Coral reefs support approximately 25% of all marine species while covering less than 0.1% of the ocean floor (Knowlton et al., 2010). These ecosystems provide essential ecological and economic services, including fisheries, tourism, and coastal protection, with reef-related economic activities estimated to generate $38.5 billion annually (Moberg and Folke, 1999; Ferrario et al., 2014; Spalding et al., 2017). However, reef stability is increasingly threatened by anthropogenic stressors, such as climate change, pollution, and sedimentation from land-based runoff (Fabricius, 2005; Vega Thurber et al., 2014; Risk, 2014; Hughes et al., 2017). Sediment carried by runoff from deforestation, agriculture, and urbanization reduces light-availability, smothers coral tissues, and alters reef biogeochemistry (Anthony and Fabricius, 2000; Fabricius, 2005; Junjie et al., 2014; Risk, 2014). Sedimentation further exacerbates other stressors affecting coral health, such as widespread coral bleaching and disease outbreaks, and together these stressors accelerate reef degradation (Tuttle and Donahue, 2022).

Sedimentation affects corals not only through direct physiological stress, but also by altering the surrounding ecological and microbial environment (Fabricius, 2005). Suspended sediments indirectly limit photosynthesis by coral-associated Symbiodiniaceae by decreasing light availability, while direct sediment exposure can impair gas exchange and nutrient uptake by the coral animal itself (Weber et al., 2012; Junjie et al., 2014). Sedimentation also introduces organic matter that fuels microbial metabolism, altering microbial interactions within the coral reef environment (Weber et al., 2012). The severity of these impacts depends on sediment grain size, concentration, and duration of exposure, with fine sediments that remain suspended in the water column longer having the greatest impact on coral reef ecosystems (Fabricius, 2005). While increased sedimentation has been associated with shifts in the microbial community taxonomic composition (Risk, 2014; Tuttle and Donahue, 2022), particularly under chronic conditions, the effects of short-term sedimentation events on coral-associated microbial communities remain relatively unexplored.

The coral surface mucus layer (SML) is a critical interface between corals and their environment, serving as both a physical barrier and niche habitat for diverse microbial communities (Brown and Bythell, 2005; Glasl et al., 2016; Briggs et al., 2021). These microbial assemblages, collectively referred to as the SML microbiome, include bacteria, archaea, fungi, and viruses that contribute to nutrient cycling, pathogen defense, and environmental adaptation (Rohwer et al., 2002; Ritchie, 2006; Bourne et al., 2016; Sweet and Bythell, 2017; Lima et al., 2022). Microbial community composition within the SML microbiome is highly dynamic and shifts in response to fluctuations in water quality, temperature, and coral health (Mouchka et al., 2010; Zou et al., 2022). Stability and diversity in these microbial assemblages are often associated with greater coral health and resilience, however, stress-induced changes can also increase diversity through the introduction of opportunistic or pathogenic taxa, a form of microbial dysbiosis that may signal coral health decline (Kline and Vollmer, 2011; Zaneveld et al., 2016; Hughes et al., 2017; Sweet and Bythell, 2017; Huntley et al., 2022). Some SML-associated microbes play beneficial roles through the production of antimicrobial compounds, but these interactions can be disrupted under environmental stress (Rosenberg and Falkovitz, 2004). For example, thermal stress has been linked to compositional changes and the proliferation of known coral pathogens (Lee et al., 2015), whilenutrient runoff can restructure microbial communities by promoting the growth of bacteria adapted to high-nutrient, low-oxygen conditions (Fabricius, 2005). Sedimentation presents a distinct type of disturbance byphysically smothering coralsand altering the chemical environment of the SML (Weber et al., 2012), favoring heterotrophic bacteria capable of degrading organic matter while suppressing photoautotrophic taxa dependent on light availability (Vega Thurber et al., 2014; Sutherland et al., 2011). Given the central role of microbial interactions in coral health, understanding whether sedimentation-induced changes in microbial diversity and composition are transient or indicative of chronic stress is essential for evaluating coral resilience.

Recent research suggests that prolonged sedimentation can increase microbial diversity in the SML microbiome, often introducing rare or transient microbial taxa during periods of under high sediment loads (Fifer et al., 2022; Miller and Bentlage, 2024). However, the timing and reversibility of these changes remain poorly understood. Specifically, it is unclear how quickly the SML microbiome responds to sediment input and whether short-term sedimentation events lead to similar increases in diversity or community restructuring. Similar taxonomic shifts have been observed under other stressors, such as hypoxia, where elevated abundances of anaerobic bacteria suggest rapid changes in microbial turnover (Howard et al., 2023). Sediment-driven restructuring may similarly favor anaerobic or terrestrial-associated bacteria, potentially displacing host-associated taxa. While some studies have characterized microbial responses to chronic sedimentation, fewer have investigated how acute sedimentation events affect the taxonomic composition and diversity of coral-associated microbiomes or whether such responses are transient or persistent (Fifer et al., 2022). These knowledge gaps limit our ability to evaluate short-term disturbances and predict recovery trajectories in coral microbial communities.

This study examines the effects of sedimentation on the SML microbiome of Porites lobata and aims to identify microbial indicators of sediment-induced stress. Specifically, three research questions are addressed: (1) How does sedimentation affect microbiome diversity within the SML of P. lobata? (2) How does the taxonomic composition of the SML microbiome change in response to sedimentation? (3) Which bacterial taxa in the P. lobata SML microbiome are most responsive to sedimentation events? This study further enhances the understanding of how sedimentation influences coral-associated microbiomes and contributes to the identification of microbial signatures reflective of sedimentation impacts and potential recovery. These insights can help inform the development of microbiome-based tools for monitoring coral reef health and support resilience-based approaches to conservation and management.

This study demonstrates that acute sedimentation induced measurable changes in the SML microbiome of P. lobata coral, based on observations from five monitored colonies during a documented sedimentation event (HDOH, 2024). Alpha and beta diversity metrics were compared across three sedimentation periods to demonstrate both immediate and lasting sedimentation-driven shifts in the SML microbiome, with the most significant changes observed after sediment exposure. The significant decline in alpha diversity after sedimentation aligns with previous findings that environmental stressors reduce microbial evenness and taxonomic richness (Maher et al., 2020; Bui et al., 2024). Beta diversity analysis further showed that microbial communities were compositionally distinct among sedimentation periods, with the post-event microbiome showing the most divergence from pre- and during-event communities. The patterns of decreased diversity and compositional shifts are consistent with experimental studies of corals exposed to different stressors, such as antibiotics, disease, and hypoxia, suggesting that sedimentation not only decreases microbial diversity, but also restructures community composition (Bent et al., 2021; Guo et al., 2022; Huntley et al., 2022; Howard et al., 2023). These findings demonstrate that acute sedimentation events can drive measurable shifts in both the richness and structure of the P. lobata SML microbiome.

Indicator species analyses revealed distinct microbial signatures across sedimentation periods. Before sedimentation, the presence of the coral-associated bacterial families OM60, Synechococcaceae, and Vibrionaceae suggests that a stable, host-associated microbiome is present in the absence of environmental disturbances (McKew et al., 2016; Webster et al., 2016; Greff et al., 2017). During sedimentation 121 families were identified as indicator taxa, reflecting the influx of environmental microbes during sedimentation events. Although commonly associated with coral microbiomes, Flavobacteriaceae was enriched during sedimentation, aligning with prior studies that have observed an enrichment of this group in stressed and diseased corals (Miller and Richardson, 2011; Meyer et al., 2019; Delgadillo-Ordoñez et al., 2022).

Many taxa associated with sedimentation were not retained after the event, suggesting that these microbes may only have a brief influence on the coral SML but do not persist in shaping the microbiome over time. Only three indicator taxa were identified after sedimentation—Endozoicimonaceae, Brevibacteriaceae, and an unassigned family in the order R76-B128—indicating that a more selective community may persist post-disturbance. Among these, Endozoicimonaceae are well-known coral-associated symbionts involved in nutrient cycling, immune modulation, and antimicrobial activity (Neave et al., 2016; Bourne et al., 2016). For instance, Endozoicomonas marisrubi has been shown to contribute to the exchange of essential metabolites that could play a role in coral recovery following disturbances (Pogoreutz et al., 2022). Endozoicimonaceae also comprised a large portion of the microbial community during all periods, but was most dominant after sedimentation, suggesting a return to a core microbiome during post-sediment microbiome stabilization (Bernasconi et al., 2019). Brevibacteriaceae and taxa within the R76-B128 order are commonly found in sediments, especially in saline environments, indicating the incorporation of sediment-associated taxa into the SML microbiome post-sedimentation (Forquin-Gomez et al., 2014; van Vliet et al., 2019). The low relative abundance of both Brevibacteriaceae and the unassigned family in the order R76-B128 after sedimentation may be reflective of transient infiltration rather than long-term colonization. Together, these results indicate that while sedimentation can introduce novel microbial taxa to the coral SML, only some are retained beyond the disturbance period. The post-event community appears to reflect both residual sediment-associated taxa and a resurgence of core coral symbionts, highlighting a possible early recovery stage where coral-associated microbes begin to reestablish dominance. The observed trends in microbial community composition across sedimentation periods suggest that microbiome restructuring is a delayed response rather than an immediate shift. Alpha diversity analyses showed that taxonomic richness temporarily increased during sedimentation but significantly declined once environmental conditions returned to pre-event levels. This increase in transient microbe diversity mirrors patterns observed in corals exposed to prolonged sedimentation, where microbial turnover continues beyond the disturbance event itself (Ziegler et al., 2016). Although the subsequent decline in diversity may indicate the onset of recovery, the post-sedimentation microbiome remained compositionally distinct and did not revert to its pre-event state. Moreover, indicator species analysis identified 58 taxa shared between the periods before and during sedimentation and only one taxon shared between the during and after periods, while no taxa were shared between the before and after periods. This progression supports a gradual transition in microbial composition, where few microbial lineages introduced during sedimentation persisted into the recovery period.

While these findings provide new insights into the SML microbiome’s response to an acute sedimentation event, several aspects warrant further investigation. This study focused on a single site, which provided a controlled environmental context, but microbiome composition has been observed to vary over small geographic scales (Wainwright et al., 2019), highlighting the need for multi-site comparisons. Additionally, while 16S rRNA gene sequencing allowed for taxonomic classification, the functional traits and physiological roles of identified taxa remain inferred rather than directly measured. Metagenomic and transcriptomic approaches have proven useful in other studies for identifying microbial genes involved in nutrient cycling, immune modulation, and stress tolerance and could better validate the ecological roles of the taxa highlighted here (Lima et al., 2022; Pogoreutz et al., 2022). The temporal resolution of this study, limited tothe single post-sedimentation time point, provides a snapshot of the SML microbiome nearly 2 months after the sedimentation event and makes it difficult to determine whether the observed composition reflects a temporary disturbance, an intermediate recovery phase, or a longer-term shift in microbiome state. Acute sedimentation events, like the event monitored in this study, are thought to be key drivers of microbiome structuring, but longitudinal sampling is needed to determine whether the microbiome stabilizes over longer periods of time or remains in an altered state (Fifer et al., 2022). Furthermore, microbial shifts may reflect not only host selection, but also changes in the surrounding microbial pool following environmental disturbance. For example, persistent restructuring of microbial communities has been observed in human skin microbiomes after environmental exposures such as water contact and urbanization (Callewart et al., 2020), and similar dynamics may apply to the coral SML microbiome following sedimentation. These changes may represent not only adaptive responses but also the passive acquisition of environmental taxa. Consequently, physiological impacts on the coral host may be influenced as much by environmental disturbance and microbial availability as by selective recovery processes. Despite these considerations, this study provides foundational insights into the taxonomic shifts associated with acute sedimentation and identifies key bacterial families that may serve as indicators of sedimentation stress.

Building on the single-site design of this study, future research should expand to multiple reef locations and incorporate functional analyses to better understand the ecological significance of sedimentation-induced microbiome shifts. Future studies using metagenomic and transcriptomic tools could determine whether observed taxonomic shifts correspond to functional changes, such as antimicrobial compound production or nutrient processing, that directly influence coral health and resilience (Wright et al., 2019; Glaze et al., 2022). Notably, this study revealed short-term loss of diversity, the emergence of sediment-associated and opportunistic taxa during sedimentation, and the retention of potential recovery-associated bacterial families, such as Endozoicimonaceae, after sedimentation. Although the functional roles of taxa associated with the post-sediment microbiome, their identification could help to identify microbial patterns associated with sedimentation stress. These findings highlight the value of identifying sediment-responsive microbial taxa as a first step toward understanding how environmental disturbances shape coral microbiomes, and they underscore the importance of linking taxonomic shifts with both microbial function and coral health outcomes in future studies.

Microbial responses to sedimentation are likely to be habitat-specific, thus future studies should include multiple reef sites impacted by acute sedimentation to determine whether consistent patterns in microbial shifts emerge across locations (Glasl et al., 2019). Extended time series from multiple seasons and recovery stages will help differentiate natural variability from disturbance-driven shifts, particularly given the failure of the microbiome to return to pre-event composition nearly 2 months after the initial sediment exposure and seasonal variability reported in corals elsewhere (Miller and Bentlage, 2024). Controlled sediment exposure experiments could further establish causal links between sedimentation and microbial community restructuring. For example, the persistence and increase in taxa such as Endozoicimonaceae warrants further investigation into its potential role in post-sedimentation microbial community dynamics and recovery processes (Pogoreutz et al., 2022). These foundational insights are a necessary precursor to the development of microbiome-based restoration strategies, such as probiotics or microbial transplants, to mitigate sedimentation stress and enhance coral resilience (Moradi et al., 2023; Delgadillo-Ordoñez et al., 2024).

Understanding how sedimentation-driven microbiome shifts relate to overall coral resilience is essential for predicting coral responses to increasing sedimentation pressure. If microbial restructuring following sedimentation disrupts key microbial functions, such as nutrient cycling, pathogen defense, or symbiosis, corals may become more vulnerable to additional stressors, including warming, pollution, or disease outbreaks (Vezzulli et al., 2013; Neave et al., 2016; Webster et al., 2016). However, it remains unclear whether these shifts represent a temporary stress response or a functional adaptation that enhances coral resilience. Clarifying the ecological roles of sediment-responsive taxa is therefore critical for developing microbiome-based conservation strategies (Boilard et al., 2020; Terzin et al., 2024). Building on this study’s findings, future research should also consider how microbiome assembly is influenced by environmentally available microbes, recognizing that community shifts may be driven as much by stochastic colonization as by host filtering. As land-based runoff continues to threaten nearshore coral reefs, these insights underscore the importance of integrating microbiome dynamics into coral conservation frameworks and provide a foundation for identifying microbial signatures of sedimentation stress and recovery (Staley et al., 2017; Carlson et al., 2019).