Environmental conditions affect activity and associated microorganisms of marine sponges

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.

Antibacterial and antibiofilm activity of extracts from sponge-associated bacterial endophytes

Sponges forms association with many bacteria that serve as sources of new bioactive compounds. The compounds are produced in response to environmental and nutritional conditions of the environment that enable them to protect their host from colonization. In this study, three sponge bacterial endophytes were isolated, identified, and subjected to solvent extraction processes. The identified bacteria are Bacillus amyloquifaciens, Bacillus paramycoides, and Enterobacter sp. The bacteria were cultured in two different fermentation media with varying nutritional composition for the extraction process. The extracts were evaluated for antibacterial and antibiofilm activity against microfouling bacteria and the chemical composition of each extract was analyzed via gas chromatography-mass spectrometry (GC-MS). The extract from the endophytes shows varying antibacterial and antibiofilm activity against the tested strains. Several compounds were detected from the extracts including some with known antibacterial/antibiofilm activity. The results showed variations in activity and secondary metabolite production between the extracts obtained under different nutritional composition of the media. In conclusion, this study indicated the role of nutrient composition in the activity and secondary metabolites production by bacteria associated with sponge Also, this study confirmed the role of sponge bacterial endophytes as producers of bioactive compounds with potential application as antifouling (AF) agents.

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.

Environmental DNA persistence and fish detection in captive sponges

Large and hyperdiverse marine ecosystems pose significant challenges to biodiversity monitoring. While environmental DNA (eDNA) promises to meet many of these challenges, recent studies suggested that sponges, as "natural samplers" of eDNA, could further streamline the workflow for detecting marine vertebrates. However, beyond pilot studies demonstrating the ability of sponges to capture eDNA, little is known about the dynamics of eDNA particles in sponge tissue, and the effectiveness of the latter compared to water samples. Here, we present the results of a controlled aquarium experiment to examine the persistence and detectability of eDNA captured by three encrusting sponge species and compare the sponge's eDNA capturing ability with established water filtration techniques. Our results indicate that sponges and water samples have highly similar detectability for fish of different sizes and abundances, but different sponge species exhibit considerable variance in performance. Interestingly, one sponge appeared to mirror the eDNA degradation profile of water samples, while another sponge retained eDNA throughout the experiment. A third sponge yielded virtually no DNA sequences at all. Overall, our study suggests that some sponges will be suitable as natural samplers, while others will introduce significant problems for laboratory processing. We suggest that an initial optimization phase will be required in any future studies aiming to employ sponges for biodiversity assessment. With time, factoring in technical and natural accessibility, it is expected that specific sponge taxa may become the "chosen" natural samplers in certain habitats and regions.

Antimicrobial Biosynthetic Potential and Phylogenetic Analysis of Culturable Bacteria Associated with the Sponge Ophlitaspongia sp. from the Yellow Sea, China

Sponge-derived bacteria are considered to be a promising source of novel drugs, owing to their abundant secondary metabolites that have diverse biological activities. In this study, we explored the antimicrobial biosynthetic potential and phylogenetics of culturable bacteria associated with the sponge Ophlitaspongia sp. from the Yellow Sea, China. Using culture-dependent methods, we obtained 151 bacterial strains, which were then analysed for their antimicrobial activities against seven indicator strains. The results indicate that 94 (62.3%) of the 151 isolated strains exhibited antimicrobial activities and inhibited at least one of the indicator strains. Fifty-two strains were selected for further phylogenetic analysis using 16S rRNA gene sequencing, as well as for the presence of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes. These 52 strains belonged to 20 genera from 18 families in 4 phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Five strains with PKS genes and ten strains with NRPS genes were detected. Among them, two strains contained both PKS and NRPS genes. Notoacmeibacter sp. strain HMA008 (class Alphaproteobacteria) exhibited potent antimicrobial activity; thus, whole genome sequencing methods were used to analyse its secondary metabolite biosynthetic gene clusters. The genome of HMA008 contained 12 biosynthetic gene clusters that potentially encode secondary metabolites belonging to compound classes such as non-ribosomal peptides, prodigiosin, terpene, β-lactones, and siderophore, among others. This study indicates that the sponge Ophlitaspongia sp. harbours diverse bacterial strains with antimicrobial properties and may serve as a potential source of bioactive compounds.

Marine Sponges in a Snowstorm – Extreme Sensitivity of a Sponge Holobiont to Marine Oil Snow and Chemically Dispersed Oil Pollution

Holobionts formed by a host organism and associated symbionts are key biological units in marine ecosystems where they are responsible for fundamental ecosystem services. Therefore, understanding anthropogenic impacts on holobionts is essential. Sponges (Phylum Porifera) are ideal holobiont models. They host a complex microbial community and provide ecosystem services including nutrient cycling. At bathyal depths, sponges can accumulate forming dense sponge ground habitats supporting biodiverse associated communities. However, the impacts of spilled oil and dispersants on sponge grounds cannot be understood without considering exposures mediated through sponge filtration of marine snow particles. To examine this, we exposed the model sponge Halichondria panicea to oil, dispersant and “marine oil snow” contaminated seawater and elucidate the complex molecular response of the holobiont through metatranscriptomics. While the host response included detoxification and immune response pathways, the bacterial symbiotic response differed and was at least partially the result of a change in the host environment rather than a direct response to hydrocarbon exposure. As the sponge host reduced its pumping activity and internal tissue oxygen levels declined, the symbionts changed their metabolism from aerobic to anaerobic pathways possibly via quorum sensing. Furthermore, we found evidence of hydrocarbon degradation by sponge symbionts, but sponge mortality (even when exposed to low concentrations of hydrocarbons) implied this may not provide the holobiont with sufficient resilience against contaminants. Given the continued proposed expansion of hydrocarbon production into deep continental shelf and slope settings where sponge grounds form significant habitats it is important that dispersant use is minimised and that environmental impact assessments carefully consider the vulnerability of sponge holobionts.

Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera

Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges.

The Red Sea marine sponge Spongia irregularis: metabolomic profiling and cytotoxic potential supported by in silico studies

The current study discusses the chemical composition of the marine sponge Spongia irregularis using LC-HRESIMS. The metabolomic profiling resulted in the annotation of 17 metabolites of different chemical classes. Additionally, evaluation of the cytotoxic activities of the total extract and different fractions were carried out against three different cell lines where the n-butanol fraction exhibited the highest cytotoxic effects against HepG-2, MCF-7 and CACO-2 cell lines with IC₅₀ values of 9.6 ± 0.02, 4.3 ± 0.10 and 5.6 ± 0.03 µg/mL, respectively. Also, the study was supported by docking study of the identified compounds for binding affinity to MSK1.

Natural products potential of Dictyoceratida sponges-associated micro-organisms

The marine environment represents one of the most underexplored environments in the world. Marine sponges have a higher taxonomic diversity according to definite environmental conditions. They have been considered interesting sources for bioactive compounds. Dictyoceratida sponges are divided into five families which are widely distributed and habituating different types of micro-organisms. However, some secondary metabolites are probably not produced by the sponges themselves, but rather by their associated micro-organisms. These secondary metabolites are characterized by different chemical structures and consequently different biological activities. This review outlines the reported secondary metabolites from micro-organisms associated with Dictyoceratida sponges and their investigated biological activities from 1991 to 2019. The increasing research studies in this field can play a major role in marine microbial natural products drug discovery in the future.

Metavirome datasets from two endemic Baikal sponges Baikalospongia bacillifera

Sponges are ecologically important components of marine and freshwater benthic environments; these holobionts contain a variety of microorganisms and viruses. For the metagenomic characterization of potential taxonomic and functional diversity of sponge-associated dsDNA viruses, we surveyed two samples of Baikal endemic sponge Baikalospongia bacillifera (diseased and visually healthy). In total, after quality processing, we have obtained 3 375 063 and 4 063 311 reads; of these 97 557 and 88 517 sequences, accounting for ca. 2.9 and 2.2% of datasets, have been identified as viral. We have revealed approximately 28 viral families, among which the bacteriophages of the Myoviridae, Siphoviridae and Podoviridae families, as well as the viruses of the Phycodnaviridae and Poxviridae families, dominated in the samples. Analysis of viral sequences using the COG database has indicated 22 functional categories of proteins. Viral communities of visually healthy and diseased Baikal sponges were significantly different. The metagenome sequence data were deposited to NCBI SRA as BioProject PRJNA577390.

The oceans are changing: impact of ocean warming and acidification on biofouling communities

Climate change (CC) is driving modification of the chemical and physical properties of estuaries and oceans with profound consequences for species and ecosystems. Numerous studies investigate CC effects from species to ecosystem levels, but little is known of the impacts on biofilm communities and on bioactive molecules such as cues, adhesives and enzymes. CC is induced by anthropogenic activity increasing greenhouse emissions leading to rises in air and water temperatures, ocean acidification, sea level rise and changes in ocean gyres and rainfall patterns. These environmental changes are resulting in alterations within marine communities and changes in species ranges and composition. This review provides insights and synthesis of knowledge about the effect of elevated temperature and ocean acidification on microfouling communities and bioactive molecules. The existing studies suggest that CC will impact production of bioactive compounds as well as the growth and composition of biofouling communities. Undoubtedly, with CC fouling management will became an even greater challenge.