already been implemented in the Mediterranean to assess the quality of IRR (Infralittoral Rocky Reefs). The CARLIT index (Ballesteros et al., 2007; Blanfuné et al., 2017) has been in use along the French and Spanish coasts since 2007 for the purposes of the Water Framework Directive (WFD). Based on the assessment of the cover of macroalgal communities along the upper limit of the infralittoral zone (0–1 m depth), the CARLIT monitoring network highlights a relatively high ecological status along the French Mediterranean coast, corresponding to an overall improvement of water quality. Our findings, by applying reef-EBQI show a different trend, highlighting the influence of different stressors, local specificities and management; this shows again the issue in using different indicators for different purposes (Table 1). The reef-EBQI might be suitable for future regional monitoring networks for both MSFD and HD purposes, allowing the use of a single integrated indicator. Indeed, the implementation of the reef-EBQI remains easy and cost-effective, with demonstrated feasibility by MPA managers after training (Astruch et al., 2022). Our study also reveals its robust response to anthropogenic pressures and management practices across the Mediterranean (Thibaut et al., 2017; Bevilacqua et al., 2020; Savin et al., 2023), targeting the infralittoral zone (5–10 m depth) with an ecosystem-based approach, originally designed for the MSFD. It provides a varied dataset relevant for descriptors D1 (biological diversity), D2 (NIS), D3 (exploited fish), D4 (food webs), D5 (human-induced eutrophication) and D6 (sea-floor integrity). The reef-EBQI protocol provides a diverse set of descriptors suitable for assessing the conservation status of IRR, particularly the structure and the functions. This meets the requirements of the HD (Delavenne et al., 2023). However, our work emphasizes the importance of caution in interpreting results from such indicators. Furthermore, the status is determined spatially, thus not accounting for natural fluctuations and changes in management practices and level of pressure. This is why monitoring over time is needed.

## 5. Conclusion

The ecological status of infralittoral rocky reefs along the French Mediterranean coast has been assessed using the reef-EBQI. Results showed an overall 'good' and 'moderate' status consistent with previous surveys. Notably, 'high' sites appear as characteristic of the western Mediterranean. However, caution is needed in interpreting this general assessment, considering the complexity of the ecosystem quality and the need to analyze in details the functional compartments. The reef-EBQI indicator highlights the significance of MPOs and teleosts in determining ecological status in this area. In addition, the reef-EBQI is sensitive to the level of pressure but even more to local specificities. Management level significantly influences status, with unregulated areas often associated with low status sites. Geomorphology also affects status, though caution is needed in interpretation due to semi-quantitative estimation. Comparing the reef-EBQI with the ECOfast index reveals similarities but also discrepancies, particularly in assessing invertebrates and teleosts, underscoring the need to carefully choose
indicators based on specific assessment objectives. The reef-EBQI proves suitable for long-term monitoring for the requirements of European Directives, providing relevant data for MSFD and HD purposes and potentially in different Mediterranean regions. However, careful interpretation and consideration of temporal variability are mandatory.

Supplementary data to this article can be found online at https://doi.org/10.1016/j.marpolbul.2024.117050.

## CRediT authorship contribution statement

**Élodie Jacob:** Writing – original draft, Visualization, Methodology, Investigation, Formal analysis, Data curation. **Mélanie Cabral:** Writing – review & editing, Investigation, Data curation. **Thomas Schohn:** Writing – review & editing, Methodology, Investigation, Data curation. **Bruno Belloni:** Investigation, Data curation. **Charles-François Boudouresque:** Writing – review & editing, Conceptualization. **Thierry Thibaut:** Writing – review & editing. **Sandrine Ruitton:** Investigation. **Patrick Astruch:** Writing – review & editing, Supervision, Investigation, Funding acquisition, Conceptualization.

## Declaration of competing interest

The authors have declared that there are no competing interests.

## Data availability

Data will be made available on request.

## Acknowledgments

This work was carried out in the frame of several projects: LIFE 16PE FR001 Marha, GECOMED and GECORISK. We warmly thank the Marine Protected Area Agency (Agence des Aires Marines Protégées), the French Water Agency (Agence de l'Eau Rhône-Méditerranée-Corse), Port-Cros National Park, the French Biodiversity Agency, the Department of the Environment of Monaco and the Alpes-Maritimes Department Council for financial and logistical support, and Michael Paul, a native English speaker, for the proof-reading of the text. All this work would not have been possible without the dedication of managers and rangers from Marine Protected Areas involved in the data sampling: the Nature Marine Park of the Gulf of Lions, Nature Marine Reserve of Cerbère-Banyuls, Cap d'Agde MPA, Côte Bleue Marine Park, Port-Cros National Park, Collectivity of the Gulf of Saint-Tropez, Marine Park of Théoule-Estérel, Department of the Environment of Monaco, Nature Marine Park of Cap Corsica and Agriate and Nature Reserve of Scandola.

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