Holobiont dysbiosis or acclimatation? Shift in the microbial taxonomic diversity and functional composition of a cosmopolitan sponge subjected to chronic pollution in a Patagonian bay

Dysbiosis and acclimatization are two starkly opposing outcomes of altered holobiont associations in response to environmental pollution. This study assesses whether shifts in microbial taxonomic composition and functional profiles of the cosmopolitan sponge Hymeniacidon perlevis indicate dysbiotic or acclimatized responses to water pollution. To do so, sponge and water samples were collected in a semi-enclosed environment (San Antonio Bay, Patagonia, Argentina) from variably polluted sites (i.e., eutrophication, heavy metal contamination). We found significant differences in the microbiome of H. perlevis with respect to the pollution history of the sites. Several indicators suggested that acclimatization, rather than dysbiosis, explained the microbiome response to higher pollution: 1) the distinction of the sponge microbiome from the water microbiome; 2) low similarity between the sponge and water microbiomes at the most polluted site; 3) the change in microbiome composition between sponges from the different sites; 4) a high similarity in the microbiome among sponge individuals within sites; 5) a similar ratio of common sponge microbes to opportunistic microbes between sponges at the most and least polluted sites; and 6) a distinctive functional profile of the sponge microbiome at the most polluted site. This profile indicated a more expansive metabolic repertoire, including the degradation of pollutants and the biosynthesis of secondary metabolites, suggesting a relevant role of these microbial communities in the adaptation of the holobiont to organic pollution. Our results shed light on the rearrangement of the H. perlevis microbiome that could allow it to successfully colonize sites with high anthropogenic impact while resisting dysbiosis.

The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions

Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.

High compositional and functional similarity in the microbiome of deep-sea sponges

Sponges largely depend on their symbiotic microbes for their nutrition, health, and survival. This is especially true in high microbial abundance (HMA) sponges, where filtration is usually deprecated in favor of a larger association with prokaryotic symbionts. Sponge-microbiome association is substantially less understood for deep-sea sponges than for shallow water species. This is most unfortunate, since HMA sponges can form massive sponge grounds in the deep sea, where they dominate the ecosystems, driving their biogeochemical cycles. Here, we assess the microbial transcriptional profile of three different deep-sea HMA sponges in four locations of the Cantabrian Sea and compared them to shallow water HMA and LMA (low microbial abundance) sponge species. Our results reveal that the sponge microbiome has converged in a fundamental metabolic role for deep-sea sponges, independent of taxonomic relationships or geographic location, which is shared in broad terms with shallow HMA species. We also observed a large number of redundant microbial members performing the same functions, likely providing stability to the sponge inner ecosystem. A comparison between the community composition of our deep-sea sponges and another 39 species of HMA sponges from deep-sea and shallow habitats, belonging to the same taxonomic orders, suggested strong homogeneity in microbial composition (i.e. weak species-specificity) in deep sea species, which contrasts with that observed in shallow water counterparts. This convergence in microbiome composition and functionality underscores the adaptation to an extremely restrictive environment with the aim of exploiting the available resources.

Validation of key sponge symbiont pathways using genome-centric metatranscriptomics

The sponge microbiome underpins host function through provision and recycling of essential nutrients in a nutrient poor environment. Genomic data suggest that carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism and supplementation of B-vitamins are central microbial functions. However, validation beyond the genomic potential of sponge symbiont pathways is rarely explored. To evaluate metagenomic predictions, we sequenced the metagenomes and metatranscriptomes of three common coral reef sponges: Ircinia ramosa, Ircinia microconulosa and Phyllospongia foliascens. Multiple carbohydrate active enzymes were expressed by Poribacteria, Bacteroidota and Cyanobacteria symbionts, suggesting these lineages have a central role in assimilating dissolved organic matter. Expression of entire pathways for carbon fixation and multiple sulphur compound transformations were observed in all sponges. Gene expression for anaerobic nitrogen metabolism (denitrification and nitrate reduction) were more common than aerobic metabolism (nitrification), where only the I. ramosa microbiome expressed the nitrification pathway. Finally, while expression of the biosynthetic pathways for B-vitamins was common, the expression of additional transporter genes was far more limited. Overall, we highlight consistencies and disparities between metagenomic and metatranscriptomic results when inferring microbial activity, while uncovering new microbial taxa that contribute to the health of their sponge host via nutrient exchange.

Sponge functional roles in a changing world

Sponges are ecologically important benthic organisms with many important functional roles. However, despite increasing global interest in the functions that sponges perform, there has been limited focus on how such functions will be impacted by different anthropogenic stressors. In this review, we describe the progress that has been made in our understanding of the functional roles of sponges over the last 15 years and consider the impacts of anthropogenic stressors on these roles. We split sponge functional roles into interactions with the water column and associations with other organisms. We found evidence for an increasing focus on functional roles among sponge-focused research articles, with our understanding of sponge-mediated nutrient cycling increasing substantially in recent years. From the information available, many anthropogenic stressors have the potential to negatively impact sponge pumping, and therefore have the potential to cause ecosystem level impacts. While our understanding of the importance of sponges has increased in the last 15 years, much more experimental work is required to fully understand how sponges will contribute to reef ecosystem function in future changing oceans.

From friends to foes: fungi could be emerging marine sponge pathogens under global change scenarios

Global change, experienced in the form of ocean warming and pollution by man-made goods and xenobiotics, is rapidly affecting reef ecosystems and could have devastating consequences for marine ecology. Due to their critical role in regulating marine food webs and trophic connections, sponges are an essential model for studying and forecasting the impact of global change on reef ecosystems. Microbes are regarded as major contributors to the health and survival of sponges in marine environments. While most culture-independent studies on sponge microbiome composition to date have focused on prokaryotic diversity, the importance of fungi in holobiont behavior has been largely overlooked. Studies focusing on the biology of sponge fungi are uncommon. Thus, our current understanding is quite limited regarding the interactions and “crosstalk” between sponges and their associated fungi. Anthropogenic activities and climate change may reveal sponge-associated fungi as novel emerging pathogens. Global change scenarios could trigger the expression of fungal virulence genes and unearth new opportunistic pathogens, posing a risk to the health of sponges and severely damaging reef ecosystems. Although ambitious, this hypothesis has not yet been proven. Here we also postulate as a pioneering hypothesis that manipulating sponge-associated fungal communities may be a new strategy to cope with the threats posed to sponge health by pathogens and pollutants. Additionally, we anticipate that sponge-derived fungi might be used as novel sponge health promoters and beneficial members of the resident sponge microbiome in order to increase the sponge's resistance to opportunistic fungal infections under a scenario of global change.

Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta

Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.

Future ocean conditions induce necrosis, microbial dysbiosis and nutrient cycling imbalance in the reef sponge Stylissa flabelliformis

Oceans are rapidly warming and acidifying in the context of climate change, threatening sensitive marine biota including coral reef sponges. Ocean warming (OW) and ocean acidification (OA) can impact host health and associated microbiome, but few studies have investigated these effects, which are generally studied in isolation, on a specific component of the holobiont. Here we present a comprehensive view of the consequences of simultaneous OW and OA for the tropical sponge Stylissa flabelliformis. We found no interactive effect on the host health or microbiome. Furthermore, OA (pH 7.6 versus pH 8.0) had no impact, while OW (31.5 °C versus 28.5 °C) caused tissue necrosis, as well as dysbiosis and shifts in microbial functions in healthy tissue of necrotic sponges. Major taxonomic shifts included a complete loss of archaea, reduced proportions of Gammaproteobacteria and elevated relative abundances of Alphaproteobacteria. OW weakened sponge-microbe interactions, with a reduced capacity for nutrient exchange and phagocytosis evasion, indicating lower representations of stable symbionts. The potential for microbially-driven nitrogen and sulphur cycling was reduced, as was amino acid metabolism. Crucially, the dysbiosis annihilated the potential for ammonia detoxification, possibly leading to accumulation of toxic ammonia, nutrient imbalance, and host tissue necrosis. Putative defence against reactive oxygen species was greater at 31.5 °C, perhaps as microorganisms capable of resisting temperature-driven oxidative stress were favoured. We conclude that healthy symbiosis in S. flabelliformis is unlikely to be disrupted by future OA but will be deeply impacted by temperatures predicted for 2100 under a "business-as-usual" carbon emission scenario.

Bacterial aerobic methane cycling by the marine sponge-associated microbiome

BACKGROUND

Methanotrophy by the sponge-hosted microbiome has been mainly reported in the ecological context of deep-sea hydrocarbon seep niches where methane is either produced geothermically or via anaerobic methanogenic archaea inhabiting the sulfate-depleted sediments. However, methane-oxidizing bacteria from the candidate phylum Binatota have recently been described and shown to be present in oxic shallow-water marine sponges, where sources of methane remain undescribed.

RESULTS

Here, using an integrative -omics approach, we provide evidence for sponge-hosted bacterial methane synthesis occurring in fully oxygenated shallow-water habitats. Specifically, we suggest methane generation occurs via at least two independent pathways involving methylamine and methylphosphonate transformations that, concomitantly to aerobic methane production, generate bioavailable nitrogen and phosphate, respectively. Methylphosphonate may be sourced from seawater continuously filtered by the sponge host. Methylamines may also be externally sourced or, alternatively, generated by a multi-step metabolic process where carnitine, derived from sponge cell debris, is transformed to methylamine by different sponge-hosted microbial lineages. Finally, methanotrophs specialized in pigment production, affiliated to the phylum Binatota, may provide a photoprotective function, closing a previously undescribed C₁-metabolic loop that involves both the sponge host and specific members of the associated microbial community.

CONCLUSION

Given the global distribution of this ancient animal lineage and their remarkable water filtration activity, sponge-hosted methane cycling may affect methane supersaturation in oxic coastal environments. Depending on the net balance between methane production and consumption, sponges may serve as marine sources or sinks of this potent greenhouse gas. Video Abstract.

Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp

Sponges are widely distributed in the global ocean and harbor diverse symbiotic microbes with mutualistic relationships. However, sponge symbionts in the deep sea remain poorly studied at the genome level. Here, we report a new glass sponge species of the genus Bathydorus and provide a genome-centric view of its microbiome. We obtained 14 high-quality prokaryotic metagenome-assembled genomes (MAGs) affiliated with the phyla Nitrososphaerota, Pseudomonadota, Nitrospirota, Bdellovibrionota, SAR324, Bacteroidota, and Patescibacteria. In total, 13 of these MAGs probably represent new species, suggesting the high novelty of the deep-sea glass sponge microbiome. An ammonia-oxidizing Nitrososphaerota MAG B01, which accounted for up to 70% of the metagenome reads, dominated the sponge microbiomes. The B01 genome had a highly complex CRISPR array, which likely represents an advantageous evolution toward a symbiotic lifestyle and forceful ability to defend against phages. A sulfur-oxidizing Gammaproteobacteria species was the second most dominant symbiont, and a nitrite-oxidizing Nitrospirota species could also be detected, but with lower relative abundance. Bdellovibrio species represented by two MAGs, B11 and B12, were first reported as potential predatory symbionts in deep-sea glass sponges and have undergone dramatic genome reduction. Comprehensive functional analysis indicated that most of the sponge symbionts encoded CRISPR-Cas systems and eukaryotic-like proteins for symbiotic interactions with the host. Metabolic reconstruction further illustrated their essential roles in carbon, nitrogen, and sulfur cycles. In addition, diverse putative phages were identified from the sponge metagenomes. Our study expands the knowledge of microbial diversity, evolutionary adaption, and metabolic complementarity in deep-sea glass sponges.

Uptake of inorganic and organic phosphorus compounds by two marine sponges and their associated bacterial communities in aquaria

Marine sponges are abundant filter-feeders in benthic ecosystems and many host copious microorganisms. Sponges and their symbionts have emerged as major players within marine biogeochemical cycles, facilitating uptake and release of carbon, nitrogen, and sulfur. Sponge holobionts' role in transforming dissolved carbon and nitrogen is well established; however, the same depth of understanding has not yet been extended to phosphorus. In this aquaria-based study, ³² P-labelled orthophosphate and ATP were used to determine that two sponges, Lendenfeldia chondrodes and Hymeniacidon heliophila, both take up ambient dissolved inorganic phosphate (DIP) and dissolved organic phosphorus (DOP). Subsequent genetic analyses and chemical extraction showed that sponge symbionts have the potential to synthesise polyphosphate (poly-P) and that this energy-rich form of stored phosphorus is present in both sponges. L. chondrodes, an oligotrophic sponge with a microbiome dominated by cyanobacteria, stores more phosphorus as poly-P (6%-8% of total phosphorus) than H. heliophila (0.55%), a eutrophic sponge with low cyanobacterial abundance. DIP/DOP uptake, as well as poly-P storage, may be driven by two factors: cyanobacterial abundance and nutrient availability. Considering their prevalence in phosphorus-limited ecosystems and their ability to pump large amounts of seawater, sponge holobionts are likely to be key players within benthic phosphorus cycles.

Fluxes of the Amazon River plume nutrients and microbes into marine sponges

Sponges have co-evolved with microbes for over 400 myr. Previous studies have demonstrated that sponges can be classified according to the abundance of microbes in their tissues as Low Microbial Abundance (LMA) and High Microbial Abundance (HMA). While LMA sponges rely mainly on water column microbes, HMA appear to rely much more on symbiotic fermentative and autotrophic microbes maintained in their tissues. However, it is unclear if this pattern holds when comparing different species of tropical sponges under extreme nutrient conditions and sediment loads in the water column, such as the Great Amazon Reef System (GARS), which covers an area of ~56,000 km² off the Amazon River mouth. Sponges are the major GARS benthic components. However, these sponges' microbiome across the GARS is still unknown. Here, we investigated water quality, isotopic values (δ¹³C and δ¹⁵N), metagenomic and lipidomic profiles of sponges obtained from different sectors throughout the GARS. >180 million shotgun metagenomic reads were annotated, covering 22 sponge species. Isotopic and lipidomic analyses suggested LMA sponges rely on the Amazon River Plume for nutrition. HMA sponges (N = 15) had higher Roseiflexus and Nitrospira abundance, whereas LMA sponges (N = 7) had higher Prochlorococcus and Pelagibacter abundance. Functional data revealed that the LMA sponge microbiomes had greater number of sequences related to phages and prophages as well as electron transport and photophosphorylation which may be related to photosynthetic processes associated with the Prochlorococcus and Synechococcus found in the LMA. The higher phages abundance in LMA sponges could be related to these holobionts' reduced defense towards phage infection. Meanwhile, HMA sponge microbiomes had higher Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR abundance, which may be involved in defense against phage infection. This study sheds light on the nutrient fluxes and microbes from the Amazon River plume into the sponge holobionts.

Microbiome diversity and metabolic capacity determines the trophic ecology of the holobiont in Caribbean sponges

Sponges are increasingly recognized as an ecologically important taxon on coral reefs, representing significant biomass and biodiversity where sponges have replaced scleractinian corals. Most sponge species can be divided into two symbiotic states based on symbiont community structure and abundance (i.e., the microbiome), and are characterized as high microbial abundance (HMA) or low microbial abundance (LMA) sponges. Across the Caribbean, sponge species of the HMA or LMA symbiotic states differ in metabolic capacity, as well as their trophic ecology. A metagenetic analysis of symbiont 16 S rRNA and metagenomes showed that HMA sponge microbiomes are more functionally diverse than LMA microbiomes, offer greater metabolic functional capacity and redundancy, and encode for the biosynthesis of secondary metabolites. Stable isotope analyses showed that HMA and LMA sponges primarily consume dissolved organic matter (DOM) derived from external autotrophic sources, or live particulate organic matter (POM) in the form of bacterioplankton, respectively, resulting in a low degree of resource competition between these symbiont states. As many coral reefs have undergone phase shifts from coral- to macroalgal-dominated reefs, the role of DOM, and the potential for future declines in POM due to decreased picoplankton productivity, may result in an increased abundance of chemically defended HMA sponges on tropical coral reefs.

Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges

Sponges are known for hosting diverse communities of microbial symbionts, but despite persistent interest in the sponge microbiome, most research has targeted marine sponges; freshwater sponges have been the focus of less than a dozen studies. Here, we used 16 S rRNA gene amplicon sequencing and shotgun metagenomics to characterize the microbiome of the freshwater sponge Ephydatia muelleri and identify potential indicators of sponge-microbe mutualism. Using samples collected from the Sooke, Nanaimo, and Cowichan Rivers on Vancouver Island, British Columbia, we show that the E. muelleri microbiome is distinct from the ambient water and adjacent biofilms and is dominated by Sediminibacterium, Comamonas, and unclassified Rhodospirillales. We also observed phylotype-level differences in sponge microbiome taxonomic composition among different rivers. These differences were not reflected in the ambient water, suggesting that other environmental or host-specific factors may drive the observed geographic variation. Shotgun metagenomes and metagenome-assembled genomes further revealed that freshwater sponge-associated bacteria share many genomic similarities with marine sponge microbiota, including an abundance of defense-related proteins (CRISPR, restriction-modification systems, and transposases) and genes for vitamin B12 production. Overall, our results provide foundational information on the composition and function of freshwater sponge-associated microbes, which represent an important yet underappreciated component of the global sponge microbiome.

Global patterns in symbiont selection and transmission strategies in sponges

Sponges host dense and diverse communities of microbes (known as the microbiome) beneficial for the host nutrition and defense. Symbionts in turn receive shelter and metabolites from the sponge host, making their relationship beneficial for both partners. Given that sponge-microbes associations are fundamental for the survival of both, especially the sponge, such relationship is maintained through their life and even passed on to the future generations. In many organisms, the microbiome has profound effects on the development of the host, but the influence of the microbiome on the reproductive and developmental pathways of the sponges are less understood. In sponges, microbes are passed on to oocytes, sperm, embryos, and larvae (known as vertical transmission), using a variety of methods that include direct uptake from the mesohyl through phagocytosis by oocytes to indirect transmission to the oocyte by nurse cells. Such microbes can remain in the reproductive elements untouched, for transfer to offspring, or can be digested to make the yolky nutrient reserves of oocytes and larvae. When and how those decisions are made are fundamentally unanswered questions in sponge reproduction. Here we review the diversity of vertical transmission modes existent in the entire phylum Porifera through detailed imaging using electron microscopy, available metabarcoding data from reproductive elements, and macroevolutionary patterns associated to phylogenetic constraints. Additionally, we examine the fidelity of this vertical transmission and possible reasons for the observed variability in some developmental stages. Our current understanding in marine sponges, however, is that the adult microbial community is established by a combination of both vertical and horizontal (acquisition from the surrounding environment in each new generation) transmission processes, although the extent in which each mode shapes the adult microbiome still remains to be determined. We also assessed the fundamental role of filtration, the cellular structures for acquiring external microbes, and the role of the host immune system, that ultimately shapes the stable communities of prokaryotes observed in adult sponges.

Meta-transcriptomic comparison of two sponge holobionts feeding on coral- and macroalgal-dissolved organic matter

Background

Sponge holobionts (i.e., the host and its associated microbiota) play a key role in the cycling of dissolved organic matter (DOM) in marine ecosystems. On coral reefs, an ecological shift from coral-dominated to algal-dominated ecosystems is currently occurring. Given that benthic corals and macroalgae release different types of DOM, in different abundances and with different bioavailability to sponge holobionts, it is important to understand how the metabolic activity of the host and associated microbiota change in response to the exposure to both DOM sources. Here, we look at the differential gene expression of two sponge holobionts 6 hours after feeding on naturally sourced coral- and macroalgal-DOM using RNA sequencing and meta-transcriptomic analysis.

Results

We found a slight, but significant differential gene expression in the comparison between the coral- and macroalgal-DOM treatments in both the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Haliclona vansoesti. In the hosts, processes that regulate immune response, signal transduction, and metabolic pathways related to cell proliferation were elicited. In the associated microbiota carbohydrate metabolism was upregulated in both treatments, but coral-DOM induced further lipid and amino acids biosynthesis, while macroalgal-DOM caused a stress response. These differences could be driven by the presence of distinct organic macronutrients in the two DOM sources and of small pathogens or bacterial virulence factors in the macroalgal-DOM.

Conclusions

This work provides two new sponge meta-transcriptomes and a database of putative genes and genetic pathways that are involved in the differential processing of coral- versus macroalgal-DOM as food source to sponges with high and low abundances of associated microbes. These pathways include carbohydrate metabolism, signaling pathways, and immune responses. However, the differences in the meta-transcriptomic responses of the sponge holobionts after 6 hours of feeding on the two DOM sources were small. Longer-term responses to both DOM sources should be assessed to evaluate how the metabolism and the ecological function of sponges will be affected when reefs shift from coral towards algal dominance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08893-y.

Microbiome composition of the marine sponge Cliona varians at the Neotropical Southern Caribbean Sea displays a predominant core of Rhizobiales and Nitrosopumilaceae

AIMS

This work aims to characterize the microbial diversity of the encrusting sponge Cliona varians, a pore-forming and coral reef bioeroding marine sponge of emerging spread related to ocean acidification.

METHODS AND RESULTS

We analyzed the microbiome composition by 16S V4 amplicon next-generation sequencing in a community of the bioeroding coral-reef encrusting/excavating marine sponge Cliona varians thriving at the Southern Caribbean Sea. 87.21% and 6.76% of the sequences retrieved were assigned to the domain Bacteria and Archaea. The most predominant operational taxonomic units were classified as members of the order Rhizobiales and family Nitrosopumilaceae, representing members of not yet characterized genera. Features found strictly conserved in the strain/genomic representatives reported in those microbial taxa are nitrogen fixation and transformation.

CONCLUSION

Our results suggest, in accordance with recent results, that these microbiome members and associated functions could be contributing to the biological fitness of the sponge to be able to colonize and bioerode in environments with low access and scarce availability of nitrogen source.

SIGNIFICANCE AND IMPACT OF STUDY

Coral reefs bioresources such as sponge holobionts are intriguing and complex ecosystems units. This study contributes to the knowledge of how C. varians microbiota is composed or shaped, which is crucial to understand its ecological functions.

Near-future extreme temperatures affect physiology, morphology and recruitment of the temperate sponge Crella incrustans

Current rates of greenhouse gas emissions are leading to a rapid increase in global temperatures and a greater occurrence of extreme climatic events such as marine heatwaves. In this study, we assessed the effects of thermal conditions predicted to occur within the next 40 years (SSP3-7.0 scenario of IPCC, 2021) on the respiration rate, buoyant weight, morphology and recruitment of the temperate model sponge Crella incrustans. Under predicted average temperatures (+ 2.5 °C, over the local mean), C. incrustans did not show any physiological and morphological changes compared to current conditions. However, when exposed to a simulated marine heatwave (16 days duration and a thermal peak at 22 °C), there was a large increase in sponge respiration rate, significant weight loss resulting from tissue regression, and sponge mortality. The simulated marine heatwave resulted also in a shorter period of recruitment, lower recruitment rate and higher mortality of settlers. Despite the tissue regression, the majority of sponges that survived the extreme temperatures showed respiration rates similar to controls 13 days after the thermal peak, indicating some resilience of C. incrustans to extreme thermal events. Our study shows that marine heatwaves will significantly impact the physiology, morphology, and recruitment of temperate sponges under near-future conditions, but that these sponges are likely to persist in warmer oceans.

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.

Marine sponges maintain stable bacterial communities between reef sites with different coral to algae cover ratios

Marine sponges play a major ecological role in recycling resources on coral reef ecosystems. The cycling of resources may largely depend on the stability of the host-microbiome interactions and their susceptibility to altered environmental conditions. Given the current coral to algal phase shift on coral reefs, we investigated whether the sponge-associated bacterial communities of four sponge species, with either high or low microbial abundances (HMA and LMA), remain stable at two reefs sites with different coral to algae cover ratios. Additionally, we assessed the bacterial community composition of two of these sponge species before and after a reciprocal transplantation experiment between the sites. An overall stable bacterial community composition was maintained across the two sites in all sponge species, with a high degree of host-specificity. Furthermore, the core bacterial communities of the sponges remained stable also after a 21-day transplantation period, although a minor shift was observed in less abundant taxa (< 1%). Our findings support the conclusion that host identity and HMA-LMA status are stronger traits in shaping bacterial community composition than habitat. Nevertheless, long-term microbial monitoring of sponges along with benthic biomass and water quality assessments are needed for identifying ecosystem tolerance ranges and tipping points in ongoing coral reef phase shifts.

Streptomyces poriferorum sp. nov., a novel marine sponge-derived Actinobacteria species expressing anti-MRSA activity

Marine sponges represent a rich source of uncharacterized microbial diversity, and many are host to microorganisms that produce biologically active specialized metabolites. Here, a polyphasic approach was used to characterize two Actinobacteria strains, P01-B04^T and P01-F02, that were isolated from the marine sponges Geodia barretti (Bowerbank, 1858) and Antho dichotoma (Esper, 1794), respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains P01-B04^T and P01-F02 are closely related to Streptomyces beijiangensis DSM 41794^T, Streptomyces laculatispora NRRL B-24909^T, and Streptomyces brevispora NRRL B-24910^T. The two strains showed nearly identical 16S rRNA gene sequences (99.93%), and the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness values were 99.96% and 99.6%, respectively, suggesting that these strains are affiliated with the same species. Chemotaxonomic and culture characteristics of both strains were also consistent with the genus Streptomyces, while phenotypic properties, genome-based comparisons, and phylogenomic analyses distinguished strains P01-B04^T and P01-F02 from their closest phylogenetic relatives. In silico analysis predicted that the 8.9 Mb genome of P01-B04^T contains at least 41 biosynthetic gene clusters (BGCs) encoding secondary metabolites, indicating that this strain could express diverse bioactive metabolites; in support of this prediction, this strain expressed antibacterial activity against Gram-positive bacteria including a clinical isolate of methicillin-resistant Staphylococcus aureus (MRSA) EAMC30. Based on these results, the marine sponge-associated isolates represent a novel species of the genus Streptomyces, for which the name Streptomyces poriferorum sp. nov. is proposed, with P01-B04^T (=DSM 111306^T = CCM 9048^T) as the type strain.

Ocean Acidification and Direct Interactions Affect Coral, Macroalga, and Sponge Growth in the Florida Keys

Coral reef community composition, function, and resilience have been altered by natural and anthropogenic stressors. Future anthropogenic ocean and coastal acidification (together termed “acidification”) may exacerbate this reef degradation. Accurately predicting reef resilience requires an understanding of not only direct impacts of acidification on marine organisms but also indirect effects on species interactions that influence community composition and reef ecosystem functions. In this 28-day experiment, we assessed the effect of acidification on coral–algal, coral–sponge, and algal–sponge interactions. We quantified growth of corals (Siderastrea radians), fleshy macroalgae (Dictyota spp.), and sponges (Pione lampa) that were exposed to local summer ambient (603 μatm) or elevated (1105 μatm) pCO2 seawater. These species are common to hard-bottom communities, including shallow reefs, in the Florida Keys. Each individual was maintained in isolation or paired with another organism. Coral growth (net calcification) was similar across seawater pCO2 and interaction treatments. Fleshy macroalgae had increased biomass when paired with a sponge but lost biomass when growing in isolation or paired with coral. Sponges grew more volumetrically in the elevated seawater pCO2 treatment (i.e., under acidification conditions). Although these results are limited in temporal and spatial scales due to the experimental design, they do lend support to the hypothesis that acidification may facilitate a shift towards increased sponge and macroalgae abundance by directly benefiting sponge growth which in turn may provide more dissolved inorganic nitrogen to macroalgae in the Florida Keys.

Assessing the Diversity and Biomedical Potential of Microbes Associated With the Neptune's Cup Sponge, Cliona patera

Marine sponges are known to host a complex microbial consortium that is essential to the health and resilience of these benthic invertebrates. These sponge-associated microbes are also an important source of therapeutic agents. The Neptune's Cup sponge, Cliona patera, once believed to be extinct, was rediscovered off the southern coast of Singapore in 2011. The chance discovery of this sponge presented an opportunity to characterize the prokaryotic community of C. patera. Sponge tissue samples were collected from the inner cup, outer cup and stem of C. patera for 16S rRNA amplicon sequencing. C. patera hosted 5,222 distinct OTUs, spanning 26 bacterial phyla, and 74 bacterial classes. The bacterial phylum Proteobacteria, particularly classes Gammaproteobacteria and Alphaproteobacteria, dominated the sponge microbiome. Interestingly, the prokaryotic community structure differed significantly between the cup and stem of C. patera, suggesting that within C. patera there are distinct microenvironments. Moreover, the cup of C. patera had lower diversity and evenness as compared to the stem. Quorum sensing inhibitory (QSI) activities of selected sponge-associated marine bacteria were evaluated and their organic extracts profiled using the MS-based molecular networking platform. Of the 110 distinct marine bacterial strains isolated from sponge samples using culture-dependent methods, about 30% showed quorum sensing inhibitory activity. Preliminary identification of selected QSI active bacterial strains revealed that they belong mostly to classes Alphaproteobacteria and Bacilli. Annotation of the MS/MS molecular networkings of these QSI active organic extracts revealed diverse classes of natural products, including aromatic polyketides, siderophores, pyrrolidine derivatives, indole alkaloids, diketopiperazines, and pyrone derivatives. Moreover, potential novel compounds were detected in several strains as revealed by unique molecular families present in the molecular networks. Further research is required to determine the temporal stability of the microbiome of the host sponge, as well as mining of associated bacteria for novel QS inhibitors.

DNA-stable isotope probing (DNA-SIP) identifies marine sponge-associated bacteria actively utilizing dissolved organic matter (DOM)

Sponges possess exceptionally diverse associated microbial communities and play a major role in (re)cycling of dissolved organic matter (DOM) in marine ecosystems. Linking sponge-associated community structure with DOM utilization is essential to understand host-microbe interactions in the uptake, processing, and exchange of resources. We coupled, for the first time, DNA-stable isotope probing (DNA-SIP) with 16S rRNA amplicon sequencing in a sponge holobiont to identify which symbiotic bacterial taxa are metabolically active in DOM uptake. Parallel incubation experiments with the sponge Plakortis angulospiculatus were amended with equimolar quantities of unlabelled (¹² C) and labelled (¹³ C) DOM. Seven bacterial amplicon sequence variants (ASVs), belonging to the phyla PAUC34f, Proteobacteria, Poribacteria, Nitrospirae, and Chloroflexi, were identified as the first active consumers of DOM. Our results support the predictions that PAUC34f, Poribacteria, and Chloroflexi are capable of organic matter degradation through heterotrophic carbon metabolism, while Nitrospirae may have a potential mixotrophic metabolism. We present a new analytical application of DNA-SIP to detect substrate incorporation into a marine holobiont with a complex associated bacterial community and provide new experimental evidence that links the identity of diverse sponge-associated bacteria to the consumption of DOM.

Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea

Marine sponges are excellent examples of invertebrate-microbe symbioses. In this holobiont, the partnership has elegantly evolved by either transmitting key microbial associates through the host germline and/or capturing microorganisms from the surrounding seawater. We report here on the prokaryotic microbiota during different developmental stages of Plakina cyanorosea and their surrounding environmental samples by a 16S rRNA metabarcoding approach. In comparison with their source adults, larvae housed slightly richer and more diverse microbial communities, which are structurally more related to the environmental microbiota. In addition to the thaumarchaeal Nitrosopumilus, parental sponges were broadly dominated by Alpha- and Gamma-proteobacteria, while the offspring were particularly enriched in the Vibrionales, Alteromonodales, Enterobacterales orders and the Clostridia and Bacteroidia classes. An enterobacterial operational taxonomic unit (OTU) was the dominant member of the strict core microbiota. The most abundant and unique OTUs were not significantly enriched amongst the microbiomes from host specimens included in the sponge microbiome project. In a wider context, Oscarella and Plakina are the sponge genera with higher divergence in their associated microbiota compared to their Homoscleromorpha counterparts. Our results indicate that P. cyanorosea is a low microbial abundance sponge (LMA), which appears to heavily depend on the horizontal transmission of its microbial partners that likely help the sponge host in the adaptation to its habitat.

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.

Microbial symbionts and ecological divergence of Caribbean sponges: A new perspective on an ancient association

Marine sponges host diverse communities of microbial symbionts that expand the metabolic capabilities of their host, but the abundance and structure of these communities is highly variable across sponge species. Specificity in these interactions may fuel host niche partitioning on crowded coral reefs by allowing individual sponge species to exploit unique sources of carbon and nitrogen, but this hypothesis is yet to be tested. Given the presence of high sponge biomass and the coexistence of diverse sponge species, the Caribbean Sea provides a unique system in which to investigate this hypothesis. To test for ecological divergence among sympatric Caribbean sponges and investigate whether these trends are mediated by microbial symbionts, we measured stable isotope (δ13C and δ15N) ratios and characterized the microbial community structure of sponge species at sites within four regions spanning a 1700 km latitudinal gradient. There was a low (median of 8.2 %) overlap in the isotopic niches of sympatric species; in addition, host identity accounted for over 75% of the dissimilarity in both δ13C and δ15N values and microbiome community structure among individual samples within a site. There was also a strong phylogenetic signal in both δ15N values and microbial community diversity across host phylogeny, as well as a correlation between microbial community structure and variation in δ13C and δ15N values across samples. Together, this evidence supports a hypothesis of strong evolutionary selection for ecological divergence across sponge lineages and suggests that this divergence is at least partially mediated by associations with microbial symbionts.

Coral Reef Microorganisms in a Changing Climate

Coral reefs are one of the most diverse and productive ecosystems on the planet, yet they have suffered tremendous losses due to anthropogenic disturbances and are predicted to be one of the most adversely affected habitats under future climate change conditions. Coral reefs can be viewed as microbially driven ecosystems that rely on the efficient capture, retention, and recycling of nutrients in order to thrive in oligotrophic waters. Microorganisms play vital roles in maintaining holobiont health and ecosystem resilience under environmental stress; however, they are also key players in positive feedback loops that intensify coral reef decline, with cascading effects on biogeochemical cycles and marine food webs. There is an urgent need to develop a fundamental understanding of the complex microbial interactions within coral reefs and their role in ecosystem acclimatization, and it is important to include microorganisms in reef conservation in order to secure a future for these unique environments.