DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species

Novotny, Andreas; Zamora-Terol, Sara; Winder, Monika

doi:10.1098/rspb.2021.0908

Cited by 29 publications

(49 citation statements)

References 69 publications

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“…The copepods that were shared in the diet of stickleback, sprat, and herring were Temora , Acartia, and Centropages have increased over the last decades, as opposed to Pseudocalanus 32 . Our results show that stickleback are able to feed on a broader spectrum of prey and highlight that stickleback utilizes the rotifer Synchaeta baltica as prey, which is an important component of the plankton community composition in the Baltic Sea 18 , 20 . Due to the difference of prey size, we can expect an overrepresentation of copepod to rotifer sequences compared with microscopic count data.…”

Section: Discussionmentioning

confidence: 70%

“…A possible explanation is the difficulty observing them microscopically, as their digestion rate is faster than crustaceans 29 , and no hard parts remain in the digestive system. Further, COI detected the presence of cladocerans, which was confirmed by the microscopic survey, but underrepresented with 18S that strongly amplify copepods 20 . Interestingly, more than twice annelid COI reads, including the benthic macroinvertebrates Bylgides and Marenzellaria , were associated to stickleback (15%) and herring (8%) than to sprat (4%), highlighting their ability to migrate vertically.…”

Section: Discussionmentioning

confidence: 75%

“…An increasing trend in biomass of the two main rotifer genera ( Synchaeta and Keratella ) was observed since the 1990s 36 . In a recent study, we showed that rotifers might occupy a unique feeding niche, as direct grazers of dinoflagellate spring bloom, as well as in the recycling of organic matter in summer 20 . The low level of predation on rotifers by clupeid adults (< 1% of the reads) observed here indicate that this trophic niche may not be fully utilized.…”

Section: Discussionmentioning

confidence: 99%

“…As a result, copepods and cladocerans are described being the main food for planktivorous fish, leading to a high diet overlap between sprat, herring, and stickleback in the Baltic Sea 12 . At the same time, soft and gelatinous zooplankton (i.e., rotifers and ctenophores) can at times dominate the zooplankton biomass in the Baltic Sea 18 – 20 . However, the digestion rate for soft and gelatinous prey is faster compared to crustaceans 21 , and potentially contribute to an overestimation of reported empty fish gut content.…”

Section: Introductionmentioning

confidence: 99%

“…However, the digestion rate for soft and gelatinous prey is faster compared to crustaceans 21 , and potentially contribute to an overestimation of reported empty fish gut content. DNA metabarcoding has proven to be a successful tool investigating diverse groups of diets of zooplankton, being able to detect a broad diversity of prey items for zooplankton in the pelagic ecosystem 20 , 22 . A recent study using DNA metabarcoding conducted in coastal spawning areas was able to detect a much broader diversity of stickleback prey preference than previously described, indicating flexibility and adaptivity of the stickleback 23 .…”

Section: Introductionmentioning

confidence: 99%

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Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy

Novotny

Jan

Dierking

et al. 2022

Sci Rep

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Marine communities undergo rapid changes related to human-induced ecosystem pressures. The Baltic Sea pelagic food web has experienced several regime shifts during the past century, resulting in a system where competition between the dominant planktivorous mesopredatory clupeid fish species herring (Clupea harengus) and sprat (Sprattus sprattus) and the rapidly increasing stickleback (Gasterosteus aculeatus) population is assumed to be high. Here, we investigate diet overlap between these three planktivorous fishes in the Baltic Sea, utilizing DNA metabarcoding on the 18S rRNA gene and the COI gene, targeted qPCR, and microscopy. Our results show niche differentiation between clupeids and stickleback, and highlight that rotifers play an important role in this pattern, as a resource that is not being used by the clupeids nor by other zooplankton in spring. We further show that all the diet assessment methods used in this study are consistent, but also that DNA metabarcoding describes the plankton-fish link at the highest taxonomic resolution. This study suggests that rotifers and other understudied soft-bodied prey may have an important function in the pelagic food web and that the growing population of pelagic stickleback may be supported by the open feeding niche offered by the rotifers.

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Section: Discussionmentioning

confidence: 70%

Section: Discussionmentioning

confidence: 75%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy

Novotny

Jan

Dierking

et al. 2022

Sci Rep

Self Cite

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Brute force prey metabarcoding to explore the diets of small invertebrates

Flo,

Vader,

Præbel

2024

Ecology and Evolution

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Prey metabarcoding has become a popular tool in molecular ecology for resolving trophic interactions at high resolution, from various sample types and animals. To date, most predator–prey studies of small‐sized animals (<1 mm) have met the problem of overabundant predator DNA in dietary samples by adding blocking primers/peptide nucleic acids. These primers aim to limit the PCR amplification and detection of the predator DNA but may introduce bias to the prey composition identified by interacting with sequences that are similar to those of the predator. Here we demonstrate the use of an alternative method to explore the prey of small marine copepods using whole‐body DNA extracts and deep, brute force metabarcoding of an 18S rDNA fragment. After processing and curating raw data from two sequencing runs of varying depths (0.4 and 5.4 billion raw reads), we isolated 1.3 and 52.2 million prey reads, with average depths of ~15,900 and ~120,000 prey reads per copepod individual, respectively. While data from both sequencing runs were sufficient to distinguish dietary compositions from disparate seasons, locations, and copepod species, greater sequencing depth led to better separation of clusters. As computation and sequencing are becoming ever more powerful and affordable, we expect the brute force approach to become a general standard for prey metabarcoding, as it offers a simple and affordable solution to consumers that is impractical to dissect or unknown to science.

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Feeding strategy and dietary preference shape the microbiome of epipelagic copepods in a warm nutrient‐impoverished ecosystem

et al. 2022

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Copepods provide a rich organic microenvironment allowing the settlement and proliferation of microorganisms, forming dynamic microbial hotspots in the oceans. Such symbiotic associations in the plankton were previously hypothesized to be especially developed in warm oligotrophic seas, as they may serve as alternative sources of nutrients in biologically poor waters. Aiming to better understand how copepod microbiomes are shaped in an oligotrophic sea, we characterized microbiota associated with three dominant coastal epipelagic copepod species in the ultra‐oligotrophic Eastern Mediterranean Sea using amplicon sequencing of the 16S rRNA gene. Our results show that copepod‐associated microbial communities were host‐specific rather than determined by seasonal environmental changes. In the filter‐feeding copepod with a tendency to herbivory, Temora stylifera, microbial diversity was low and relatively stable throughout the year. In contrast, omnivorous copepods, the ambush‐feeding Oithona nana, and the mixed‐feeding Centropages ponticus harbored more diverse microbiomes dominated by transient taxa. We suggest that filter‐feeding strategy and narrow food spectrum can limit copepod–microbe interactions, while the ambush and mixed feeding strategies combined with omnivory confer higher microbial diversity. Filter feeders may reduce the recruitment of opportunistic microbes by maintaining high fidelity associations, as indicated by the large number of core taxa in T. stylifera. We underline the importance of the copepod–microbe associations in nutrient‐impoverished ecosystems, based on predicted enrichment of nitrogen metabolism in the core microbiome, mostly during summer when the shallow coastal waters are nitrogen‐depleted.

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DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species

Cited by 29 publications

References 69 publications

Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy

Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy

Brute force prey metabarcoding to explore the diets of small invertebrates

Feeding strategy and dietary preference shape the microbiome of epipelagic copepods in a warm nutrient‐impoverished ecosystem

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