In this study, we investigated the biodiversity of eukaryotes associated with sponges along the Red Sea coast of Saudi Arabia via metagenomic approaches. Our metagenomic analysis provided a comprehensive evaluation of the eukaryotic biodiversity within these sponge communities. By employing metataxonomic annotation, we were able to explore phylogenetic relationships at the genus and species levels, constructing detailed phylogenetic trees that elucidate the evolutionary connections among these eukaryotes.

Metagenomic analysis of the eukaryotic community associated with sponges in the Red Sea revealed diverse and rich ecosystems. The presence of various taxa, including Ascomycota, Bacillariophyta, Chlorophyta, Chytridiomycota, Rhodophyta, and several unclassified species, highlights the biodiversity of this marine environment. Ascomycota is a fungal phylum that is well known for its ecological roles, including decomposition and nutrient cycling. The presence of these compounds in the sponge microbiome suggests potential symbiotic relationships, possibly assisting in the breakdown of organic materials and contributing to the overall health of the sponge. Bacillariophyta are commonly known as diatoms, and these algae are crucial for primary production in marine ecosystems. Their abundance indicates a robust photosynthetic community, which supports the broader food web by providing essential nutrients through photosynthesis. Chlorophyta are also known as green algae, and these organisms contribute significantly to primary production and oxygen generation. The presence of these fungi underscores the photosynthetic capacity of the sponge-associated community, enhancing the nutritional intake of the sponge and promoting a stable habitat. Chytridiomycota is a group of fungi that can degrade chitin and keratin, suggesting a role in nutrient recycling within the sponge ecosystem.

Their detection points to complex interactions and a dynamic microbial environment. Rhodophyta are red algae known for their ecological and economic importance, particularly in coral reef ecosystems. The association of algae with sponges indicates potential mutualistic relationships, where algae provide oxygen and other nutrients while benefiting from the sponge's habitat. The detection of unclassified eukaryotic species highlights the potential for discovering novel organisms and further underscores the unexplored biodiversity within the Red Sea sponge microbiome. These unclassified entities could represent new species or groups that play unique roles in the ecosystem.

The presence of these diverse eukaryotic communities in the sponge-associated microbiome indicates a rich and complex environment. The interplay between these different taxa likely contributes to the resilience and adaptability of the sponge, allowing it to thrive in the variable conditions of the Red Sea. This biodiversity not only enhances the ecological functions of sponges but also suggests that the Red Sea is a hotspot for marine microbial diversity, offering valuable insights into marine biology and potential biotechnological applications.

Our data indicate the presence of Candida albicans within the sponge-associated microbiome. This yeast is known for its dual role as both a commensal organism and a pathogen in humans. In marine environments, its role can vary from symbiotic interactions with host organisms to opportunistic colonization. The detection of Candida albicans in the Red Sea sponge microbiome suggests a potential symbiotic relationship, where the yeast may benefit from the nutrient-rich environment provided by the sponge while possibly contributing to the host's microbial balance and health. Studies that align with our data have reported the presence of Candida species in various marine habitats, including coastal waters and sediments. For example, a study by Sen et al. documented the occurrence of Candida species in Mediterranean Sea sediments, highlighting their role in organic matter degradation and nutrient cycling (Sen et al. 2022). Another study (Raes et al. 2024) revealed the presence of Candida species in North Sea water samples, emphasizing the ubiquity and ecological versatility of this genus in different marine environments. This study revealed that Candida spp. are capable of surviving in diverse marine conditions, contributing to the microbial diversity and ecological functions in these habitats.

In our study of the sponge-associated microbiome in the Red Sea, we identified the genus Saccharomyces, which plays significant roles in marine ecosystems. These yeasts contribute to nutrient cycling and organic matter decomposition within the sponge environment. Their presence in the Red Sea, which is characterized by high salinity and temperature extremes, may influence their adaptability and interactions with the sponge host. Saccharomyces species are known for their role in decomposing organic matter, which releases essential nutrients such as nitrogen and phosphorus. This process supports the growth of other marine organisms and helps maintain ecosystem balance and primary productivity. In marine sediments of the Mediterranean Sea, Saccharomyces also contributes to organic matter decomposition and nutrient recycling (Said Hassane et al. 2020). Similarly, in the North Atlantic Ocean, these yeasts interact with phytoplankton, affecting nutrient availability and playing a role in the marine nutrient cycle (Breyer and Baltar 2023).

Pichia species are vital contributors to nutrient cycling in sponge-associated environments across different marine regions. They decompose organic matter, such as detritus and dead cells, releasing essential nutrients such as nitrogen and phosphorus, which support marine ecosystem health and primary productivity (Al Sodany and Diab 2023). In the Red Sea, owing to their extreme salinity and temperatures, Pichia species may have evolved unique adaptations to optimize nutrient cycling, influencing the dynamics of sponge-associated microbiomes (Tarman 2020). Their ability to break down complex organic compounds into simpler forms helps maintain the stability and functionality of sponge ecosystems. Pichia species also produce bioactive compounds with pharmaceutical and industrial applications. In the Red Sea, extreme environmental conditions may lead to the generation of novel metabolites with potential biotechnological uses, including drug development and enzyme production (El-Hossary et al. 2017).

In the Mediterranean Sea, Pichia species are essential for organic matter decomposition and nutrient recycling within sponge-associated environments. Their activity contributes significantly to ecosystem health and marine biodiversity by enhancing nutrient release and recycling (Bovio et al. 2017). The diverse Mediterranean environment has revealed Pichia strains with considerable biotechnological potential, producing enzymes and metabolites for industrial processes such as bioremediation and specialty chemical production (Bovio et al. 2017). In the North Atlantic Ocean, Pichia species similarly support nutrient cycling by decomposing organic matter in marine sediments and sponge habitats, which contributes to ecosystem stability. These species are also known for producing enzymes and bioactive metabolites with industrial and pharmaceutical applications, including antimicrobial and antifungal properties (Bonugli-Santos et al. 2015).

Additionally, our metagenomic analysis of sponge samples from the Red Sea coastal region of Saudi Arabia revealed diverse assemblages of eukaryotic microbial communities. The genera identified included Hyalosynedra sp., Navicula sp., Papiliocellulus sp., Psammodictyon sp., Pynococcus sp., Ostreococcus sp., Micromonas sp., and several unclassified species. The phylogenetic tree constructed from these samples provides insights into the ecological roles and potential biotechnological applications of these genera.

The Hyalosynedra genus is known for its presence in freshwater environments and its role in silica biogeochemistry. Its occurrence in sponges suggests that it may contribute to silica cycling within the sponge microbiome, possibly influencing sponge health through nutrient cycling and structural support (McNair et al. 2018). The Navicula genus is known as the diatom genus and is widely recognized for its ecological role in aquatic environments as a primary producer. In sponges, Navicula might play a role in nutrient cycling and as a food source for other microorganisms within the sponge. Its presence could be indicative of nutrient availability and environmental conditions (Colman 2015). Papiliocellulus is less well studied, but the presence of this genus in sponge samples suggests that it may contribute to the sponge microbiome by influencing microbial interactions and potentially producing bioactive compounds. Its role in sponge health and disease resistance requires further investigation (Gardner and Crawford 1992). The Psammodictyon genus is known for its role in benthic environments. Its association with sponges could reflect its ability to adapt to various environmental conditions and contribute to the sponge's ecological niche by participating in nutrient recycling and organic matter decomposition (Krishnaswami et al. 2024).

Pynococcus is considered a lesser-known genus, and Pynococcus might play a role in the breakdown of complex organic matter within the sponge microbiome. Understanding its function could provide insights into its contribution to sponge health and resilience (Finkel et al. 2007). The Ostreococcus genus includes some of the smallest known eukaryotic phytoplankton, which are important for primary production in marine environments. The presence of these compounds in sponges could indicate their role in nutrient acquisition and overall sponge health (Vaulot et al. 2008). Micromonas is similar to Ostreococcus, and Micromonas is a key primary producer in marine ecosystems. Its role in sponges may involve nutrient cycling and symbiotic relationships with the host sponge, contributing to its overall health (Karlusich et al. 2022).

Comparing our findings with other marine regions, such as the Mediterranean or Pacific Oceans, provides context for the ecological roles of these genera. For example, Navicula and Ostreococcus are also found in diverse marine environments and play crucial roles in primary production and nutrient cycling (Countway and Caron 2006; DeMaster 2001). The specific genera identified in our study reflect the unique conditions of the Red Sea, including its high salinity and temperature variations, which influence the microbial community composition.

In contrast to those in other marine regions, the presence of Hyalosynedra and Psammodictyon in our samples indicates potential adaptations to the extreme conditions of the Red Sea, highlighting the adaptability and resilience of these genera. The unique ecological interactions observed in Red Sea sponges may differ from those in cooler or less saline environments, suggesting that sponge-associated microbial communities are highly specialized and adapted to their specific habitats.

The identified genera contribute to the sponge microbiome by participating in nutrient cycling, organic matter decomposition, and primary production. Their interactions with sponge hosts can influence sponge health, resilience, and ecological function. Several genera, such as Ostreococcus and Micromonas, are known for their potential in biotechnology, including biofuel production and bioremediation (Marques et al. 2011; Pulz and Gross 2004). The discovery of novel species within the sponge microbiome could lead to new biotechnological applications, such as the development of novel antimicrobial compounds or enzymes with industrial relevance.

The presence of unclassified species highlights the potential for discovering novel microbial taxa with unique ecological and biotechnological roles. Further characterization of these species could reveal new insights into sponge-associated microbial communities and their functions.

Metagenomic analysis of sponge samples from the Red Sea coastal region of Saudi Arabia revealed the presence of several unclassified genera, including Kryptoperidinium, Amoebophyra, Amphidinium, Karlodinium, Geminiger, Blastocystis, Spiniferites, Blixaea, Protodinium, Symbiodinium, Galeidinium, Haliphthoros, Bysmatrum, Chytriodinium, and Euduboscquella. These genera represent a diverse array of eukaryotic microbial communities, each potentially playing unique roles in sponge health and offering various biotechnological applications.

The Cryptoperidinium genus is known for its complex life cycle, including symbiotic relationships with other microorganisms. In sponges, Kryptoperidinium may contribute to nutrient cycling and symbiotic interactions, enhancing sponge resilience in extreme environments such as the Red Sea (Ellegaard et al. 2013). Amoebacea is a parasite of dinoflagellates, and amoebacea could play a role in controlling the population of harmful algal blooms within the sponge microbiome. Its presence might indicate a regulatory mechanism within the sponge's microbial community, ensuring a balanced ecosystem (Annenkova et al. 2011). Amphidinium is known for its ability to produce bioactive compounds, and Amphidinium could contribute to sponge health by producing secondary metabolites that protect sponges from pathogens. Its role in the sponge microbiome may include providing chemical defense mechanisms (Okolodkov et al. 2022). The Karlodinium genus is also known for its production of toxins, which can influence the microbial community structure within sponges. Karlodinium may contribute to the sponge's defense against microbial invasions by producing compounds with antimicrobial properties (Shang et al. 2019). The Blastocystis genus includes species that are known to be parasitic or commensal. In sponges, Blastocystis may contribute to the overall health of the microbiome by regulating microbial population dynamics and influencing host immune responses (Stensvold and Clark 2016). Spiniferites is known primarily as a fossil dinoflagellate genus, and Spiniferites might be involved in the long-term stability and resilience of the sponge's microbial community, contributing to its adaptability in the dynamic Red Sea environment (Rochon et al. 1999). Blixaea is a relatively unknown genus, and Blixaea may play a role in the structural support of sponges or biogeochemical cycling within the sponge microbiome. However, further research is needed to elucidate its function (Matsuoka and Fukuyo 2000). Symbiodinium is known for its symbiotic relationship with corals, and Symbiodinium sponges may provide photosynthetic products that contribute to sponge nutrition and health. Its presence suggests a potential role in energy acquisition and symbiotic balance within the sponge (Baker 2003). Haliphthoros is a genus of water molds, and Haliphthoros might play a role in the decomposition of organic matter within the sponge microbiome. Its function could be linked to the nutrient cycling and overall health of the sponge (Raghukumar 2017). The Chytriodinium genus is associated with parasitism by other microorganisms. In sponges, Chytriodinium may play a role in controlling the population of specific microbial species, contributing to the balance and stability of the microbiome (Strassert et al. 2018).

When the microbial genera found in Red Sea sponges are compared with those from other marine regions, certain unique aspects become evident. The Red Sea's extreme conditions, such as high salinity and temperature, likely influence the composition and function of sponge-associated microbial communities. For example, the presence of genera such as Symbiodinium and Karlodinium, which are also found in other tropical marine environments, suggests a shared role in symbiosis and chemical defense (Stat et al. 2013; Van Wagoner et al. 2010). However, the discovery of genera such as Blixaea in Red Sea sponges indicates a potentially unique adaptation to this environment, which may not be as prevalent in other regions.

In contrast, sponges from cooler or less saline environments might host different microbial communities, reflecting the influence of environmental conditions on microbial composition. For example, genera such as Kryptoperidinium and Amoebophyra, known for their parasitic and symbiotic roles, may interact differently in the Red Sea than in other marine ecosystems, highlighting the importance of the environmental context in shaping sponge‒microbe interactions (Ellegaard et al. 2013; Pandeirada et al. 2017).

In conclusion, our metagenomic analysis of Red Sea sponges uncovered a diverse eukaryotic microbiome that includes fungi, algae, and a variety of unclassified species, underscoring the region's extensive marine biodiversity. Candida, Saccharomyces, and Pichia sp. are genera that contribute to the decomposition of organic matter and the cycling of nutrients. Their unique adaptations to the extreme conditions of the Red Sea have the potential to serve as biotechnological applications.

The Red Sea sponge microbiomes are further distinguished from those in other marine environments by the presence of Hyalosynedra sp., Navicula sp., and other genera, which suggests that they play intricate ecological roles in nutrient cycling and sponge health. Novel symbiotic and defensive mechanisms are suggested by unclassified genera such as Kryptoperidinium sp. and Amoebophyra sp., underscoring the necessity of additional research to explore the complete potential of these sponge-associated microbial communities for biotechnological advancements.