Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins

Abstract

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.

The Epibiotic Microbiota of Wild Caribbean Sea Urchin Spines Is Species Specific

“…A quality meter Pro 2030 ( , accessed on 10 December 2019) was used to measure water temperature, salinity, and pH. More information about the site can be found in Rodríguez-Barreras et al [ 4 ]. Temperature, salinity, and pH were similar among sites, ranging from 25.6–26.8 °C, 33.2–33.8, and 8.33–8.40, respectively ( Supplementary Table S1 ).…”

“…Over the last two decades, microbiological studies have advanced from traditional cultures and microscopy to sophisticated genomic and molecular analyses [ 1 , 2 ]. The developments of refined genomic sequencing and bioinformatic tools have revolutionized the traditional microbiology approaches, exponentially increasing the existing knowledge of prokaryotes and host microbiomes [ 3 , 4 ]. Several studies using high-throughput 16S rRNA gene sequencing have been published in vertebrates such as fish, birds, and mammals [ 5 , 6 , 7 ], while marine invertebrates have received less attention [ 8 , 9 , 10 ].…”

“…However, the importance of external microbiota, even though critical for immunity response, has been understudied in invertebrates [ 10 , 45 , 46 ]. Microbiome studies in echinoderms have been focused primarily on the coelomic fluid and gut microbiota [ 4 , 47 , 48 ], whereas the external microbiota remains unstudied.…”

Bacterial composition along the digestive tract of the Horned Screamer (Anhima cornuta), a tropical herbivorous bird

“…DNA was extracted from these samples using the PowerSoil DNA Isolation kit (MO BIO, Inc., Carlsbad, CA, USA). DNA from the GIT content samples were normalized to 4 nM during 16S library prep and the hypervariable region V4 of the 16S ribosomal RNA gene (~291 bp) was amplified using the universal bacterial primers: 515F (5′GTGCCAGCMGCCGCGGTAA3′) and 806R (5′GGACTACHVGGGTWTCTAAT3′) in the Earth Microbiome Project ( ) ( Caporaso et al, 2012 ) using previously reported conditions in projects from our group ( Rodriguez-Barreras, Tosado-Rodriguez & Godoy-Vitorino, 2021 ; Ruiz Barrionuevo et al, 2022 ; Abarca et al, 2018 ). We used the Illumina MiSeq Reagent kit 2 × 250 bp to sequence the 16S amplicons.…”

“…Singletons and reads matching chloroplasts or mitochondria were removed from downstream analyses. Data were collected as previously described ( Rodriguez-Barreras, Tosado-Rodriguez & Godoy-Vitorino, 2021 ; Ruiz Barrionuevo et al, 2022 ). Data analysis was done using a rarefaction level of 1,000 sequences per sample considering the gut sections: proventriculus n = 3, small intestine n = 1, large intestine n = 4 and cecum n = 2.…”