Journal Articles - UP - MSI
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- Transcriptome analysis of growth variation in early juvenile stage sandfish Holothuria scabraOrdoñez, June Feliciano F.; Galindez, Gihanna Gaye S.T.; Gulay, Karina Therese; Ravago-Gotanco, Rachel (Elsevier, 2021-12)The sandfish Holothuria scabra is a high-value tropical sea cucumber species representing a major mariculture prospect across the Indo-Pacific. Advancements in culture technology, rearing, and processing present options for augmenting capture production, stock restoration, and sustainable livelihood activities from hatchery-produced sandfish. Further improvements in mariculture production may be gained from the application of genomic technologies to improve performance traits such as growth. In this study, we performed de novo transcriptome assembly and characterization of fast- and slow-growing juvenile H. scabra from three Philippine populations. Analyses revealed 66 unigenes that were consistently differentially regulated in fast-growing sandfish and found to be associated with immune response and metabolism. Further, we identified microsatellite and single nucleotide polymorphism markers potentially associated with fast growth. These findings provide insight on potential genomic determinants underlying growth regulation in early juvenile sandfish which will be useful for further functional studies.The authors are grateful to the following individuals and institutions for providing samples and facilitating their collection: D. Ticao of (Finfish Hatcheries, Inc.); Dr. M.A. Juinio-Menez, ˜ J.R. Gorospe, C. Edullantes, B. Rodriguez, A. Rioja, T. Catbagan, and G. Peralta of Bolinao Marine Laboratory, University of the Philippines Marine Science Institute; and E. Tech (Palawan Aquaculture Corp.).
- Associated effects of shading on the behavior, growth, and survival of Stichopus cf. horrens juvenilesRioja, Rose Angeli; Palomar-Abesamis, Nadia; Juinio–Meñez, Marie Antonette (Springer Science and Business Media LLC, 2021-07-07)Stichopus cf. horrens is an emergent culture species. It is known to be nocturnal and negatively phototactic; hence, determining its behavioral and growth responses to different light regimes is essential in optimizing culture protocols. This study examined the interactive effects of shading and relative food availability on the feeding pattern, absolute growth rates, and survival of juvenile S. cf. horrens. Six-month-old juveniles (4.27 to 19.41 g) were reared in replicate aquaria with three different shading treatments (covered, exposed, and half-covered aquaria) under ambient light conditions for 30 days. Juveniles in the exposed treatment with high microalgal biomass (13.44 ± 4.57 mg/g) had the highest growth rates (0.10 ± 0.05 g/day) but also the highest mortality (50%). In contrast, juveniles in the covered treatment had the lowest growth (−0.07 ± 0.03 g/day) but the highest survival (100%). Growth rates in the half-covered treatment were comparable with the exposed, and survival was higher than in the covered treatment. These indicate a trade-off between growth associated with more food and mortality risks due to light-induced stress. Juveniles in the half-covered treatment showed a significant preference to stay in the shaded portion whenever they were inactive during the day, suggesting avoidance to high light intensities (4726.51 ± 1582.43 Lux). Results of this study suggest that careful calibration of light intensities in nursery systems may help enhance juvenile growth. For indoor systems that may have limited space or surfaces for microalgal growth, cultured benthic diatom can be added to the partially covered tanks to increase the food available for the juveniles.
- Sargassum sp. juice as an early juvenile supplemental feed for Stichopus cf. horrensIbañez, Glaiza; Cabanayan-Soy, Rona; Baure, Jerwin; Juinio-Meñez, Marie Antonette (Springer, 2022-09-28)The development of an efficient and low-cost feed is important to reduce the production and maintenance costs of microalgae. In this study, two experiments were conducted to evaluate the feasibility of using Sargassum sp. juice (SARG) to boost the growth and survival of post-settled Stichopus cf. horrens juveniles. Experiment 1 tested whether SARG improves growth compared with live microalgae diets, Chaetoceros calcitrans (Cc), combined Cc and Navicula ramosissima (Nr), and an unfed treatment. Experiment 2 determined the best SARG concentration—high feeding regime (HFR; 1 mL ind−1), medium (MFR; 0.5 mL ind−1), or low (LFR; 0.25 ml ind−1), relative to live microalgae Chaetoceros muelleri (CM). Juveniles in both experiments were reared for 30 days. In Experiment 1, the average daily growth rate (DGRL) of juveniles in SARG (0.04 ± 0.01 cm d−1) was the highest although not significantly different from Cc and Cc + Nr, but was significantly higher than the control. In Experiment 2, DGRL at day 14 in HFR (− 0.02 ± 0.02 cm d−1) was significantly lower than LFR (0.01 ± 0.01 cm d−1) and MFR (0.02 ± 0.02 cm d−1). Survival was higher in all SARG treatments compared with CM, while a significant decrease in feeding activity was observed in HFR by day 30. Results indicate that concentrations of 0.25–0.5 mL SARG per juvenile can boost growth and be an alternate diet for post-settled juveniles during early rearing. However, SARG alone is not sufficient to maintain growth beyond 3 weeks. With SARG feed supplementation and water quality management, the scaling-up of juvenile production of this emergent culture species can be accelerated.Our sincere gratitude to Mr. Tirso Catbagan and Mr. Garry Bucol for their assistance in the set-up of the experiments. We also thank Ms. Rose Angeli Rioja and Ms. JayR Gorospe for providing inputs to improve this paper. We also thank the Sea cucumber Research Team and the staff of the University of the Philippines—Marine Science Institute, Bolinao Marine Laboratory for their support and assistance during the conduct of the study.
- Evolving governance structures in community-based sandfish mariculture and their interactions with livelihood outcomes: Evidence from the PhilippinesFabinyi, Michael; Gorospe, Jay R; McClean, Nicholas; Juinio–Meñez, Marie Antonette (Frontiers Media SA, 2022-11-02)Sea cucumber mariculture is an important emerging field of practice and applied research in the coastal tropics. This is due to the existing importance of tropical sea cucumber fisheries for wealth generation and poverty reduction, and the potential for mariculture to contribute to the longer term sustainability of these fisheries while generating benefits additional to those from wild caught sea cucumber. Understanding the optimal institutional arrangements for sea cucumber mariculture is an important area of focus in this field, with a variety of arrangements currently in place. This paper documents the establishment of a communal form of sea ranching in the Philippines, as a case study of community level institutional processes. It describes the background to establishment of the sea ranch in the community of Victory, challenges encountered and how these were managed, and the evolution of governance arrangements. In charting this process, we assess the impacts on livelihood outcomes, highlighting this as a crucial aspect influencing this evolution and the nature of community involvement in the sea ranch. While the sea ranching project generated a range of benefits for livelihoods, including possible spillover effects for the surrounding fishery, substantial economic returns from harvests did not occur. Thus, the system of governing the sea ranch evolved from a communal model to a more exclusive household model primarily to improve operational efficiency. In order for possible benefits of the sea ranch to be sustained and enhanced, greater integration with fisheries management and government support will be needed.We are grateful to the Samahan ng Maliliit na Mangingisda ng Barangay Victory, Inc., the local government unit of Barangay Victory and Bolinao for their support to the Sea cucumber Research Program. We are also thankful to Tirso Catbagan, Josh Caasi, Rona Cabanayan-Soy, and Garry Bucol for their invaluable assistance during the field monitoring of sandfish in the sea ranch.
- Size-dependent predation on juvenile sandfish, Holothuria scabra by seagrass-associated crabsCaasi, Olivier Josh C.; Gosselin, Louis A.; Juinio–Meñez, Marie Antonette (Cambridge University Press, 2023-10-23)High mortality of juvenile Holothuria scabra in seagrass nursery areas has been attributed to predation. In this study, laboratory and field experiments were conducted to determine the effect of the size of two seagrass–associated crabs, Thalamita crenata and Dardanus megistos, on the survival of juvenile sandfish at different sizes (1–10 g). Small juvenile sandfish (1–2 g) offered in field trials were more preferred by small Thalamita and large Dardanus. Non-lethal damage caused by both crabs were also evident, indicating differences in the mode of attack and consumption. The incidence of non-lethal wounds in medium and large juveniles in the laboratory indicate higher incidences of unsuccessful attacks by the crabs. Differences in consumption rate may be related to cheliped morphology and handling techniques, and activity patterns affecting encounter rates. Mortality rates of juvenile sandfish due to T. crenata (CW: 4.30–7.05 cm) ranged from 10–43%, while those by D. megistos (SL: 0.90–2.3 cm) was even higher at 34–53% after 24 h trials. This is the first report that a hermit crab D. megistos is a significant predator of juvenile sandfish. Results provide new insights on crab–soft-bodied prey interactions in tropical seagrass areas. These are also important considerations in stock restoration and ocean-based culture. Given that juveniles (≤10 g) are very vulnerable to predation by these common crab species, growing sandfish to larger sizes is essential prior to release in the field.This study was funded by Australian Centre for International Agricultural Research (ACIAR) through the project FIS/2016/ 122 ‘Increasing technical skills supporting community–based sea cucumber production in Vietnam and the Philippines’ and administrative support from the Marine Environment and Resources Foundation (MERF), Inc. We are grateful to the Bolinao Marine Laboratory of the University of the Philippines Marine Science Institute for the use of facilities and equipment. Special thanks to Tirso Catbagan, Garry Bucol, and Tomilyn Jan Garpa for their assistance with field and laboratory work. We also thank JayR Gorospe and Jerwin Baure for comments on the draft versions of the manuscript.
- Physicochemical and biochemical characterization of collagen from Stichopus cf. horrens tissues for use as stimuli-responsive thin filmsSisican, Kim Marie D.; Torreno, Vicenzo Paolo M.; Yu, Eizadora T.; Conato, Marlon T. (American Chemical Society, 2023-09-20)The mutable collagenous tissue (MCT) of sea cucumber, with its ability to rapidly change its stiffness and extensibility in response to different environmental stress conditions, serves as inspiration for the design of new smart functional biomaterials. Collagen, extracted from the body wall of Stichopus cf. horrens, a species commonly found in the Philippines, was characterized for its suitability as stimuli-responsive films. Protein BLAST search showed the presence of sequences commonly found in type VII and IX collagen, suggesting that Stichopus horrens collagen is heterotypic. The maximum transition temperature recorded was 56.0 ± 2 °C, which is higher than those of other known sources of marine collagen. This suggests that S. horrens collagen has better thermal stability and durability. Collagen-based thin films were then prepared, and atomic force microscopy (AFM) imaging showed the visible collagen network comprising the films. The thin films were subjected to thermomechanical analysis with degradation starting at >175 °C. At 100–150 °C, the collagen-based films apparently lose their translucency due to the removal of moisture. Upon exposure to ambient temperature, instead of degrading, the films were able to revert to the original state due to the readsorption of moisture. This study is a demonstration of a smart biomaterial developed from S. cf. horrens collagen with potential applications in food, pharmaceutical, biomedical, and other collagen-based research.This research was funded by the Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development of the Department of Science and Technology (DOST-PCAARRD).
- Comprehensive metabolomics of Philippine Stichopus cf. horrens reveals diverse classes of valuable small molecules for biomedical applicationsTorreno, Vicenzo Paolo M.; Molino, Ralph John Emerson J.; Junio, Hiyas A.; Yu, Eizadora T. (Public Library of Science (PLoS), 2023-12-06)Stichopus cf. horrens is an economically important sea cucumber species in Southeast Asia due to their presumed nutritional and medicinal benefits. However, compared to other sea cucumbers such as Apostichopus japonicus, there are no biochemical studies on which compounds contribute to the purported bioactivities of S. cf. horrens. To address this, a high-throughput characterization of the global metabolite profile of the species was performed through LC-MS/MS experiments and utilizing open-access platforms such as GNPS, XCMS, and metaboAnalyst. Bioinformatics-based molecular networking and chemometrics revealed the abundance of phospholipids such as phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), phosphatidylinositols (PIs), and phosphatidylserines (PSs) in the crude samples. Body wall extracts were observed to have higher levels of structural, diacylated PCs, while the viscera have higher relative abundance of single-tail PCs and PEs that could be involved in digestion via nutrient absorption and transport for sea cucumbers. PEs and sphingolipids could also be implicated in the ecological response and morphological transformations of S. cf. horrens in the presence of predatory and other environmental stress. Interestingly, terpenoid glycosides and saponins with reported anti-cancer benefits were significantly localized in the body wall. The sulfated alkanes and sterols present in S. cf. horrens bear similarity to known kairomones and other signaling molecules. All in all, the results provide a baseline metabolomic profile of S. cf. horrens that may further be used for comparative and exploratory studies and suggest the untapped potential of S. cf. horrens as a source of bioactive molecules.The authors would like to thank the Marine Invertebrate Ecology Laboratory under Dr. Marie Antonette Juinio-Meñez for the collection and maintenance of animals, and the Mass Spectrometry Facility at the Institute of Chemistry, UP Diliman for instrument use.
- Transcriptome-derived SNP markers for population assignment of sandfish, Holothuria (Metriatyla) scabraOrdoñez, June F.; Ravago-Gotanco, Rachel (Elsevier, 2024-01-30)The sandfish, Holothuria scabra is a commercially important fishery and aquaculture species contributing to the high-value sea cucumber industry. Overexploited across many areas throughout its distributional range, natural populations are considered in decline. Accurate genetic assignment to population of origin is becoming increasingly important for genetics-based marine fisheries management and monitoring, especially for species experiencing depletion of natural stocks and decline in fisheries productivity due to overfishing and illegal, unreported, and unregulated (IUU) fishing. Initiatives for genetics-based applications on economically important seafood such as H. scabra have been limited by the lack of comprehensive genome or transcriptome resources. The present study developed and evaluated the use of gene-associated single nucleotide polymorphism (SNP) markers to assign sandfish to three locations in the Philippines, in the proximity of existing and emerging hatchery production centers. In silico SNP discovery pipeline using pooled RNA-Seq libraries and medium-throughput genotyping approach generated a dataset comprising 115 individuals genotyped at 88 SNPs. Population assignment using machine-learning analysis and Bayesian approach revealed that the 88 transcriptome-derived SNPs allowed the assignment of sandfish individuals to population of origin, with an overall assignment accuracy of >80%. The novel SNPs developed could find their utility in facilitating the development of geographic traceability tools applicable in the context of sandfish aquaculture, fisheries management and conservation.
- Metamorphic success and production cost of Holothuria scabra reared on microalgae concentrates compared with live microalgaeGarpa, Tomilyn Jan; Caasi, Olivier Josh C.; Juinio–Meñez, Marie Antonette (Bureau of Fisheries and Aquatic Resources, 2024-03-07)The production of live microalgae poses challenges for the expansion of sandfish hatcheries, hindered by high costs and limited technical resources. In relation to this, the use of three imported commercial concentrates (Instant Algae®) - TW1200 (Thalassiosira weisflogii), TISO1800 (Isochrysis sp.), and Shellfish1800 (mixed diatom) - were compared with live Chaetoceros calcitrans (CC). The diet efficacy was evaluated based on larval development, growth, and survival to late auricularia (LA) with hyaline spheres (HS), and the number of post-settled juveniles. Larvae reared with TW did not progress beyond LA, while those fed CC exhibited earlier LA development, larger sizes (1028.43 ± 19.38 µm), and significantly more post–settled juveniles (9,268 ± 2,183.79) compared to SHELL and TISO. Although TISO larvae reached a larger size during LA (855.7 ± 62.67 µm), SHELL resulted in a higher number of post-settled juveniles. The better performance of CC and SHELL may be attributed to their higher carbohydrate content. Despite SHELL and TISO having lower juvenile yields and longer feeding durations, the estimated cost per juvenile using SHELL, TISO, and CC were PHP 2.00, PHP 11.77, and PHP 0.52, respectively. Results showed that microalgae concentrates are not a cost-effective option under the studied conditions. The potential use of microalgae concentrates as supplemental feeds and further research to develop the use of local microalgae concentrates to sandfish larval culture are discussed.This study was funded by Australian Centre for International Agricultural Research (ACIAR) through the project FIS/2016/122 “Increasing technical skills supporting community-based sea cucumber production in Vietnam and the Philippines” and administrative support from the Marine Environment and Resources Foundation (MERF), Inc. We would also like to thank the Bolinao Marine Laboratory of the University of the Philippines Marine Science Institute for the use of facilities and equipment. We are grateful to our collaborators, Jon Altamirano and Roselyn Noran, and SEAFDEC AQD for guidance on the methods used for preparation and protocols of microalgae concentrate feeding regimen. Special thanks to JayR Gorospe for comments on the earlier draft and Jerwin Baure for copyediting this manuscript. The assistance of Mr. Tirso Catbagan in the culture of larvae and maintenance of the experimental tanks was invaluable during the experiment.
- Pseudocryptic diversity and species boundaries in the sea cucumber Stichopus cf. horrens (Echinodermata: Stichopodidae) revealed by mitochondrial and microsatellite markersLizano, Apollo Marco D.; Kim, Kenneth M.; Juinio-Meñez, Marie Antonette; Ravago-Gotanco, Rachel (Nature Research, 2024)Morphologically cryptic and pseudo-cryptic species pose a challenge to taxonomic identification and assessments of species diversity and distributions. Such is the case for the sea cucumber Stichopus horrens, commonly confused with Stichopus monotuberculatus. Here, we used mitochondrial cytochrome oxidase subunit I (COI) and microsatellite markers to examine genetic diversity in Stichopus cf. horrens throughout the Philippine archipelago, to aid species identification and clarify species boundaries. Phylogenetic analysis reveals two recently diverged COI lineages (Clade A and Clade B; c. 1.35–2.54 Mya) corresponding to sequence records for specimens identified as S. monotuberculatus and S. horrens, respectively. Microsatellite markers reveal two significantly differentiated genotype clusters broadly concordant with COI lineages (Cluster 1, Cluster 2). A small proportion of individuals were identified as later-generation hybrids indicating limited contemporary gene flow between genotype clusters, thus confirming species boundaries. Morphological differences in papillae distribution and form are observed for the two species, however tack-like spicules from the dorsal papillae are not a reliable diagnostic character. An additional putative cryptic species was detected within Clade B-Cluster 2 specimens warranting further examination. We propose that these lineages revealed by COI and genotype data be referred to as Stichopus cf. horrens species complex. © The Author(s) 2024.