Symbiont community stability through severe coral bleaching in a thermally extreme lagoon

Smith, Edward G.; Vaughan, Grace O.; Ketchum, Remi N.; McParland, Dain; Burt, John A.

doi:10.1038/s41598-017-01569-8

Cited by 47 publications

(40 citation statements)

References 59 publications

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“…For example, ITS2 type C3 (and additional types characterized by sequences from the C3 radiation; Thornhill, Lewis, Wham, & LaJeunesse, ) for Acropora sp. in Eastern Africa (Chauka, ), the Chagos Archipelago (Yang et al, ), Red Sea (Ziegler, Eguíluz et al, ) and Persian‐Arabian Gulf (Hume et al, ; Smith, Ketchum et al, ; Smith, Vaughan et al, ). The C3 sequence represents one of several major radiations within the genus Cladocopium (Thornhill et al, ) and our C3z type profile among Acropora sp.…”

Section: Discussionmentioning

confidence: 99%

“…For Symbiodiniaceae typing, amplification of the ribosomal Internal Transcribed Spacer 2 (ITS2) region, a multicopy genetic marker commonly used to assess Symbiodiniaceae diversity was used (Arif et al, ; Smith, Ketchum, et al, ; Smith, Vaughan, Ketchum, McParland, & Burt, ). For amplicon‐specific PCRs, we used the primers ITSintfor2 5'‐TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GAA TTG CAG AAC TCC GTG‐3' and ITS2‐reverse 5'‐GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGG GAT CCA TAT GCT TAA GTT CAG CGG GT‐3' with concatenated Illumina sequencing adapters (underlined).…”

Section: Methodsmentioning

confidence: 99%

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Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave

Gardner

Camp

Smith

et al. 2019

Ecology and Evolution

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Repeat marine heat wave‐induced mass coral bleaching has decimated reefs in Seychelles for 35 years, but how coral‐associated microbial diversity (microalgal endosymbionts of the family Symbiodiniaceae and bacterial communities) potentially underpins broad‐scale bleaching dynamics remains unknown. We assessed microbiome composition during the 2016 heat wave peak at two contrasting reef sites (clear vs. turbid) in Seychelles, for key coral species considered bleaching sensitive (Acropora muricata, Acropora gemmifera) or tolerant (Porites lutea, Coelastrea aspera). For all species and sites, we sampled bleached versus unbleached colonies to examine how microbiomes align with heat stress susceptibility. Over 30% of all corals bleached in 2016, half of which were from Acropora sp. and Pocillopora sp. mass bleaching that largely transitioned to mortality by 2017. Symbiodiniaceae ITS2‐sequencing revealed that the two Acropora sp. and P. lutea generally associated with C3z/C3 and C15 types, respectively, whereas C. aspera exhibited a plastic association with multiple D types and two C3z types. 16S rRNA gene sequencing revealed that bacterial communities were coral host‐specific, largely through differences in the most abundant families, Hahellaceae (comprising Endozoicomonas), Rhodospirillaceae, and Rhodobacteraceae. Both Acropora sp. exhibited lower bacterial diversity, species richness, and community evenness compared to more bleaching‐resistant P. lutea and C. aspera. Different bleaching susceptibility among coral species was thus consistent with distinct microbiome community profiles. These profiles were conserved across bleached and unbleached colonies of all coral species. As this pattern could also reflect a parallel response of the microbiome to environmental changes, the detailed functional associations will need to be determined in future studies. Further understanding such microbiome‐environmental interactions is likely critical to target more effective management within oceanically isolated reefs of Seychelles.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave

Gardner

Camp

Smith

et al. 2019

Ecology and Evolution

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“…Furthermore, it is not known whether the DMS antioxidant system and/or the proposed DMS‐aerosol‐cloud feedback will assist corals in coping with these impacts. Corals may change their endosymbiont composition via symbiont switching and/or shuffling to favor thermo‐tolerant species and lower oxidative stress (Bay et al, 2016; Smith et al, 2017). For example, Acropora spp.…”

Section: Discussionmentioning

confidence: 99%

Coral Reef Emissions of Atmospheric Dimethylsulfide and the Influence on Marine Aerosols in the Southern Great Barrier Reef, Australia

et al. 2020

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Variability in atmospheric dimethylsulfide (DMSa) and the potential influence on atmospheric aerosols was investigated at Heron Island in the southern Great Barrier Reef (GBR), Australia. This work compiles previously published DMSa data (reported in Swan, Jones, Deschaseaux, & Eyre, 2017, https://doi.org/10.1007/s00216-017-0385-8), with additional surveys of DMSa, atmospheric particle number concentration, and other oceanic and atmospheric data sets. DMSa was higher in summer (mean 3.2 nmol m−3/78 ppt) than winter (mean 1.3 nmol m−3/32 ppt), reflective of seasonal shifts in phytoplankton biomass and emissions from corals in the southern GBR. Seasonally extreme spikes in DMSa were detected during low tide and low wind speed, supporting findings that the coral reef can be an important source of DMSa above background oceanic emissions. A significant link was present between DMSa and aerosol concentration (ranging from 0.5 to 2.5 μm) during calm, daylight hours, when conditions were optimal for the local oxidation of DMSa to sulfate aerosol precursors. This link may reflect condensational growth of existing fine particles (< 0.5 μm), which is the dominant pathway by which biogenic trace gases influence aerosols in the marine boundary layer. Aerosol concentration significantly correlated with reduced surface solar irradiance and sea surface temperature, which is potential evidence of a local negative feedback mitigating coral physiological stress. These findings provide a step toward a better understanding of the processes influencing DMSa and aerosol concentrations and of the consequences for the local radiative balance over coral reefs; an increasingly important topic with ongoing ocean warming and coral bleaching.

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“…Given the inability to align some ITS2 sequences from different genera within the Symbiodiniaceae, pairwise differences are calculated for genus‐separated groupings of ITS2 sequences. Distance matrices are calculated based on either a Bray–Curtis method (sensu Smith, Vaughan, Ketchum, McParland, & Burt, ) or using the weighted UniFrac method (Lozupone, Lladser, Knights, Stombaugh, & Knight, ). UniFrac is often used to compare bacterial communities by assessing similarity between sets of 16S rDNA sequences representative of bacterial taxa (Lozupone et al, ).…”

Section: Methodsmentioning

confidence: 99%

“…Data from the original Smith, Vaughan et al () study are deposited in the Dryad Digital Repository (http://dx.doi.org/10.5061/dryad.h6s54). The data used to create Figure are available through the SymPortal wiki hosted on GitHub: https://github.com/didillysquat/SymPortal_framework/wiki.…”

Section: Data Accessibilitymentioning

confidence: 99%

SymPortal: A novel analytical framework and platform for coral algal symbiont next‐generation sequencing ITS2 profiling

Hume

Smith

Ziegler

et al. 2019

Molecular Ecology Resources

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We present SymPortal (SymPortal.org), a novel analytical framework and platform for genetically resolving the algal symbionts of reef corals using next‐generation sequencing (NGS) data of the ITS2 rDNA. Although the ITS2 marker is widely used to genetically characterize taxa within the family Symbiodiniaceae (formerly the genus Symbiodinium) , the multicopy nature of the marker complicates its use. Commonly, the intragenomic diversity resultant from this multicopy nature is collapsed by analytical approaches, thereby focusing on only the most abundant sequences. In contrast, SymPortal employs logic to identify within‐sample informative intragenomic sequences, which we have termed ‘defining intragenomic variants' (DIVs), to identify ITS2 ‐type profiles representative of putative Symbiodiniaceae taxa. By making use of this intragenomic ITS2 diversity, SymPortal is able to resolve genetic delineations using the ITS2 marker at a level that was previously only possible by using additional genetic markers. We demonstrate this by comparing this novel approach to the most commonly used alternative approach for NGS ITS2 data, the 97% similarity clustering to operational taxonomic units (OTUs). The SymPortal platform accepts NGS raw sequencing data as input to provide an easy‐to‐use, standardization‐enforced, and community‐driven framework that integrates with a database to gain resolving power with increased use. We consider that SymPortal, in conjunction with ongoing large‐scale sampling and sequencing efforts, should play an instrumental role in making future sampling efforts more comparable and in maximizing their efficacy in working towards the classification of the global Symbiodiniaceae diversity.

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Symbiont community stability through severe coral bleaching in a thermally extreme lagoon

Cited by 47 publications

References 59 publications

Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave

Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave

Coral Reef Emissions of Atmospheric Dimethylsulfide and the Influence on Marine Aerosols in the Southern Great Barrier Reef, Australia

SymPortal: A novel analytical framework and platform for coral algal symbiont next‐generation sequencing ITS2 profiling

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