Influence of environmental variation on symbiotic bacterial communities of two temperate sponges

Effects of titanium dioxide nanoparticle exposure on the gut microbiota of pearl oyster (Pinctada fucata martensii)

With the advancement of nanotechnology and the growing utilization of nanomaterials, titanium dioxide (TiO2) has been released into aquatic environments, posing potential ecotoxicological risks to aquatic organisms. In this study, the toxicological effects of TiO2 nanoparticles were investigated on the intestinal health of pearl oyster (Pinctada fucata martensii). The pearl oysters were subjected to a 14-day exposure to 5-mg/L TiO2 nanoparticle, followed by a 7-day recovery period. Subsequently, the intestinal tissues were analyzed using 16S rDNA high-throughput sequencing. The results from LEfSe analysis revealed that TiO2 nanoparticle increased the susceptibility of pearl oysters to potential pathogenic bacteria infections. Additionally, the TiO2 nanoparticles led to alterations in the abundance of microbial communities in the gut of pearl oysters. Notable changes included a decrease in the relative abundance of Phaeobacter and Nautella, and an increase in the Actinobacteria, which could potentially impact the immune function of pearl oysters. The abundance of Firmicutes and Bacteroidetes, as well as the expression of genes related to energy metabolism (AMPK, PK, SCS-1, SCS-2, SCS-3), were down-regulated, suggesting that TiO2 nanoparticles exposure may affect the digestive and energy metabolic functions of pearl oysters. Furthermore, the short-term recovery of seven days did not fully restore these levels to normal. These findings provide crucial insights and serve as an important reference for understanding the toxic effects of TiO2 nanoparticles on bivalves.

Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial

Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.

Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO2 vents

Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3-V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.

Stability of the Microbiome of the Sponge Mycale (Oxymycale) acerata in the Western Antarctic Peninsula

The sponge microbiome, especially in Low Microbial Abundance (LMA) species, is expected to be influenced by the local environment; however, contrasting results exist with evidence showing that host specificity is also important, hence suggesting that the microbiome is influenced by host-specific and environmental factors. Despite sponges being important members of Southern Ocean benthic communities, their relationships with the microbial communities they host remain poorly studied. Here, we studied the spatial and temporal patterns of the microbiota associated with the ecologically important LMA sponge M. acerata at sites along ∼400 km of the Western Antarctic Peninsula (WAP) to assess patterns in the core and variable microbial components of the symbiont communities of this sponge species. The analyses of 31 samples revealed that the microbiome of M. acerata is composed of 35 prokaryotic phyla (3 Archaea, 31 Bacteria, and one unaffiliated), being mainly dominated by Proteobacteria with Gammaproteobacteria as the most dominant class. The core community was composed of six prokaryotic OTUs, with gammaproteobacterial OTU (EC94 Family), showing a mean abundance over 65% of the total abundance. Despite some differences in rare OTUs, the core community did not show clear patterns in diversity and abundance associated with specific sites/environmental conditions, confirming a low variability in community structure of this species along the WAP. The analysis at small scale (Doumer Island, Palmer Archipelago) showed no differences in space and time in the microbiome M. acerata collected at sites around the island, sampled in three consecutive years (2016–2018). Our results highlight the existence of a low spatial and temporal variability in the microbiome of M. acerata, supporting previous suggestions based on limited studies on this and other Antarctic sponges.

Oceanographic setting influences the prokaryotic community and metabolome in deep-sea sponges

Marine sponges (phylum Porifera) are leading organisms for the discovery of bioactive compounds from nature. Their often rich and species-specific microbiota is hypothesised to be producing many of these compounds. Yet, environmental influences on the sponge-associated microbiota and bioactive compound production remain elusive. Here, we investigated the changes of microbiota and metabolomes in sponges along a depth range of 1232 m. Using 16S rRNA gene amplicon sequencing and untargeted metabolomics, we assessed prokaryotic and chemical diversities in three deep-sea sponge species: Geodia barretti, Stryphnus fortis, and Weberella bursa. Both prokaryotic communities and metabolome varied significantly with depth, which we hypothesized to be the effect of different water masses. Up to 35.5% of microbial ASVs (amplicon sequence variants) showed significant changes with depth while phylum-level composition of host microbiome remained unchanged. The metabolome varied with depth, with relative quantities of known bioactive compounds increasing or decreasing strongly. Other metabolites varying with depth were compatible solutes regulating osmolarity of the cells. Correlations between prokaryotic community and the bioactive compounds in G. barretti suggested members of Acidobacteria, Proteobacteria, Chloroflexi, or an unclassified prokaryote as potential producers.

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.

Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts

The fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution. IMPORTANCE Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa (Entoporibacteria, SAUL, and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. Finally, it appears that the Entoporibacteria are associated primarily with high-microbial abundance sponges, while the Tethybacterales associate with low-microbial abundance sponges.

Application of Networking Approaches to Assess the Chemical Diversity, Biogeography, and Pharmaceutical Potential of Verongiida Natural Products

This study provides a review of all isolated natural products (NPs) reported for sponges within the order Verongiida (1960 to May 2020) and includes a comprehensive compilation of their geographic and physico-chemical parameters. Physico-chemical parameters were used in this study to infer pharmacokinetic properties as well as the potential pharmaceutical potential of NPs from this order of marine sponge. In addition, a network analysis for the NPs produced by the Verongiida sponges was applied to systematically explore the chemical space relationships between taxonomy, secondary metabolite and drug score variables, allowing for the identification of differences and correlations within a dataset. The use of scaffold networks as well as bipartite relationship networks provided a platform to explore chemical diversity as well as the use of chemical similarity networks to link pharmacokinetic properties with structural similarity. This study paves the way for future applications of network analysis procedures in the field of natural products for any order or family.

Transmission of the sponge microbiome: moving towards a unified model

Sponges have co-evolved for millions of years alongside several types of microorganisms, which aside from participating in the animal's diet, are mostly symbionts. Since most of the genetic repertoire in the holobiont genome is provided by microbes, it is expected that the host-associated microbiome will be at least partially heritable. Sponges can therefore acquire their symbionts in different ways. Both vertical transmission (VT) and horizontal transmission (HT) have different advantages and disadvantages in the life cycle of these invertebrates. However, a third mode of transmission, called leaky vertical transmission or mixed mode of transmission (MMT), which incorporates both VT and HT modes, has gained relevance and seems to be the most robust model. In that regard, the aim of this review is to present the evolving knowledge on these main modes of transmission of the sponge microbiome. Our conclusions lead us to suggest that MMT may be more common for all sponges, with its frequency varying across the transmission spectrum between species and the environment. This hybrid model supports the stable and specific transmission of these microbial partners and reinforces their assistance in the resilience of sponges over the years.

Bacterial diversity associated with a newly described bioeroding sponge, Cliona thomasi, from the coral reefs on the West Coast of India

The bacterial diversity associated with eroding sponges belonging to the Cliona viridis species complex is scarcely known. Cliona thomasi described from the West Coast of India is a new introduction to the viridis species complex. In this study, we determined the bacterial diversity associated with C. thomasi using next-generation sequencing. The results revealed the dominance of Proteobacteria followed by Cyanobacteria, Actinobacteria and Firmicutes. Among Proteobacteria, the Alphaproteobacteria were found to be the most dominant class. Furthermore, at the genus level, Rhodothalassium were highly abundant followed by Endozoicomonas in sponge samples. The beta-diversity and species richness measures showed remarkably lower diversity in Cliona thomasi than the ambient environment. The determined lower bacterial diversity in C. thomasi than the environmental samples, thus, categorized it as a low microbial abundance (LMA). Functional annotation of the C. thomasi-associated bacterial community indicates their possible role in photo-autotrophy, aerobic nitrification, coupling of sulphate reduction and sulphide oxidization. The present study unveils the bacterial diversity in bioeroding C. thomasi, which is a crucial step to determine the functions of the sponge holobiont in coral reef ecosystem.

Assessing the strength and sensitivity of the core microbiota approach on a highly diverse sponge reef

Marine sponge reefs usually comprise a complex array of taxonomically different sponge species, many of these hosting highly diverse microbial communities. The number of microbial species known to occupy a given sponge ranges from tens to thousands, bringing numerous challenges to their analysis. One way to deal with such complexity is to use a core microbiota approach, in which only prevalent and abundant microbes are considered. Here we aimed to test the strength and sensitivity of the core microbiota approach by applying different core definitions to 20 host sponge species. Application of increasingly stringent relative abundance and/or percentage occurrence thresholds to qualify as part of the core microbiota decreased the number of 'core' OTUs and phyla and, consequently, changed both alpha- and beta-diversity patterns. Moreover, microbial co-occurrence patterns explored using correlation networks were also affected by the core microbiota definition. The application of stricter thresholds resulted in smaller and less compartmentalized networks, with different keystone species. These results highlight that the application of different core definitions to phylogenetically disparate host species can result in the drawing of markedly different conclusions. Consequently, we recommend to assess the effects of different core community definitions on the specific system of study before considering its application.

Sponges from Zanzibar host diverse prokaryotic communities with potential for natural product synthesis

Sponges are one of the most dominant organisms in marine ecosystems. One reason for their success is their association with microorganisms that are besides the host itself responsible for the chemical defence. Sponge abundances have been increasing on coral reefs in the Western Indian Ocean (WIO) and are predicted to increase further with rising anthropogenic impacts on coral reefs. However, there is a paucity of information on chemical ecology of sponges from the WIO and their prokaryotic community composition. We used a combination of Illumina sequencing and a predictive metagenomic analysis to (i) assess the prokaryotic community composition of sponges from Zanzibar, (ii) predict the presence of KEGG metabolic pathways responsible for bioactive compound production and (iii) relate their presence to the degree of observed chemical defence in their respective sponge host. We found that sponges from Zanzibar host diverse prokaryotic communities that are host species-specific. Sponge-species and respective specimens that showed strong chemical defences in previous studies were also predicted to be highly enriched in various pathways responsible for secondary metabolite production. Hence, the combined sequencing and predictive metagenomic approach proved to be a useful indicator for the metabolic potential of sponge holobionts.

Freshwater Sponge Tubella variabilis Presents Richer Microbiota Than Marine Sponge Species

Sponges can host diverse and abundant communities of microorganisms, which constitute an interesting source of bioactive compounds. Thus, to broaden our knowledge about the diversity of the microbiota that is found in freshwater sponges, the microbial community of Tubella variabilis was analyzed using culture-independent and culture-dependent approaches. Additionally, sponge-associated bacteria were compared with those living in the surrounding waters. Bacteria were also tested for antimicrobial production. Overall, the microbial composition identified comprises at least 44 phyla belonging mainly to Proteobacteria and low percentages of Bacteroidetes, Acidobacteria, and Verrucomicrobia. Alphaproteobacteria was the dominant class in T. variabilis while Betaproteobacteria was dominant in freshwater. Our data also revealed a high richness of bacteria in comparison to another freshwater sponge and 32 marine sponges. A global comparison of the structure of microbiota of different sponges showed that the main structuring factor may be the sponge environment, with T. variabilis and all freshwater sponges clustering together, and far away from the marine sponges. Bacterial strains from sponges and from freshwater were isolated and 163 morphotypes were phylogenetically identified. These belong to 26 genera, of which 12 were exclusively found in sponge samples and three only in freshwater. Inhibitory activities were also detected among 20–25% of the isolates from sponges and freshwater, respectively. This study presents new information on the composition of the microbial community found in freshwater sponges, which is diverse, abundant and distinct from some marine sponges. Moreover, the antimicrobial activity observed from the bacterial strains might play an important role in shaping microbial communities of the environment.

Temporal Stability of Bacterial Communities in Antarctic Sponges

Marine sponges host dense, diverse, and species-specific microbial communities around the globe; however, most of the current knowledge is restricted to species from tropical and temperate waters. Only recently, some studies have assessed the microbiome of a few Antarctic sponges; however, contrary to low mid-latitude sponges, the knowledge about temporal (stability) patterns in the bacterial communities of Antarctic sponges is absent. Here, we studied the temporal patterns of bacterial communities in the Antarctic sponges Mycale (Oxymycale) acerata, Isodictya sp., Hymeniacidon torquata, and Tedania (Tedaniopsis) wellsae that were tagged in situ and monitored during three austral summers over a 24-month period. By using amplicon sequencing of the bacterial 16S rRNA gene we found that the microbiome differed between species. In general, bacterial communities were dominated by gammaproteobacterial OTUs; however, M. acerata showed the most distinct pattern, being dominated by a single betaproteobacterial OTU. The analysis at OTU level (defined at 97% sequence similarity) showed a highly stable bacterial community through time, despite the abnormal seawater temperatures (reaching 3°C) and rates of temperature increase of 0.15°C day-1 recorded in austral summer 2017. Sponges were characterized by a small core bacterial community that accounted for a high percentage of the abundance. Overall, no consistent changes in core OTU abundance were recorded for all studied species, confirming a high temporal stability of the microbiome. In addition, predicted functional pathway profiles showed that the most abundant pathways among all sponges belonged mostly to metabolism pathway groups (e.g., amino acid, carbohydrate, energy, and nucleotide). The predicted functional pathway patterns differed among the four sponge species. However, no clear temporal differences were detected supporting what was found in terms of the relatively stable composition of the bacterial communities.

Sponges and Their Microbiomes Show Similar Community Metrics Across Impacted and Well-Preserved Reefs

Sponge diversity has been reported to decrease from well-preserved to polluted environments, but whether diversity and intra-species variation of their associated microbiomes also change as function of environmental quality remains unknown. Our study aimed to assess whether microbiome composition and structure are related to the proliferation of some sponges and not others under degraded conditions. We characterized the most frequent sponges and their associated bacteria in two close areas (impacted and well-preserved) of Nha Trang Bay (Indo-Pacific). Sponge assemblages were richer and more diverse in the well-preserved reefs, but more abundant (individuals/m. transect) in the impacted environments, where two species (Clathria reinwardti and Amphimedon paraviridis) dominated. Sponge microbiomes from the polluted zones had, in general, lower bacterial diversity and core size and consequently, higher intra-species dispersion than microbiomes of sponges from the well-preserved environments. Microbial communities reflect the reduction of diversity and richness shown by their host sponges. In this sense, sponges with less complex and more variable microbiomes proliferate under degraded environmental conditions, following the ecological paradigm that negatively correlates community diversity and environmental degradation. Thereby, the diversity and structure of sponge microbiomes might indirectly determine the presence and proliferation of sponge species in certain habitats.

Microbiome of the Black-Lipped Pearl Oyster Pinctada margaritifera, a Multi-Tissue Description With Functional Profiling

Elucidating the role of prokaryotic symbionts in mediating host physiology has emerged as an important area of research. Since oysters are the world’s most heavily cultivated bivalve molluscs, numerous studies have applied molecular techniques to understand the taxonomic and functional diversity of their associated bacteria. Here, we expand on this research by assessing the composition and putative functional profiles of prokaryotic communities from different organs/compartments of the black-lipped pearl oyster Pinctada margaritifera, a commercially important shellfish valued for cultured pearl production in the Pacific region. Seven tissues, in addition to mucous secretions, were targeted from P. margaritifera individuals: the gill, gonad, byssus gland, haemolymph, mantle, adductor muscle, mucus, and gut. Richness of bacterial Operational Taxonomic Units (OTUs) and phylogenetic diversity differed between host tissues, with mucous layers displaying the highest richness and diversity. This multi-tissues approach permitted the identification of consistent microbial members, together constituting the core microbiome of P. margaritifera, including Alpha- and Gammaproteobacteria, Flavobacteriia, and Spirochaetes. We also found a high representation of Endozoicimonaceae symbionts, indicating that they may be of particular importance to oyster health, survival and homeostasis, as in many other coral reef animals. Our study demonstrates that the microbial communities and their associated predicted functional profiles are tissue specific. Inferred physiological functions were supported by current physiological data available for the associated bacterial taxa specific to each tissue. This work provides the first baseline of microbial community composition in P. margaritifera, providing a solid foundation for future research into this commercially important species and emphasises the important effects of tissue differentiation in structuring the oyster microbiome.

Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities

The disease of freshwater sponges was first discovered in 2011, when pink samples were found in the Central Basin of Lake Baikal. Subsequently, the visible signs of the disease have changed, and now sponges appear with various symptoms of damage to the body, such as discoloration, tissue necrosis, the formation of brown patches and dirty-purple biofilms on some branches. These signs of the disease are accompanied by the mass death of sponges. We identified differences in microbiomes by sequencing 16S rRNA genes and found changes in the consortium of microorganisms of freshwater Baikal sponges. We found that the observed imbalance in the studied microbial communities of diseased sponges is caused by several different conditionally pathogenic microorganisms that increase their negative effect by acting together and in concert, which leads to the death of photosynthetic microalgae and sponges. Sponges are an important component of coastal communities, and the massive loss of sponges can obviously affect the structure of benthic communities and the purity of water.

Sponge-microbe partnerships are stable under eutrophication pressure from mariculture

Sponges harbor a great diversity of symbiotic microorganisms. However, environmental stresses can affect this partnership and influence the health and abundance of the host sponges. In Bolinao, Pangasinan, Philippines, chronic input of organic materials from mariculture activities contributes to a eutrophic coastal environment. To understand how these conditions might affect sponge-microbial partnerships, transplantation experiments were conducted with the marine sponge Gelliodes obtusa. High-throughput sequencing of 16S rRNA revealed that the associated microbial community of the sponges did not exhibit significant shifts after six weeks of transplantation at a eutrophic fish farm site compared to sponges grown at a coral reef or a seagrass area. However, sponges at the fish farm revealed higher abundance of the amoA gene, suggesting that microbiome members are responsive to increased ammonium levels at the site. The stable association between G. obtusa and its microbiome indicates that the sponge holobiont can withstand eutrophication pressure from mariculture.

A controlled aquarium system and approach to study the role of sponge-bacteria interactions using Aplysilla rosea and Vibrio natriegens

Sponge-bacteria interactions are very important due to their ecological and biological significance. To understand the impact of interactions between sponges and bacteria (both associated with and external to sponges) on sponge-associated microbial diversity, sponge metabolite profiles and bioactivity, we used a controlled aquarium system and designed an experimental approach that allows the study of sponge-bacteria interactions in a well-defined manner. To test the feasibility of this approach, this system was used to study the interaction between a sponge Aplysilla rosea and a marine bacterium commonly found in seawater, Vibrio natriegens. Sponge explants were exposed to V. natriegens, at 5 × 106 cfu/ml, and changes were monitored for 48 hours. Pyro-sequencing revealed significant shifts in microbial communities associated with the sponges after 24 to 48 hours. Both the control (sponge only without added bacteria) and Vibrio-exposed sponges showed a distinct shift in bacterial diversity and abundance with time. Vibrio exposure significantly increased bacterial diversity, the abundance of a number of taxa compared to control sponges. The result experimentally supports the notion of dynamic and concerted responses by the sponge when interacting with a bacterium, and demonstrates the feasibility of using this controlled aquarium system for the study of sponge-bacteria interactions.

High similarity in the microbiota of cold-water sponges of the Genus Mycale from two different geographical areas

Sponges belonging to genus Mycale are common and widely distributed across the oceans and represent a significant component of benthic communities in term of their biomass, which in many species is largely composed by bacteria. However, the microbial communities associated with Mycale species inhabiting different geographical areas have not been previously compared. Here, we provide the first detailed description of the microbiota of two Mycale species inhabiting the sub-Antarctic Magellan region (53°S) and the Western Antarctic Peninsula (62-64°S), two geographically distant areas (>1,300 km) with contrasting environmental conditions. The sponges Mycale (Aegogropila) magellanica and Mycale (Oxymycale) acerata are both abundant members of benthic communities in the Magellan region and in Antarctica, respectively. High throughput sequencing revealed a remarkable similarity in the microbiota of both sponge species, dominated by Proteobacteria and Bacteroidetes, with both species sharing more than 74% of the OTUs. In contrast, 16% and 10% of the OTUs were found only in either M. magellanica or M. acerata, respectively. Interestingly, despite slight differences in the relative abundance, the most dominant OTUs were present in both species, whereas the unique OTUs had very low abundances (less than 1% of the total abundance). These results show a significant overlap among the microbiota of both Mycale species and also suggest the existence of a low level of specificity of the most dominant symbiont groups.

The sponge holobiont in a changing ocean: from microbes to ecosystems

The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as "nested ecosystems." In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities-a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans.

Sponge Prokaryote Communities in Taiwanese Coral Reef and Shallow Hydrothermal Vent Ecosystems

Previously, it was believed that the prokaryote communities of typical 'low-microbial abundance' (LMA) or 'non-symbiont harboring' sponges were merely subsets of the prokaryote plankton community. Recent research has, however, shown that these sponges are dominated by particular clades of Proteobacteria or Cyanobacteria. Here, we expand on this research and assess the composition and putative functional profiles of prokaryotic communities from LMA sponges collected in two ecosystems (coral reef and hydrothermal vent) from vicinal islands of Taiwan with distinct physicochemical conditions. Six sponge species identified as Acanthella cavernosa (Bubarida), Echinodictyum asperum, Ptilocaulis spiculifer (Axinellida), Jaspis splendens (Tetractinellida), Stylissa carteri (Scopalinida) and Suberites sp. (Suberitida) were sampled in coral reefs in the Penghu archipelago. One sponge species provisionally identified as Hymeniacidon novo spec. (Suberitida) was sampled in hydrothermal vent habitat. Each sponge was dominated by a limited set of operational taxonomic units which were similar to sequences from organisms previously obtained from other LMA sponges. There was a distinct bacterial community between sponges collected in coral reef and in hydrothermal vents. The putative functional profile revealed that the prokaryote community from sponges collected in hydrothermal vents was significantly enriched for pathways related to DNA replication and repair.

Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks

Sponges (Porifera) are abundant and diverse members of benthic filter feeding communities in most marine ecosystems, from the deep sea to tropical reefs. A characteristic feature is the associated dense and diverse prokaryotic community present within the sponge mesohyl. Previous molecular genetic studies revealed the importance of host identity for the community composition of the sponge-associated microbiota. However, little is known whether sponge host-specific prokaryotic community patterns observed at 97% 16S rRNA gene sequence similarity are consistent at high taxonomic ranks (from genus to phylum level). In the present study, we investigated the prokaryotic community structure and variation of 24 sponge specimens (seven taxa) and three seawater samples from Sweden. Results show that the resemblance of prokaryotic communities at different taxonomic ranks is consistent with patterns present at 97% operational taxonomic unit level.

Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila

Microbial symbionts in sponges are ubiquitous, forming complex and highly diverse host-specific communities. Conspecific sponges display remarkable stability in their symbiont communities, both spatially and temporally, yet extreme fluctuations in environmental factors can cause shifts in host-symbiont associations. We previously demonstrated that the marine sponge Hymeniacidon heliophila displayed significant community-level differences in microbial symbiont diversity, structure and composition when sampled from intertidal and subtidal environments. Here, we conducted a 70-day reciprocal transplant experiment to directly test the effect of tidal exposure on the microbiome of H. heliophila, using next-generation Illumina sequencing of 16S rRNA gene sequences to characterize symbiont communities. While sponges transplanted between habitats displayed shifts in microbial communities after 70 days, temporal variation was the dominant factor affecting microbial community composition. Further, we identified core symbionts that persisted across these spatio-temporal scales and used a metagenomic approach to show that these dominant members of the microbiome of H. heliophila represent nitrogen cycling taxa that have the potential to contribute to a diverse array of nitrogen transformations in the sponge holobiont. Together, these results indicate that despite moderate spatio-temporal shifts in symbiont composition, core symbiont functions (e.g. nitrogen cycling) can be maintained in sponge microbiomes through functional redundancy.

Analysis of bacterial composition in marine sponges reveals the influence of host phylogeny and environment

Bacterial communities associated with sponges are influenced by environmental factors; however, some degree of genetic influence of the host on the microbiome is also expected. In this work, 16S rRNA gene amplicon sequencing revealed diverse bacterial phylotypes based on the phylogenies of three tropical sponges (Aplysina fulva, Aiolochroia crassa and Chondrosia collectrix). Despite their sympatric occurrence, the studied sponges presented different bacterial compositions that differed from those observed in seawater. However, lower dissimilarities in bacterial communities were observed within sponges from the same phylogenetic group. The relationships between operational taxonomic units (OTUs) recovered from the sponges and database sequences revealed associations among sequences from unrelated sponge species and sequences retrieved from diverse environmental samples. In addition, one Proteobacteria OTU retrieved from A. fulva was identical to sequences previously reported from A. fulva specimens collected along the Brazilian coast. Based on these results, we conclude that bacterial communities associated with marine sponges are shaped by host identity, while environmental conditions seem to be less important in shaping symbiont communities. This is the first study to assess bacterial communities associated with marine sponges in the remote St. Peter and St. Paul Archipelago using amplicon sequencing of the 16S rRNA gene.

Restructuring of the sponge microbiome favors tolerance to ocean acidification

Ocean acidification is increasing and affects many marine organisms. However, certain sponge species can withstand low-pH conditions. This may be related to their complex association with microbes. We hypothesized that species with greater microbial diversity may develop functional redundancy that could enable the holobiont to survive even if particular microbes are lost at low-pH conditions. We evaluated the effects of acidification on the growth and associated microbes of three ubiquitous Mediterranean sponges by exposing them to the present pH level and that predicted for the year 2100. We found marked differences among the species in the acquisition of new microbes, being high in Dysidea avara, moderate in Agelas oroides and null in Chondrosia reniformis; however, we did not observe variation in the overall microbiome abundance, richness or diversity. The relative abilities to alter the microbiomes contributes to survivorship in an OA scenario as demonstrated by lowered pH severely affecting the growth of C. reniformis, halving that of A. oroides, and unaffecting D. avara. Our results indicate that functional stability of the sponge holobiont to withstand future OA is species-specific and is linked to the species' ability to use horizontal transmission to modify the associated microbiome to adapt to environmental change.

In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity

Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities remain less understood. On tropical coral reefs, sponge habitats can span from shallow areas to deeper, mesophotic sites. These habitats differ in terms of environmental factors such as light, temperature, and food availability, as well as anthropogenic impact. In order to study the host specificity and potential influence of varying habitats on the sponge microbiota within a local area, four tropical reef sponges, Rhabdastrella globostellata, Callyspongia sp., Rhaphoxya sp., and Acanthella cavernosa, were collected from exposed shallow reef slopes and a deep reef drop-off. Based on 16S rRNA gene pyrosequencing profiles, beta diversity analyses revealed that each sponge species possessed a specific microbiota that was significantly different to those of the other species and exhibited attributes that are characteristic of high- and/or low-microbial-abundance sponges. These findings emphasize the influence of host identity on the associated microbiota. Dominant sponge- and seawater-associated bacterial phyla were Chloroflexi, Cyanobacteria, and Proteobacteria. Comparison of individual sponge taxa and seawater samples between shallow and deep reef sites revealed no significant variation in alpha diversity estimates, while differences in microbial beta diversity (variation in community composition) were significant for Callyspongia sp. sponges and seawater samples. Overall, the sponge-associated microbiota is significantly shaped by host identity across all samples, while the effect of habitat differentiation seems to be less predominant in tropical reef sponges.

Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens

Sponges are well known for hosting dense and diverse microbial communities, but how these associations vary with biogeography and environment is less clear. Here we compared the microbiome of an ecologically important sponge species, Carteriospongia foliascens, over a large geographic area and identified environmental factors likely responsible for driving microbial community differences between inshore and offshore locations using co-occurrence networks (NWs). The microbiome of C. foliascens exhibited exceptionally high microbial richness, with more than 9,000 OTUs identified at 97% sequence similarity. A large biogeographic signal was evident at the OTU level despite similar phyla level diversity being observed across all geographic locations. The C. foliascens bacterial community was primarily comprised of Gammaproteobacteria (34.2% ± 3.4%) and Cyanobacteria (32.2% ± 3.5%), with lower abundances of Alphaproteobacteria, Bacteroidetes, unidentified Proteobacteria, Actinobacteria, Acidobacteria and Deltaproteobacteria. Co-occurrence NWs revealed a consistent increase in the proportion of Cyanobacteria over Bacteroidetes between turbid inshore and oligotrophic offshore locations, suggesting that the specialist microbiome of C. foliascens is driven by environmental factors.

Intraspecific Variation in Microbial Symbiont Communities of the Sun Sponge, Hymeniacidon heliophila, from Intertidal and Subtidal Habitats

Sponges host diverse and complex communities of microbial symbionts that display a high degree of host specificity. The microbiomes of conspecific sponges are relatively constant, even across distant locations, yet few studies have directly examined the influence of abiotic factors on intraspecific variation in sponge microbial community structure. The contrast between intertidal and subtidal environments is an ideal system to assess the effect of environmental variation on sponge-microbe symbioses, producing two drastically different environments on a small spatial scale. Here, we characterized the microbial communities of individual intertidal and subtidal Hymeniacidon heliophila sponges, ambient seawater, and sediment from a North Carolina oyster reef habitat by partial (Illumina sequencing) and nearly full-length (clone libraries) 16S rRNA gene sequence analyses. Clone library sequences were compared to H. heliophila symbiont communities from the Gulf of Mexico and Brazil, revealing strong host specificity of dominant symbiont taxa across expansive geographic distances. Sediment and seawater samples yielded clearly distinct microbial communities from those found in H. heliophila. Despite the close proximity of the sponges sampled, significant differences between subtidal and intertidal sponges in the diversity, structure, and composition of their microbial communities were detected. Differences were driven by changes in the relative abundance of a few dominant microbial symbiont taxa, as well as the presence or absence of numerous rare microbial taxa. These findings suggest that extreme abiotic fluctuations, such as periodic air exposure in intertidal habitats, can drive intraspecific differences in complex host-microbe symbioses.

Characterization of Bacterial, Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem

Sponge-associated microbial communities include members from the three domains of life. In the case of bacteria, they are diverse, host specific and different from the surrounding seawater. However, little is known about the diversity and specificity of Eukarya and Archaea living in association with marine sponges. This knowledge gap is even greater regarding sponges from regions other than temperate and tropical environments. In Antarctica, marine sponges are abundant and important members of the benthos, structuring the Antarctic marine ecosystem. In this study, we used high throughput ribosomal gene sequencing to investigate the three-domain diversity and community composition from eight different Antarctic sponges. Taxonomic identification reveals that they belong to families Acarnidae, Chalinidae, Hymedesmiidae, Hymeniacidonidae, Leucettidae, Microcionidae, and Myxillidae. Our study indicates that there are different diversity and similarity patterns between bacterial/archaeal and eukaryote microbial symbionts from these Antarctic marine sponges, indicating inherent differences in how organisms from different domains establish symbiotic relationships. In general, when considering diversity indices and number of phyla detected, sponge-associated communities are more diverse than the planktonic communities. We conclude that three-domain microbial communities from Antarctic sponges are different from surrounding planktonic communities, expanding previous observations for Bacteria and including the Antarctic environment. Furthermore, we reveal differences in the composition of the sponge associated bacterial assemblages between Antarctic and tropical-temperate environments and the presence of a highly complex microbial eukaryote community, suggesting a particular signature for Antarctic sponges, different to that reported from other ecosystems.

Marine sponge derived natural products between 2001 and 2010: trends and opportunities for discovery of bioactives

Marine sponges belonging to the phylum Porifera (Metazoa), evolutionarily the oldest animals are the single best source of marine natural products. The present review presents a comprehensive overview of the source, taxonomy, country of origin or geographical position, chemical class, and biological activity of sponge-derived new natural products discovered between 2001 and 2010. The data has been analyzed with a view to gaining an outlook on the future trends and opportunities in the search for new compounds and their sources from marine sponges.