Potential prey of Rice's whales based on seawater eDNA 2019

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Wilcox Talbot L, Silliman K, Applegate M, Aichinger Dias L, Garrison L, Paterson C, Thompson L, Vollmer N, Rosel P (2025). Potential prey of Rice's whales based on seawater eDNA 2019. Version 1.2. NOAA Oceanic and Atmospheric Research. Occurrence dataset. https://ipt-obis.gbif.us/resource?r=rices-diet-edna&v=1.2

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Palabras clave

eDNA; metabarcoding; marine biodiversity; environmental DNA; Occurrence

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Contactos

Cobertura geográfica

USA: Gulf of Mexico

Cobertura taxonómica

Marine vertebrates identified through eDNA metabarcoding

Cobertura temporal

Datos del proyecto

Understanding the foraging ecology of endangered marine mammals is crucial for their conservation yet remains challenging due to the inaccessibility of their feeding habitats. This study used environmental DNA (eDNA) metabarcoding with two complementary 12S rRNA markers (MiFish and Riaz) to characterize potential fish prey communities available to the critically endangered Rice's whale (Balaenoptera ricei) in its core habitat in the northeastern Gulf of America. Water samples (N = 21) collected during a July 2019 survey detected 99 unique fish species across 62 families. The combined metabarcoding approach revealed 74 fish species not recorded in concurrent trawl surveys, while 16 trawl-caught species went undetected by eDNA. Notably, eDNA yielded higher detection rates for several potential prey taxa previously identified through stable isotope analysis, suggesting key prey species may be more prevalent than previously documented. This study demonstrates the value of eDNA as a complementary tool for monitoring the prey community of this critically endangered cetacean.

Personas asociadas al proyecto:

Métodos de muestreo

During July 2019, a fish trawl (31.7 m footrope length, 0.6 cm sq codend mesh liner) was deployed from the NOAA Ship Gordon Gunter to collect potential Rice’s whale fish prey during daylight hours within Rice’s whale feeding areas in the northeastern Gulf of America (formerly known as the Gulf of Mexico). Trawl stations were selected by locating near-bottom aggregations of backscattering organisms (i.e., fishes) based on observations from a Simrad EK80 echosounder (transducer frequencies 18 kHz, 38 kHz and 120 kHz). Seawater samples (N = 21), collected between 120-320 m depth, were collected concurrently with the trawling using Niskin bottles (5 L total capacity) attached to a conductivity, temperature, and depth sensor (CTD) unit (Figure 1). Bottles were triggered to close via remote command at the desired sampling depth (Table S1). CTDs were deployed for seawater collection at one depth immediately after the trawl was retrieved at 18 stations, except for one trawl station where CTD sampling was repeated at two depths. Two additional CTD deployments collected seawater when no trawling was occurring while Rice’s whales were in the immediate vicinity and displaying feeding behavior. After each sample was collected, approximately 2 L of seawater was transferred from the Niskin bottle into a 2 L sterile Nalgene bottle (cleaned as described for the Niskin bottles prior to use) and placed into a cooler with ice until filtration. All samples were filtered within 35 minutes of collection. Filtration, cleaning, and sample storage followed that as described in (Wilcox Talbot et al., 2025), using a 47 mm diameter mixed cellulose ester (MCE) filter with a 0.45-µm pore size. Using sterile forceps, each MCE filter was placed in a 4 mL screw cap vial containing approximately 3 mL of sterile Longmire’s lysis buffer (Longmire et al., 1997). The preserved filters were stored at room temperature and in the dark until eDNA extraction.

Descripción de la metodología paso a paso:

1. Sample Collection Method Seawater was collected using 5 L Niskin bottles attached to a conductivity, temperature, and depth (CTD) sensor unit. Bottles were triggered remotely at depths between 120 and 320 meters. Approximately 2 L of seawater from each Niskin bottle was transferred to a sterile 2 L Nalgene bottle, placed in a cooler with ice, and filtered within 35 minutes of collection
2. Sample Processing Filtration was conducted using a 47 mm diameter mixed cellulose ester (MCE) filter with a 0.45-µm pore size. Using sterile forceps, each filter was placed in a 4 mL screw cap vial containing approximately 3 mL of sterile Longmire’s lysis buffer. Preserved filters were stored at room temperature in the dark until extraction.
3. Molecular Methods - eDNA Extraction: eDNA was extracted from the filters using a phenol:chloroform (1:1) method, followed by DNA precipitation using 5M NaCl and ice-cold 100% ethanol . - Metabarcoding: The 12S rRNA gene was amplified using two different fish-specific primer sets: modified MiFish-U-F/R2 primers and the Riaz primers. - Sequencing: Library pools were sequenced on an Illumina MiSeq in a 2x250 bp paired-end format using a MiSeq v2 500 cycle reagent cartridge. - Bioinformatics: Raw reads were processed using cutadapt v4.4 and Tourmaline v1.1.1 (which implements QIIME2 and DADA2) to infer amplicon sequence variants (ASVs). - Taxonomic Assignment: Taxonomy was assigned using Naïve Bayes classifiers trained on custom 12S reference sequence databases for each marker. To support this, 12S rRNA gene sequences from 15 regional fish species collected in the trawls were generated for this study and added to the reference databases

Metadatos adicionales