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Microorganisms play a significant role in biofouling and biocorrosion within the maritime industry. Addressing these challenges requires an innovative and integrated approach utilizing marine natural products with beneficial properties. A comprehensive screening of 173 non-toxic EtOAc and H₂O extracts derived from diverse marine organisms collected in Indonesian waters was conducted using a robust panel of assays. These included antimicrobial tests and classical biosurfactant assays (drop collapse and oil displacement), as well as anti-quorum-sensing (QS) and anti-biofilm assays. These screening efforts identified five active extracts with promising activities. Among these, EtOAc extracts of the marine tunicate Sigilina cf. signifera (0159-22e) and the marine sponge Lamellodysidea herbacea (0194-24c) demonstrated significant anti-biofouling activity against Perna indica and anti-biocorrosion performance (mpy 10.70 ± 0.70 for S. cf. signifera; 7.87 ± 0.86 for L. herbacea; 13.60 ± 1.70 for positive control Tetracorr CI-2915). Further chemical analyses of the active extracts, including LC-HR-MS/MS, MS-based molecular networking, and chemoinformatics, revealed the presence of both known and new bioactive compounds. These included tambjamines and polybrominated diphenyl ethers (PBDEs), which are likely contributors to the observed bioactivities. Subsequent investigations uncovered new anti-QS and anti-biofilm properties in synthetic and natural PBDEs 1–12 previously derived from L. herbacea. Among these, 8 exhibited the most potent anti-QS activity, with an IC50 value of 15 µM, while 4 significantly reduced biofilm formation at a concentration of 1 µM. This study highlights the potential of marine-derived compounds in addressing biofouling and biocorrosion challenges in a sustainable and effective manner.

Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity. Here, we present an extensive survey of the prokaryote communities of a wide range of biotopes from Indo-Pacific coral reef environments. We find a large variation in operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing the most diverse prokaryote communities. These biotopes share a higher percentage and number of OTUs with sediment and are particularly enriched in members of the phylum Planctomycetes. Despite having lower OTU richness, sponges share the greatest percentage (>90%) of OTUs with >100 sequences with the environment (sediment and/or seawater) although there is considerable variation among sponge species. Our results, furthermore, highlight that prokaryote microorganisms are shared among multiple coral reef biotopes, and that, although compositionally distinct, the sponge prokaryote community does not appear to be as sponge-specific as previously thought.

Abstract Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems. However, the specific effects of HS on sponge-associated microbial symbionts have largely been neglected. Here, we used a randomized-controlled microcosm setup to investigate the independent and interactive effects of HS, elevated temperature, and UVB radiation on bacterial communities associated with the sponge Chondrilla sp. Our results indicated the presence of a core bacterial community consisting of relatively abundant members, apparently resilient to the tested environmental perturbations, alongside a variable bacterial community. Elevated temperature positively affected the relative abundances of ASVs related to Planctomycetales and members of the families Pseudohongiellaceae and Hyphomonadaceae. HS increased the relative abundances of several ASVs potentially involved in recalcitrant organic matter degradation (e.g., the BD2-11 terrestrial group, Saccharimonadales, and SAR202 clade). There was no significant independent effect of UVB and there were no significant interactive effects of HS, heat, and UVB on bacterial diversity and composition. The significant, independent impact of HS on the composition of sponge bacterial communities suggests that alterations to HS inputs may have cascading effects on adjacent marine ecosystems. Humic substances modified bacterial composition within Chondrilla sp. sponges and enriched bacteria potentially involved in recalcitrant organic matter degradation while temperature and exposure to UVB had only minor and negligible effects, respectively.

BackgroundMarine ecosystems are hosts to a vast array of organisms, being among the most richly biodiverse locations on the planet. The study of these ecosystems is very important, as they are not only a significant source of food for the world but also have, in recent years, become a prolific source of compounds with therapeutic potential. Studies of aspects of marine life have involved diverse fields of marine science, and the use of metabolomics as an experimental approach has increased in recent years. As part of the “omics” technologies, metabolomics has been used to deepen the understanding of interactions between marine organisms and their environment at a metabolic level and to discover new metabolites produced by these organisms.Aim of reviewThis review provides an overview of the use of metabolomics in the study of marine organisms. It also explores the use of metabolomics tools common to other fields such as plants and human metabolomics that could potentially contribute to marine organism studies. It deals with the entire process of a metabolomic study, from sample collection considerations, metabolite extraction, analytical techniques, and data analysis. It also includes an overview of recent applications of metabolomics in fields such as marine ecology and drug discovery and future perspectives of its use in the study of marine organisms.Key scientific concepts of reviewThe review covers all the steps involved in metabolomic studies of marine organisms including, collection, extraction methods, analytical tools, statistical analysis, and dereplication. It aims to provide insight into all aspects that a newcomer to the field should consider when undertaking marine metabolomics.

A chemical study of the CH2Cl2−MeOH (1:1) extract from the sponge Ernsta naturalis collected in Rodrigues (Mauritius) based on a molecular networking dereplication strategy highlighted one novel aminopyrimidone alkaloid compound, ernstine A (1), seven new aminoimidazole alkaloid compounds, phorbatopsins D–E (2, 3), calcaridine C (4), naamines H–I (5, 7), naamidines J–K (6, 8), along with the known thymidine (9). Their structures were established by spectroscopic analysis (1D and 2D NMR spectra and HRESIMS data). To improve the investigation of this unstudied calcareous marine sponge, a metabolomic study by molecular networking was conducted. The isolated molecules are distributed in two clusters of interest. Naamine and naamidine derivatives are grouped together with ernstine in the first cluster of twenty-three molecules. Phorbatopsin derivatives and calcaridine C are grouped together in a cluster of twenty-one molecules. Interpretation of the MS/MS spectra of other compounds of these clusters with structural features close to the isolated ones allowed us to propose a structural hypothesis for 16 compounds, 5 known and 11 potentially new.

Four new bisabolane-type sesquiterpenoids, aspergiterpenoid A (1), (−)-sydonol (2), (−)-sydonic acid (3), and (−)-5-(hydroxymethyl)-2-(2′,6′,6′-trimethyltetrahydro-2H- pyran-2-yl)phenol (4) together with one known fungal metabolite (5) were isolated from the fermentation broth of a marine-derived fungus Aspergillus sp., which was isolated from the sponge Xestospongia testudinaria collected from the South China Sea. Four of them (1–4) are optically active compounds. Their structures and absolute configurations were elucidated by using NMR spectroscopic techniques and mass spectrometric analysis, and by comparing their optical rotations with those related known analogues. Compounds 1–5 showed selective antibacterial activity against eight bacterial strains with the MIC (minimum inhibiting concentrations) values between 1.25 and 20.0 µM. The cytotoxic, antifouling, and acetylcholinesterase inhibitory activities of these compounds were also examined.

Screening of a marine derived crude natural product extract library, followed by bioactivity guided fractionation, has led to isolation and structural elucidation of 10 natural products as hits active against Mycobacterium tuberculosis (Mtb). Among them, three (3, 4 and 5) were identified for the first time and the remaining 7 compounds (1, 2, 6, 7, 8, 9 and 10) were previously reported, but now assigned with anti-mycobacterial activity. Among identified hits, the oligo cyclic depsipeptide discodermin B (7) exhibited the highest potency with an MIC90 value of 0.5 µM. The polysufide alkaloid lissoclinotoxin F (1) displayed a good balance of anti Mtb potency (MIC90 = 2.6 µM) and selectivity (SI = 19 in HEK293 cells). Lissoclinotoxin F (1) was found to be active against intracellular Mtb as well as non-replicating forms of Mtb, with higher activity against Mtb compared to other gram-negative and gram-positive bacteria. Consequently, lissoclinotoxin F (1) could be used as a lead compound for development of new TB drugs. Details regarding screening techniques, structural elucidation and preliminary structural activity relationships (SAR) of the isolated hits are discussed.

Certain sponge species are difficult to identify using classical taxonomic characters, and other techniques are often necessary. Here we used 454-pyrosequencing of the 16S rRNA gene to investigate bacterial and archaeal communities of two distinct Cinachyrella morphospecies collected from two Indonesian marine lakes with differing degrees of connection to the surrounding sea. Our main goal was to assess whether these morphospecies hosted distinct bacterial and archaeal communities and to what extent these differed from those found in lake water. A recently developed bioinformatic tool (PICRUSt) was used to predict metagenomic gene content of the studied communities. Compositionally, sponge samples clustered according to morphospecies as opposed to marine lake indicating that each morphospecies hosted distinct bacterial and archaeal communities. There were, however, also differences in higher taxon abundance among lakes. In the less connected lake, for example, both Cinachyrella morphospecies had higher levels of the order Synechococcales. With respect to metabolic gene content, although there were pronounced differences in predicted enrichment between both morphospecies, both were putatively enriched for KOs involved in pathways related to stress response, energy metabolism, environmental information processing and the production of secondary metabolites compared to prokaryote communities in water. These morphospecies may thus prove to be interesting sources of novel compounds of potential pharmaceutical and/or biotechnological importance.

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.

Two new sesterterpenoids, 1 and 2, were isolated from the sponge Luffariella variabilis. Their planar structures were characterized with spectroscopic analyses. The sole chiral center of compound 1 was elucidated as 12R by comparing observed and calculated optical rotation values. The configurations of compound 2 were determined by NMR and electronic circular dichroism (ECD) studies. Furthermore, compound 2 showed cytotoxicity at IC50 1.0 µM against NBT-T2 cells.