18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species

The potential of the 18S rRNA V9 metabarcoding approach for diet assessment was explored using MiSeq paired-end (PE; 2 9 150 bp) technology. To critically evaluate the method's performance with degraded/digested DNA, the diets of two zooplanktivorous fish species from the Bay of Biscay, European sardine (Sardina pilchardus) and European sprat (Sprattus sprattus), were analysed. The taxonomic resolution and quantitative potential of the 18S V9 metabarcoding was first assessed both in silico and with mock and field plankton samples. Our method was capable of discriminating species within the reference database in a reliable way providing there was at least one variable position in the 18S V9 region. Furthermore, it successfully discriminated diet between both fish species, including habitat and diel differences among sardines, overcoming some of the limitations of traditional visual-based diet analysis methods. The high sensitivity and semi-quantitative nature of the 18S V9 metabarcoding approach was supported by both visual microscopy and qPCR-based results. This molecular approach provides an alternative cost and time effective tool for food-web analysis.

Diet composition of fish species from the southern continental shelf of Colombia

The diet composition of 30 fish species belonging to 16 families from the Pacific Coast of Colombia is described. Benthic crustaceans (37.5%) and bony fishes (23.7%, chiefly demersal) were the most important food items for the fish species analyzed. Data on diet composition of the fish species are presented for the first time which can be a source of information for trophic modeling.

Diet composition and daily ration estimates of selected trawl-caught fishes in San Miguel Bay, Philippines

The diet composition of fish caught in San Miguel Bay, Philippines, in April and May 1993 was studied. The diets of tiger-tooth croaker (Otolithes ruber), commerson's anchovy (Stolephorus commersonii); and the Indian anchovy (Stolephorus indicus) consisted mainly of zooplankton, primarily crustaceans. The stomach content of orangefin ponyfish (Leiognathus bindus) was found to consist mostly of detritus and unidentified materials. Daily rations estimated were: 1.90 g day super(1) for O. ruber of 17.3 g mean body weight (BW), 0.078 g day super(1) for S. commersonii) of 3.8 g mean BW, 0.062 g day super(1) for S. indicus of 3.9 g mean BW and 0.56 g day super(1) for L. bindus of 7.7 g mean BW.

Diet of oceanic loggerhead sea turtles (Caretta caretta) in the central North Pacific

Diet analysis of 52 loggerhead sea turtles (Caretta caretta) collected as bycatch from 1990 to 1992 in the high-seas driftnet fishery operating between lat. 29.5°N and 43°N and between long. 150°E and 154°W demonstrated that these turtles fed predominately at the surface; few deeper water prey items were present in their stomachs. The turtles ranged in size from 13.5 to 74.0 cm curved carapace length. Whole turtles (n =10) and excised stomachs (n= 42) were frozen and transported to a laboratory for analysis of major faunal components. Neustonic species accounted for four of the five most common prey taxa. The most common prey items were Janthina spp. (Gastropoda); Carinaria cithara Benson 1835 (Heteropoda); a chondrophore, Velella velella (Hydrodia); Lepas spp. (Cirripedia), Planes spp. (Decapoda: Grapsidae), and pyrosomas (Pyrosoma spp.).

Diet of Bottlenose Dolphins Tursiops truncatus in the Northwest Panhandle and Foraging Behavior Near Savannah, Georgia

The foraging ecology of bottlenose dolphins Tursiops truncatus in the Northwest Florida Panhandle and estuaries in northern Georgia was determined using diet analysis and behavioral surveys. Stomach content analysis was completed on bottlenose dolphins(N = 25) that stranded in the Northwest Florida Panhandle from November 2006 to March 2009. The most abundant prey species were spot Leiostomus xanthurus (20.4%), squid (10.9%), pinfish Lagodon rhombiodes (10.3%), and Atlantic croaker Micropogonias undulatus (8.5%). Dolphins that stranded during months with a red tide Karenia brevis bloom consumed more pinfish, and spot; whereas dolphins that stranded in non-bloom months consumed more squid, Atlantic croaker, and silver perch Bairdiella chrysoura. Differences in diet were also identified for dolphins that stranded inside bays/sound and dolphin that stranded outside of bays along the coast, and male and female dolphins. Surveys were conducted from south of the Savannah River to north of Ossabaw Sound in Georgia where foraging behaviors were classified. Multivariate Generalized Additive Models were used to test correlations of behaviors to dolphin group size, depth, salinity, temperature, creek width, and tide. Sightings with headstands (p = 0.009), hard stops (p = 0.019), chasing (p = 0.004), mudbank whacking (p < 0.001), herding/circling (p = 0.024), and strand feeding (p = 0.006) were correlated with shallow water or small creeks. Sightings with kerplunking (p = 0.031), mudbank whacking (p = 0.001), strand feeding (p = 0.003), and herding/circling (p = 0.026) were significantly correlated with low tide. The results of the Savannah, Georgia study were the first to characterize foraging behaviors in this area and demonstrate how bottlenose dolphins utilize the salt marsh estuary in terms of foraging. Studies like these are important to determine how dolphins forage efficiently and to provide background information on diet and foraging behavior for use in monitoring future impacts to dolphins in the Northwest Florida Panhandle and near Savannah, Georgia.

Habitat and diet overlap of 4 piscivorous fishes: variation on the inner continental shelf off New Jersey

Piscivorous fishes, many of which are economically valuable, play an important role in marine ecosystems and have the potential to affect fish and invertebrate populations at lower trophic levels. Therefore, a quantitative understanding of the foraging ecology of piscivores is needed for ecosystem-based fishery management plans to be successful. Abundance and stomach contents of seasonally co-occurring piscivores were examined to determine overlap in resource use for Summer Flounder (Paralichthys dentatus; 206–670 mm total length [TL]), Weakfish (Cynoscion regalis; 80–565 mm TL), Bluefish (Pomatomus saltatrix; 55–732 mm fork length [FL]), and Striped Bass (Morone saxatilis; 422–920 mm FL). We collected samples from monthly, fishery-independent trawl surveys conducted on the inner continental shelf (5–27 m) off New Jersey from June to October 2005. Fish abundances and overlaps in diet and habitat varied over this study period. A wide range of fish and invertebrate prey was consumed by each species. Diet composition (determined from 1997 stomachs with identifiable contents) varied with ontogeny (size) and indicated limited overlap between most of the species size classes examined. Although many prey categories were shared by the piscivores examined, different temporal and spatial patterns in habitat use seemed to alleviate potential competition for prey. Nevertheless, the degree of overlap in both fish distributions and diets increased severalfold in the fall as species left estuaries and migrated across and along the study area. Therefore, the transitional period of fall migration, when fish densities are higher than at other times of the year, may be critical for unraveling resource overlap for these seasonally migrant predators.

Spatial and temporal variation in the diet of the California sea lion (Zalophus californianus) in the Gulf of California, Mexico

Between June 1995 and May 1996 seven rookeries in the Gulf of California were visited four times in order to collect scat samples for studying spatial and seasonal variability California sea lion prey. The rookeries studied were San Pedro Mártir, San Esteban, El Rasito, Los Machos, Los Cantiles, Isla Granito, and Isla Lobos. The 1273 scat samples collected yielded 4995 otoliths (95.3%) and 247 (4.7%) cephalopod beaks. Fish were found in 97.4% of scat samples collected, cephalopods in 11.2%, and crustaceans in 12.7%. We identified 92 prey taxa to the species level, 11 to genus level, and 10 to family level, of which the most important were Pacific cutlassfish (Trichiurus lepturus), Pacific sardine (Sardinops caeruleus), plainfin midshipman (Porichthys spp.), myctophid no. 1, northern anchovy (Engraulis mordax), Pacific mackerel (Scomber japonicus), anchoveta (Cetengraulis mysticetus), and jack mackerel (Trachurus symmetricus). Significant differences were found among rookeries in the occurrence of all main prey (P≤0.04), except for myctophid no. 1 (P>0.05). Temporally, significant differences were found in the occurrence of Pacific cutlassfish, Pacific sardine, plainfin midshipman, northern anchovy, and Pacific mackerel (P<0.05), but not in jack mackerel (χ 2=2.94, df=3, P=0.40), myctophid no. 1 (χ 2=1.67, df= 3, P=0.64), or lanternfishes (χ 2=2.08, df=3, P=0.56). Differences were observed in the diet and in trophic diversity among seasons and rookeries. More evident was the variation in diet in relation to availability of Pacific sardine.