Metabarcoding analysis of the Pacific harbor seal diet in Mexico

Brassea-Pérez, Elizabeth; Schramm, Yolanda; Heckel, Gisela; Chong-Robles, Jennyfers; Lago‐Lestón, Asunción

doi:10.1007/s00227-019-3555-8

Cited by 22 publications

(25 citation statements)

References 63 publications

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“…The diet analysis previously conducted on the harbor seals colonies of Todos Santos, San Jeronimo, Natividad, and San Roque islands had been characterized via metabarcoding analysis [9]. The same fecal samples were used in this study to characterize the gut microbial composition and complete the diet characterization.…”

Section: Methodsmentioning

confidence: 99%

“…Harbor seals are considered opportunistic predators with a high trophic level that feed on benthic or pelagic or both species predominantly fish and cephalopods [3]. Mexican harbor seals feed at low depths, between 5–50 m [4,5], mainly on benthic or demersal prey [6–9]. Of the pinnipeds found in Mexico, the harbor seal has enabled the most amount of information to be obtained on the quality of their local environment, due to their fidelity to haul-out sites, where they remain all year [2].…”

Section: Introductionmentioning

confidence: 99%

“…Of the pinnipeds found in Mexico, the harbor seal has enabled the most amount of information to be obtained on the quality of their local environment, due to their fidelity to haul-out sites, where they remain all year [2]. Based on satellite transmitter data, it is now known that harbor seals forage near their colonies (at distance of between 25 km [10] and 30 km [4]); therefore, differences in the type of prey consumed are expected [8,9], because most of the harbor seal colonies in Baja California are separated by greater distances. However, differences in the diet have also been found in colonies separated by only 16 km [7].…”

Section: Introductionmentioning

confidence: 99%

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The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences

et al. 2019

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Diet is a primary driver of the composition of gut microbiota and is considered one of the main routes of microbial colonization. Prey identification is fundamental for correlating the diet with the presence of particular microbial groups. The present study examined how diet influenced the composition and function of the gut microbiota of the Pacific harbor seal ( Phoca vitulina richardii ) in order to better understand the role of prey consumption in shaping its microbiota. This species is a good indicator of the quality of the local environment due to both its foraging and haul-out site fidelity. DNA was extracted from 20 fecal samples collected from five harbor seal colonies located in Baja California, Mexico. The V4 region of 16S rRNA gene was amplified and sequenced using the Illumina technology. Results showed that the gut microbiota of the harbor seals was dominated by the phyla Firmicutes (37%), Bacteroidetes (26%) and Fusobacteria (26%) and revealed significant differences in its composition among the colonies. Funtional analysis using the PICRUSt software suggests a high number of pathways involved in the basal metabolism, such as those for carbohydrates (22%) and amino acids (20%), and those related to the degradation of persistent environmental pollutants. In addition, a DNA metabarcoding analysis of the same samples, via the amplification and sequencing of the mtRNA 16S and rRNA 18S genes, was used to identify the prey consumed by harbor seals revealing the consumption of prey with mainly demersal habits. Functional redundancy in the seal gut microbiota was observed, irrespective of diet or location. Our results indicate that the frequency of occurrence of specific prey in the harbor seal diet plays an important role in shaping the composition of the gut microbiota of harbor seals by influencing the relative abundance of specific groups of gut microorganisms. A significant relationship was found among diet, gut microbiota composition and OTUs assigned to a particular metabolic pathway.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences

et al. 2019

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“…Little is known regarding the trophic ecology of the Pacific harbor seal colonies along the Baja California Peninsula. Although there is a wide composition of prey species in the colonies studied here, the harbor seal tends to feed mostly on two to five items at each site, leading to the conclusion that this subspecies is a specialist consumer [21][22][23][24].…”

Section: Introductionmentioning

confidence: 99%

“…Moreover, the δ 15 N values of residual nitrate tend to be enriched in 15 N near the tropics due to extensive denitrification regions in minimum oxygen zones (MOZs) [41,44,45]. Values of δ 13 C at the base of the food web are generally depleted in 13 C at higher latitudes due to the lower sea surface temperature than that found at lower latitudes [35,46], combined with light-limited low photosynthetic rates [24,29].…”

Section: Introductionmentioning

confidence: 99%

Trophic ecology of Mexican Pacific harbor seal colonies using carbon and nitrogen stable isotopes

et al. 2020

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There is limited information that provides a comprehensive understanding of the trophic ecology of Mexican Pacific harbor seal (Phoca vitulina richardii) colonies. While scat analysis has been used to determine the diet of some colonies, the integrative characterization of its feeding habits on broader temporal and spatial scales remains limited. We examined potential feeding grounds, trophic niche width, and overlap, and inferred the degree of dietary specialization using stable carbon and nitrogen isotope ratios (δ 13 C and δ 15 N) in this subspecies. We analyzed δ 13 C and δ 15 N on fur samples from pups collected at five sites along the western coast of the Baja California Peninsula, Mexico. Fur of natal coat of Pacific harbor seal pups begins to grow during the seventh month in utero until the last stage of gestation. Therefore pup fur is a good proxy for the mother's feeding habits in winter (~December to March), based on the timing of gestation for the subspecies in this region. Our results indicated that the δ 13 C and δ 15 N values differed significantly among sampling sites, with the highest mean δ 15 N value occurring at the southernmost site, reflecting a well-characterized north to south latitudinal 15 N-enrichment in the food web. The tendency identified in δ 13 C values, in which the northern colonies showed the most enriched values, suggests nearshore and benthic-demersal feeding habits. A low variance in δ 13 C and δ 15 N values for each colony (<1‰) and relatively small standard ellipse areas suggest a specialized foraging behavior in adult female Pacific harbor seals in Mexican waters.

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DNA‐metabarcoding supports trophic flexibility and reveals new prey species for the Galapagos sea lion

Urquía,

Anslan,

Asadobay

et al. 2024

Ecology and Evolution

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Tropical ecosystems are challenging for pinnipeds due to fluctuating food availability. According to previous research, the Galapagos sea lion (GSL, Zalophus wollebaeki) adopts trophic flexibility to face such conditions. However, this hypothesis comes from studies using traditional methods (hard‐parts analysis of scat and isotopic analysis from tissue). We studied the diet of five rookeries in the southeastern Galapagos bioregion (which harbors the highest GSL density), via DNA‐metabarcoding of scat samples. The DNA‐metabarcoding approach may identify consumed prey with a higher taxonomic resolution than isotopic analysis, while not depending on hard‐parts remaining through digestion. Our study included five different rookeries to look for evidence of trophic flexibility at the bioregional level. We detected 98 prey OTUs (124 scats), mostly assigned to bony‐fish taxa; we identified novel prey items, including a shark, rays, and several deep‐sea fish. Our data supported the trophic flexibility of GSL throughout the studied bioregion since different individuals from the same rookery consumed prey coming from different habitats and trophic levels. Significant diet differentiations were found among rookeries, particularly between Punta Pitt and Santa Fe. Punta Pitt rookery, with a more pronounced bathymetry and lower productivity, was distinguished by a high trophic level and consumption of a high proportion of deep‐sea prey; meanwhile, Santa Fe, located in more productive, shallow waters over the shelf, consumed a high proportion of epipelagic planktivorous fish. Geographic location and heterogeneous bathymetry of El Malecon, Española, and Floreana rookeries would allow the animals therein to access both, epipelagic prey over the shelf, and deep‐sea prey out of the shelf; this would lead to a higher prey richness and diet variability there. These findings provide evidence of GSL adopting a trophic flexibility to tune their diets to different ecological contexts. This strategy would be crucial for this endangered species to overcome the challenges faced in a habitat with fluctuating foraging conditions.

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Metabarcoding analysis of the Pacific harbor seal diet in Mexico

Cited by 22 publications

References 63 publications

The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences

The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences

Trophic ecology of Mexican Pacific harbor seal colonies using carbon and nitrogen stable isotopes

DNA‐metabarcoding supports trophic flexibility and reveals new prey species for the Galapagos sea lion

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