1
|
Walker NS, Nestor V, Golbuu Y, Palumbi SR. Coral bleaching resistance variation is linked to differential mortality and skeletal growth during recovery. Evol Appl 2023; 16:504-517. [PMID: 36793702 PMCID: PMC9923480 DOI: 10.1111/eva.13500] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 09/19/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022] Open
Abstract
The prevalence of global coral bleaching has focused much attention on the possibility of interventions to increase heat resistance. However, if high heat resistance is linked to fitness tradeoffs that may disadvantage corals in other areas, then a more holistic view of heat resilience may be beneficial. In particular, overall resilience of a species to heat stress is likely to be the product of both resistance to heat and recovery from heat stress. Here, we investigate heat resistance and recovery among individual Acropora hyacinthus colonies in Palau. We divided corals into low, moderate, and high heat resistance categories based on the number of days (4-9) needed to reach significant pigmentation loss due to experimental heat stress. Afterward, we deployed corals back onto a reef in a common garden 6-month recovery experiment that monitored chlorophyll a, mortality, and skeletal growth. Heat resistance was negatively correlated with mortality during early recovery (0-1 month) but not late recovery (4-6 months), and chlorophyll a concentration recovered in heat-stressed corals by 1-month postbleaching. However, moderate-resistance corals had significantly greater skeletal growth than high-resistance corals by 4 months of recovery. High- and low-resistance corals on average did not exhibit skeletal growth within the observed recovery period. These data suggest complex tradeoffs may exist between coral heat resistance and recovery and highlight the importance of incorporating multiple aspects of resilience into future reef management programs.
Collapse
Affiliation(s)
- Nia S. Walker
- Department of BiologyHopkins Marine Station of Stanford UniversityPacific GroveCaliforniaUSA
- Hawaiʻi Institute of Marine BiologyUniversity of Hawai‘i at MānoaKāneʻoheHawaiiUSA
| | | | | | - Stephen R. Palumbi
- Department of BiologyHopkins Marine Station of Stanford UniversityPacific GroveCaliforniaUSA
| |
Collapse
|
2
|
Rinsky M, Weizman E, Ben-Asher HW, Eyal G, Zhu B, Levy O. Temporal gene expression patterns in the coral Euphyllia paradivisa reveal the complexity of biological clocks in the cnidarian-algal symbiosis. SCIENCE ADVANCES 2022; 8:eabo6467. [PMID: 36112690 PMCID: PMC9481131 DOI: 10.1126/sciadv.abo6467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/02/2022] [Indexed: 05/25/2023]
Abstract
Studying chronobiology in reef-building corals is challenging due to the tightly coupled symbiosis with their photosynthetic algae, Symbiodiniaceae. Although symbiosis requires metabolic synchronization and coordination of cellular processes in the holobiont, the cross-talk between the host and symbiont's clocks is still puzzling. Here, we use the mesophotic coral Euphyllia paradivisa to examine temporal gene expression patterns in symbiotic and aposymbiotic morphs exposed to natural light/dark cycles and constant darkness. Our comparative transcriptomic analyses revealed circadian and circatidal cycles of gene expression with a predominant diel pattern in both coral morphs. We found a substantial number of transcripts consistently rhythmic under both light conditions, including genes likely involved in the cnidarians' circadian clock, thus indicating that an endogenous clock, which can oscillate independently from the Symbiodiniaceae clock, exists in E. paradivisa. The analysis further manifests the remarkable impacts of symbiosis on transcriptional rhythms and implies that the algae's presence influences the host's biorhythm.
Collapse
Affiliation(s)
- Mieka Rinsky
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eviatar Weizman
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Hiba Waldman Ben-Asher
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Gal Eyal
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, University of Queensland St. Lucia, Queensland 4072, Australia
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| |
Collapse
|
3
|
Schomaker RA, Dudycha JL. De novo transcriptome assembly of the green alga Ankistrodesmus falcatus. PLoS One 2021; 16:e0251668. [PMID: 33989339 PMCID: PMC8121315 DOI: 10.1371/journal.pone.0251668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/30/2021] [Indexed: 01/11/2023] Open
Abstract
Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. BUSCO analysis recovered 83.3% of total chlorophyte BUSCOs and 82.5% of the eukaryotic BUSCOs. A portion (7.9%) of these supposedly single-copy genes were found to have transcriptionally active, distinct duplicates. We annotated the assembly using the dammit annotation pipeline, resulting in putative functional annotation for 68.89% of the assembly. Using available rbcL sequences from 16 strains (10 species) of Ankistrodesmus, we constructed a neighbor-joining phylogeny to illustrate genetic distances of our A. falcatus strain to other members of the genus. This assembly will be valuable for researchers seeking to identify Ankistrodesmus sequences in metatranscriptomic and metagenomic field studies and in experiments where separating expression responses of zooplankton and their algal food sources through bioinformatics is important.
Collapse
Affiliation(s)
- Rachel A Schomaker
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States of America
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States of America
| |
Collapse
|
4
|
Onyango CA, Glassom D, MacDonald A. De novo assembly of the transcriptome of scleractinian coral, Anomastraea irregularis and analyses of its response to thermal stress. Mol Biol Rep 2021; 48:2083-2092. [PMID: 33660094 DOI: 10.1007/s11033-021-06184-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
Rising seawater temperatures cause coral bleaching. The molecular responses of the coral holobiont under stress conditions, determine the success of the symbiosis. Anomastraea irregularis is a hard coral commonly found in the harsh intertidal zones of the south coast of KwaZulu-Natal (KZN), South Africa, where it thrives at the very margins of hard coral distribution in the Western Indian Ocean. To identify the possible molecular and cellular mechanisms underlying its resilience to heat stress, experimental and control nubbins were exposed to temperatures of 29 and 19 °C respectively for 24 h. The transcriptome was assembled de novo from 42.8 million quality controlled 63 bp paired-end short sequence reads obtained via RNA sequencing (RNA-seq). The assembly yielded 333,057 contigs (> 500 bp = 55,626, Largest = 6341 bp N50 = 747 bp). 1362 (1.23%) of the transcripts were significantly differentially expressed between heat stressed and control samples. Log fold change magnitudes among individual genes ranged from - 4.6 to 7.2. Overall, the heat stress response in the A. irregularis constituted a protective response involving up regulation of apoptosis and SUMOylation. Gene ontology (GO) analyses revealed that heat stress in the coral affected the metabolism, protein synthesis, photosynthesis, transport and cytoskeleton. This is the first study to produce a reference transcriptome of this coral species and analyze its response to heat stress. The assembled transcriptome also presents a valuable resource for further transcriptomic and genomic studies.
Collapse
Affiliation(s)
- Christine A Onyango
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa. .,School of Natural Sciences, Masinde Muliro University of Science and Technology, Kakamega, 50100, Kenya.
| | - David Glassom
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Angus MacDonald
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| |
Collapse
|
5
|
Cleves PA, Krediet CJ, Lehnert EM, Onishi M, Pringle JR. Insights into coral bleaching under heat stress from analysis of gene expression in a sea anemone model system. Proc Natl Acad Sci U S A 2020; 117:28906-28917. [PMID: 33168733 PMCID: PMC7682557 DOI: 10.1073/pnas.2015737117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Loss of endosymbiotic algae ("bleaching") under heat stress has become a major problem for reef-building corals worldwide. To identify genes that might be involved in triggering or executing bleaching, or in protecting corals from it, we used RNAseq to analyze gene-expression changes during heat stress in a coral relative, the sea anemone Aiptasia. We identified >500 genes that showed rapid and extensive up-regulation upon temperature increase. These genes fell into two clusters. In both clusters, most genes showed similar expression patterns in symbiotic and aposymbiotic anemones, suggesting that this early stress response is largely independent of the symbiosis. Cluster I was highly enriched for genes involved in innate immunity and apoptosis, and most transcript levels returned to baseline many hours before bleaching was first detected, raising doubts about their possible roles in this process. Cluster II was highly enriched for genes involved in protein folding, and most transcript levels returned more slowly to baseline, so that roles in either promoting or preventing bleaching seem plausible. Many of the genes in clusters I and II appear to be targets of the transcription factors NFκB and HSF1, respectively. We also examined the behavior of 337 genes whose much higher levels of expression in symbiotic than aposymbiotic anemones in the absence of stress suggest that they are important for the symbiosis. Unexpectedly, in many cases, these expression levels declined precipitously long before bleaching itself was evident, suggesting that loss of expression of symbiosis-supporting genes may be involved in triggering bleaching.
Collapse
Affiliation(s)
- Phillip A Cleves
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Cory J Krediet
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Department of Marine Science, Eckerd College, St. Petersburg, FL 33711
| | - Erik M Lehnert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Masayuki Onishi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - John R Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305;
| |
Collapse
|
6
|
Giovannetti L, Viti C. Editorial for the Special Issue: Macro and Microorganism Interactions. Microorganisms 2020; 8:E1751. [PMID: 33171804 PMCID: PMC7695024 DOI: 10.3390/microorganisms8111751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/04/2020] [Indexed: 11/24/2022] Open
Abstract
The knowledge of symbiotic, parasitic, and commensal interactions between macro and microorganisms is fundamental to explaining their coexistence, ecology, and productivity [...].
Collapse
Affiliation(s)
| | - Carlo Viti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, I-50144 Firenze, Italy;
| |
Collapse
|
7
|
van Oppen MJH, Medina M. Coral evolutionary responses to microbial symbioses. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190591. [PMID: 32772672 PMCID: PMC7435167 DOI: 10.1098/rstb.2019.0591] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 12/19/2022] Open
Abstract
This review explores how microbial symbioses may have influenced and continue to influence the evolution of reef-building corals (Cnidaria; Scleractinia). The coral holobiont comprises a diverse microbiome including dinoflagellate algae (Dinophyceae; Symbiodiniaceae), bacteria, archaea, fungi and viruses, but here we focus on the Symbiodiniaceae as knowledge of the impact of other microbial symbionts on coral evolution is scant. Symbiosis with Symbiodiniaceae has extended the coral's metabolic capacity through metabolic handoffs and horizontal gene transfer (HGT) and has contributed to the ecological success of these iconic organisms. It necessitated the prior existence or the evolution of a series of adaptations of the host to attract and select the right symbionts, to provide them with a suitable environment and to remove disfunctional symbionts. Signatures of microbial symbiosis in the coral genome include HGT from Symbiodiniaceae and bacteria, gene family expansions, and a broad repertoire of oxidative stress response and innate immunity genes. Symbiosis with Symbiodiniaceae has permitted corals to occupy oligotrophic waters as the algae provide most corals with the majority of their nutrition. However, the coral-Symbiodiniaceae symbiosis is sensitive to climate warming, which disrupts this intimate relationship, causing coral bleaching, mortality and a worldwide decline of coral reefs. This article is part of the theme issue 'The role of the microbiome in host evolution'.
Collapse
Affiliation(s)
- Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, 3010 Victoria, Australia
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, 4810 Queensland, Australia
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, 208 Mueller Lab, University Park, PA 16802, USA
| |
Collapse
|
8
|
Studivan MS, Voss JD. Transcriptomic plasticity of mesophotic corals among natural populations and transplants of
Montastraea cavernosa
in the Gulf of Mexico and Belize. Mol Ecol 2020; 29:2399-2415. [DOI: 10.1111/mec.15495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/14/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Michael S. Studivan
- Harbor Branch Oceanographic Institute Florida Atlantic University Fort Pierce FL USA
- Cooperative Institute for Marine and Atmospheric Studies University of Miami Rosenstiel School of Marine and Atmospheric Sciences Miami FL USA
| | - Joshua D. Voss
- Harbor Branch Oceanographic Institute Florida Atlantic University Fort Pierce FL USA
| |
Collapse
|
9
|
Meron D, Maor-Landaw K, Eyal G, Elifantz H, Banin E, Loya Y, Levy O. The Complexity of the Holobiont in the Red Sea Coral Euphyllia paradivisa under Heat Stress. Microorganisms 2020; 8:E372. [PMID: 32155796 PMCID: PMC7143197 DOI: 10.3390/microorganisms8030372] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 11/16/2022] Open
Abstract
The recognition of the microbiota complexity and their role in the evolution of their host is leading to the popularization of the holobiont concept. However, the coral holobiont (host and its microbiota) is still enigmatic and unclear. Here, we explore the complex relations between different holobiont members of a mesophotic coral Euphyllia paradivisa. We subjected two lines of the coral-with photosymbionts, and without photosymbionts (apo-symbiotic)-to increasing temperatures and to antibiotics. The different symbiotic states were characterized using transcriptomics, microbiology and physiology techniques. The bacterial community's composition is dominated by bacteroidetes, alphaproteobacteria, and gammaproteobacteria, but is dependent upon the symbiont state, colony, temperature treatment, and antibiotic exposure. Overall, the most important parameter determining the response was whether the coral was a symbiont/apo-symbiotic, while the colony and bacterial composition were secondary factors. Enrichment Gene Ontology analysis of coral host's differentially expressed genes demonstrated the cellular differences between symbiotic and apo-symbiotic samples. Our results demonstrate the significance of each component of the holobiont consortium and imply a coherent link between them, which dramatically impacts the molecular and cellular processes of the coral host, which possibly affect its fitness, particularly under environmental stress.
Collapse
Affiliation(s)
- Dalit Meron
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
- Morris Kahn Marine Research Station, University of Haifa, Haifa 3498838, Israel
| | - Keren Maor-Landaw
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Gal Eyal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland St. Lucia, Qld 4072, Australia
| | - Hila Elifantz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
| | - Ehud Banin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
- The Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Yossi Loya
- Department of Zoology, Tel-Aviv University, Tel Aviv 6997801, Israel;
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (D.M.); (K.M.-L.); (G.E.); (H.E.); (E.B.)
| |
Collapse
|