A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

Carradec, Quentin; Poulain, Julie; Boissin, Émilie; Hume, Benjamin C. C.; Voolstra, Christian R.; Ziegler, Maren; Engelen, Stéfan; Cruaud, Corinne; Planes, Serge; Wincker, Patrick

doi:10.1038/s41598-020-72589-0

Cited by 9 publications

(6 citation statements)

References 60 publications

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“…Most attention to date has focused on fishes and stony corals (Figure 5), mirroring their ecological and economic importance as fishery targets and foundation species. The ability to bring long-read DNA sequencers to the field provides a novel opportunity to rapidly expand the availability of genomic resources for coral reef taxa (27,39) by expediting sequencing timelines, involving local scientists, and simplifying permit logistics.…”

Section: Genomic Resources For Reef Speciesmentioning

confidence: 99%

Coral Reef Population Genomics in an Age of Global Change

2023

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Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated. Expected final online publication date for the Annual Review of Genetics, Volume 57 is November 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Section: Genomic Resources For Reef Speciesmentioning

confidence: 99%

Coral Reef Population Genomics in an Age of Global Change

2023

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“…Large datasets, such as obtained for the Earth Microbiome Project, maximize the comparability among studies (Thompson et al, 2017), but the employed primers are prone to misamplification in corals and provide limited coverage of some taxonomic groups (Bayer et al, 2013;Robbins et al, 2019;van de Water et al, 2020). Such methodological constraints may resolve in the near future with the availability of direct full-length sequencing of 16S rRNA genes (Carradec et al, 2020). Fewer studies have utilized shotgun metagenomic sequencing to obtain prokaryotic genomes via metagenome-assembled genomes (MAGs) (Neave et al, 2017a;Cárdenas et al, 2018;Robbins et al, 2019).…”

Section: The Prokaryotic Communitymentioning

confidence: 99%

Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

et al. 2021

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Coral research is being ushered into the genomic era. To fully capitalize on the potential discoveries from this genomic revolution, the rapidly increasing number of high-quality genomes requires effective pairing with rigorous taxonomic characterizations of specimens and the contextualization of their ecological relevance. However, to date there is no formal framework that genomicists, taxonomists, and coral scientists can collectively use to systematically acquire and link these data. Spurred by the recently announced “Coral symbiosis sensitivity to environmental change hub” under the “Aquatic Symbiosis Genomics Project” - a collaboration between the Wellcome Sanger Institute and the Gordon and Betty Moore Foundation to generate gold-standard genome sequences for coral animal hosts and their associated Symbiodiniaceae microalgae (among the sequencing of many other symbiotic aquatic species) - we outline consensus guidelines to reconcile different types of data. The metaorganism nature of the coral holobiont provides a particular challenge in this context and is a key factor to consider for developing a framework to consolidate genomic, taxonomic, and ecological (meta)data. Ideally, genomic data should be accompanied by taxonomic references, i.e., skeletal vouchers as formal morphological references for corals and strain specimens in the case of microalgal and bacterial symbionts (cultured isolates). However, exhaustive taxonomic characterization of all coral holobiont member species is currently not feasible simply because we do not have a comprehensive understanding of all the organisms that constitute the coral holobiont. Nevertheless, guidelines on minimal, recommended, and ideal-case descriptions for the major coral holobiont constituents (coral animal, Symbiodiniaceae microalgae, and prokaryotes) will undoubtedly help in future referencing and will facilitate comparative studies. We hope that the guidelines outlined here, which we will adhere to as part of the Aquatic Symbiosis Genomics Project sub-hub focused on coral symbioses, will be useful to a broader community and their implementation will facilitate cross- and meta-data comparisons and analyses.

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“…To test this hypothesis, we analyzed the structure of the microbiota in T. aurea collected from acidified (HV), polluted (CM), and normal environments (NPP and CZ) by using a third-generation DNA sequencing platform from Oxford Nanopore Technologies (ONT). Oxford nanopore sequencing provides long reads, which allow us to efficiently and costeffectively cover the entire 16S rRNA gene (V1-V9 regions) with a high throughput; thus, we can rapidly monitor bacterial communities (Carradec et al, 2020;Ho et al, 2021). Utilizing ONT, we examined the variation in the bacterial communities of T. aurea.…”

Section: Introductionmentioning

confidence: 99%

Microbiome variability in invasive coral (Tubastraea aurea) in response to diverse environmental stressors

Girija,

Tseng,

Chen

et al. 2023

Front. Mar. Sci.

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The Indo-Pacific native azooxanthellate Tubastraea (Scleractinia) has been identified as an invasive marine species with substantial environmental, economic, and social implications worldwide. Despite their exceptional invasive capacity, our understanding of the role of their symbiotic microbiota in host resilience, as well as their response to ambient environmental conditions, remains limited. In this study, we analyzed the symbiotic bacterial communities found in the tissue and mucus of Tubastraea aurea from different habitats along the northeastern coast of Taiwan. These habitats included two extreme sites (a hydrothermal vent [HV] and a copper mining [CM] site) and two normal environments (inlet of a nuclear power plant [NPP] and a habitat adjacent to a conservation zone [CZ]). We employed full-length 16S rRNA sequencing (~1.5 kilobases) to determine coral-associated microbiome responses to local environments. Results showed significant variations in bacterial communities between corals from extreme and normal habitats. Chemoheterotrophic Endozoicomonas bacteria dominated the tissue samples from the HV and CM sites, whereas phototrophic Synechococcus cyanobacteria dominated the NPP and CZ sites. Hydrographic parameters such as pH, salinity, biological oxygen demand, turbidity, and concentration of heavy metals (e.g., Cu and Fe) increased at the HV and CM sites compared with those at the NPP and CZ sites. This difference created more stressful conditions at the HV and CM sites. The microbial assemblages associated with T. aurea exhibited a prevalence of diverse symbiotic bacteria that could potentially contribute to the host’s ability to adapt and survive in challenging ecological conditions. Therefore, these advantageous microorganisms, along with the host’s physiological mechanisms of dispersion, range expansion, and invasiveness, may enhance the resilience and ability of T. aurea to thrive in extreme environments.

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A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

Cited by 9 publications

References 60 publications

Coral Reef Population Genomics in an Age of Global Change

Coral Reef Population Genomics in an Age of Global Change

Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

Microbiome variability in invasive coral (Tubastraea aurea) in response to diverse environmental stressors

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