scholarly journals DNA metabarcoding provides insights into the diverse diet of a dominant suspension feeder, the giant plumose anemone Metridium farcimen

2020 ◽  
Author(s):  
Christopher D. Wells ◽  
Gustav Paulay ◽  
Bryan N. Nguyen ◽  
Matthieu Leray
Keyword(s):  
Taxonomic Resolution ◽  
Gut Contents ◽  
Prey Selectivity ◽  
Gut Content ◽  
Marine Food Webs ◽  
Dna Metabarcoding ◽  
Terrestrial Input ◽  
Marine Food ◽  
Mating Flights ◽  
Plankton Communities

ABSTRACTBenthic suspension feeders have significant impacts on plankton communities by depleting plankton or modifying composition of the plankton through prey selectivity. Quantifying diets of planktivorous animals can be difficult because plankton are frequently microscopic, may lack diagnostic characters, and are digested at variable rates. With DNA metabarcoding, the identification of gut contents has become faster and more accurate, and the technique allows for higher taxonomic resolution-n while also identifying rare and highly degraded items that would otherwise not be detected. We used DNA metabarcoding to examine the diet of the giant plumose anemone Metridium farcimen, a large, abundant, competitively-dominant anemone on subtidal rock surfaces and floating docks in the northeast Pacific Ocean. Gut contents of 12 individuals were compared to 80- and 330-μm filtered plankton samples collected one hour prior between 0.02 and 1.5 km from the anemones. The objectives of this study were to determine if M. farcimen has a selective diet and compare our findings with traditional gut content analyses. Metridium farcimen captured a wider range of prey than previously suspected and metabarcoding found many more taxa than traditional sampling techniques. Gut contents were less diverse than 80-μm filtered plankton samples, but more diverse than 330-μm filtered plankton samples. The diet of the anemones was 52% arthropods with a surprisingly high relative abundance of an ant (10%) that has mating flights in August when this study was conducted. The gut contents of M. farcimen likely include all prey that it can detect and that cannot escape. There were no overrepresented taxa in the gut contents compared to the plankton but there were underrepresented taxa. This study highlights the usefulness of the metabarcoding method in identifying prey within the gut of planktivorous animals and the significant terrestrial input into marine food webs.

scholarly journals The potential of aquatic haematophagous, liquidosomatophagous and macrophagous leeches as a tool for iDNA characterisation

2021 ◽  
Author(s):  
Christina Lynggaard ◽  
Alejandro Oceguera-Figueroa ◽  
Sebastian Kvist ◽  
M. Thomas P. Gilbert ◽  
Kristine Bohmann
Keyword(s):  
Parasitic Nematode ◽  
Feeding Habits ◽  
Taxonomic Resolution ◽  
Gut Contents ◽  
Proof Of Concept ◽  
Gut Content ◽  
Dna Metabarcoding ◽  
Taxonomic Groups ◽  
Animal Monitoring ◽  
Potential Use

Leeches play important roles in food webs due to their abundance, diversity and feeding habits. Studies using invertebrate-derived DNA (iDNA) extracted from leech gut contents to target vertebrate DNA have focused on the Indo-Pacific region and mainly leveraged the leech family Haemadipsidae, composed of haematophagous terrestrial leeches, while the aquatic haematophagous, liquidosomatophagous and macrophagous counterparts have largely been disregarded. While there is general knowledge regarding the taxonomic groups that leeches prefer to feed on, detailed taxonomic resolution is still missing and therefore, their potential use for monitoring animals is not known. In this study, 116 non-haemadipsid leeches belonging to 12 species and spanning the three feeding habits were collected in Mexico and Canada. We used DNA metabarcoding to investigate their diet and assess their potential use for vertebrate monitoring. We detected vertebrate taxa from five orders including fish, turtles and birds in the diet of the aquatic haematophagous leeches; eight invertebrate orders of annelids, arthropods and molluscs in the liquidosomatophagous leeches; and ten orders of invertebrates belonging to Arthropoda and Annelida, as well as one vertebrate and one parasitic nematode, in the macrophagous leeches. These results show the potential use of iDNA from the gut content of aquatic haematophagous leeches for retrieving vertebrate taxa, and from macrophagous and liquidosomatophagous counterparts for invertebrates. Our study provides information about the dietary range of the freshwater leeches and the non-haemadipsid terrestrial leech and proof-of-concept for the use of non-haemadipsid leeches for animal monitoring, expanding our knowledge of the use of iDNA from leech gut contents to North America.

scholarly journals Gut content metabarcoding reveals potential importance of fisheries discards consumption in marine fauna

2021 ◽  
Author(s):  
Benjamin Lejeune ◽  
Maud Aline Mouchet ◽  
Sonia Mehault ◽  
Dorothée Kopp
Keyword(s):  
Ecosystem Approach ◽  
Gut Contents ◽  
The European Union ◽  
Fish Prey ◽  
Marine Fauna ◽  
Marine Food Webs ◽  
Dna Metabarcoding ◽  
Fisheries Policy ◽  
Reconstructed Network ◽  
Marine Food

Fisheries discards have become a source of concern for the perennation of marine resources. To reduce discards, the European Union adopted a Landing Obligation under the reform of its Common Fisheries Policy. However, food web consequences of reducing discards remain uncertain since their degree and pathway of reintegration are understudied. We used multi-marker DNA metabarcoding of gut contents and an ecological network approach to quantify marine fauna reliance on discarded fish and functional importance of discard consumers in coastal fishing grounds. We show that potential discard consumption is widespread across fish and invertebrates, but particularly important for decapods which were also pinpointed as functionally important. Potential discard consumption may represent up to 66% of all interactions involving fish prey in the reconstructed network. We highlight that discard reliance may be more important than previously assessed in some fishing areas and support functionally important taxa. While reducing discarding remains a conservation priority, it is crucial to understand discards reintegration in marine food webs to anticipate changes in the context of an ecosystem approach to fisheries management.

scholarly journals Background and interpretation of the ‘Marine Trophic Index’ as a measure of biodiversity

2005 ◽  
Vol 360 (1454) ◽  
pp. 415-423 ◽  
Author(s):  
Daniel Pauly ◽  
Reg Watson
Keyword(s):  
Biological Diversity ◽  
Taxonomic Resolution ◽  
Convention On Biological Diversity ◽  
Data Series ◽  
Marine Food Webs ◽  
Trophic Index ◽  
The World ◽  
Marine Food ◽  
Fisheries Statistics ◽  
Agricultural Organization

Since the demonstration, in 1998, of the phenomenon now widely known as ‘fishing down marine food webs’, and the publication of a critical rejoinder by Food and Agricultural Organization (FAO) staff, a number of studies have been conducted in different parts of the world, based on more detailed data than the global FAO fisheries statistics originally used, which established the validity and ubiquity of this phenomenon. In this contribution, we briefly review how, rather than being an artefact of biased data, this phenomenon was in fact largely masked by such data, and is in fact more widespread than was initially anticipated. This is made visible here by comparing two global maps of trophic level (TL) changes from the early 1950s to the present. The first presents the 50-year difference of the grand mean TL values originally used to demonstrate the fishing down effect, while the second is based on means above a cut-off TL (here set at 3.25), thus eliminating the highly variable and abundant small pelagic fishes caught throughout the world. Based on this, we suggest that using mean TL as ‘Marine Trophic Index’ (MTI), as endorsed by the Convention on Biological Diversity , always be done with an explicitly stated cut-off TL (i.e. cut MTI), chosen (as is the case with our proposed value of 3.25) to emphasize changes in the relative abundance of the more threatened, high-TL fishes. We also point out the need to improve the taxonomic resolution, completeness and accuracy of the national and international fisheries catch data series upon which the cut MTI is to be based.

scholarly journals Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

2018 ◽  
Author(s):  
Aimee L van der Reis ◽  
Olivier Laroche ◽  
Andrew G Jeffs ◽  
Shane D Lavery
Keyword(s):  
New Zealand ◽  
Preliminary Analysis ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Gut Contents ◽  
Rrna Gene ◽  
Diverse Range ◽  
Dna Metabarcoding

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view of M. challengeri diet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable, but metabarcoding outcomes indicated that the ethanol samples produced better results from the COI gene. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta, however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of M. challengeri identified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctate), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitza), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

scholarly journals Feeding by Calanus glacialis in a high arctic fjord: potential seasonal importance of alternative prey

2017 ◽  
Vol 74 (7) ◽  
pp. 1937-1946 ◽  
Author(s):  
Alison C. Cleary ◽  
Janne E. Søreide ◽  
Daniela Freese ◽  
Barbara Niehoff ◽  
Tove M. Gabrielsen
Keyword(s):  
Spring Bloom ◽  
High Arctic ◽  
Gut Contents ◽  
Larval Abundance ◽  
Early Life Stages ◽  
Marine Food Webs ◽  
Calanus Glacialis ◽  
Arctic Fjord ◽  
Marine Food ◽  
Generation Sequencing

Abstract The copepod species Calanus glacialis is an important component of arctic marine food webs, where it is the numerically dominant zooplankton grazer and serves as a major prey item for fish, seabirds, and other predators. These copepods are typically considered to be phytoplanktivorous, although they are also known to feed on microzooplankton, and little is known about their diet in fall and winter. To investigate their feeding, C. glacialis gut contents were analyzed over an annual cycle in a seasonally ice covered arctic fjord using next generation sequencing of 18S rDNA. During the spring bloom, diatoms, particularly Thalassiosira spp., were important contributors to the dietary sequence reads. In addition to diatoms, Chytridiomycetes, fungal parasites of diatoms, also made up a large proportion of dietary sequence reads during this productive season. This provides one of the first indications of the potential importance of the mycoloop in marine environments. Just prior to the spring bloom, chaetognath sequences dominated the prey sequence reads from C. glacialis, suggesting potential predation on eggs or other early life stages of chaetognaths by C. glacialis. Other indications of omnivorous feeding outside of the spring bloom period included sequence reads from polychaetes in summer, at the time of peak polychaete larval abundance, and from Metridia spp. (Copepoda) in winter in prey sequences from C. glacialis. Incorporating such predation into our knowledge of Calanus spp. behaviour may help refine our understanding of Calanus spp. ecology, and potential responses of C. glacialis to ongoing climate change.

scholarly journals Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5641 ◽  
Author(s):  
Aimee L. van der Reis ◽  
Olivier Laroche ◽  
Andrew G. Jeffs ◽  
Shane D. Lavery
Keyword(s):  
New Zealand ◽  
Preliminary Analysis ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Gut Contents ◽  
Rrna Gene ◽  
Diverse Range ◽  
Dna Metabarcoding

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view ofM.challengeridiet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta; however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet ofM.challengeriidentified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctata), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitzai), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

scholarly journals Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

2018 ◽  
Author(s):  
Aimee L van der Reis ◽  
Olivier Laroche ◽  
Andrew G Jeffs ◽  
Shane D Lavery
Keyword(s):  
New Zealand ◽  
Preliminary Analysis ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Gut Contents ◽  
Rrna Gene ◽  
Diverse Range ◽  
Dna Metabarcoding

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of foregut and hindgut contents of the New Zealand (NZ) scampi (Metanephrops challengeri), but a number of methodological concerns need to first be overcome to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were trialled to determine the optimum protocols for DNA metabarcoding, and provide a first view of the NZ scampi diet. Several PCR protocols were trialled, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from frozen and ethanol preserved samples of both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable, but metabarcoding results showed that ethanol samples resulted in better results from the COI gene. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta, however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of the NZ scampi identified a range of species, which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctate), tall sea pen (Funiculina quadrangularis ) and salp (Ihlea racovitza), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

scholarly journals Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

2018 ◽  
Author(s):  
Aimee L van der Reis ◽  
Olivier Laroche ◽  
Andrew G Jeffs ◽  
Shane D Lavery
Keyword(s):  
New Zealand ◽  
Preliminary Analysis ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Gut Contents ◽  
Rrna Gene ◽  
Diverse Range ◽  
Dna Metabarcoding

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view of M. challengeri diet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable, but metabarcoding outcomes indicated that the ethanol samples produced better results from the COI gene. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta, however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of M. challengeri identified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctate), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitza), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

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