A metabarcoding approach for the feeding habits of European hake in the Adriatic Sea

Insights into trophic interactions: DNA metabarcoding reveals species composition in black-tailed gull fecal samples in coastal environments of South Korea

This study explored the algae, zooplankton, macroinvertebrate, fish, and parasitic single-celled organism communities in Larus crassirostris (black-tailed gull) fecal samples from Baengnyeongdo, Hongdo, and Ulleungdo in South Korea. The fecal samples can identify key species consumed by black-tailed gull, providing insights into their, trophic interactions, and habitat dependencies. Using DNA metabarcoding, we identified algae, zooplankton, macroinvertebrate, fish, and intestinal and single-celled parasite species in the fecal samples. Parasitic single-celled organisms, such as Rhogostoma sp., Rhogostoma schuessleri, Eimeria furonis, and Aggregata eberthi, showed differing relative abundances at each sampling location, indicating variability in parasite diversity in the fecal DNA analysis of birds at each site. Intestinal parasites showed similar site-specific variability, though Clistobothrium sp. and Tetrabothrius sp. were common at all locations. Algae species, including Heterocapsa steinii, Heterocapsa niei, and Sargassum cristaefolium, also displayed habitat-specific patterns, as did zooplankton, with Calanus sp., Corycaeus speciosus, and Caprella californica being dominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. In the macroinvertebrate communities, Octopus sinensis was prevalent at all locations but at varying abundances. Site-specific dominant fish species were also identified, with Ammodytes personatus, Decapterus maruadsi, and Arctoscopus japonicus highly predominant on Baengnyeongdo, Hongdo, and Ulleungdo, respectively. Other fish species, such as Ammodytes hexapterus, were detected in lower frequencies, suggesting a diverse diet for the seabirds. These results offer insights into the species composition and ecological dynamics in black-tailed gull populations across disparate Korean islands.

Trophic Interactions of European Hake Merluccius merluccius (Linnaeus, 1758) in Benthic Communities off the Moroccan Mediterranean Coastline: Seasonal and Ontogenetic Shifts

The European hake, Merluccius merluccius (Linnaeus, 1758), is one of the most important resources for Mediterranean fisheries. Due to its pivotal role in energy transfer from lower to higher trophic levels, this species is a crucial component of the ecosystem's functioning. The ecological role of Merluccius merluccius, off the Moroccan Mediterranean Sea (southern Alboran Sea), was investigated, exploring seasonal and ontogenetic shifts, geographical variations in prey composition, and feeding strategy. Between November 2020 and July 2022, a total of 402 hake specimens were collected by oceanographic bottom trawl surveys (MEDITS) that were carried out during warm and cold seasons to assess their diet and feeding habits. The sample was analyzed according to fish sizes and seasons, and qualitative/quantitative feeding indices were calculated. The trophic spectrum of Merluccius merluccius included 24 prey items in total, mainly belonging to Osteichthyes (12), Crustacea (10), Cephalopoda (1), and Polychaeta (1), suggesting a generalist behavior of this predator as in numerous regions of the Mediterranean Sea, with several species that occasionally occurs in its diet. In the Moroccan Mediterranean Sea, Osteichthyes proved to be the most important prey item (%IRI = 78.56) among the different zoological groups, followed by Crustacea (%IRI = 16.22). The other food items were occasionally and randomly consumed, and cannibalism was low (0.8%). Hierarchical cluster analysis and nonmetric multidimensional scaling (nMDS) showed different feeding habits of two main groups separated at 60% similarity: small specimens <10 cm TL, primarily feed on zooplanktonic prey, while medium and large specimens hold a diet based on Osteichthyes with crustaceans. Furthermore, a significant positive relationship between hake and fish prey size was confirmed. Seasonally, mesopelagic Osteichthyes were the main food prey in the summer season, while pelagic species were predominant during the autumn. SIMPER analysis revealed that the prey items contributing the most to the differences between seasons and length classes were Engraulis encrasicolus, Micromesistius poutassou, Boops boops, Macroramphosus scolopax, gobids, Gadiculus argenteus, and most of Crustacea. The diet does not appear to be influenced by sex (>0.05). A trophic level (TROPH) of 4.1 was calculated, indicating that the species is a top predator (quaternary consumers). The TROPH values ranged between 2.58 and 4.38 from juveniles to adults, increasing asymptotically with the size of specimens. In contrast to what has previously been found in other Mediterranean regions, where ichthyophagous hake feed mostly on pelagic Osteichthyes, such as Engraulis encrasicolus, Sardina pilchardus, and Micromesistius poutassou, the study points up the vital role played by Atlantic horse mackerel Trachurus trachurus for hake diet in the Moroccan Mediterranean Sea. Information on the feeding ecology of fish species as provided in this study is essential to improve ecosystem conservation in accordance with multispecies approach to fishery management, leading to a better understanding of the role of hake in the Moroccan Mediterranean Sea demersal communities.

Metabarcoding Used for the First Time to Identify Prey of Wild Totoaba macdonaldi

Totoaba macdonaldi is an endangered endemic fish of the Gulf of California. Overexploitation resulted in the Mexican government banning the fishing of this species in 1975, and it being listed as endangered. However, the species is still subject to illegal fishing. Despite its conservation status, little is known about totoaba biology. The present study aimed to implement, for the first time, a metabarcoding protocol to describe the totoaba diet. Four wild totoaba individuals, seized by Mexican law enforcement agents, were dissected, and their stomach contents were collected. Three representative amplicon libraries were generated for cephalopods, chordates, and eukaryotes. After sequencing, 18 different taxa were identified, of which 11 species were recognized as prey. The totoaba were found to have consumed Pacific anchovy (Cetengraulis mysticetus), flathead grey mullet (Mugil cephalus), bigeye croaker (Micropogonias megalops), northern anchovy (Engraulis mordax), ocean whitefish (Caulolatilus princeps), milkfish (Chanos chanos), and Pacific sardine (Sardinops sagax). Members of the Euphausiidae family (krill) were also identified. This study identified up to four times more species in much fewer samples than previous studies based on morphological recognition, thus confirming metabarcoding as an effective method for studying the feeding habits of this species and one providing the tools required for further analysis of the totoaba diet.

Ontogenetic shift and feeding habits of the European hake (Merluccius merluccius L., 1758) in Central and Southern Tyrrhenian Sea (Western Mediterranean Sea): A comparison between past and present data

The present paper aims to investigate the ecological role of Merluccius merluccius, Linnaeus, 1758, in southern and central Tyrrhenian Sea (GSA 10, Resolution GFCM/33/2009/2 General Fisheries Commission for the Mediterranean), analyzing ontogenetic diet shifts, geographical variations on prey composition, and feeding habits. A total of 734 hake specimens ranging in size between 6 cm and 73 cm (Total Length, TL) were collected in 2018. In order to evaluate ontogenetic shifts in prey composition, samples were divided into five size classes and for each class the quantitative feeding indices have been calculated. The statistical analysis, based on index of relative importance percentage (%IRI), resulted in three trophic groups. The most abundant prey found in the immature hake specimens (size class I) were the Euphausiids, Stylocheiron longicorne and Mysidacea, while for samples with a total length over 10.5 cm were crustaceans and fish. Engraulis encrasicolus was the most abundant fish prey identified, followed by Boops boops and Myctophids. The high presence of Euphausiids, Mysids, Myctophidae, and Sternoptychidae in classes I, II, II, and IV (6–23 cm) showed the relevant role of mesopelagic fauna in hake diets, with an essential organic matter and energy flow from the mesopelagic to the epipelagic environment. Additionally, decapod crustaceans were found in the stomach contents of hakes belonging to class V (with size over 36 cm TL), which is notable considering that our study area includes an important decapod crustacean fishing area.

DNA metabarcoding suggests dietary niche partitioning in the Adriatic European hake

The Northern Adriatic Sea (FAO Geographical Sub-Area 17) is one of the most productive fishing areas of the Mediterranean Sea and it includes a broad diversity of habitats. In the Northern Adriatic basin, the Pomo Pit (200-273 m of depth) is one of the most important areas of aggregation for some demersal stocks shared in the Adriatic Sea and it is an important spawning/nursery area of the European hake (Merluccius merluccius). Through a metabarcoding approach we investigated the feeding habits of European hake, both inside and outside the Pomo Pit, and their temporal variability comparing samples collected in 2016 and 2014. Our analyses proved the presence of an ontogenetic shift from a diet based mainly on crustaceans in juveniles to a more piscivorous feeding behaviour in adult hakes and suggested the presence of a specific niche partitioning and food preferences between hakes living inside and outside the Pomo Pit. The main differences among adult hakes refer to the presence of molluscs in the stomachs of hakes collected within the Pomo Pit and the presence of high depth prey species (i.e., Micromesistius poutassou). Metabarcoding revealed the relevant ecological role played by the Pomo Pit in M. merluccius feeding behaviour and ontogenetic development, promoting a careful ecosystem-based management of fisheries in this area through focused conservation measures.

Trophic niche overlap between round sardinella (Sardinella aurita) and sympatric pelagic fish species in the Western Mediterranean

The northward expansion of round sardinella (Sardinella aurita) in the Mediterranean Sea, together with declines and fluctuations in biomass and landings of European sardine (Sardina pilchardus) and anchovy (Engraulis encrasicolus) observed in recent decades, may suggest potential inter-specific competition in the pelagic domain. The coexistence of sympatric zooplanktivorous fish species might therefore be exposed in part to trophic niche overlap and competition for food. Combining visual diet characterization under the microscope with DNA metabarcoding from stomach contents of fish collected in spring results show that predation on relatively large krill is equally important for sardinella than for the other two niche overlapping species. Furthermore, an important overlap is found in their isotopic niche, especially with anchovy, using nitrogen (δ15N) and carbon (δ13C) stable isotopes in muscle tissue. In fact, the three fish species are able to feed effectively in the whole prey size spectrum available during the sampled season, from the smallest diatoms and copepods to the larger prey (i.e., decapods and euphausiids), including fish larvae. Moreover, effective predation upon other large prey like siphonophores, which is observed only when multi-proxy analyses in stomach contents are applied, might also be relevant in the diet of sardinella. The overlapping diet composition in spring, together with the effective use of food resource by sardinella, can be of special interest in potential future scenarios with warmer water temperature leading to lower zooplankton and/or higher jellyfish availability, where sardinella may take advantage over other species due to its feeding plasticity.

Diet of the Deep-Sea Shark Galeus melastomus Rafinesque, 1810, in the Mediterranean Sea: What We Know and What We Should Know

We reviewed literature on the diet of the Galeus melastomus Rafinesque, 1810, from the Mediterranean Sea. Specific keywords (“Galeus melastomus diet”, “feeding habits”, “trophic position”, “biology”, “deep environment adaptation”) in the principal data sources, such as Web of Science, PubMed, and Google Scholar were used. Seventeen studies conducted on the diet and trophic position of G. melastomus have been considered for Mediterranean Sea regions. The feeding habits have been analyzed in many areas of the western basin; instead, for the Tyrrhenian, Adriatic, and central Mediterranean Seas, information is outdated and fragmentary. In all investigated sub areas, the data showed that G. melastomus is an opportunistic demersal supra benthic predator, benthic feeder, and scavenger, that adapts its diet to the seasonal and geographical fluctuations of the prey availability. It occupies a generalist niche showing individual specialization. In all reviewed Mediterranean sub areas, the most important prey groups were crustaceans, cephalopods, and teleost fishes. Taxa percentage in its diet composition can vary depending on different habitats with ontogenetic development of individuals, depth (that is correlated with the ontogenetic development), seasonal availability, and distribution of different prey groups. Widening knowledge of G. melastomus feeding habits is a fundamental tool for better understand meso and bathy-pelagic ecosystems.

Fish as predators and prey: DNA-based assessment of their role in food webs

Fish are both consumers and prey, and as such part of a dynamic trophic network. Measuring how they are trophically linked, both directly and indirectly, to other species is vital to comprehend the mechanisms driving alterations in fish communities in space and time. Moreover, this knowledge also helps to understand how fish communities respond to environmental change and delivers important information for implementing management of fish stocks. DNA-based methods have significantly widened our ability to assess trophic interactions in both marine and freshwater systems and they possess a range of advantages over other approaches in diet analysis. In this review we provide an overview of different DNA-based methods that have been used to assess trophic interactions of fish as consumers and prey. We consider the practicalities and limitations, and emphasize critical aspects when analysing molecular derived trophic data. We exemplify how molecular techniques have been employed to unravel food web interactions involving fish as consumers and prey. In addition to the exciting opportunities DNA-based approaches offer, we identify current challenges and future prospects for assessing fish food webs where DNA-based approaches will play an important role.

A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758)

High‐throughput sequencing has become an accurate method for the identification of species present in soil, water, faeces, gut or stomach contents. However, information at the species level is limited due to the choice of short barcodes and based on the idea that DNA is too degraded to allow longer sequences to be amplified. We have therefore developed a long DNA metabarcoding method based on the sequencing of short reads followed by de novo assembly, which can precisely identify the taxonomic groups of organisms associated with complex diets, such as omnivorous individuals. The procedure includes 11 different primer pairs targeting the COI gene, the large subunit of the ribulose‐1,5‐bisphosphate carboxylase gene, the maturase K gene, the 28S rRNA and the trnL‐trnF chloroplastic region. We validated this approach using 32 faeces samples from an omnivorous reptile, the European pond turtle (Emys orbicularis, L. 1758). This metabarcoding approach was assessed using controlled experiments including mock communities and faecal samples from captive feeding trials. The method allowed us to accurately identify prey DNA present in the diet of the European pond turtles to the species level in most of the cases (82.4%), based on the amplicon lengths of multiple markers (168–1,379 bp, average 546 bp), and produced by de novo assembly. The proposed approach can be adapted to analyse various diets, in numerous conservation and ecological applications. It is consequently appropriate for detecting fine dietary variations among individuals, populations and species as well as for the identification of rare food items.

Feeding studies take guts - critical review and recommendations of methods for stomach contents analysis in fish

Studies on the feeding ecology of fish are essential for exploring and contrasting trophic interactions and population and community dynamics within and among aquatic ecosystems. In this respect, many different methods have been adopted for the analysis of fish stomach contents. No consensus has, however, been reached for a standardised methodology despite that for several decades there has been an ongoing debate about which methodical approaches that should be preferred. Here, we critically review and scrutinise methods, addressing their strengths and weaknesses and emphasising inherent problems and possible pitfalls in their use. Although our critical assessment reveals that no completely ideal approach exists, appropriate and reliable procedures can be adopted through careful considerations and implementation. In particular, we advocate that different objectives require different methodical approaches and the choice of method should therefore be closely linked to the research questions that are addressed. For a standardisation of methods, we recommend a combination of the relative-fullness and presence-absence methods as the optimal approach for the commonly applied feeding studies addressing relative dietary composition in terms of prey diversity and abundance. Additionally, we recommend the gravimetric method for objectives related to the quantification of food consumption rates and the numerical method for prey selection studies. DNA-based dietary analysis provides a new and promising complementary approach to visual examination of stomach contents, although some technical challenges still exist. The suggested method standardisation facilitates comparisons across species, ecosystems and time and will enhance the applicability and benefits of fish feeding studies in trophic ecology research.