The microbial biosphere of the coral <i>Acropora cervicornis</i> in Northeastern Puerto Rico

Godoy-Vitorino, Filipa; Ruiz-Diaz, Claudia Patricia; Rivera-Seda, Abigail; Ramírez-Lugo, Juan S.; Toledo-Hernández, Carlos

doi:10.7717/peerj.3717

Cited by 36 publications

(31 citation statements)

References 46 publications

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“…The observed dominance of members of Proteobacteria, Bacteroidetes and Cyanobacteria phyla was expected considering findings from the global oceans (Sunagawa et al, 2015;Zinger et al, 2011) as well as previous studies of coral reefs and coastal associated niches (Curren & Leong, 2019;Feng et al, 2009;Godoy-Vitorino et al, 2017;Wegley et al, 2007). As expected, different classes of Proteobacteria phylum dominated water and sediment samples (Feng et al, 2009;Zinger et al, 2011): members of Gammaproteobacteria class were the most abundant in water samples whereas in the sediment samples Deltaproteobacteria were predominant.…”

Section: Discussionsupporting

confidence: 83%

“…Furthermore, shifts in population composition of coral-associated microorganisms often correlate with the onset of diseases and coral-bleaching (Krediet et al, 2013), suggesting a likely role of microbes in coral health and, therefore, the stability of reef ecosystems. Besides health, microbes are also known to be critical for coral nutrition (Rosenberg et al, 2007) homeostasis and protection against diseases (Godoy-Vitorino et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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A peek into Western Indian Ocean microbial richness: a pilot for a coral microbiome study

Wambua

Gourlé

Villiers

et al. 2019

Preprint

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Microbial communities are essential components of natural ecosystems. Of the global oceans, the Indian Ocean remains the least studied in terms of its microbial diversity, despite it being a highly dynamic tropical water body. Metagenomics methods have significantly advanced studies in marine microbial ecology in recent years. Preliminary metabarcoding assessments are recommended to mitigate against the associated costs, prior to the metagenomics study, to give an impression of the diversity expected and determine the sequencing effort required.We report here the first metabarcoding survey of bacterial diversity of the western Indian Ocean (WIO) using samples used for optimizing environmental DNA (eDNA) isolation as pilot experiment for a metagenomic study investigating the coral-reef microbiome of the region. Sampling of water and sediment samples was done near-shore sublittoral and within the coral reef.About 3,000 microbial ribotypes were inferred, from which 41 phyla were uncovered. Sediments registered higher alpha diversity than seawater samples. The phylum Proteobacteria was dominant with its members constituting over 60% of the ribosomal sequence variants (RSVs). The other abundant bacteria were members of Bacteroidetes and Cyanobacteria phyla. We identified bacterial species with potential broad biotechnological applications, underscoring the WIO's richness and the usefulness of eDNA metabarcoding approaches in bioprospecting as well as monitoring and/or surveying marine ecosystems.

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Section: Discussionsupporting

confidence: 83%

Section: Introductionmentioning

confidence: 99%

A peek into Western Indian Ocean microbial richness: a pilot for a coral microbiome study

Wambua

Gourlé

Villiers

et al. 2019

Preprint

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“…The observation that differences between Heliconius species were restricted to rare OTUs can be rather important since rare taxa have been shown to be important in other biological systems. Distinct studies in soils ( Hausmann et al, 2016 ), human skin, human gut and the coral holobiont ( Shade et al, 2014 ; Godoy-Vitorino et al, 2017 ) have suggested that phylotypes with very low abundance (rare taxa) are likely to be functionally relevant.…”

Section: Discussionmentioning

confidence: 99%

Conserved microbiota among young Heliconius butterfly species

Schooten

Godoy-Vitorino

McMillan

et al. 2018

PeerJ

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BackgroundInsects are the most diverse group of animals which have established intricate evolutionary interactions with bacteria. However, the importance of these interactions is still poorly understood. Few studies have focused on a closely related group of insect species, to test the similarities and differences between their microbiota. Heliconius butterflies are a charismatic recent insect radiation that evolved the unique ability to use pollen as a protein source, which affected life history traits and resulted in an elevated speciation rates. We hypothesize that different Heliconius butterflies sharing a similar trophic pollen niche, harbor a similar gut flora within species, population and sexes.MethodsTo test our hypothesis, we characterized the microbiota of 38 adult male and female butterflies representing six species of Heliconius butterflies and 2 populations of the same species. We sequenced the V4 region of the 16S rRNA gene with the Roche 454 system and analyzed the data with standard tools for microbiome analysis.ResultsOverall, we found a low microbial diversity with only 10 OTUs dominating across all individuals, mostly Proteobacteria and Firmicutes, which accounted for 99.5% of the bacterial reads. When rare reads were considered, we identified a total of 406 OTUs across our samples. We identified reads within Phyla Chlamydiae, found in 5 butterflies of four species. Interestingly, only three OTUs were shared among all 38 individuals (Bacillus, Enterococcus and Enterobacteriaceae). Altogether, the high individual variation overshadowed species and sex differences. Thus, bacterial communities were not structured randomly with 13% of beta-diversity explained by species, and 40 rare OTUs being significantly different across species. Finally, 13 OTUs, including the intercellular symbiont Spiroplasma, varied significantly in relative abundance between males and females.DiscussionThe Heliconius microbial communities in these 38 individuals show a low diversity with few differences in the rare microbes between females, males, species or populations. Indeed, Heliconius butterflies, similarly to other insects, are dominated by few OTUs, mainly from Proteobacteria and Firmicutes. The overall low microbial diversity observed contrasts with the high intra-species variation in microbiome composition. This could indicate that much of the microbiome maybe acquired from their surroundings. The significant differences between species and sexes were restricted to rare taxa, which could be important for microbial community stability under changing conditions as seen in other host-microbiome systems. The presence of symbionts like Spiroplasma or Chlamydiae, identified in this study for the first time in Heliconius, could play a vital role in their behavior and evolution by vertical transmission. Altogether, our study represents a step forward into the description of the microbial diversity in a charismatic group of closely related butterflies.

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“…gibbosa were from Streptococcus. All three of these bacterial genera have been observed in coral microbiomes (Beleneva et al, 2005;de Castro et al, 2010;Godoy-Vitorino et al, 2017).…”

Section: Influence Of Bleachingmentioning

confidence: 99%

Microbial Associations of Four Species of Algal Symbiont-bearing Foraminifers from the Florida Reef Tract, Usa

Martin

Kellogg

Hallock

2019

Journal of Foraminiferal Research

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While microbiome research is a rapidly expanding field of study, relatively little is known of the microbiomes associated with Foraminifera. This preliminary study investigated microbes associated with four species of Foraminifera, representing two taxonomic orders, which host three kinds of algal endosymbionts. A major objective was to explore potential influences on the microbiome composition, including phylogenetic relatedness among the host species, similarities in algal symbionts hosted, and environmental conditions from which the specimens were collected. Samples examined from two locations along the middle Florida Keys reef tract included 45 foraminiferal specimens and four environmental samples. Bacterial DNA extraction from individual specimens was followed by amplification and amplicon sequencing of the V4 variable region of the 16S rRNA gene; results were obtained from 21 specimens. The Order Miliolida, Family Soritidae, was represented by 5–8 specimens of each of three species: Archaias angulatus and Cyclorbiculina compressa, which both host chlorophyte symbionts, and Sorites orbiculus, which hosts dinoflagellate symbionts. Three Ar. angulatus specimens from which the microbiome was successfully sequenced shared 177 OTUs. Six C. compressa specimens successfully sequenced shared 58 OTUs, of which 31 were also shared by the three specimens of Ar. angulatus. Four successfully sequenced S. orbiculus specimens shared 717 unique OTUs. The 13 soritid specimens shared 26 OTUs, 23 of which represented Proteobacteria, predominantly of the bacterial family Rhodobacteraceae. The fourth foraminiferal species, Amphistegina gibbosa (Order Rotaliida) hosts diatom endosymbionts. Bacterial DNA extraction was attempted on 16 Am. gibbosa, including both normal-appearing and partly-bleached specimens. Only six OTUs, four of which represented Proteobacteria, were found in all eight specimens successfully sequenced. The partly bleached specimens shared nearly twice as many unique microbial OTUs (32) as the normal-appearing specimens (19). All Am. gibbosa specimens shared only four microbial OTUs with the soritid species, three of which may have been contaminants, indicating minimal commonality between the microbiomes of Am. gibbosa and the soritid taxa.

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The microbial biosphere of the coral Acropora cervicornis in Northeastern Puerto Rico

Cited by 36 publications

References 46 publications

A peek into Western Indian Ocean microbial richness: a pilot for a coral microbiome study

A peek into Western Indian Ocean microbial richness: a pilot for a coral microbiome study

Conserved microbiota among young Heliconius butterfly species

Microbial Associations of Four Species of Algal Symbiont-bearing Foraminifers from the Florida Reef Tract, Usa

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