Marine biodiversity: an exploration of São Paulo coastal islands using environmental DNA metabarcoding

• Grant number: 19/10201-0
• Support Opportunities: BIOTA-FAPESP Program - Young Investigators Grants
• Start date: May 01, 2022
• End date: April 30, 2027
• Field of knowledge: Physical Sciences and Mathematics - Oceanography - Biological Oceanography
• Principal Investigator: Rodrigo Rodrigues Domingues
• Grantee: Rodrigo Rodrigues Domingues
• Host Institution: Instituto de Biociências (IB-CLP). Universidade Estadual Paulista (UNESP). Campus Experimental do Litoral Paulista. São Vicente , SP, Brazil
• Associated researchers: Agostinho Antunes Pereira ; Marcelo Visentini Kitahara ; Naiara Guimaraes Sales ; Paulo Yukio Gomes Sumida ; Tito Monteiro da Cruz Lotufo
• Associated scholarship(s): 25/01448-2 - Composition, structure, and distribution of ichthyofauna in the coastal islands of São Paulo using environmental DNA, BP.MS; 24/16716-0 - Eukaryotic biodiversity of coastal islands of São Paulo through environmental DNA and metabarcoding, BP.DD; 24/05452-1 - Application of environmental DNA metabarcoding in protected and non-protected marine areas of the State of São Paulo., BP.TT; + associated scholarships 24/00480-7 - Hidden marine biodiversity: applications of e-DNA on marine biodiversity and conservation, BP.JC; 24/00485-9 - Hidden marine biodiversity: applications of e-DNA on marine biodiversity and conservation, BP.JC; 23/12613-9 - Characterization of eukaryotic biodiversity of the Laje de Santos using 18s rRNA, BP.IC; 23/09317-9 - Development and validation of metabarcoding primers for the survey of Porifera and Cnidaria from the São Paulo coastal islands, BP.IC; 22/14631-1 - Multilocus DNA barcode of marine species not represented in sequences database: subsidies for DNA metabarcoding off the São Paulo coast, BP.IC; 22/05068-1 - Marine biodiversity: an exploration of São Paulo coastal islands using environmental DNA metabarcoding, AP.BTA.JP - associated scholarships

Abstract

Biological diversity is an ecosystem property that has received increasing attention in recent years, mainly because biodiversity loss is one of the most critical current environmental problems. Specifically, marine biodiversity may be subject to rapid changes due to anthropogenic influences such as fishing, oil and gas exploration, nonindigenous species introduction, environmental destruction, and climate change. To gather data to support future monitoring plans, mainly in depauperate populations and remote ecosystems, the development of non-invasive techniques that minimize the risks of injury or death of animals is imperative. Biodiversity surveys using DNA derived from environmental samples, known as "environmental DNA" (eDNA), allow the detection of traces of genetic material of cellular or extracellular form released into the environment through mucus, excrements, gametes, skin cells, and decomposing carcasses of different organisms. Environmental DNA can be retrieved from the environment, amplified, sequenced, and taxonomically assigned using high-throughput sequencing (HTS) metabarcoding. Despite being a widely used, rapid and efficient biodiversity monitoring tool in temperate regions, eDNA metabarcoding has not been used yet to assess the Brazilian marine biodiversity. Therefore, this pioneering project proposal will work towards filling the knowledge gap concerning marine biodiversity of protected and unprotected ecosystems via eDNA metabarcoding. Specifically, we will use massive sequence data to provide a better understanding of the current marine eukaryotic biodiversity at community (high taxonomic levels - phylum) and assemblages of fish, porifera and anthozoa at species-specific level, testing hypotheses about the possible causes of biodiversity changes. Biomonitoring data that will be performed over two years within four geographic regions in the São Paulo state, including Laje de Santos Marine State Park, Alcatrazes Archipelago Wildlife Refuge, Queimada Grande Island, and Búzios Island. Hypotheses will be tested to examine wheter eukaryotic community and some metazoan taxa (porifera, anthozoan, and fish) identified through eDNA metabarcoding differ among the various regions and the two collection years. We will compare oceanographic conditions within the two sampling years to correlate different environmental conditions with biodiversity patterns. Therefore, this project will provide crucial lacking information about marine biodiversity, which will be disseminated to both scientists and policy managers, contributing to better conservation management actions of the marine realm. By the end of this project, we expect to have contributed to a better knowledge of São Paulo marine biodiversity, implemented a new research line at the Oceanographic Institute, University of São Paulo (USP), and trained researchers and students in different disciplines such as genomics, oceanography, marine molecular ecology, evolution, bioinformatics, and statistical analysis. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

DOMINGUES, RODRIGO R.; MASTROCHIRICO-FILHO, VITO ANTONIO; MENDES, NATALIA J.; HASHIMOTO, DIOGO T.; COELHO, RUI; ANTUNES, AGOSTINHO; FORESTI, FAUSTO; MENDONCA, FERNANDO F.. Gene-associated markers as a genomic and transcriptomic resource for a highly migratory and apex predator shark (Isurus oxyrinchus). Marine Biology, v. 169, n. 9, p. 12-pg., 2022-09-01. (14/19740-7, 17/02420-8, 19/10201-0)

SEIXAS, MANUEL J.; DOMINGUES, RODRIGO R.; ANTUNES, AGOSTINHO. Decoding the Transcriptome of Sharks, Rays, and Chimaeras: Insights into Their Physiology, Morphology, Evolution, and Biomedical Applications. FISHES, v. 8, n. 5, p. 22-pg., 2023-05-19. (19/10201-0, 22/05068-1)

SILVA, LARA E.; DOMINGUES, RODRIGO R.; SALES, NAIARA G.; VILLELA, PRISCILA M. S.; SILVA, CAMILA BARBOSA; HILSDORF, ALEXANDRE W. S.. Amazonian ichthyoplankton assessment via DNA metabarcoding: A baseline for detecting spawning sites of migratory fishes. Biological Conservation, v. 284, p. 11-pg., 2023-07-05. (19/10201-0, 22/05068-1)