# Gut microbiome plasticity and host resistance in response to ocean warming in sub-Antarctic sea urchins.

Guillaume Schwob, Mélanie Delleuze, Sébastien Motreuil, Christian Marschal, Thomas Saucède, Julieta Orlando, Elie Poulin, Léa Cabrol

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Guillaume Schwob, Mélanie Delleuze, Sébastien Motreuil, Christian Marschal, Thomas Saucède, et al.. Gut microbiome plasticity and host resistance in response to ocean warming in sub-Antarctic sea urchins.. BMC Biology, 2025, 23 (1), pp.343. 10.1186/s12915-025-02448-9. hal-05375211

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# Gut microbiome plasticity and host resistance in response to ocean warming in sub-Antarctic sea urchins

Guillaume Schwob¹,²*, Mélanie Delleuze¹,³,⁴, Sébastien Motreuil⁵, Christian Marschal⁶, Thomas Saucède⁵, Julieta Orlando¹,³, Elie Poulin¹,³ and Léa Cabrol¹,⁷*

**Abstract**

**Background** Sub-Antarctic marine ecosystems are highly vulnerable to climate change, with rising ocean temperatures threatening key benthic species. *Abatus cordatus*, an endemic sea urchin of the Kerguelen Islands with limited dispersal capacity, has been hypothesised to possess a narrow thermal niche, which would render it particularly susceptible to environmental shifts. However, microbiome-mediated acclimation may provide a potential mechanism of resilience to ocean warming. To test these hypotheses, this study evaluates host survival and gut microbiome responses of *A. cordatus* to medium-term seawater warming under near-future temperature scenarios using 16S rRNA gene sequencing to compare these changes with those observed in sediment microbiomes.

**Results** Host mortality remained relatively low across all temperatures, showing no association with warming intensity and thereby suggesting thermal tolerance. While gut microbiome alpha-diversity remained stable, its composition shifted and variability increased with experiment duration and temperature, leading to greater inter-individual divergence and a decline in both the richness and abundance of core taxa. In contrast, sediment microbiomes remained more stable, exhibiting more deterministic assembly and increased core stability over time. At the taxonomic level, specific gut bacterial ASVs showed temperature-dependent abundance shifts, with greater flexibility at moderate thermal stress. Notably, the depleted and enriched ASVs were affiliated to known sulphate-reducing and fermentative taxa, respectively, suggesting a possible functional shift.

**Conclusions** Overall, our findings suggest that *A. cordatus* can tolerate medium-term warming, with gut microbiome plasticity representing a potential mechanism supporting host resilience.

**Keywords** Global climate change, Host microbiome, Thermal tolerance, Seawater warming, Sea urchins, Sub-Antarctic ecosystem

<footnote>*Correspondence:
Guillaume Schwob
guillaume_schwob@hotmail.fr
Léa Cabrol
lea.cabrol@mio.osupytheas.fr
Full list of author information is available at the end of the article</footnote>
## Background

Sub-Antarctic islands are remote, ecologically valuable regions with pristine coastal marine ecosystems [1, 2]. Due to their location at the transition zone between subtropical and Antarctic waters, these regions are particularly at risk from the impacts of the southward shift of marine fronts [3], and are currently facing rapid warming [4]. The high endemicity and cold-temperature adaptations of sub-Antarctic marine species make these islands among the most sensitive ecoregions of the Southern Ocean [5]. As natural laboratories, sub-Antarctic islands provide unique insights into the resilience and adaptability of marine communities in the face of climate change [6].

Benthic organisms in the coastal zones of sub-Antarctic islands are particularly sensitive to environmental perturbations, especially to shifts in temperature regime, due to their slow growth, reproduction rates, and limited dispersal capabilities [7–9]. Sea urchins (echinoids class) are key components of these benthic ecosystems, playing a substantial role in trophic networks, promoting benthic diversity, and maintaining ecosystem functions [10–12]. Previous studies predict major changes in echinoid assemblages in the sub-Antarctic region, including the Kerguelen Plateau, with high extinction rates driven by the southward migration of the Antarctic Circumpolar Current and associated shifts in marine fronts [13, 14].

Abatus cordatus is a common echinoid species in the nearshore benthic communities in soft bottom environments of the Kerguelen islands [15]. While this species is endemic to the Kerguelen Plateau, the genus is broadly distributed throughout the sub-Antarctic and Antarctic regions, with closely related species inhabiting similar environments [16]. It forms patchy yet high-density populations, reaching up to 70 individuals per 0.5 m² in shallow (0–3 m depth) sheltered bays of the Kerguelen archipelago [15]. It is an infaunal, burrowing species feeding from the organic matter in the ingested sediment (also called “deposit-feeder”) [17], which has been suggested to facilitate horizontal acquisition of microbes from the sediment, thereby influencing gut microbiome composition and function [18]. Abatus cordatus plays a key ecological role in sub-Antarctic soft-sediment ecosystems as a dominant bioturbator, contributing to sediment oxygenation, nutrient cycling, and the redistribution of organic matter [19]. Its ecological niche is narrow, restricted to places with mean seafloor temperatures ranging from 3 to 4 °C [13, 15]. As a brooding species with no larval stage, A. cordatus has limited dispersal capacity, making populations vulnerable to environmental perturbations [12]. Ecological niche modelling revealed that A. cordatus already occupies the entire available niche space around the Kerguelen Islands, with

its distribution constrained by the seafloor's steep drop beyond the plateau, preventing southward dispersal to potential refuges [13]. In the SO, projections anticipate mean sea surface temperature increases of 1.8 to 3.7 °C by the end of the century, along with more frequent and intense marine heatwaves during austral summers for the Kerguelen Plateau [13, 20, 21]. The species is thus expected to exhibit high thermal sensitivity and limited resilience to near-future seawater warming, with its response to global change depending on its ability to adapt through physiological plasticity [22]. In marine invertebrates, a suite of physiological mechanisms, including the heat shock response, oxidative stress management, membrane remodelling, and metabolic depression, may contribute to thermal stress resilience [23–25]. Among these, microbiome-mediated host acclimation may be crucial for enhancing A. cordatus' resilience to rising seawater temperatures [26].

The gut microbiome plays a fundamental role in host development, nutrition, immunity, and behaviour, with broad implications for both host ecology and ecosystem functioning [27–29]. Its plasticity enables rapid acclimation to environmental changes through various microbiome-mediated mechanisms, potentially mitigating the impact of stressors more efficiently than the host alone [30–32]. Over longer timescales, the microbiome may also contribute to host evolutionary potential by facilitating novel ecological interactions and expanding phenotypic variability [33]. Conversely, shifts in microbiome diversity can lead to dysbiosis, defined as a disruption in microbial community structure that negatively affects host physiological performance and fitness [34]. For instance, alterations in the gut microbiome, such as those caused by antibiotic exposure, have been associated with reduced immunity and increased mortality, likely due to a greater susceptibility to opportunistic infections [35]. While the importance of gut microbiomes in sea urchin ecology and evolution is increasingly recognized [18, 36, 37], the impact of temperature on their microbiomes remains understudied.

A recent meta-analysis of over 1300 microbiomes from 43 terrestrial and aquatic host species revealed that experimental warming typically reduce microbiome phylogenetic diversity and alter community composition [38]. However, this global analysis included no data from sub-Antarctic or Antarctic ecosystems, exposing a critical geographic and climatic gap in our understanding of microbiome responses to temperature increase in cold-adapted species. In echinoids specifically, most available studies focused on tropical species, reporting natural seasonal shifts in microbiome composition influenced by temperature among other abiotic factors [39, 40]. However, these in situ approaches
often struggle to isolate temperature effects due to
multiple confounding factors. To our knowledge, only
three experimental studies have examined the effects of
near-future warming on sea urchin microbiomes under
controlled conditions, focusing on warm-adapted (sub)
tropical echinoid species *Echinometra* sp. A and *Lytechinus variegatus*. These studies reported minor altera-
tions in gut microbiome composition but significant
predicted functional shifts at 30 °C and a 50% mortality
rate after 14 days at 32 °C for *Lytechinus variegatus* [41,
42]. Additionally, temperature increase and elevated
pCO₂ induced bacterial taxa-specific responses in the
gonad microbiome of *Echinometra* sp. A [43].

Given their cold-water specialization, ecological rel-
evance and expected vulnerability to global change [13,
44], it is crucial to assess the microbiome responses
of sea urchins like *A. cordatus* under warming scenar-
ios. This study evaluates the gut mucosa microbiome
responses of *A. cordatus* exposed to two near-future
seawater temperature treatments (7.5 °C and 10.5 °C),
assessed at three time points (day 2, day 5 and day 13).
A third treatment at 6 °C, corresponding to the local
average summer temperature, was used as a control.
In addition, samples were collected from in situ sea
urchins prior to the experimental setup, serving as a
baseline for natural microbiome structure. At each
experimental time points, we contextualised the gut
microbiome responses with those of the surround-
ing sediment microbiome, which represents the feed-
ing source for *A. cordatus*. This approach allowed us to
assess whether observed shifts in the gut microbiome
are host-specific or reflect changes occurring in the
environmental microbial inputs from ingested sedi-
ments. We hypothesise that *A. cordatus* would exhibit
high thermal sensitivity and that its gut microbiome
exhibits plasticity in response to seawater warming,
undergoing temperature-driven shifts in diversity and
composition that may contribute to host resilience
under thermal stress.

Results

Negligible impact of temperature on *A. cordatus* mortality

During the experiment, six of 60 *A. cordatus* individu-
als died, not necessarily at the highest temperature or
longest experiment duration: three at 6 °C (two on day
2 and one on day 12), one at 7.5 °C (on day 3), and two
at 10.5 °C (on days 4 and 7). Thus, only 3 of 60 indi-
viduals died under elevated temperature conditions. No
significant differences in sea urchin ellipsoidal volume
were detected among temperatures at any experiment
duration (Kruskal–Wallis, D2: $\chi^2=2.94$, $p=0.23$; D5:

$\chi^2 = 4.94, p = 0.09; \text{D13: } \chi^2 = 0.23, p = 0.89)$, indicating
that sea urchin size was comparable across experimen-
tal groups.

Sequencing output and pooling strategy

A total of 19,256,095 raw reads were obtained from 40 external sediment and 54 gut mucosa samples. After curation, the dataset comprised 6,730,721 sequences representing 4527 unique Amplicon Sequence Variants (ASVs). As no significant aquarium effect was detected on *A. cordatus* microbiome composition within each experimental condition (gut mucosa; F = 1.28, R² = 0.03, *p* = 0.163, sediment: F = 1.92, R² = 0.06, *p* = 0.065), samples from replicate aquaria were pooled per condition for downstream analyses.

Stable alpha-diversity in sediment and *A. cordatus*
microbiomes across conditions

Alpha-diversity indices in external sediment (total ASVs, Faith's phylogenetic diversity, Pielou's evenness, Chao1 richness and Simpson diversity) showed no statistically significant differences across temperatures and experiment durations. The only exception was observed on day 13 (D13), where diversity values (total ASVs, Chao1 and Faith's phylogenetic diversity) were significantly higher than at day 5 (D5) under 7.5 °C (Dunn test, *p* < 0.05) (Fig. 1, Additional File 1: Fig. S1). In contrast, gut mucosa samples showed no significant variation in alpha diversity across temperatures or experimental durations, regardless of the index considered (Fig. 1, Additional File 1: Fig. S1).

Letters above the boxplots indicate the significance of
the pairwise comparisons using Dunn test; conditions
with the same letter are not significantly different, while
conditions with different letter are significantly differ-
ent (*p* < 0.05). On the *x*-axis, D2, D5 and D13 respec-
tively indicate the day 2, 3 and 13 of sampling.

Relative standard deviation (RSD) analysis of alpha-
diversity indices showed no significant differences
across temperatures or durations in either sediment
or gut mucosa microbiomes (Dunn tests; *p* > 0.05)
(Additional File 1: Fig. S2). However, when grouped
by durations, post hoc Dunn tests indicated a signifi-
cant increase in gut mucosa alpha-diversity dispersion
between in situ and D13 groups (*p* = 0.023) and a trend
of increasing values between D2 and D13 (*p* = 0.053).
No significant temporal differences of alpha-diversity
were observed in sediment microbiomes (Dunn tests:
D0 vs. D2, *p* = 1.00; D0 vs. D5, *p* = 0.46; D0 vs. D13,
*p* = 1.00; D2 vs. D5, *p* = 1.00; D2 vs. D13, *p* = 1.00; D5 vs.
D13, *p* = 0.81) (Additional File 1: Fig. S1).
<figure><img src="image_3.png" /><figcaption>**Fig. 1** Alpha diversity, measured as total ASVs, Faith's phylogenetic diversity, and Pielou's evenness, in external sediment and *A. cordatus* gut mucosa under natural conditions ("in situ") and experimental conditions at different temperatures and times</figcaption></figure>

Shift in *A. cordatus* microbiome composition in response
to temperature and experiment duration

Experiment duration and, to a lesser extent, the tempera-
ture significantly influenced the gut mucosa microbiome
composition of *A. cordatus*, affecting presence-absence
(Jaccard distance; duration: *p*=0.022, temperature:
*p*=0.003), abundance (Bray–Curtis distance; duration:
*p*=0.026, temperature: *p*=0.005), and phylogenetic rela-
tionships (weighted Unifrac distance; duration: *p*=0.035,
temperature: *p*=0.002) (Fig. 2 and Additional File 1:
Table S1).

In contrast, experiment duration and temperature had
no significant effect on the sediment microbiome compo-
sition, with no detectable influence on presence-absence
(Jaccard distance; *p*=0.965 and *p*=0.146), abundance
(Bray–Curtis distance; *p*=0.927 and *p*=0.071), or phy-
logenetic relationships (weighted UniFrac distances;
*p*=0.937 and *p*=0.119) (Additional File 1: Table S1).
Exceptions included sporadic significant differences on

day 13 (“D13”) and trends approaching significance on
day 5 (“Day 5”) between 7.5 and 10.5 °C, and between D5
and D13 at 7.5 °C (Additional File 1: Table S2), indicat-
ing that sediment and gut mucosa microbiome dynamics
are largely decoupled. For both microbiomes, the strong-
est differences were between in situ and experimental
conditions (Additional File 1: Table S2). Despite overall
effect of temperature and experiment duration on the gut
mucosa microbiome detected by general PERMANOVA,
few pairwise comparisons among experimental condi-
tions were significant (Additional File 1: Table S2). Focus-
ing on the core common to each experimental condition
reduced the inter-replicate variability, revealing stronger
effect of temperature (R²=0.102, *p*<0.011) and dura-
tion (R²=0.120, *p*<0.001) on Bray–Curtis distances
of gut mucosa microbiomes, while the interaction of
both factors was not significant (R²=0.097, *p*=0.061).
In sediment core microbiomes, only temperature was
approaching significance (R²=0.131, *p*=0.059).
<figure><img src="image_4.png" /><figcaption>**Fig. 2** Non-metric multidimensional scaling (NMDS) plots based on Bray–Curtis distances computed from the Hellinger-transformed ASV abundance matrix of external sediment and *A. cordatus* gut mucosa. The NMDS solution had a stress value of 0.01. The shapes and colours of symbols indicate the type of sample (external sediment and gut mucosa) and the experimental condition (temperature and experiment duration), respectively. Unfilled symbols represent samples from the other temperature and experiment duration conditions</figcaption></figure>

## Increased microbiome dissimilarity in *A. cordatus* due to experiment duration

Neither temperature nor the interaction between temperature and experiment duration significantly influenced microbiome dispersion in the gut mucosa of *A. cordatus* (*p* > 0.05, Additional File 1: Table S3), as assessed using β-diversity dispersion (Betadisper). However, the gut microbiome dispersion significantly increased with experiment duration (*p* = 0.001, Additional File 1: Table S3), at all tested temperatures, including the control temperature. In contrast, no significant effects of temperature or experiment duration were detected on microbiome dispersion in the external sediment (Additional File 1: Table S3).

The fixed baseline analysis across experiment durations revealed a significant accumulation of *A. cordatus* gut microbiome dissimilarity when comparing in situ and day 13 (“D0–D13”) versus in situ and day 2 (“D0–D2”) at all temperatures, while sediment microbiomes remained stable (Fig. 3). The fixed baseline analysis across temperatures showed that gut microbiomes harboured at least one significantly different pairwise comparison between two of the three temperatures (Additional File 1: Fig. S3). In contrast, sediment microbiomes dissimilarity remained homogeneous across temperatures in “D0–D2” and “D0–D5,” but dissimilarity significantly increased between 6 and 7.5 °C and between 7.5 and 10.5 °C.

## Contrasting core microbiome dynamics in external sediment vs. gut mucosa

To minimize inter-replicate variability, we focused on the core microbiomes of external sediment (Fig. 4a and c) and gut mucosa (Fig. 4b and d) for each temperature-duration combination, defined as taxa consistently present across samples. Core microbiomes highlight stable components of these communities, while functional implications are not assessed here. In gut mucosa, core abundance and richness decreased across temperatures (Fig. 4b), from levels close to in situ conditions down to 30%. At 6 and 7.5 °C, reductions in core abundance were observed on Day 13, whereas at 10.5 °C, a more immediate impact was observed on Day 5, followed by partial recovery on Day 13.

Within the 10 most abundant core gut taxa, Spirochaeta 2 increased over time at all temperatures, whereas Proteobacteria genera (e.g. *Amaricoccus*, *Enhydrobacter* and *Halioglobus*) decreased. Notably, on Day 13 at 10.5 °C, new taxa such as *Desulfatiglans*, *Persicirhabdus* and *Elusimicrobium* emerged, marking a shift in the composition of the gut core (Fig. 4d). In contrast, sediment microbiome replicates converged over time, with core abundance and richness increasing over time at all temperatures, rising up to 60% and surpassing in situ levels (Fig. 4a). Taxonomic shifts included increased abundances of *Lactobacillus*, *Marinilabiliaceae* and *Spirochaeta* at 10.5 °C on Day 13, alongside the loss of
<figure><img src="image_5.png" /><figcaption>**Fig. 3** Fixed baseline analysis: Accumulated divergence of microbiome communities, estimated by the pairwise Bray–Curtis dissimilarity between each experimental duration (D2, D5 or D13) and the in situ samples (D0). The comparison values are calculated independently for each temperature condition. Results for external sediment and *A. cordatus* gut mucosa are shown in the left and right panels, respectively. The asterisks correspond to the significance levels (***; *p* < 0.001, **; *p* < 0.01, *; *p* < 0.05) assessed through Dunn's tests. *NS.* no significant difference (*p* > 0.05)</figcaption></figure>

*Microtrichaceae* from the core (Fig. 4c); additional shifts are detailed in Additional File 1: Text 1.

**Experiment duration, rather than increased temperature, primarily drives divergence of *A. cordatus* gut microbiome**

To assess the ecological processes shaping microbial community assembly, we examined the standardized effect size of mean nearest taxon distances (ses.MNTD) in both gut and sediment microbiomes. In the gut microbiome, a shift towards relatively more divergent

assembly under prolonged experimentation duration was observed, with ses.MNTD values significantly higher at Day 13 than Day 2 across all temperatures (Fig. 5). While no significant differences were detected among temperatures at a given time point, a trend of increasing ses.MNTD with temperature was observed, with values generally closer to or above 0 at 7.5 and 10.5 °C compared to 6.0 °C. In contrast, ses.MNTD values in sediment microbiomes remained relatively low compared to the gut microbiome, with minor variations in response across temperatures.
<figure><img src="image_6.png" /><figcaption>**Fig. 4** Core microbiome of each experimental condition for external sediment and gut mucosa. a, b Core microbiome abundance (ASVs common to all replicates at each temperature-day) for external sediment and gut mucosa, with numbers above bars indicating core ASVs. Relative abundance is based on total abundance for each condition. c, d Taxonomic composition at the genus level for the core microbiome, showing the 10 most abundant taxa per condition for sediment and gut mucosa. Relative abundance is based on core abundance. Colours represent taxonomic affiliation, with consistent colours for shared genera between external sediment and gut mucosa</figcaption></figure>

Temperature increases are mostly associated
with depletion of bacterial ASVs in the gut microbiome
of *A. cordatus*

To detect bacterial shifts at a finer taxonomic scale, and better identify temperature-related responses that might be masked at the community level, we used DESeq2 to compare ASV relative abundances at 7.5 and 10.5 °C against the control (6 °C) at each time point. Across all temperatures and experiment durations, most gut microbiome ASVs (71.3–99.1%) showed no significant changes in their relative abundances (Additional File 1: Table S4). In the gut microbiome, ASV depletions were more frequent than enrichments, with 133 ASVs depleted and only 33 enriched in treatments compared to the control. The sharpest ASV depletion occurred at 7.5 °C on Day 5, where 102 ASVs were significantly depleted compared with the control. These ASVs accounted for 64.2% of the total relative abundance in the control, but their cumulative abundance dropped to 0.24% under the 7.5 °C treatment. More limited depletion occurred on Day 2 (8 ASVs; 13.9% in control vs. 0.02% in treatment) and on Day 13 (4 ASVs; 1.2% vs. 0.01%). At 10.5 °C, depletion was comparatively weaker, with 7 ASVs on Day 2 (5.0% vs. 0.00%), 10 ASVs on Day 5 (3.7% vs. 0.00%), and only 2 ASVs on

Day 13 (0.5% vs. 0.00%) (Additional File 1: Table S4). In total, more ASVs were depleted at 7.5 °C (n=114) than at 10.5 °C (n=19). Most of the depleted ASVs on Day 5 at both 7.5 and 10.5 °C belonged to sulphate-reducing Desulfobacterota (e.g. *Desulfobacula*, *Desulfocarbo*, *Desulfoconvexum*, *Desulfovibrio*) (Fig. 6). In contrast, enrichment events were observed in both 7.5 and 10.5 °C treatments (Additional File 1: Table S4). These enrichments were particularly important on Day 5, involving five ASVs at 7.5 °C and two ASVs at 10.5 °C, which initially represented 0.2 and 0.08% of the gut microbiome in the control condition, and reached relative abundances of 19.2 and 11.9% of the total community in the 7.5 and 10.5 °C conditions, respectively. The enriched ASVs primarily belonged to Gammaproteobacteria, especially Pseudomonadales (e.g. *Enhydrobacter*, *Pseudomonas*) and *Enterobacteriaceae*, in both treatment temperatures, with an additional enrichment of Firmicutes (e.g. *Exiguobacterium*, *Hungateiclostridia*, *Enterococcus*) at 7.5 °C (Fig. 6).

Some genera exhibited contrasting temperature
responses at the ASV level. Within *Spirochaeta* 2—pre-
viously identified as a potential keystone taxon in the
*Abatus* microbiome—three ASVs were depleted at 7.5 °C
<figure><img src="image_7.png" /><figcaption>**Fig. 5** Phylogenetic structure of external sediment (upper panel) and *A. cordatus* gut mucosa (lower panel) microbiomes under natural conditions ("in situ"), and across different temperatures and experiment durations, based on standardized effect sizes of mean nearest taxon distance (ses. MNTD). Letters above the boxplots indicate the significance of the pairwise comparisons using the Dunn test (*p* < 0.05). Negative ses.MNTD values indicate phylogenetic clustering, while positive values reflect overdispersion</figcaption></figure>

across all time points, while three others were enriched at 10.5 °C (Fig. 6). This contrasts with the overall increase of *Spirochaeta* 2 in the core microbiome on Day 13 across all temperatures (Fig. 4).

Few altered ASVs were shared between sediment and gut microbiomes, indicating distinct responses to temperature and experiment duration (Additional File 1: Fig. S4). For example, two ASVs depleted in sediment at 7.5 °C on Day 2 were enriched in the gut, while one ASV was consistently enriched in both microbiomes at 10.5 °C on Day 2.

## Discussion

Climate change, and particularly the pronounced seawater warming observed in recent decades, poses a major threat to the—predominantly endemic—wildlife of the SO through [45–47]. Microbiomes are increasingly recognized as key mediators of host adaptation, contributing to thermal tolerance and resilience [48, 49]. Yet, the effects of rising temperatures on the microbiomes of marine invertebrate in this region

remain poorly understood [50]. Our study indicates that *A. cordatus* can tolerate a +5 °C temperature increase over 2 weeks, as suggested by low mortality rates (5% at 7.5 °C and 10% at 10.5 °C). While its upper thermal limit remains to be determined, our results challenge previous observations and predictions that linked *A. cordatus* survival strictly to a narrow seafloor temperature range of 3–4 °C [12, 13, 15]. Although sea urchins were handled carefully during sampling, transport and experimental setup to minimize stress, we cannot exclude the possibility that minor impacts caused undetected shell damage, possibly explaining the observed mortality independent of experimental conditions. Our findings suggest that, under the conditions tested in this study, short- to mid-term seawater warming in the Kerguelen Plateau may not constitute an immediate threat to *A. cordatus* populations. However, mortality alone is insufficient to fully assess species tolerance to warming [51], and additional host physiological, ecological and environmental responses (e.g. reproduction, growth, behaviour, and stress
<figure><img src="image_8.png" /><figcaption>**Fig. 6** Most significantly enriched or depleted ASVs in *Abatus cordatus* gut microbiome at treatment temperatures (7.5 or 10.5 °C) compared to the control temperature (6 °C) at different times during the experiment. Only ASVs with −log10 *p*-value greater than 5 are shown. The colour gradient represents log2 fold change between treatment and control, while the colours of the tree tips indicate the taxonomic affiliation of the ASVs. The same colours are used for common taxa in both plots to facilitate comparisons</figcaption></figure>

physiology) warrant further investigation [52–54]. For instance, rising temperatures can alter the timing and magnitude of phytoplankton blooms, disrupting organic matter deposition on the seafloor [55], which is critical for deposit feeders like *A. cordatus* [56, 57]. Indeed, recent evidence suggests that food resources

may be a more decisive factor in determining *A. cordatus* population densities than temperature [44].

Despite having limited effects on the organism's mortality rate, increasing temperature impacted the structure and composition of gut microbiomes, with potential consequences for host fitness. These effects
may be either beneficial (e.g. promoting microbial taxa that enhance thermal tolerance or metabolic efficiency) or detrimental (e.g. dysbiosis, impairing digestion, immunity or reproductive performance) [58]. At the community level, our results showed that the gut microbiomes of *A. cordatus* were less stable than those of the surrounding sediment during the experiment, particularly in terms of composition, although no significant loss of alpha-diversity was observed. Other indicators of gut microbiome plasticity included a higher phylogenetic divergence in bacterial community assembly and a lower abundance of the core microbiome community, compared to sediment. Albeit low, temperature played a statistically significant role in altering the gut microbiome composition at the whole community level. While additional evidence would be required for further confirmation, these findings suggest that the low mortality of *A. cordatus* may be supported, at least in part, by microbiome plasticity, allowing some adaptive response to thermal stress rather than relying on a highly stable microbiome. The sensitivity of the *A. cordatus* gut microbiome to both temperature fluctuations and experiment duration contrasts with a previous experiment involving the tropical sea urchin *Lytechinus variegatus*, where gut microbial community composition remained unchanged in response to increased seawater temperature [41]. This discrepancy suggests that sub-Antarctic species may exhibit greater sensitivity to rising seawater temperatures, due to their adaptation to cold and stable environments [59, 60]. Although daily variations in gut microbiome composition have been observed in some benthic organisms [61], such dynamics remain unexplored in *A. cordatus*. In our study, all temperature treatments shared the same photoperiod conditions, minimizing diurnal influences. While seasonal effects have been demonstrated in other sea urchin species microbiome [39], our short-term experiment (2 weeks) and simultaneous setup of all treatments likely excludes any seasonal effects. Nevertheless, the temporal dynamics of the gut microbiome in *A. cordatus* remain to be investigated. Conversely, the enhanced stability of sediment microbiome in response to temperature increases is intriguing and contrasts with previous reports in coastal sediments [62]. External microbiomes, like those in sediment, are typically more influenced by environmental factors than host-associated microbiomes [63]. This stability raises the hypothesis that sediment microbiomes in sub-Antarctic environments might possess inherent resilience to thermal variations, which could be due to the dominance of generalist taxa capable of thriving across a wide range of environmental fluctuations. Accordingly, a recent study revealed a significantly

higher proportion of generalists in Antarctic and sub-Antarctic sediment microbiomes compared to *Abatus* gut mucosa microbiomes [64].

The limited temperature-driven alterations in *A. cordatus* microbiome—especially the absence of a common shift at the community level—could be explained first by the high inter-individual variability, masking community-level responses. In this case, the majority of the gut community would diverge among individuals over time, while only some minor taxa would respond consistently to temperature increase in all individuals. Consistently, when focusing on core microbiomes per experimental condition, this variability was mitigated, enhancing the detection of temperature compositional effects on gut mucosa microbiome. Second, the weak temperature influence may reflect the overwhelming impact of transitioning from wild to captive conditions, which drastically alters diversity and destabilizes host-associated microbiomes, including those of marine invertebrates, through handling, transport and confinement-related environmental changes [65–67]. This strong initial perturbation may have obscured the direct effects of temperature on *A. cordatus* gut microbiome composition. It is also worth noting that the seawater supplied to the aquaria was collected at 7 m depth, whereas *A. cordatus* individuals were sampled in shallow waters (0–3 m) at a different site. Seawater microbiomes can vary with both depth and location [68], which may partly explain the initial shift between in situ gut microbiome composition and that observed at D2, as well as the progressive divergence observed along the experiment. Third, the experimentation duration may have been too short to detect community-scale shifts. Although studies on warming effects in sea urchins are limited, microbiome responses in other marine invertebrates have been observed over periods ranging from 3 days in mussels [69] to 15 days in Antarctic sponges [50], similar to our study's timeframe. Lastly, elevated temperature may have affected the host immune system, potentially altering its capacity to regulate the microbiome and leading to increased temporal variability and more phylogenetically divergent gut microbial communities throughout the experiment [70–72]. This variability could partly explain why temperature had a weaker effect on microbiome composition compared to the duration of the experiment. While a significant effect of experiment duration on *A. cordatus* gut microbiome composition was observed, this pattern is unlikely to result solely from altered microbial acquisition due to captivity. *Abatus* individuals maintained natural feeding behaviour throughout the experiment, and the sediment microbiome became increasingly stable over time, in contrast to the more dynamic and divergent trajectories observed in the gut. Furthermore, temperature-altered
ASVs were inconsistent between gut and sediment samples. Taken together, these results suggest that internal, host-related processes (such as physiological acclimatization to temperature or modulation of immune responses) rather than shifts in the surrounding sediment microbiome, are the primary drivers of the observed changes in gut microbiome composition. Ultimately, given the absence of visible host impairment, the observed compositional shifts likely reflect gut microbiome plasticity, with functionally redundant taxa potentially compensating for community taxonomic changes to help host-associated function under thermal stress [73].

Beyond community-level changes, subtle but consistent temperature-driven shifts in bacterial ASVs were detected within the gut microbiomes of *A. cordatus*. Although the physiological consequences for the host remain to be fully elucidated, these compositional adjustments suggest potential functional reorganization of the microbiome that could mitigate thermal stress [74]. Sulphur metabolism plays a key role in various sea urchin species [18, 40, 75]. Here, sulphate-reducing bacteria (SRB), including *Desulfobacula*, *Desulfovibrio*, *Desulfo-carbo* and *Desulfoconvexum*, were consistently depleted at higher temperatures. *Desulfobacula* was identified as a potential keystone taxon in the gut of *Abatus agasizii*, a congeneric Antarctic species of *Abatus cordatus* [18], while *Desulfocarbo* and *Desulfoconvexum* were previously reported as specific to the gut of *Brisaster townsendi*, another deposit-feeding sea urchin [76]. SRB's abundance decline with increasing temperatures aligns with previous findings in cold environments where SRB psychrophilic members such as *Desulfoconvexum* and *Desulfotalea* have been isolated [77–79]. SRB are key players in sulphur cycling of anoxic-to-microoxic transitions zones [80], reducing sulphate and other sulphur compounds, such as sulphated polysaccharides from marine algae debris in the *Abatus* diet, into hydrogen sulphide (H₂S) [81]. Moreover, SRB like *Desulfobacula* also contribute to sulphide detoxification by precipitating sulphides with iron, thereby preventing the harmful H₂S accumulation in the gut [82, 83]. Additionally, some SRB oxidize fermentation products from other microbial community members into acetate, a short-chain fatty acid (SCFA) that is particularly abundant in the gut of the deposit-feeding sea urchin *Echinocardium cordatum*, where it supports host metabolism and nutrition [82–84]. Consistent with findings in *B. townsendi* [76], both complete and incomplete oxidizers coexist in *A. cordatus* gut, with *Desulfobacula* and *Desulfoconvexum* as potential partial oxidizers [78, 85] and *Desulfocarbo* linked to complete oxidation [86]. Furthermore, while typically anaerobic, some SRB can tolerate low levels of oxygen and perform aerobic respiration at high rates [83, 87]. By

consuming residual oxygen, these SRB help maintain an anaerobic gut environment, preventing the oxidation of acetate and supporting host nutrition. While SRB depletion has been linked to disease in other sea urchins [88, 89], and with reduced detoxification and nutrient acquisition under thermal stress in vertebrate ectotherms [90], the high survival rate of *A. cordatus* in our study suggests resilience, potentially supported by compensatory enrichment of other ASVs.

Fermentative bacteria, including facultative and obligate anaerobes such as *Enterococcus* [91], *Hun gateclostridia* [92] and *Exiguobacterium* [93], comprised a substantial fraction of enriched ASVs across both temperature treatments, reflecting a possible metabolic shift in *A. cordatus* gut in response to thermal stress-induced alterations. In sediment-burrowing sea urchins, fermenters degrade polysaccharides from detrital particles into SCFAs, which can supply energy to host epithelial cells [82, 84, 94]. Although the contribution of fermentation to *A. cordatus* metabolism is unknown, estimates in the regular sea urchin species *Paracentrotus lividus* suggest that gut bacterial fermentation may provide up to 10% of host metabolic energy [95]. The concurrent enrichment of fermenters and depletion of SRB may reflect competition for the substrate, or reduced oxygen solubility at higher temperatures [96], potentially favouring fermenters, which also tolerate higher temperature than SRB, as observed in Arctic marine sediments [97]. While this metabolic shift is less thermodynamically efficient [98], it could mitigate toxic H₂S accumulation, potentially reducing the host's detoxification requirements. Similar declines in metabolic activity has been observed in the sediment-burrowing sea urchin *Brissopsis lyrifera* under oxygen depletion [99]. Thus, the taxonomic shift from SRB- to fermentation-based SCFA production may represent an energy trade-off that helps maintain digestive function under thermal stress.

Other altered taxa exhibited complex patterns, notably *Spirochaeta*, previously identified as a potential key-stone genus in *Abatus* gut microbiomes [18, 100]. While genus-level abundance increased along the experiment, temperature-specific responses were evident at the ASV level, with some ASVs being depleted at 7.5 °C and others enriched at 10.5 °C. These shifts suggest that different *Spirochaeta* strains may fulfil distinct ecological roles under thermal stress. Variations in *Spirochaeta* strains with differing lifestyles (attached or free floating) and SCFA production pathways have been reported in other schizasterid sea urchins [76]. Maintaining a diverse set of symbionts, whose abundance and composition adapt under suboptimal conditions, can support functional redundancy and persistence of essential host functions [101].
The directionality of the interaction between gut
microbiome and *A. cordatus* remains to be elucidated.
Microbiome shifts may result from temperature-induced
selection pressures or indirectly through host physiologi-
cal responses to warming, as observed in other marine
invertebrates [102, 103]. Similarly, host responses them-
selves may be driven by temperature itself or mediated
by microbiota-mediated effects, highlighting a com-
plex, bidirectional interplay between the host and its
microbiome. This dynamic relationship suggests that
compositional plasticity of the gut microbiome could
contribute to host phenotypic adaptability under envi-
ronmental stress [104], potentially accelerating evolution-
ary responses by allowing selection to act on both direct
and microbiota-mediated traits [105]. In our experiment,
several observations support this hypothesis. The low
host mortality, the absence of gut microbiome diversity
loss, and the high gut microbiome variability collectively
suggest that temperature-induced taxonomic shifts may
result from the horizontal acquisition of new bacterial
taxa and/or the expansion of rare, pre-existing minor
taxa, facilitating *A. cordatus* acclimatization to thermal
stress. Furthermore, high microbiome variability among
individuals may itself represent an adaptive trait, enhanc-
ing population-level phenotypic plasticity and potentially
improving population fitness under environmental per-
turbations [101]. This trait could be particularly relevant
for *A. cordatus*, whose limited dispersal capacity restricts
its ability to escape shifting environmental conditions.

Conclusions

In summary, this is the first study to demonstrate the
ability of *Abatus cordatus* to cope with short-term sea-
water warming at near future temperatures, along with
the dynamic restructuring of its gut microbiome. Our
findings support the idea that microbiome plasticity may
serve as a key mechanism supporting the resilience of
benthic invertebrates facing rapid environmental change,
particularly in ecologically vulnerable sub-Antarctic eco-
systems. While the compositional shifts observed here
may reflect adaptive responses, the long-term ecologi-
cal and evolutionary implications remain to be fully elu-
cidated. Given the correlative nature of our approach,
future research should incorporate more comprehen-
sive assessments of host physiological and molecular
responses to thermal stress, through transcriptomic or
metabolomic profiling, to fully understand the func-
tional outcomes of temperature-induced microbiome
changes. Experimental approaches targeting microbiome
manipulation, including antibiotic treatments, micro-
biota transplants or substrate-tracing experiments (e.g.
labelled sulphate or acetate to track microbial consump-
tion and potential transfer to the host) will be needed to

establish causal links between microbiome dynamics and
host thermal tolerance. Understanding the specific roles
of thermally responsive microbial taxa will be essential to
predict the adaptive capacity of polar invertebrates under
climate change.

Methods

Sample collection

*Abatus cordatus* individuals were hand-collected from sediment by scuba diving at Île Haute, Kerguelen Islands (seawater temperature 7.0 °C, 2.0-m depth, 49° 23′ 14.856″ S, 69° 56′ 28.211″ E) in December 2022. Surfi- cial coastal sediment from the immediate vicinity of the *Abatus* population was also collected. Both the sea urchins and sediments were transferred to the “Port- aux-Français” French research station in a 50-L sealed drum filled with in situ seawater, with boat transport lasting <1 h. As baseline controls, gut mucosa samples from five sea urchins and five sediment samples from the sampling site were processed immediately upon arrival, to represent in situ conditions (hereafter “T0”; Additional File 1: Table S5).

Experimental design

Six 30-L aquaria (45 cm height×30 cm width×30 cm
length) were set up, each containing a 10-cm layer of sed-
iment (3–3.5 L) and housing 20 sea urchins randomly dis-
tributed after careful inspection; only apparently healthy
individuals were included in the experiment. Each aquar-
ium was filled with 20 L of seawater, continuously sup-
plied at a rate of 1.5 L min⁻¹ via a pump drawing coarsely
filtered seawater (Ø 5 mm) from Port-au-Français Bay at
a depth of 7 m. Seawater was aerated using airstones con-
nected to a 4000 L h⁻¹ Aquamedic aquarium air pump.
The experimental design included two control aquaria
(6.0 °C) and four temperature-increased aquaria (two at
7.5 °C and two at 10.5 °C), resulting in two independent
replicates per temperature condition. The control tem-
perature was maintained with three Teco TK500 chill-
ers and a Blue Marine BM Chiller 400 arranged in series,
while the increased temperature treatments were con-
trolled with Inkbird ITC-306 T and AquaMedic 300 W
TH-300 heaters. The control temperature reflects the
average summer seawater temperature (6.2 °C) recorded
at Île Haute during the experiment year. The 7.5 °C tem-
perature treatment represents the upper quartile temper-
ature from the hottest month (March) over 2012–2023,
while the 10.5 °C treatment corresponds to the highest
recorded temperature during the same period (Addi-
tional File 1: Fig. S5). Sea urchins were acclimated at
6.0 °C under natural photoperiod conditions for 24 h,
after which the temperature was increased by 1.5 °C per
day to reach the target conditions, with the experiment
duration set to 13 days due to climatic and logistical fac-
tors (i.e. <20 days between ship rotations). Sea urchin
mortality was monitored through observations of spine
movement absence, spine loss, and tissue necrosis lead-
ing to an exposed test. Dead individuals were removed
from the tanks along the experiment.

Sample preparation and genomic DNA extraction

Sea urchins and sediment were collected from all aquaria
after 2, 5 and 13 days of the experiment. For each tem-
perature treatment, 5–7 sea urchins were randomly
selected, aiming for an even distribution between the two
replicate aquaria (typically 2–4 individuals per aquar-
ium). Sea urchins were measured (Length: 2.58 ± 0.08 cm,
Width: 2.36 ± 0.07 cm, Height: 1.32 ± 0.04 cm), and their
gut mucosa was aseptically sampled for microbiome
analysis, following previously described procedures [18]
(Additional File 1: Table S5, Additional File 2: Table S6).
Simultaneously, 3–5 sediment samples (350 mg each)
were collected from each aquarium, avoiding *Abatus*
individuals to prevent disturbance. The number of sam-
pling points varied depending on the spatial distribution
of individuals, with fewer points available when indi-
viduals were more dispersed. All samples were frozen
at –20 °C immediately after collection and stored until
DNA extraction.

Prior to DNA extraction, samples were homogenized
using a FastPrep-24® instrument (MP Biomedicals,
USA) for three cycles of 15 s at 4 m s⁻¹ with 2.5-min
rests between cycles. Genomic DNA was subsequently
extracted from thawed gut mucosa and sediment samples
using the DNeasy PowerSoil Pro Kit (Qiagen, CA, USA),
following the manufacturer's protocol. Extractions were
performed under a sterile laminar flow hood using newly
opened, sealed reagents.

Metabarcoding and sequence analysis

The metabarcoding approach targeted the V3–V4 region
of the 16S rRNA gene using 341F/806R primers [106].
Amplification, library preparation and sequencing on the
Illumina NovaSeq PE250 platform were performed by
Novogene (Beijing, China), following Schwob et al. [107].
As part of Novogene's standard procedure, negative PCR
controls were included to monitor potential contamina-
tion during amplification. FASTQ files were processed
in R using DADA2 (v 1.32.0) [108]. Briefly, raw forward
and reverse reads were quality-filtered and trimmed
using the standard parameters (maxN = 0, maxEE = 2,
truncQ = 2, rm.phix = TRUE). Chimaeras were removed
using the *removeBimeraDenovo* function with the *con-
sensus* method. Taxonomic assignments of the ampli-
con sequence variants (ASVs) were made with SILVA
v138.1 database. The contingency table of 16S rRNA

ASVs and samples metadata (Additional File 2: Table S6 and Table S7) were imported in R and processed with the PHYLOSEQ package (v 1.48.0) [109]. ASVs assigned to Archaea, Eukarya, chloroplasts, or mitochondria were removed. To reduce the influence of spurious or contaminant sequences, ASVs occurring in fewer than two samples or represented by fewer than 10 total reads across all samples were filtered out. The aligned ASV sequences were used to reconstruct a phylogenetic tree following the methodology previously described [110]. The sediment and gut mucosa ASV tables were rarefied to 35,084 and 16,874 sequences per sample, respectively.

Statistical analysis

To assess potential aquarium-specific effects, a PER-
MANOVA was performed separately on sediment and
gut mucosa samples, using the strata option to account
for the nesting of samples within each experimental con-
dition (i.e. temperature and sampling day). Ellipsoidal
volume (V = 4/3 × π × Length/2 × Width/2 × Height/2)
was calculated as a proxy for overall sea urchin body
size, and compared across temperatures at each experi-
ment durations (i.e. 2, 5 and 13 days) to evaluate poten-
tial confounding effect (Additional File 2: Table S6).
Alpha-diversity indices (total ASVs, Faith's phylogenetic
diversity, Pielou's evenness, Chao1 richness and Simpson
diversity) were estimated from rarefied datasets using
PHYLOSEQ and PICANTE packages [109, 111]. Outliers
identified using the interquartile range (IQR) method
were excluded from alpha-diversity analysis. Relative
standard deviation (RSD) was calculated in R using a
custom script. Differences across experimental condi-
tions were tested using Dunn's post hoc tests with Holm
correction.

Beta-diversity metrics (Jaccard, Bray-Curtis and
weighted UniFrac indices) were calculated from unrar-
efied datasets. The effects of temperature, experiment
duration and their interaction on bacterial composi-
tion in sediment and gut mucosa were assessed through
PERMANOVA using VEGAN package [112]. Pairwise
PermanovaG analyses integrating the three beta-diver-
sity metrics into a single omnibus test were performed
to identify significant differences among groups [110].
These analyses were carried out either on the global
community or on core subset communities common to
all the replicates of a given condition (i.e. a given com-
bination of temperature and time) to reduce individual
variability. Community composition in sediment and gut
mucosa across experimental conditions was visualized
using non-metric multidimensional scaling (NMDS) on
Bray-Curtis distances computed from the rarefied ASV
tables, applying the formula *temperature* + *duration*. The
homogeneity of beta-diversity dispersion (Bray-Curtis
values) among experimental conditions was assessed using the *betadisper* function, followed by ANOVA tests. Bray-Curtis pairwise dissimilarity means were compared among experimental conditions using Dunn's tests. A fixed baseline analysis was conducted to assess variability accumulation over time by comparing the mean dissimilarity in in situ samples (D0) to later time points (D2, D5 or D13), and the differences were tested using Wilcoxon tests.

Core microbiomes were determined separately for each gut mucosa and sediment under each experimental condition using a 70% prevalence threshold with no minimum abundance criterion. The 10 most abundant ASVs within each core were identified, and their relative abundances were calculated for each condition.

Phylogenetic relatedness in external sediment and gut mucosa microbiomes was assessed using the standardized effect size of phylogenetic community structure (ses. MNTD) in the R package *PICANTE* [111]. This metric compares the differences between observed communities and null communities generated with 999 randomizations, standardized by the standard deviation of phylogenetic distances. Negative values indicate that species are more phylogenetically related than expected by chance (i.e. convergence), while positive values suggest an overdispersion (i.e. divergence), with greater absolute values reflecting stronger deterministic processes.

Differential abundance analysis for gut mucosa and sediment microbiomes was performed independently using DESeq2 [113]. ASVs were classified as enriched (*p* < 0.055 and log2FC > 0.5), depleted (*p* < 0.055 and log2FC < -0.5) or unchanged ASVs (*p* > 0.055 and -0.5 < log2FC < 0.5) by comparing each treatment temperature (7.5 °C; 10.5 °C) to the control (6.0 °C) at a given time point (Day 2, 5 or 13).

**Abbreviations**

ASVs Amplicon sequence variants

IQR Interquartile range

RSD Relative standard deviation

ses.MNTD Standardized effect size of phylogenetic community structure

SCFA Short-chain fatty acid

SRBs Sulphate reducing bacteria

**Supplementary Information**

The online version contains supplementary material available at https://doi.org/10.1186/s12915-025-02448-9.

Additional File 1: Fig. S1. Alpha diversity, measured as Chao1 and Simpson indices, in external sediment and *A. cordatus* gut mucosa and experimental conditions at different temperatures and times. Letters above the boxplots indicate the significance of the pairwise comparisons using Dunn test; conditions with the same letter are not significantly different, while conditions with different letter are significantly different. On the x-axis, D2, D5 and D13 respectively indicate the day 2, 3 and 13 of sampling. Fig. S2. Relative Standard Deviation of alpha-diversity indices in microbiomes of external sediment and gut mucosa under natural and experimental conditions, across varying temperatures and time points

of sampling. *p*; *p*-values of post-hoc Dunn tests to assess the difference among time conditions. Only significant *p*-values are shown. Table S1. Influence of temperature and time on microbiome composition of external sediment and *A. cordatus* gut mucosa evaluated by permutational multivariate analysis of variance using multiple distance matrices. The tested datasets excluded the in situ samples. The distinct distance matrices were combined in an omnibus test, with the reported *p*-values representing the minimum *p*-value from individual distance matrices. Bold *p*-values indicate statistical significance, while italicized *p*-values indicate a tendency or approaching significance. *;* interaction between temperature and duration factors. Table S2. Influence of treatment temperature and duration on *A. cordatus* gut microbiome and surrounding sediment evaluated by pairwise permutational multivariate analysis of variance using multiple distance matrices. Global *p*-values are reported, testing the null hypothesis that none of the explanatory variables account for variation in microbiome composition. Bold *p*-values indicate statistical significance, while italicized *p*-values indicate a tendency or approaching significance. Table S3. Influence of temperature and experiment duration on microbiome beta-diversity dispersion in sediment and gut mucosa analysed using Betadisper. The 'condition' factor refers to the experimental combination of a given temperature at a given treatment duration. *p*-values in bold are considered as significant. The datasets tested excluded the in situ samples. Fig. S3. Moving frame analysis of Bray-Curtis pairwise dissimilarity distances among external sediment and gut mucosa samples within exposure duration across temperature conditions. 'D0' corresponds to the in situ samples. Colours indicate the temperature treatment. *NS*; no significant comparison. The asterisks correspond to the significance level. Text S1. On day 2, all temperature conditions exhibited a reduction in both the number and cumulative relative abundance of core ASVs compared to in situ conditions, likely due to alterations of the sediment structure during sampling and transportation, which increased the spatial heterogeneity naturally found in the environment. This loss was accompanied by taxonomical shifts within the 10 most abundant core taxa. The most pronounced shift occurred between in situ condition and 6°C on day 2, where the core microbiome was dominated by *Roseomonas*, *Desulfatiglans*, and *Sulforovum*. *Enhydrobacter*, which constituted over 10% of the in situ core sediment, was absent from the 10 most abundant taxa in the core of the other experimental conditions. Table S4. Number and relative abundance of depleted, enriched, and non-significant ASVs identified in the comparisons between treatment and control conditions in *Abatus* gut microbiome at different times of the experiment. The relative abundance of these ASVs is indicated in both the control and treatment conditions for each time. Fig. S4. Shared enriched and depleted ASVs between sediment and gut microbiomes across experimental conditions. The colour gradient represents the number of shared ASVs. The tile corresponding to the single ASV that was simultaneously enriched in both sediment and gut microbiomes at the same temperature and time point is highlighted with black borders. Table S5. Experimental design outlining the 20 conditions tested and the samples' nomenclature. The number of replicates within each experimental condition is indicated in parentheses. Fig. S5. Annual variation in mean seawater temperature at *A. cordatus* sampling site at a depth of five meters. from 2012 to 2023. The curve colours represent individual years and monthly boxplots summarize data across the twelve-year period. Table S6. Samples metadata.

Additional file 2: Table S6. Samples metadata. Table S7. Contingency table of 16S rRNA ASVs.

**Acknowledgements**

The authors thank Dr. Jean-Pierre Féral for his assistance in obtaining the sampling authorization. Powered@NLHPC: This research was partially supported by the supercomputing infrastructure of the NLHPC (CCSS210001).

**Authors' contributions**

G.S.: Conceptualization, Methodology, Formal Analysis, Investigation, Visualization, Data Curation, Writing – Original Draft, Writing – Review & Editing. M.D.: Formal Analysis, Visualization, Writing – Original Draft, Writing – Review & Editing. S.M. & C.M.: Methodology, Investigation. T.S.: Resources, Writing – Review & Editing, Project Administration, Funding Acquisition. J.O. & E.P.
Conceptualization, Methodology, Resources, Writing - Review & Editing. L.C.: Conceptualization, Writing - Review & Editing, Project Administration, Funding Acquisition. All authors read and approved the final manuscript.

## Funding

Funding for this work was provided by the Regular FONDECYT (grant #1211672) and the Millennium Science Initiative Program (Millennium Institute BASE, grant #ICN2021_002) from the Chilean National Agency of Research and Innovation (ANID). Field access facilities to the Kerguelen Islands were supported by the French Polar Institute-IPEV (program No. 1044 PROTEKER).

## Data availability

All NextGen raw sequence data files are deposited in the NCBI Sequence Read Archive for public access (Accession no. PRJNA1164138).

## Declarations

### Ethics approval and consent to participate

Sampling and experimental setups in the Kerguelen Islands were carried out with the permission of the French Polar Institute and the Environmental Directorate of the French Southern and Antarctic Lands (reference 2022–198).

### Consent for publication

Not applicable.

### Competing interests

The authors declare no competing interests.

### Author details

¹Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile. ²Université Claude Bernard Lyon 1, Laboratoire d'Écologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Research Team "Bacterial Opportunistic Pathogens and Environment" (BPOE), Marcy L'Étoile 69280, France. ³Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile. ⁴Marine Biology Lab, CP160/15, Université Libre de Bruxelles (ULB), Brussels, Belgium. ⁵Biogéosciences UMR 6282, Université Bourgogne Europe, CNRS, Dijon F-21000, France. ⁶IMBE-Institut Méditerranéen de Biologie et d'Ecologie marine et continentale, UMR 7263 Aix Marseille Université/CNRS/IRD/UAPV, Station Marine d'Endoume, Marseille, France. ⁷Aix-Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (M.I.O.) UM 110, Marseille, France.

Received: 25 June 2025 Accepted: 21 October 2025

Published online: 18 November 2025

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