Challenge 09: Skills, knowledge, and technology for all

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Ocean Decade

Challenge 09:
Skills, knowledge, and technology for all

Ensure comprehensive capacity development and equitable access to data, information, knowledge and technology across all aspects of ocean science and for all stakeholders.

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Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta
Matriano, Danielle M.; Alegado, Rosanna A.; Conaco, Cecilia (Springer, 2021-03-16)
Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome—evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.
We thank Joshua Dizon and Francis Tablizo of the Philippine Genome Center Core Facility for Bioinformatics for assistance with scripts and database construction. We thank Becca Lensing (University of Hawai’i), Cheryl Andam (University of New Hampshire), Deo Onda and Ron Leonard Dy (University of the Philippines) for insightful comments and suggestions on the analysis and interpretation of the data. This work was supported by thesis grants from the Department of Science and Technology Accelerated Science and Technology Human Resource Development Program-National Science Consortium (DOST-ASTHRDP-NSC) and the University of the Philippines Marine Science Institute to DM.
Sexual reproduction in the soft coral Lobophytum schoedei in Bolinao‐Anda Reef Complex, Pangasinan, northwestern Philippines
Baran, Christine C.; Baria‐Rodriguez, Maria Vanessa (Wiley, 2021-04-02)
The characterization of early life-history strategies of soft corals is important in understanding population maintenance, replenishment, and recovery in disturbed coral reefs. This study examined the sexual reproduction of the soft coral Lobophytum schoedei in the Bolinao-Anda Reef Complex (BARC), a degraded reef in northwestern Philippines. Reproductive strategies such as sexuality, sex ratio, fecundity, and reproductive timing were examined. Random colonies of L. schoedei were sampled a few weeks before the predicted time of spawning to assess fecundity (n = 73 colonies), and sexuality and sex ratio (n = 221 colonies). Monthly sampling of tagged colonies of L. schoedei (n = 20) was done over 13 months to determine the reproductive timing through polyp dissection. Peak of annual spawning was inferred based on the presence of large gametes and their absence in the next sampling period. Results showed that L. schoedei is a gonochoric broadcast spawner with 1:1.1 sex ratio. Although oogenesis and spermatogenesis exhibited overlapping cycles, both gametes matured and spawned in April, coinciding with increasing sea surface temperature. Prior to spawning, oocytes and spermaries ranged 300–633 µm and 150–337 µm in diameter, respectively. Mean female fecundity was 6.7 ± 3.9 oocytes per polyp and male fecundity was 39.2 ± 22.5 (±SD) spermaries per polyp. Some of these results, including the low number of oocytes produced by female polyps, may be caused by sexual reproduction in a degraded reef environment. Understanding these reproductive traits may be useful for predicting the resiliency of populations of L. schoedei in response to ongoing and future environmental change.
Limited progress in improving gender and geographic representation in coral reef science
Ahmadia, Gabby N.; Cheng, Samantha H.; Andradi-Brown, Dominic A.; Baez, Stacy K.; Barnes, Megan D.; Bennett, Nathan J.; Campbell, Stuart J.; Darling, Emily S.; Gill, David; Gress, Erika; Gurney, Georgina G.; Horigue, Vera; Jakub, Raymond; Kennedy, Emma V.; Mahajan, Shauna L.; Mangubhai, Sangeeta; Matsuda, Shayle B.; Muthiga, Nyawira A.; Navarro, Michael O.; Santodomingo, Nadia; Vallès, Henri; Veverka, Laura; Villagomez, Angelo; Wenger, Amelia S.; Wosu, Adaoma (Frontiers Media SA, 2021-09-29)
Despite increasing recognition of the need for more diverse and equitable representation in the sciences, it is unclear whether measurable progress has been made. Here, we examine trends in authorship in coral reef science from 1,677 articles published over the past 16 years (2003–2018) and find that while representation of authors that are women (from 18 to 33%) and from non-OECD nations (from 4 to 13%) have increased over time, progress is slow in achieving more equitable representation. For example, at the current rate, it would take over two decades for female representation to reach 50%. Given that there are more coral reef non-OECD countries, at the current rate, truly equitable representation of non-OECD countries would take even longer. OECD nations also continue to dominate authorship contributions in coral reef science (89%), in research conducted in both OECD (63%) and non-OECD nations (68%). We identify systemic issues that remain prevalent in coral reef science (i.e., parachute science, gender bias) that likely contribute to observed trends. We provide recommendations to address systemic biases in research to foster a more inclusive global science community. Adoption of these recommendations will lead to more creative, innovative, and impactful scientific approaches urgently needed for coral reefs and contribute to environmental justice efforts.
We acknowledge the contributions of the many unrecognized and undervalued individuals in coral reef research whose efforts have made it possible for the field to progress. These scientists have collected data, translated across languages, coordinated field work, welcomed foreign visitors to their countries, shared ideas, trained and mentored students, become friends, inspired, and built the foundation for the discipline we know today. We acknowledge the work of all coral reef scientists who continue day after day to pursue equity, inclusion, and justice in the field and for their colleagues and themselves.
Thecal tabulation, body scale morphology and phylogeny of Heterocapsa philippinensis sp. nov. (Peridiniales, Dinophyceae) from the Philippines
Benico, Garry; Lum, Wai Mun; Takahashi, Kazuya; Yñiguez, Aletta T.; Iwataki, Mitsunori (Elsevier, 2021-08)
The thecal tabulation and body scale structure of the marine armoured dinoflagellate Heterocapsa, isolated from Philippines, were examined using LM, SEM and TEM, and its phylogenetic position was inferred from ITS and LSU rDNA sequences. Cells were ovoid and the plate tabulation (Po, cp, X, 5′, 3a, 7′′, 6c, 5s, 5′′′, 2′′′′) was consistent with most Heterocapsa species. The second anterior intercalary plate (2a) had a circular pattern with a thick marginal border free of pores. The nucleus was longitudinally elongated and curved, and located at the dorsal side of the cell. Discoid lobes of brownish chloroplast were peripherally distributed, and a pyrenoid was positioned at the centre. The triradiate body scales, measuring 250–300 nm in diameter, consisted of a roundish basal plate with six radiating ridges, nine peripheral uprights/spines, and three radiating spines. These components were identical to those of H. pseudotriquetra and H. steinii, except for the roundish outline of basal plate. Molecular phylogeny showed that the species clustered with H. pseudotriquetra and H. steinii. This species was differentiated from all other Heterocapsa species in the sausage-shaped nucleus and circular pattern on the 2a plate. This study proposed a novel species Heterocapsa philippinensis sp. nov. for the isolate.
Spatial planning insights for Philippine coral reef conservation using larval connectivity networks
Pata, Patrick R.; Yñiguez, Aletta T. (Frontiers Media SA, 2021-10-06)
The marine habitats of the Philippines are recognized to be some of the most biodiverse systems globally yet only 1.7% of its seas are designated as marine protected areas (MPAs) with varying levels of implementation. Many of these MPAs were established based on local-scale conservation and fisheries objectives without considering larger-scale ecological connections. The connectivity of reefs through larval dispersal is important in the regional-scale resilience against anthropogenic disturbances and is considered a significant criterion in planning for MPAs. In this study, we provide insights into the delineation of ecologically connected MPA networks using larval dispersal modeling and network analysis. We characterized the network properties of the Philippine coral reefs, organized as 252 reef nodes, based on the larval connectivity networks of a branching coral, sea urchin, and grouper. We then evaluated the distribution of the existing 1,060 MPAs relative to the connectivity patterns. All reef nodes were found to be highly interconnected with a mean shortest path ranging from 1.96 to 4.06. Reef nodes were then ranked according to their relative importance in regional connectivity based on five connectivity indices. Despite the between-organism and between-index variability in rankings, there were reefs nodes, mostly located offshore and at major straits, which consistently ranked high. We found that the distribution of existing MPAs partially capture some of the regional connectivity functions but there is a spatial mismatch between the primarily coastal MPAs and the high-ranking reef nodes. Furthermore, network partitioning identified subnetworks and dispersal barriers. The existing MPAs were found to be disproportionately distributed to a few subnetworks and that the largest subnetworks do not contain the greatest number of MPAs. Considering these gaps, we suggest expanding the coverage of protected areas especially in underrepresented reef networks to meaningfully capture national-scale connectivity and meet global conservation objectives.
We would like to thank Dr. Vera Horigue and Andrew Torres for constructive comments and suggestions during the early versions of this paper. We also thank the members of the Biological Oceanography and Modeling of Ecosystems (BiOME) Laboratory who assisted in running model simulations.
Manzaea minuta gen. & comb. nov. (Scytosiphonaceae, Phaeophyceae) from the tropical Northwestern Pacific Ocean
Santiañez, Wilfred John E.; Kogame, Kazuhiro (Philippine Journal of Systematic Biology, 2022-07-11)
Recent molecular-assisted taxonomic studies on the brown algal genus Hydroclathrus has resulted in discoveries of new taxa in the family Scytosiphonaceae, both at the genus and species level. However, phylogenetic studies on Hydroclathrus based on wide geographical sampling also suggested that the genus is not monophyletic. That is, one of the recently described species Hydroclathrus minutus is consistently segregated from the Hydroclathrus main clade. We propose here to segregate H. minutus from the brown algal genus Hydroclathrus and establish the new monotypic genus Manzaea (i.e., Manzaea minuta gen. & comb. nov.) based on information on molecular phylogenetics and morpho-anatomy. Morphologically, M. minuta is similar to Hydroclathrus and Tronoella in having clathrate (net-like) and spreading thalli but is differentiated from the latter two genera in having membranous thalli that are sometimes interadhesive resulting in portions of the thallus forming amorphous clumps. Additionally, Manzaea is distinguished from both clathrate genera in having thick-walled medullary cells and short closely arranged quadriseriate plurangia. Phylogenetic analyses (Maximum Likelihood and Bayesian Inference) based on single (plastidial psaA and rbcL genes) and concatenated (cox3 + psaA + rbcL) genes showed that M. minuta is consistently segregated from the highly supported clade of Hydroclathrus species and often clustering with Tronoella and/or Rosenvingea. Our proposal further increases the diversity of monotypic genera in the Scytosiphonaceae and underscores the need to conduct further studies on tropical seaweed biodiversity.
WJES thanks Dr. Gavino C. Trono, Jr. and Dr. Edna T. Ganzon-Fortes for the inspiration and encouragement to conduct seaweed biodiversity and systematics research. WJES is funded by the University of the Philippines through the Balik PhD Program of the Office of the Vice President for Academic Affairs (OVPAA-BPhD-2018-05), the University of the Philippines Diliman through the In-house research grant of the Marine Science Institute, and the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of the Government of Japan under the Monbukagakusho Scholarship Grant. WJES also acknowledges the support of the Department of Science and Technology (DOST)-Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development (PCAARRD) of the Government of the Philippines through the DOST Balik Scientist Program.
Modified oxylipins as inhibitors of biofilm formation in Staphylococcus epidermidis
Peran, Jacquelyn E.; Salvador-Reyes, Lilibeth A. (Frontiers Media SA, 2024-05-23)
New approaches to combating microbial drug resistance are being sought, with the discovery of biofilm inhibitors considered as alternative arsenal for treating infections. Natural products have been at the forefront of antimicrobial discovery and serve as inspiration for the design of new antibiotics. We probed the potency, selectivity, and mechanism of anti-biofilm activity of modified oxylipins inspired by the marine natural product turneroic acid. Structure-activity relationship (SAR) evaluation revealed the importance of the trans-epoxide moiety, regardless of the position, for inhibiting biofilm formation. trans-12,13-epoxyoctadecanoic acid (1) and trans-9,10 epoxyoctadecanoic acid (4) selectively target the early stage of biofilm formation, with no effect on planktonic cells. These compounds interrupt the formation of a protective polysaccharide barrier by significantly upregulating the ica operon’s transcriptional repressor. This was corroborated by docking experiment with SarA and scanning electron micrographs showing reduced biofilm aggregates and the absence of thread-like structures of extrapolymeric substances. In silico evaluation revealed that 1 and 4 can interfere with the AgrA-mediated communication language in Staphylococci, typical to the diffusible signal factor (DSF) capacity of lipophilic chains.
Mining small molecules from Teredinibacter turnerae strains isolated from Philippine Teredinidae
Villacorta, Jamaine B.; Rodriguez, Camille V.; Peran, Jacquelyn E.; Batucan, Jeremiah D.; Concepcion, Gisela; Salvador-Reyes, Lilibeth A.; Junio, Hiyas A. (MDPI, 2022-11-21)
Endosymbiotic relationship has played a significant role in the evolution of marine species, allowing for the development of biochemical machinery for the synthesis of diverse metabolites. In this work, we explore the chemical space of exogenous compounds from shipworm endosymbionts using LC-MS-based metabolomics. Priority T. turnerae strains (1022X.S.1B.7A, 991H.S.0A.06B, 1675L.S.0A.01) that displayed antimicrobial activity, isolated from shipworms collected from several sites in the Philippines were cultured, and fractionated extracts were subjected for profiling using ultrahigh-performance liquid chromatography with high-resolution mass spectrometry quadrupole time-of-flight mass analyzer (UHPLC-HRMS QTOF). T. turnerae T7901 was used as a reference microorganism for dereplication analysis. Tandem MS data were analyzed through the Global Natural Products Social (GNPS) molecular networking, which resulted to 93 clusters with more than two nodes, leading to four putatively annotated clusters: lipids, lysophosphatidylethanolamines, cyclic dipeptides, and rhamnolipids. Additional clusters were also annotated through molecular networking with cross-reference to previous publications. Tartrolon D cluster with analogues, turnercyclamycins A and B; teredinibactin A, dechloroteredinibactin, and two other possible teredinibactin analogues; and oxylipin (E)-11-oxooctadec-12-enoic acid were putatively identified as described. Molecular networking also revealed two additional metabolite clusters, annotated as lyso-ornithine lipids and polyethers. Manual fragmentation analysis corroborated the putative identification generated from GNPS. However, some of the clusters remained unclassified due to the limited structural information on marine natural products in the public database. The result of this study, nonetheless, showed the diversity in the chemical space occupied by shipworm endosymbionts. This study also affirms the use of bioinformatics, molecular networking, and fragmentation mechanisms analysis as tools for the dereplication of high-throughput data to aid the prioritization of strains for further analysis.
The research was completed under the supervision of the Department of Agriculture-Bureau of Fisheries and Aquatic Resources (DA-BFAR), Philippines in compliance with Prior Informed Consent (PIC) certificate requirements and all required legal instruments and regulatory issuances covering the conduct of the research. The authors would also like to acknowledge the Department of Science and Technology-funded Discovery and Development of Health Products Program (DOST-DDHP) for the LC-MS Facility of the Institute of Chemistry, University of the Philippines Diliman.
Contrasting reproductive strategies between stress-tolerant and competitive coral taxa
Bonilla, K. G.; Guest, J. R.; Baria-Rodriguez, M. V. (Springer, 2023-04-19)
Reproductive traits such as fecundity (i.e., the number of gametes produced) and the size and age of coral colonies at reproductive onset can vary in predictable ways among life history strategies. However, most studies on the onset of reproductive maturity in corals only report the presence or absence of oocytes with little known about variation in fecundity across size and age classes. This study aimed to determine the colony size and fecundity at the onset of reproductive maturity across size classes of two scleractinian corals with contrasting life history strategies, Acropora millepora (competitive) and Favites colemani (stress-tolerant). Colonies at a site in northwestern Philippines were sampled to determine the smallest colony size class with mature oocytes and to estimate fecundity across size classes. Histological slides were also prepared to verify the presence of mature gametes. Colonies were able to produce mature oocytes when they had attained colony diameters of 4.7 cm for A. millepora and 1.5 cm for F. colemani. A. millepora had lower fecundity, but larger oocytes compared to F. colemani. Although small colonies can contribute to the larval pool, the proportion of mature colonies increased for larger size classes, suggesting that larger colonies make a disproportionately greater contribution to population reproductive output. These findings contribute to our understanding of coral population dynamics, particularly in parameterizing population and demographic models for different coral life histories.
We are grateful to Christine Baran, Jue Alef Lalas, Jerry Arboleda, Gabriel de Guzman, the students and research assistants of Community and Ecology and Interactions of Marine Bionts and Benthic Ecosystems Laboratories for their valuable assistance during field and laboratory works, Darryl Valino for the site map, and Liam Lachs for the assistance on the statistical analyses. This research was supported by the University of the Philippines Marine Science Institute’s In-house project, Department of Science and Technology – ASTHRDP Thesis Grant, and University of the Philippines – Office of the Vice President for Academic Affairs’ Balik Ph.D. project (OVPAA-BPhD-2018-02).
Synthesis and biological evaluation of cyanobacterial-inspired peptides
Casanova, Jannelle R.; Villaraza, Aaron Joseph L.; Salvador-Reyes, Lilibeth (Philippine-American Academy of Science and Engineering, 2024-03-18)
Cyanobacteria are known producers of structurally diverse and potent natural products; the majority are peptides with unique modifications. Yet, there remains a huge underexplored chemodiversity from cyanobacteria. Here, we designed a linear octapeptide as a product of combinatorial peptide design inspired by the natural products from the filamentous cyanobacteria Hapalosiphon welwitschii and Leptolyngbya sp. The target peptide was synthesized via solid-phase peptide synthesis (SPPS) using fluorenylmethyloxycarbonyl-protecting group (Fmoc) strategy. Structural diversity was expanded by the substitution of unnatural amino acids to yield five analogues. The structure and sequence of the synthesized peptides were confirmed using nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). Biological activity evaluation was done; with none of the peptides showing antimicrobial or cytotoxic activities against microbial pathogens and mammalian cells, respectively. To our knowledge, this study is the first to report a combinatorial peptide design inspired by a natural product and a predicted biosynthetic product. This strategy of peptide design expands the chemistry of a known bioactive natural product with the aid of unexplored cyanobacterial biosynthetic gene clusters.
This study was funded by the Philippine Council for Health Research and Development – Department of Science and Technology through the Discovery and Development of Health Products – Marine Component Program. J.R.C acknowledges scholarship support from the Accelerated Science and Technology Human Resource Development Program of the Department of Science and Technology – Science Education Institute. We acknowledge the assistance of Z. Malto, J. Peran and S. Susana in the conduct of the biological assays. This is MSI Contribution No. 502.