DNA metabarcoding unveils niche overlapping and competition among Caribbean sea urchins

Rodríguez-Barreras, Ruber; Godoy-Vitorino, Filipa; Præbel, Kim; Wangensteen, Owen S.

doi:10.1016/j.rsma.2020.101537

Cited by 8 publications

(8 citation statements)

References 62 publications

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“…Cyanobacteria likely come from the ingestion of seagrass compared to T. ventricosus (Tertschnig, 1989;Hendler et al, 1995), and Planctomycetes are dominant components of the epibiotic marine algae microbiota (Bondoso et al, 2017). This adds to our recent dietary survey which confirmed higher herbivory for L. variegatus (Rodríguez-Barreras et al, 2020). T. ventricosus usually grazes on T. testudinum leaves (Keller, 1983;Barrios & Reyes, 2009), however the species also migrates to the backreef zone where D. antillarum and E. lucunter inhabit (Moses & Bonem, 2001).…”

Section: Discussionsupporting

confidence: 58%

Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins

Rodríguez-Barreras

Tosado-Rodríguez

Godoy-Vitorino

2021

PeerJ

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Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species’ guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent.

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Section: Discussionsupporting

confidence: 58%

Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins

Rodríguez-Barreras

Tosado-Rodríguez

Godoy-Vitorino

2021

PeerJ

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“…Alongside the microalgal population, the phylum Ochrophyta was identified as the third most common food item in both river and weir chironomid guts. We observed outputs related to Rodríguez-Barreras et al (2020) [ 48 ] regarding the species variation and sample composition of phylum Ochrophyta identified between study habitants. Phragmoplastophyta, Cryptophyta, Dinoflagellata, and Haptophyta were the minor OTU-associated groups recorded as phytoplankton diet sources.…”

Section: Discussionsupporting

confidence: 54%

“…Abiotic factors are important drivers in the spatial distribution of the dominant communities [ 48 , 62 ]. The relationship between the environmental factors and species in an ecosystem is considered to be crucial.…”

Section: Discussionmentioning

confidence: 99%

Profiling Analysis of Filter Feeder Polypedilum (Chironomidae) Gut Contents Using eDNA Metabarcoding Following Contrasting Habitat Types—Weir and Stream

Rangaswamy

Kim

et al. 2022

IJERPH

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We analyzed the dietary composition of Polypedilum larvae among two contrasting habitats (river and weir). Our approach was (i) to apply eDNA-based sampling to reveal the gut content of the chironomid larvae, (ii) the diversity of gut contents in the two aquatic habitats, and (iii) assessment of habitat sediment condition with the food sources in the gut. The most abundant food was Chlorophyta in the gut of the river (20%) and weir (39%) chironomids. The average ratio of fungi, protozoa, and zooplankton in river chironomids gut was 5.9%, 7.2%, and 3.8%, while it was found decreased to 1.2%, 2.5%, and 0.1% in weir chironomids. Aerobic fungi in river midge guts were 3.6% and 10.34% in SC and IS, while they were in the range of 0.34–2.58% in weir midges. The hierarchical clustering analysis showed a relationship of environmental factors with food contents. Abiotic factors (e.g., pH) in the river and weir habitats correlated the clustered pattern with phytoplankton and minor groups of fungi. This study could help understand the food source diversity in the chironomid and habitat environmental conditions by using eDNA metabarcoding as an effective tool to determine dietary composition.

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“…The reverse primer used was jgHCO2198 (5′‐TAIACYTCIGGRTGICCRAARAAYCA‐3′) (Geller et al, 2013). This primer set has been succesfully used in previous trophic studies of marine broad‐diet predators (Rodríguez‐Barreras et al, 2020; Siegenthaler, Wangensteen, Benvenuto, et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

DNA metabarcoding reveals the importance of gelatinous zooplankton in the diet ofPandalus borealis, a keystone species in the Arctic

et al. 2022

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Information about the dietary composition of a species is crucial to understanding their position and role in the food web. Increasingly, molecular approaches such as DNA metabarcoding are used in studying trophic relationships, not least because they may alleviate problems such as low taxonomic resolution or underestimation of digestible taxa in the diet. Here, we used DNA metabarcoding with universal primers for cytochrome c oxidase I (COI) to study the diet composition of the northern shrimp (Pandalus borealis), an Arctic keystone species with large socio‐economic importance. Across locations, jellyfish and chaetognaths were the most important components in the diet of P. borealis, jointly accounting for 40%–60% of the total read abundance. This dietary importance of gelatinous zooplankton contrasts sharply with published results based on stomach content analysis. At the same time, diet composition differed between fjord and shelf locations, pointing to different food webs supporting P. borealis in these two systems. Our study underlines the potential of molecular approaches to provide new insights into the diet of marine invertebrates that are difficult to obtain with traditional methods, and calls for a revision of the role of gelatinous zooplankton in the diet of the key Arctic species P. borealis, and in extension, Arctic food webs.

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DNA metabarcoding unveils niche overlapping and competition among Caribbean sea urchins

Cited by 8 publications

References 62 publications

Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins

Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins

Profiling Analysis of Filter Feeder Polypedilum (Chironomidae) Gut Contents Using eDNA Metabarcoding Following Contrasting Habitat Types—Weir and Stream

DNA metabarcoding reveals the importance of gelatinous zooplankton in the diet ofPandalus borealis, a keystone species in the Arctic

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