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Ng MS, Soon N, Afiq-Rosli L, Kunning I, Mana RR, Chang Y, Wainwright BJ. Highly Diverse Symbiodiniaceae Types Hosted by Corals in a Global Hotspot of Marine Biodiversity. MICROBIAL ECOLOGY 2024; 87:92. [PMID: 38987492 PMCID: PMC11236936 DOI: 10.1007/s00248-024-02407-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024]
Abstract
Symbiotic dinoflagellates in the genus Symbiodiniaceae play vital roles in promoting resilience and increasing stress tolerance in their coral hosts. While much of the world's coral succumb to the stresses associated with increasingly severe and frequent thermal bleaching events, live coral cover in Papua New Guinea (PNG) remains some of the highest reported globally despite the historically warm waters surrounding the country. Yet, in spite of the high coral cover in PNG and the acknowledged roles Symbiodiniaceae play within their hosts, these communities have not been characterized in this global biodiversity hotspot. Using high-throughput sequencing of the ITS2 rDNA gene, we profiled the endosymbionts of four coral species, Diploastrea heliopora, Pachyseris speciosa, Pocillopora acuta, and Porites lutea, across six sites in PNG. Our findings reveal patterns of Cladocopium and Durusdinium dominance similar to other reefs in the Coral Triangle, albeit with much greater intra- and intergenomic variation. Host- and site-specific variations in Symbiodiniaceae type profiles were observed across collection sites, appearing to be driven by environmental conditions. Notably, the extensive intra- and intergenomic variation, coupled with many previously unreported sequences, highlight PNG as a potential hotspot of symbiont diversity. This work represents the first characterization of the coral-symbiont community structure in the PNG marine biodiversity hotspot, serving as a baseline for future studies.
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Affiliation(s)
- Ming Sheng Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Nathaniel Soon
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore
- Thrive Conservation, Jl. Subak Sari No. 13, Kuta Utara, Badung, Bali, 80361, Indonesia
| | - Lutfi Afiq-Rosli
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ismael Kunning
- School of Natural and Physical Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Ralph R Mana
- School of Natural and Physical Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Ying Chang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore
| | - Benjamin J Wainwright
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore.
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Gong S, Liang J, Li G, Xu L, Tan Y, Zheng X, Jin X, Yu K, Xia X. Linking coral fluorescence phenotypes to thermal bleaching in the reef-building Galaxea fascicularis from the northern South China Sea. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:155-167. [PMID: 38433965 PMCID: PMC10902222 DOI: 10.1007/s42995-023-00190-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/31/2023] [Indexed: 03/05/2024]
Abstract
Coral fluorescence phenotypes have been suggested as an adaptation to a broad range of environmental conditions, yet the mechanisms linking thermal bleaching tolerance in reef-building coral populations, associated with fluorescence phenotypes due to GFP-like proteins, remains unclear. In this study, the relationship between the thermal sensitivity and phenotypic plasticity of corals was investigated using two phenotypes of Galaxea fascicularis, green and brown. The results reveal that brown G. fascicularis was more susceptible to bleaching than green G. fascicularis when exposed to a higher growth temperature of 32 °C. Both phenotypes of G. fascicularis were associated with the thermotolerant Symbiodiniaceae symbiont, Durusdinium trenchii. However, the brown G. fascicularis showed a significant decrease in Symbiodiniaceae cell density and a significant increase in pathogenic bacteria abundance when the growth temperature was raised from 29 to 32 °C. The physiological traits and transcriptomic profiles of Symbiodiniaceae were not notably affected, but there were differences in the transcriptional levels of certain genes between the two phenotype hosts of G. fascicularis. Under heat stress of 32 °C, the gene encoding green fluorescent protein (GFP)-like and chromosome-associated proteins, as well as genes related to oxidative phosphorylation, cell growth and death showed lower transcriptional levels in the brown G. fascicularis compared to the green G. fascicularis. Overall, the results demonstrate that the green form of G. fascicularis is better able to tolerate ocean warming and defend against pathogenic bacteria, likely due to higher gene transcription levels and defense ability. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00190-1.
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Affiliation(s)
- Sanqiang Gong
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Jiayuan Liang
- Coral Reef Research Center of China, Guangxi University, Nanning, 53004 China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Lijia Xu
- South China Institute of Environmental Sciences, The Ministry of Ecology and Environment of PRC, Guangzhou, 510530 China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Xinqing Zheng
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
| | - Xuejie Jin
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi University, Nanning, 53004 China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
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Endosymbiotic Symbiodinium clades occurrence and influence on coral growth and resilience during stress. Symbiosis 2022. [DOI: 10.1007/s13199-022-00846-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Chang JJM, Ip YCA, Ng CSL, Huang D. Takeaways from Mobile DNA Barcoding with BentoLab and MinION. Genes (Basel) 2020; 11:E1121. [PMID: 32987804 PMCID: PMC7598690 DOI: 10.3390/genes11101121] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters' Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50-60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended.
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Affiliation(s)
- Jia Jin Marc Chang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
| | - Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
| | - Chin Soon Lionel Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
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Endosymbiont diversity and community structure in Porites lutea from Southeast Asia are driven by a suite of environmental variables. Symbiosis 2020. [DOI: 10.1007/s13199-020-00671-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractMany corals depend upon the highly specialised and intricate relationship they form with Symbiodiniaceae algal symbionts. Porites lutea is a massive reef-building coral found throughout Southeast Asia that hosts these endosymbionts obligately. Yet despite the prevalence and importance of P. lutea as one of the most dominant corals here, its associated Symbiodiniaceae communities have not been precisely characterised. In this study, we used high-throughput DNA amplicon sequencing of the nuclear internal transcribed spacer 2 (ITS2) to characterise the diversity, community structure and biogeographic distribution of Symbiodiniaceae in P. lutea throughout Singapore and Peninsular Malaysia. Consistent with previous studies, we found that Cladocopium was the most dominant genus among all samples, and Cladocopium C15 was the most dominant type (or subclade) with 100% occurrence in all samples from every study site. Results also revealed numerous Symbiodiniaceae types associated with P. lutea that were previously undetected in Southeast Asia. Endosymbiont diversity and community variation are driven by a combination of site-specific mean monthly cloud cover and variance in monthly sea surface temperature. This study contributes baseline data toward understanding differences in Symbiodiniaceae assemblages hosted by P. lutea, shedding light on how they might be indicative of particular environmental conditions and coral responses.
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