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1. Characterizing the secret diets of siphonophores (Cnidaria: Hydrozoa) using DNA metabarcoding

   https://doi.org/10.1371/journal.pone.0267761  

   Damian-Serrano, Alejandro ; Hetherington, Elizabeth D. ; Choy, C. Anela ; Haddock, Steven H. ; Lapides, Alexandra ; Dunn, Casey W. ( May 2022 , PLOS ONE)

   Dam, Hans G. (Ed.)

   Siphonophores (Cnidaria: Hydrozoa) are abundant and diverse gelatinous predators in open-ocean ecosystems. Due to limited access to the midwater, little is known about the diets of most deep-dwelling gelatinous species, which constrains our understanding of food-web structure and nutrient flow in these vast ecosystems. Visual gut-content methods can rarely identify soft-bodied rapidly-digested prey, while observations from submersibles often overlook small prey items. These methods have been differentially applied to shallow and deep siphonophore taxa, confounding habitat and methodological biases. DNA metabarcoding can be used to assess both shallow and deep species’ diets under a common methodological framework, since it can detect both small and gelatinous prey. We (1) further characterized the diets of open-ocean siphonophores using DNA metabarcoding, (2) compared the prey detected by visual and molecular methods to evaluate their technical biases, and (3) evaluated tentacle-based predictions of diet. To do this, we performed DNA metabarcoding analyses on the gut contents of 39 siphonophore species across depths to describe their diets, using six barcode regions along the 18S gene. Taxonomic identifications were assigned using public databases combined with local zooplankton sequences. We identified 55 unique prey items, including crustaceans, gelatinous animals, and fish across 47 siphonophore specimens in 24 species. We reported 29 novel predator-prey interactions, among them the first insights into the diets of nine siphonophore species, many of which were congruent with the dietary predictions based on tentilla morphology. Our analyses detected both small and gelatinous prey taxa underrepresented by visual methods in species from both shallow and deep habitats, indicating that siphonophores play similar trophic roles across depth habitats. We also reveal hidden links between siphonophores and filter-feeders near the base of the food web. This study expands our understanding of the ecological roles of siphonophores in the open ocean, their trophic roles within the ‘jelly-web’, and the importance of their diversity for nutrient flow and ecosystem functioning. Understanding these inconspicuous yet ubiquitous predator-prey interactions is critical to predict the impacts of climate change, overfishing, and conservation policies on oceanic ecosystems. 

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2. COI Metabarcoding of Zooplankton Species Diversity for Time-Series Monitoring of the NW Atlantic Continental Shelf

   https://doi.org/10.3389/fmars.2022.867893  

   Bucklin, Ann ; Batta-Lona, Paola G. ; Questel, Jennifer M. ; Wiebe, Peter H. ; Richardson, David E. ; Copley, Nancy J. ; O’Brien, Todd D. ( April 2022 , Frontiers in Marine Science)

   Marine zooplankton are rapid-responders and useful indicators of environmental variability and climate change impacts on pelagic ecosystems on time scales ranging from seasons to years to decades. The systematic complexity and taxonomic diversity of the zooplankton assemblage has presented significant challenges for routine morphological (microscopic) identification of species in samples collected during ecosystem monitoring and fisheries management surveys. Metabarcoding using the mitochondrial Cytochrome Oxidase I (COI) gene region has shown promise for detecting and identifying species of some – but not all – taxonomic groups in samples of marine zooplankton. This study examined species diversity of zooplankton on the Northwest Atlantic Continental Shelf using 27 samples collected in 2002-2012 from the Gulf of Maine, Georges Bank, and Mid-Atlantic Bight during Ecosystem Monitoring (EcoMon) Surveys by the NOAA NMFS Northeast Fisheries Science Center. COI metabarcodes were identified using the MetaZooGene Barcode Atlas and Database ( https://metazoogene.org/MZGdb ) specific to the North Atlantic Ocean. A total of 181 species across 23 taxonomic groups were detected, including a number of sibling and cryptic species that were not discriminated by morphological taxonomic analysis of EcoMon samples. In all, 67 species of 15 taxonomic groups had ≥ 50 COI sequences; 23 species had >1,000 COI sequences. Comparative analysis of molecular and morphological data showed significant correlations between COI sequence numbers and microscopic counts for 5 of 6 taxonomic groups and for 5 of 7 species with >1,000 COI sequences for which both types of data were available. Multivariate statistical analysis showed clustering of samples within each region based on both COI sequence numbers and EcoMon counts, although differences among the three regions were not statistically significant. The results demonstrate the power and potential of COI metabarcoding for identification of species of metazoan zooplankton in the context of ecosystem monitoring. 

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3. Otolith characterization and integrative species identification of adult mesopelagic fishes from the western North Atlantic Ocean

   https://doi.org/10.3389/fmars.2023.1217779  

   Quigley, Lucinda A ; Caiger, Paul E ; Govindarajan, Annette F ; McMonagle, Helena ; Jech, J Michael ; Lavery, Andone C ; Sosik, Heidi M ; Llopiz, Joel K ( August 2023 , Frontiers in Marine Science)

   Fish diversity and ecology in the ocean’s mesopelagic zone are understudied compared to other marine regions despite growing interest in harvesting these potential resources. Otoliths can provide a wealth of taxonomic and life history information about fish, which can help fill these knowledge gaps; however, there has been relatively little research to date on the otoliths of mesopelagic species. Here, a species-specific image library was assembled of sagittal otoliths from 70 mesopelagic fishes belonging to 29 families collected in the western North Atlantic Ocean. Images of adult sagittal otoliths from 12 species were documented and photographed for the first time. The fish were identified to species with a combination of morphological characters and DNA barcoding. Regressions between otolith size and fish length are presented for the six species with the largest sample sizes in this study. This otolith image library, coupled with otolith-length and width to fish-length relationships, can be used for prey identification and back-calculation of fish size, making it a valuable tool for studies relating to food webs in the important yet poorly understood mesopelagic zone. In addition, the 44 fish barcodes generated in this study highlight the benefit of using an integrative taxonomic approach to studies of this nature, as well as add to existing public databases that enable cryptic species and metabarcoding analyses of mesopelagic species.

    

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4. Reconstructing hyperdiverse food webs: Gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs

   https://doi.org/10.1111/2041-210X.13206  

   Casey, Jordan M. ; Meyer, Christopher P. ; Morat, Fabien ; Brandl, Simon J. ; Planes, Serge ; Parravicini, Valeriano ; Mahon, ed., Andrew ( June 2019 , Methods in Ecology and Evolution)

   Anthropogenic stressors have strong impacts on ecosystems. To understand their influence, detailed knowledge about trophic relationships among species is critical. However, this requires both exceptional resolution in dietary assessments and sampling breadth within communities, especially for highly diverse, tropical ecosystems.

   We used gut content metabarcoding across a broad range of coral reef fishes (8 families, 22 species) in Mo'orea, French Polynesia, to test whether this technique has the potential to capture the structure of a hyperdiverse marine food web. Moreover, we explored whether taxonomic groups (families) and traditional, broad‐scale trophic assignments explained fish diet across four different metrics of quantifying predator–prey interactions.

   Metabarcoding yielded a large number (4,341) of unique operational taxonomic units (i.e. prey) with high‐resolution taxonomic assignments (i.e. often to the level of genus or species). We demonstrate that across multiple metrics, taxonomic group at the family level is a consistently better, albeit still weak, predictor of empirical trophic relationships than frequently used, broad‐scale functional assignments. Our method also reveals a complex trophic network with fine‐scale partitioning among species, further emphasizing the importance of examining fish diets beyond broad trophic categories.

   We demonstrate the capacity of metabarcoding to reconstruct diverse and complex food webs with exceptional resolution, a significant advancement from traditional food web reconstruction. Furthermore, this method allows us to pinpoint the trophic niche of species with niche‐based modelling, even across hyperdiverse species assemblages such as coral reefs. In conjunction with complementary techniques such as stable isotope analysis, applying metabarcoding to whole communities will provide unparalleled information about energy and nutrient fluxes and inform their susceptibility to disturbances even in the world's most diverse ecosystems.

    

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5. Predator–prey interactions of terrestrial invertebrates are determined by predator body size and species identity

   https://doi.org/10.1002/ecy.3634  

   Miller‐ter Kuile, Ana ; Apigo, Austen ; Bui, An ; DiFiore, Bartholomew ; Forbes, Elizabeth S. ; Lee, Michelle ; Orr, Devyn ; Preston, Daniel L. ; Behm, Rachel ; Bogar, Taylor ; et al ( March 2022 , Ecology)

   Predator–prey interactions shape ecosystems and can help maintain biodiversity. However, for many of the earth's most biodiverse and abundant organisms, including terrestrial arthropods, these interactions are difficult or impossible to observe directly with traditional approaches. Based on previous theory, it is likely that predator–prey interactions for these organisms are shaped by a combination of predator traits, including body size and species‐specific hunting strategies. In this study, we combined diet DNA metabarcoding data of 173 individual invertebrate predators from nine species (a total of 305 individual predator–prey interactions) with an extensive community body size data set of a well‐described invertebrate community to explore how predator traits and identity shape interactions. We found that (1) mean size of prey families in the field usually scaled with predator size, with species‐specific variation to a general size‐scaling relationship (exceptions likely indicating scavenging or feeding on smaller life stages). We also found that (2) although predator hunting traits, including web and venom use, are thought to shape predator–prey interaction outcomes, predator identity more strongly influenced our indirect measure of the relative size of predators and prey (predator:prey size ratios) than either of these hunting traits. Our findings indicate that predator body size and species identity are important in shaping trophic interactions in invertebrate food webs and could help predict how anthropogenic biodiversity change will influence terrestrial invertebrates, the earth's most diverse animal taxonomic group.

    

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