The Potential of Indonesian Heterobranchs Found around Bunaken Island for the Production of Bioactive Compounds

Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

BACKGROUND

Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva.

RESULTS

We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously.

CONCLUSIONS

Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo. Video Abstract.

Bioactivity of bacteria associated with Red Sea nudibranchs and whole genome sequence of Nocardiopsis dassonvillei RACA-4

Microorganisms associated with marine invertebrates consider an important source of bioactive products. This study aimed to screen for antimicrobial and anticancer activity of crude extracts of bacteria associated with Red sea nudibranchs and molecular identification of the bioactive isolates using 16Sr RNA sequencing, in addition to whole-genome sequencing of one of the most bioactive bacteria. This study showed that bacteria associated with Red sea nudibranchs are highly bioactive and 16Sr RNA sequencing results showed that two isolates belonged to Firmicutes, and two isolates belonged to Proteobacteria, and Actinobacteria. The whole genome sequence data of the isolated Nocardiopsis RACA4 isolate has an estimated genome length of 6,721,839 bp and the taxonomy showed it belongs to the bacteria Nocardiopsis dassonvillei. The De novo assembly of RACA-4 paired reads using Unicycler v0.4.8 initially yielded 97 contigs with an N50 value of 214,568 bp and L50 value of 10, The resulting assembly was further mapped to the reference genome Nocardiopsis dassonvillei strain NCTC10488 using RagTag software v.2.1.0 and a final genome assembly resulted in 39 contigs and N50 value of 6,726,007 and L50 of 1. Genome mining using anti-smash showed around 9.1% of the genome occupied with genes related to secondary metabolites biosynthesis. A wide variety of secondary metabolites belonging to Polyketides, Terpenes, and nonribosomal peptides were predicted with high degree of similarity to known compounds. Non-characterized clusters were also found which suggest new natural compounds discovered by further studies.

Characterization of Onchidiid Slug (Onchidium typhae) West Kalimantan Waters as Antibacterials and Antifungal

Onchidiid slug (Onchidium typhae) is a nudibranch that coastal communities in West Kalimantan have widely used as wounds. The study aims to characterize the West Kalimantan water O. typhae as antibacterial and antifungal. The study of O. typhae was carried out in several stages: preparation and optimization, extraction by Quinn method, characterization and identification of bioactive compounds, and antibacterial and antifungal assay using the microdilution method. The result of the proximate test showed that O. typhae powder contains high protein, namely 67.68%. Phytochemical screening results from methanol, ethyl acetate, and chloroform extracts contain alkaloids and amino acids. Methanol, chloroform, and ethyl acetate extract 1% of O. typhae showed inhibitory activity against Staphylococcus aureus, Escherichia coli, and Candida albicans. The most significant inhibition value was indicated by chloroform extract 1%, where the inhibition value against S. aureus, E. coli, and C. albicans was 82±0.01%; 85.8±0.01%; 85±0.01%, respectively. From these results, O. typhae powder can be developed as a wound medicine through its antibacterial and antifungal activity.

Phyllidiidae (Nudibranchia, Heterobranchia, Gastropoda): an integrative taxonomic approach including chemical analyses

Members of the widely distributed and common nudibranch family Phyllidiidae are often easily spotted in the marine environment because of their conspicuous colours and obvious presence on the reef. They are interesting with regard to their defensive chemical compounds that may lead to new drug discoveries. Despite their abundance, the family is also well known for its taxonomic problems and the difficulties in species identification due to very similarly coloured species and lack of morphological characters. In this study, phyllidiid species were analysed using an integrative approach. Molecular analysis of the mitochondrial genes 16S and CO1 was utilised, running phylogenetic analyses, species delimitation tests, and haplotype network analyses. Additionally, for the first time, external morphological characters were analysed, museum material was re-analysed, and chemical profiles were applied for characterising species. The analyses are based on sequences of 598 specimens collected in Indonesia by the team, with the addition of published sequences available on GenBank. This study comprises 11 species of Phyllidia, seven species of Phyllidiopsis, and at least 14 species of Phyllidiella. Moreover, 11 species belonging to these three genera are probably new to science, Phyllidiopsis pipeki is synonymised with P. krempfi, and Phyllidiella albonigra is resurrected. Some of the external colouration previously used for species identification is shown to not be valid, but alternative characters are provided for most species. Chemical analyses led to species characterisation in a few examples, indicating that these species use particular sponge species as food; however, many species show a broad array of compounds and are therefore characterised more by their composition or profile than by distinct or unique compounds.

Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

Background

The soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as targets for drug discovery), the evolutionary history of cladobranch sea slugs is not yet fully understood.

Results

To enlarge the current knowledge on the phylogenetic relationships, we generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa (Berthella plumula and Polycera quadrilineata). We complemented our taxon sampling with previously published transcriptome data, resulting in a final data set covering 56 species from all but one accepted cladobranch superfamilies. We assembled all transcriptomes using six different assemblers, selecting those assemblies that provided the largest amount of potentially phylogenetically informative sites. Quality-driven compilation of data sets resulted in four different supermatrices: two with full coverage of genes per species (446 and 335 single-copy protein-coding genes, respectively) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximal statistical support for all major splits and phylogenetic relationships at the family level. Besides the questionable position of Noumeaella rubrofasciata, rendering the Facelinidae as polyphyletic, the only notable discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal.

Conclusions

Our data matrices and the inferred trees can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The placement of E. pulchra, however, proves challenging, even with large data sets and various optimization strategies. Moreover, quartet mapping results show that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01944-0.

Bioactive Compounds from Marine Heterobranchs

The natural products of heterobranch molluscs display a huge variability both in structure and in their bioactivity. Despite the considerable lack of information, it can be observed from the recent literature that this group of animals possesses an astonishing arsenal of molecules from different origins that provide the molluscs with potent chemicals that are ecologically and pharmacologically relevant. In this review, we analyze the bioactivity of more than 450 compounds from ca. 400 species of heterobranch molluscs that are useful for the snails to protect themselves in different ways and/or that may be useful to us because of their pharmacological activities. Their ecological activities include predator avoidance, toxicity, antimicrobials, antifouling, trail-following and alarm pheromones, sunscreens and UV protection, tissue regeneration, and others. The most studied ecological activity is predation avoidance, followed by toxicity. Their pharmacological activities consist of cytotoxicity and antitumoral activity; antibiotic, antiparasitic, antiviral, and anti-inflammatory activity; and activity against neurodegenerative diseases and others. The most studied pharmacological activities are cytotoxicity and anticancer activities, followed by antibiotic activity. Overall, it can be observed that heterobranch molluscs are extremely interesting in regard to the study of marine natural products in terms of both chemical ecology and biotechnology studies, providing many leads for further detailed research in these fields in the near future.

Selection of sponge-associated bacteria with high potential for the production of antibacterial compounds

The potential of sponge-associated bacteria for the biosynthesis of natural products with antibacterial activity was evaluated. In a preliminary screening 108 of 835 axenic isolates showed antibacterial activity. Active isolates were identified by 16S rRNA gene sequencing and selection of the most promising strains was done in a championship like approach, which can be done in every lab and field station without expensive equipment. In a competition assay, strains that inhibited most of the other strains were selected. In a second round, the strongest competitors from each host sponge competed against each other. To rule out that the best competitors selected in that way represent similar strains with the same metabolic profile, BOX PCR experiments were performed, and extracts of these strains were analysed using metabolic fingerprinting. This proved that the strains are different and have various metabolic profiles, even though belonging to the same genus, i.e. Bacillus. Furthermore, it was shown that co-culture experiments triggered the production of compounds with antibiotic activity, i.e. surfactins and macrolactin A. Since many members of the genus Bacillus possess the genetic equipment for the biosynthesis of these compounds, a potential synergism was analysed, showing synergistic effects between C14-surfactin and macrolactin A against methicillin-resistant Staphylococcus aureus (MRSA).

From Persian Gulf to Indonesia: interrelated phylogeographic distance and chemistry within the genus Peronia (Onchidiidae, Gastropoda, Mollusca)

The knowledge of relationships between taxa is essential to understand and explain the chemical diversity of the respective groups. Here, twelve individuals of the panpulmonate slug Peronia persiae from two localities in Persian Gulf, and one animal of P. verruculata from Bangka Island, Indonesia, were analyzed in a phylogenetic and chemotaxonomic framework. Based on the ABGD test and haplotype networking using COI gene sequences of Peronia specimens, nine well-supported clades were found. Haplotype network analysis highlighted a considerable distance between the specimens of P. persiae and other clades. Metabolomic analysis of both species using tandem mass spectrometry-based GNPS molecular networking revealed a large chemical diversity within Peronia of different clades and localities. While P. persiae from different localities showed a highly similar metabolome, only few identical chemical features were found across the clades. The main common metabolites in both Peronia species were assigned as polypropionate esters of onchitriols and ilikonapyrones, and osmoprotectant amino acid-betaine compounds. On the other hand, the isoflavonoids genistein and daidzein were exclusively detected in P. persiae, while cholesterol and conjugated chenodeoxycholic acids were only found in P. verruculata. Flavonoids, bile acids, and amino acid-betaine compounds were not reported before from Onchidiidae, some are even new for panpulmonates. Our chemical analyses indicate a close chemotaxonomic relation between phylogeographically distant Peronia species.

Antibacterial scalarane from Doriprismatica stellata nudibranchs (Gastropoda, Nudibranchia), egg ribbons, and their dietary sponge Spongia cf. agaricina (Demospongiae, Dictyoceratida)

Investigations on the biochemical relationship between Doriprismatica stellata (Chromodorididae, Doridoidea) nudibranchs, their egg ribbons, and the associated dietary sponge Spongia cf. agaricina (Demospongiae, Porifera) led to the isolation of the structurally new scalarane-type sesterterpene 12-deacetoxy-4-demethyl-11,24-diacetoxy-3,4-methylenedeoxoscalarin, with an unprecedented position of the cyclopropane ring annelated to the ring A. Unlike other scalaranes, which are most often functionalized at C-12 of ring C, it bears two acetoxy groups at C-11 and C-24 instead. The compound was present in all three samples, supporting the dietary relationship between chromodorid nudibranchs of the genus Doriprismatica and scalarane-containing dictyoceratid sponges of the Spongiidae family. The results also indicate that D. stellata passes the scalarane metabolite on to its egg ribbons, most likely for protective purposes. The scalarane showed antibacterial activity against the Gram-positive bacteria Arthrobacter crystallopoietes (DSM 20117) and Bacillus megaterium (DSM 32).

Terpenoids in Marine Heterobranch Molluscs

Heterobranch molluscs are rich in natural products. As other marine organisms, these gastropods are still quite unexplored, but they provide a stunning arsenal of compounds with interesting activities. Among their natural products, terpenoids are particularly abundant and diverse, including monoterpenoids, sesquiterpenoids, diterpenoids, sesterterpenoids, triterpenoids, tetraterpenoids, and steroids. This review evaluates the different kinds of terpenoids found in heterobranchs and reports on their bioactivity. It includes more than 330 metabolites isolated from ca. 70 species of heterobranchs. The monoterpenoids reported may be linear or monocyclic, while sesquiterpenoids may include linear, monocyclic, bicyclic, or tricyclic molecules. Diterpenoids in heterobranchs may include linear, monocyclic, bicyclic, tricyclic, or tetracyclic compounds. Sesterterpenoids, instead, are linear, bicyclic, or tetracyclic. Triterpenoids, tetraterpenoids, and steroids are not as abundant as the previously mentioned types. Within heterobranch molluscs, no terpenoids have been described in this period in tylodinoideans, cephalaspideans, or pteropods, and most terpenoids have been found in nudibranchs, anaspideans, and sacoglossans, with very few compounds in pleurobranchoideans and pulmonates. Monoterpenoids are present mostly in anaspidea, and less abundant in sacoglossa. Nudibranchs are especially rich in sesquiterpenes, which are also present in anaspidea, and in less numbers in sacoglossa and pulmonata. Diterpenoids are also very abundant in nudibranchs, present also in anaspidea, and scarce in pleurobranchoidea, sacoglossa, and pulmonata. Sesterterpenoids are only found in nudibranchia, while triterpenoids, carotenoids, and steroids are only reported for nudibranchia, pleurobranchoidea, and anaspidea. Many of these compounds are obtained from their diet, while others are biotransformed, or de novo biosynthesized by the molluscs. Overall, a huge variety of structures is found, indicating that chemodiversity correlates to the amazing biodiversity of this fascinating group of molluscs.

First Study on Marine Heterobranchia (Gastropoda, Mollusca) in Bangka Archipelago, North Sulawesi, Indonesia

As ephemeral, benthic, secondary consumers usually associated with sessile coral reef organisms, marine heterobranchs are good indicators of the health of marine tropical habitats. Thus, marine Heterobranchia have recently become a major target for monitoring programs. For this work, an extensive survey was made in Bangka Archipelago, the first of its kind in this area. Bangka Archipelago is composed of small islands and the adjacent coastline of North Sulawesi. The substrate is dominated by biogenic reefs and volcanic rocks, thus forming highly diverse habitats. In total, 149 species were collected and/or photo-documented in September 2017 and September 2018, which represents the dry season. They can be assigned to the Cephalaspidea, Aplysiida, Pleurobranchida, Nudibranchia, and Eupulmonata. Thirty-three species are new to science, highlighting the lack of knowledge about the group and especially about this region. Our data provide a baseline for future monitoring surveys, as the anthropogenic pressures on Bangka Archipelago are increasing due to enhanced touristic activities, but also due to large scale environmental changes caused by previous mining operation activities.

Bioactivity of compounds secreted by symbiont bacteria of Nudibranchs from Indonesia

The aims of this work are to isolate bacterial symbionts from nudibranchs and subsequently to determine anti-Methicillin resistant Staphylococcus aureus (MRSA), cytotoxicity and anti-Herpes simplex virus type 1 (HSV-1) activities of bio compounds. A total of 15 species of nudibranchs were collected from Karimunjawa and five species from Bali, respectively. A total of 245 bacteria isolates were obtained. The anti-MRSA activity screening activity indicated two active bacteria. Ethyl acetate extracts from supernatants, indicating extracelullar compounds, showed an inhibition zone against MRSA at concentrations of 500–1,000 µg/ml. DNA sequence analysis showed that the strain KJB-07 from Phyllidia coelestis was closely related to Pseudoalteromonas rubra, whereas the strain NP31-01 isolated from Phyllidia varicosa was closely related to Virgibacillus salarius. The extract of Pseudoalteromonas rubra was cytotoxic to Vero cells at a concentration of 75 µg/ml. The extract of V. salarius presented no cytotoxicity at concentrations of 5–1,000 µg/ml. No anti HSV-1 was observed for both isolated bacteria. This is the first study describing research on anti-MRSA, cytotoxicity and anti HSV-1 activity of bacterial symbionts from the viscera of nudibranch. Compounds produced by Pseudoalteromonas rubra and V. salarius, had potential anti-MRSA activity. However, only extracts from Pseudoalteromonas rubra showed cytotoxic effects on Vero cells. Three compounds were identified by LC/MS after purification from culture supernatant.

The Suitability of Fishes as Models for Studying Appetitive Behavior in Vertebrates

Fish have proven to be valuable models in the study of the endocrine control of appetite in response to peripheral signals of energetic and nutritional status. In parallel, a growing body of literature points to the importance of sensory experiences as factors affecting food choice in fish, with a special focus on visual and chemical signals allowing discrimination of potential foods within a 3D environment. Accordingly, waterborne compounds, such as monosaccharides or amino acids, are regarded as the main "olfactory" cues driving fish alimentary behavior. However, we recently suggested that hydrophobic molecules also allow food identification in aquatic environments and that fish actually explore a larger variety of chemosensory cues, including the olfactory/volatile compounds, when determining food palatability. In this study, we show that both homeostatic and chemosensory mechanisms involved in food intake are highly conserved in vertebrates and that the chemosensory world of fish is less different from that of terrestrial mammals than commonly thought. As a result, we support a more integrated and synthetic view of the mechanisms of chemical communication in both terrestrial and aquatic systems, which could help to ensure greater translatability of the fish models, such as the zebrafish (Danio rerio), the turquoise killifish (Nothobranchius furzeri), the goldfish (Carassius auratus), or the Japanese medaka fish (Oryzias latipes) to terrestrial vertebrates when approaching complex dynamic patterns in alimentary behavior.

Marine Heterobranchia (Gastropoda, Mollusca) in Bunaken National Park, North Sulawesi, Indonesia—A Follow-Up Diversity Study

Bunaken National Park has been surveyed for a fourth time in 14 years, in an attempt to establish the species composition of heterobranch sea slugs in a baseline study for monitoring programs and protection of this special park. These molluscs are potentially good indicators of the health of an ecosystem, as many are species-specific predators on a huge variety of marine benthic and sessile invertebrates from almost every taxonomic group. Additionally, they are known to contain bio-compounds of significance in the pharmaceutical industry. It is therefore of paramount importance not only to document the species composition from a zoogeographic point of view, but to assist in their protection for the future, both in terms of economics and aesthetics. These four surveys have documented more than 200 species, with an approximate 50% of each collection found only on that survey and not re-collected. Many species new to science have also been documented, highlighting the lack of knowledge in this field.