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

Abstract

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.

Fig 1. Gut content metabarcoding workflow used in this study.

Siphonophore colony illustrated by Freya Goetz. Silhouettes in the plankton net downloaded from phylopic.org. Solid arrows indicate physical material transfer and processing, dashed lines indicate information transfer and processing. Yellow islands indicate elements processed in the laboratory bench, green islands represent bioinformatic datasets processed in the high-performance computing cluster, and red islands represent curated data products.

Fig 2. Summary table of the siphonophore species sampled for this study indicating their vertical habitat, the number of specimens sampled, the number of specimens with recognizable prey sequences, and hypothesized feeding guild.

Guilds are based on published feeding records used in Damian-Serrano et al. [26], predicted feeding guild from the DAPC analysis in Damian-Serrano et al. [27] based on tentilla morphology, and prey found in this study. Photo credits: (A) Casey Dunn, (B, D,) Stephan Siebert, CC BY licensed and reprinted from Munro et al. [73], (C) reprinted from https://www.theredshrimp.com/ with permission from Reyn Yoshioka, original copyright (2018), (E) Steven Haddock, (F) reprinted from https://biolum.eemb.ucsb.edu/organism/pictures/bargmannia.html with permission from Steven Haddock, original copyright (1997), (G, I) Alejandro Damian-Serrano, (H) NOAA, CC BY licensed, reprinted from https://www.flickr.com/photos/noaaphotolib/19988388271 (J) reprinted from http://www.roboastra.com/Cnidaria2/brac836.htm with permission from Denis Riek, original copyright (2021).

Fig 3. Relative log-abundances of prey reads colored by taxon.

(A) For each siphonophore species, and (B) for each siphonophore specimen and barcode.

Fig 4. Species-wise grid with the frequency of the major prey types identified from the metabarcoding data and the average prey-type selectivity.

Gut content cells in white indicate absence, and cells in grey indicate presence in one specimen, or more than one specimen if labeled with a number. Selectivity colors mapped to Strauss’ L.I. values. The siphonophore cladogram (left) is a simplified version of the phylogenetic tree published in Damian-Serrano et al. [26].

Fig 5. Feeding interactions between siphonophores and their prey from different data sources.

Including prey identified by our metabarcoding results (red), observations published submersible observations (blue), observations published visual gut content analyses (green), and prey types predicted by the morphology-based DAPC model in Damian-Serrano et al. [27]. Gelatinous prey refers to ctenophores, medusae, and salps. Larvaceans were excluded as their own category since they are not gelatinous when swimming freely outside their mucous ‘houses’, which would be the only times they would be able to trigger a prey-capture response in siphonophore tentacles.