High-throughput analysis using 16S rRNA gene of bacterial communities present in selected bivalves and gastropods species from Bayug Island, Iligan City, Philippines
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Abstract. Albarido NA, Tabugo SR. 2024. High-throughput analysis using 16S rRNA gene of bacterial communities present in selected bivalves and gastropods species from Bayug Island, Iligan City, Philippines. Biodiversitas 25: 431-438. Seashells, which include bivalves and gastropods, have global recognition for their significant contributions to the economy, ecology, and medicine. They hold value as a food source and are highly regarded as effective biological indicators. The objective of this study is to identify the bacterial communities present in selected edible species of bivalves (Pinctada margaritifera Linnaeus, 1758 and Anadara granosa Linnaeus, 1758) and gastropods (Canarium urceus Linnaeus, 1758 and Conus stercusmuscarum Linnaeus, 1758), through high-throughput sequencing metabarcoding. Bacterial samples were collected via a swabbing technique on the surface and inside parts of selected mollusc species, which were then placed on sterilized seawater for DNA extraction. Genomic DNA was isolated from the samples, and the V3-V4 region of the 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform. Four amplicon libraries were generated, representing the two bivalve and two gastropod species in the study area. Data analysis was conducted using the Parallel Meta Suite software. Upon quality control and processing, 173,489 amplicon sequence variants (ASVs) were obtained. Within the bacterial community, the most abundant genera included Stenotrophomonas, Vibrio, Serratia, Photobacterium, and Shewanella. The assessment of alpha diversity, using the Shannon index, indicated a higher diversity in A. granosa. Furthermore, the analysis using the PICRUSt algorithm within the Parallel Meta Suite unveiled the involvement of specific bacteria found in the selected gastropod and bivalve species in various functions. These functions encompass protein production, xenobiotic metabolism, biodegradation, and other metabolism-related processes, supporting these organisms' ecological and physiological roles.
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References
Asakawa M, Gomez-Delan G, Barte-Quilantang M, Ito K. 2015. Paralytic Shellfish Poison (PSP) Producing Dinoflagellate and
PSP Infested Organisms. Marine Protists, 567–596. DOI: 10.1007/978-4-431-55130-0_24
Baaziz H, Lemaire ON, Jourlin-Castelli C, Iobbi-Nivol C, Méjean V, Alatou R, Fons M. 2018. Draft genome sequence of
Shewanella algidipiscicola H1, a highly chromate-resistant strain isolated from Mediterranean marine
sediments. Microbiology Resource Announcements, 7(8), 10-1128. DOI: 10.1128/mra.00905-18
Bailet B, Apothéloz-Perret-Gentil L, Bari?evi? A, Chonova T, Franc A, Frigerio JM, Kahlert M. 2020. Diatom DNA
metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries
reveals the need for standardization. Science of the Total Environment, 745, 140948.
DOI: 10.1016/j.scitotenv.2020.140948
Barendse J, Roel A, Longo C, Andriessen L, Webster LMI, Ogden R, Neat F. 2019. DNA Barcoding Validates Species Labelling
of Certified Seafood. Curr. Biol. 29, R198–R199.
Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM. 2014. Environmental conditions influence eDNA
persistence in aquatic systems. Environmental science & technology, 48(3), 1819-1827. DOI: 10.1021/es404734p
Berry TE, Osterrieder SK, Murray DC, Coghlan ML, Richardson AJ, Grealy AK, Bunce M. 2017. DNA metabarcoding for diet
analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea). Ecology and
Evolution, 7(14), 5435-5453. DOI: 10.1002/ece3.3123
Bohmann K, Evans A, Gilbert MTP, Carvalho GR, Creer S, Knapp M, De Bruyn M. 2014. Environmental DNA for wildlife
biology and biodiversity monitoring. Trends in ecology & evolution, 29(6), 358-367. DOI: 10.1016/j.tree.2014.04.003
Borrell YJ, Miralles L, Do Huu H, Mohammed-Geba K, Garcia-Vazquez E. 2017. DNA in a bottle—Rapid metabarcoding
survey for early alerts of invasive species in ports. PloS one, 12(9), e0183347. DOI: 10.1371/journal.pone.0183347
Brooke JS. 2021. Advances in the microbiology of Stenotrophomonas maltophilia. Clin Microbiol Rev 34:e00030-19. DOI:
1128/CMR.00030-19.
Calderón-Franco D, van Loosdrecht MC, Abeel T, Weissbrodt DG. 2020. A novel method to isolate free-floating extracellular
DNA from wastewater for quantitation and metagenomic profiling of mobile genetic elements and antibiotic resistance
genes. bioRxiv, 2020-05. DOI: 10.1101/2020.05.01.072397
Cáliz J, Triadó-Margarit X, Camarero L, Casamayor EO. 2018. A long-term survey unveils strong seasonal patterns in the airborne
microbiome coupled to general and regional atmospheric circulations. Proceedings of the National Academy of
Sciences, 115(48), 12229-12234. DOI: 10.1073/pnas.1812826115
Chen Y, Li J, Zhang Y, Zhang M, Sun Z, Jing G, Su X. 2022. Parallel?Meta Suite: Interactive and rapid microbiome data analysis
on multiple platforms. iMeta, 1(1), e1. DOI: 10.1002/imt2.1
Craine JM, Barberán A, Lynch RC, Menninger HL, Dunn RR, Fierer N. 2017. Molecular analysis of environmental plant DNA in
house dust across the United States. Aerobiologia, 33, 71-86. DOI: 10.1007/s10453-016-9451-5
Deiner K, Walser JC, Mächler E, Altermatt F. 2015. Choice of capture and extraction methods affect detection of freshwater
biodiversity from environmental DNA. Biological conservation, 183, 53-63. DOI: 10.1016/j.biocon.2014.11.018
Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière?Roussel A, Altermatt F, Bernatchez L. 2017. Environmental DNA
metabarcoding: Transforming how we survey animal and plant communities. Molecular ecology, 26(21), 5872-5895.
DOI: 10.1111/mec.14350
Devi AR, Susilowati A, Setyaningsih R. 2019. Morphology, molecular identification, and pathogenicity of Vibrio spp. on blood
clam (Anadara granosa) in Yogyakarta, Indonesia tourism beach areas. Biodiversitas Journal of Biological
Diversity, 20(10). DOI: 10.13057/biodiv/d201016
Ekawati ER, Yusmiati SNH. 2018. Detection of Salmonella sp., Vibrio sp. and total plate count bacteria on blood cockle
(Anadara granosa). In IOP conference series: earth and environmental science (Vol. 102, No. 1, p. 012086).
IOP Publishing. DOI: 10.1088/1755-1315/102/1/012086
Evans DM, Kitson JJ. 2020. Molecular ecology as a tool for understanding pollination and other plant–insect interactions. Current
opinion in insect science, 38, 26-33. DOI: 10.1016/j.cois.2020.01.005
Farrell MJ, Govender D, Hajibabaei M, Van Der Bank M, Davies TJ. 2019. Bacterial diversity in the waterholes of
the Kruger National Park: an eDNA metabarcoding approach. Genome, 62(3), 229-242. DOI: 10.1139/gen-2018-
@gen-dna.issue01
Fernandes TJR, Amaral JS, Mafra I. 2020. DNA Barcode Markers Applied to Seafood Authentication: An Updated Review. Crit.
Rev. Food Sci. Nutr. 1–32. DOI: 10.1080/10408398.2020.1811200
Ghosh R, Chatterjee S, Mandal NC. 2020. Stenotrophomonas. In Beneficial Microbes in Agro-Ecology (pp. 427-442). Academic
Press. DOI: 10.1016/B978-0-12-823414-3.00020-4
Gomez-Gil B, Soto-Rodríguez S, Lozano R, Betancourt-Lozano M. 2014. Draft genome sequence of Vibrio parahaemolyticus
strain M0605, which causes severe mortalities of shrimps in Mexico. Genome Announcements 2:55 -14.
DOI:10.3354/dao02621
Harrison JB, Sunday JM, Rogers SM. 2019. Predicting the fate of eDNA in the environment and implications for studying
biodiversity. Proceedings of the Royal Society B, 286(1915), 20191409. DOI: 10.1098/rspb.2019.1409
Hurley KV, Wharton L, Wheeler MJ, Skjøth CA, Niles C, Hanson MC. 2019. Car cabin filters as sampling devices to study
bioaerosols using eDNA and microbiological methods. Aerobiologia, 35, 215-225. DOI: 10.1007/s10453-018-09554-y
Ina?Salwany MY, Al?saari N, Mohamad A, Mursidi FA, Mohd?Aris A, Amal MNA, Zamri?Saad M. 2019. Vibriosis in fish: a
review on disease development and prevention. Journal of aquatic animal health, 31(1), 3-22. DOI: 10.1002/aah.10045
Ishige T, Miya M, Ushio M, Sado T, Ushioda M, Maebashi K, Matsubayashi H. 2017. Tropical-forest mammals as detected by
environmental DNA at natural saltlicks in Borneo. Biological conservation, 210, 281-285. DOI: 10.1016/j.biocon.2017.04.023
Kloska A, Cech GM, Sadowska M, Krause K, Szalewska-Pa?asz A, Olszewski P. 2020. Adaptation of the marine bacterium
Shewanella baltica to low temperature stress. International Journal of Molecular Sciences, 21(12), 4338.
DOI: 10.3390/ijms21124338
Kokashvili T, Whitehouse CA, Tskhvediani A, Grim CJ, Elbakidze T, Mitaishvili N, Tediashvili M. 2015. Occurrence and
diversity of clinically important Vibrio species in the aquatic environment of Georgia. Frontiers in public health, 3,
DOI: 10.3389/fpubh.2015.00232
Labella AM, Arahal DR, Castro D, Lemos ML, Borrego JJ. 2017. Revisiting the genus Photobacterium: taxonomy, ecology and
pathogenesis. Int Microbiol, 20(1), 1-10. DOI: 10.2436/20.1501.01.280.
Larson ER, Graham BM, Achury R, Coon JJ, Daniels MK, Gambrell DK, Suarez AV. 2020. From eDNA to citizen science:
emerging tools for the early detection of invasive species. Frontiers in Ecology and the Environment, 18(4), 194-202.
DOI: 10.1002/fee.2162
Lemaire ON, Méjean V, Iobbi-Nivol C. 2020. The Shewanella genus: ubiquitous organisms sustaining and preserving aquatic
ecosystems. FEMS microbiology reviews, 44(2), 155-170. DOI: 10.1093/femsre/fuz031
Maran MIJ. 2022. Benefits of merging paired-end reads before pre-processing environmental metagenomics data. Marine
Genomics, 61, 100914. DOI: 10.1016/j.margen.2021.100914
Moi IM, Roslan NN, Leow ATC, Ali MSM, Rahman RNZRA, Rahimpour A, Sabri S. 2017. The biology and the importance of
Photobacterium species. Applied microbiology and biotechnology, 101(11), 4371-4385. DOI: 10.1007/s00253-017-
-y
Moreira APB, Duytschaever G, Chimetto Tonon LA, Froes AM, de Oliveira ML, Amado-Filho GM, Francini-Filho RB, De Vos
P. 2014. Photobacterium sanctipauli sp. nov. isolated from bleached Madracis decactis (Scleractinia) in the St. Peter &
St Paul Archipelago, Mid-Atlantic Ridge, Brazil. Peer J 2, e427. DOI: 10.7717/peerj.427
Morris JP, Backeljau T, Chapelle G. 2019. Shells from aquaculture: a valuable biomaterial, not a nuisance waste
product. Reviews in Aquaculture, 11(1), 42-57. DOI: 10.1111/raq.12225
Muwawa EM, Obieze CC, Makonde HM, Jefwa JM, Kahindi JHP, Khasa DP. 2021. 16S rRNA Gene Amplicon-Based
Metagenomic Analysis of Bacterial Communities in the Rhizospheres of Selected Mangrove Species from Mida Creek and Gazi Bay, Kenya. PLoS one 16: 1–22. DOI: 10.1371/journal.pone.0248485.
Olson DH, Aanensen DM, Ronnenberg KL, Powell CI, Walker SF, Bielby J, Fisher MC. 2013. Mapping the global emergence of
Batrachochytrium dendrobatidis, the amphibian chytrid fungus. PloS one, 8(2), e56802. DOI: 10.1371/journal.pone.0056802
Padhi N. 2021. Kingdom of seashells: Explotation and culture of major commercial species. Int J Aquac Fish Sci 7(1): 001-004.
DOI: 10.17352/2455-8400.000065
Richards CL, Broadaway SC, Eggers MJ, Doyle J, Pyle BH, Camper AK, Ford TE. 2018. Detection of pathogenic and non-
pathogenic bacteria in drinking water and associated biofilms on the crow reservation, Montana, USA. Microbial
ecology, 76, 52-63. DOI: 10.1007/s00248-015-0595-6
Rivas AJ, Lemos ML, Osorio CR. 2013a. Photobacterium damselae subsp. damselae, a bacterium pathogenic for marine animals
and humans. Front Microbiol 4, 283–289. DOI: 3389/fmicb.2013.00283
Rosenberg G. 2014. A new critical estimate of named species-level diversity of the recent Mollusca. American Malacological
Bulletin, 32(2), 308-322. DOI: 10.4003/006.032.0204
Sirois SH, Buckley DH. 2019. Factors governing extracellular DNA degradation dynamics in soil. Environmental microbiology
reports, 11(2), 173-184. DOI: 10.1111/1758-2229.12725
Soenens A, Imperial J. 2020. Biocontrol capabilities of the genus Serratia. Phytochemistry Reviews, 19(3), 577-587. DOI:
1007/s11101-019-09657-5
Sonak SM. 2017. Molluscs and Their Shells. In: Marine Shells of Goa. Springer, Cham. DOI: 10.1007/978-3-319-55099-2_1
Stewart K, Ma H, Zheng J, Zhao J. 2017. Using environmental DNA to assess population?wide spatiotemporal reserve
use. Conservation Biology, 31(5), 1173-1182. DOI: 10.1111/cobi.12910
Summa D, Lanzoni M, Castaldelli G, Fano EA, Tamburini E. 2022. Trends and opportunities of bivalve shells’ waste
valorization in a prospect of circular blue bioeconomy. Resources, 11(5), 48. DOI: 10.3390/resources11050048
Taberlet P, Bonin A, Zinger L, Coissac E. 2018. Environmental DNA: For biodiversity research and monitoring. Oxford
University Press.
Tabugo SRM, Pattuinan JO, Sespene NJJ, Jamasali AJ. 2013. Some economically important bivalves and gastropods found in the
Island of Hadji Panglima Tahil, in the province of Sulu, Philippines. International Research Journal of Biological
Sciences, 2(7), 30-36.
Ushio M, Fukuda H, Inoue T, Makoto K, Kishida O, Sato K, Miya M. 2017. Environmental DNA enables detection of terrestrial
mammals from forest pond water. Molecular Ecology Resources, 17(6), e63-e75. DOI: 10.1111/1755-0998.12690
Valentin RE, Fonseca DM, Nielsen AL, Leskey TC, Lockwood JL. 2018. Early detection of invasive exotic insect infestations
using eDNA from crop surfaces. Frontiers in Ecology and the Environment, 16(5), 265-270. DOI: 10.1002/fee.1811
Vamosi JC, Gong YB, Adamowicz SJ, Packer L. 2017. Forecasting pollination declines through DNA barcoding: the potential
contributions of macroecological and macroevolutionary scales of inquiry. New Phytologist, 214(1), 11-18. DOI:
1016/j.cois.2020.01.005
Vito MP. 2018. Diversity and abundance of economically important bivalves in north-western Bohol, Philippines. International
Journal of Fisheries and Aquatic Studies 2018; 6(3): 44-48
Walker DM, Leys JE, Dunham KE, Oliver JC, Schiller EE, Stephenson KS, Rogers MW. 2017. Methodological considerations for
detection of terrestrial small?body salamander eDNA and implications for biodiversity conservation. Molecular Ecology
Resources, 17(6), 1223-1230. DOI: 10.1111/1755-0998.12667
Wang Z, Shi C, Wang H, Wan X, Zhang Q, Song X, Huang J. 2020. A Novel research on isolation and characterization of
Photobacterium damselae subsp. damselae from Pacific white shrimp, Penaeus vannamei, displaying black gill disease
cultured in China. Journal of fish diseases, 43(5), 551-559. DOI: 10.1111/jfd.13153
Williams KE, Huyvaert KP, Vercauteren KC, Davis AJ, Piaggio AJ. 2018. Detection and persistence of environmental DNA from
an invasive, terrestrial mammal. Ecology and Evolution, 8(1), 688-695. DOI: 10.1002/ece3.3698
Yang J, Zhang X. 2020. eDNA metabarcoding in zooplankton improves the ecological status assessment of aquatic
ecosystems. Environment international, 134, 105230. DOI: 10.1016/j.envint.2019.105230
Zarkasi KZ, Halim MA, Nazari TF, Daud F. 2018. The molecular investigation of Blood cockles (Anadara granosa) associated
bacterial communities using 16S rRNA sequencing. DOI: 10.1016/j.dib.2018.05.052
Zarkasi KZ, Nazari TF. 2018. Molecular characterisation of microbial diversity associated with oysters within a commercial
oyster farm. Turkish Journal of Fisheries and Aquatic Sciences, 18(1), 191-197. DOI: 10.4194/1303-2712-v18_1_22
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