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Yang Q, Yang B, Yang B, Zhang W, Tang X, Sun H, Zhang Y, Li J, Ling J, Dong J. Alleviating Coral Thermal Stress via Inoculation with Quorum Quenching Bacteria. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10344-6. [PMID: 39030411 DOI: 10.1007/s10126-024-10344-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 07/05/2024] [Indexed: 07/21/2024]
Abstract
In the background of global warming, coral bleaching induced by elevated seawater temperature is the primary cause of coral reef degradation. Coral microbiome engineering using the beneficial microorganisms for corals (BMCs) has become a hot spot in the field of coral reef conservation and restoration. Investigating the potential of alleviating thermal stress by quorum quenching (QQ) bacteria may provide more tools for coral microbial engineering remediation. In this study, QQ bacteria strain Pseudoalteromonas piscicida SCSIO 43740 was screened among 75 coral-derived bacterial strains, and its quorum sensing inhibitor (QSI) compound was isolated and identified as 2,4-di-tert-butylphenol (2,4-DTBP). Then, the thermal stress alleviating potential of QQ bacteria on coral Pocillopora damicornis was tested by a 30-day controlled experiment with three different treatments: control group (Con: 29 °C), high temperature group (HT: 31 °C), and the group of high temperature with QQ bacteria inoculation (HTQQ: 31 °C + QQ bacteria). The results showed that QQ bacteria SCSIO 43740 inoculation can significantly mitigate the loss of symbiotic algae and impairment of photosynthesis efficiency of coral P. damicornis under thermal stress. Significant difference in superoxide dismutase (SOD) and catalase (CAT) enzyme activities between HT and HTQQ was not observed. In addition, QQ bacteria inoculation suppressed the coral microbial community beta-dispersion and improved the stability of microbial co-occurrence network under thermal stress. It was suggested that QQ bacteria inoculation can alleviate coral thermal stress via reshaping microbial interaction and maintain community stability of coral microbiome. This study provided new evidence for the probiotic function of QQ bacteria in corals, which shedding light on the development of new microbiological tools for coral reef conservation.
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Affiliation(s)
- Qingsong Yang
- CAS 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
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, People's Republic of China
- Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China, Sea Institute of Oceanology , Chinese Academy of Sciences, Shantou, 515041, People's Republic of China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 511458, China
| | - Bing Yang
- CAS 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
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, People's Republic of China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 511458, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bin Yang
- CAS 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
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, People's Republic of China
- Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China, Sea Institute of Oceanology , Chinese Academy of Sciences, Shantou, 515041, People's Republic of China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 511458, China
| | - Wenqian Zhang
- CAS 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
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, People's Republic of China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 511458, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyu Tang
- CAS 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
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, People's Republic of China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 511458, China
| | - Huiming Sun
- CAS 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
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, People's Republic of China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 511458, China
| | - Yanying Zhang
- University of Chinese Academy of Sciences, Beijing, China
- Yantai University, Yantai, 264003, China
| | - Jie Li
- CAS 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
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, People's Republic of China
- Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China, Sea Institute of Oceanology , Chinese Academy of Sciences, Shantou, 515041, People's Republic of China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 511458, China
| | - Juan Ling
- CAS 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.
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, People's Republic of China.
- Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China, Sea Institute of Oceanology , Chinese Academy of Sciences, Shantou, 515041, People's Republic of China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 511458, China.
| | - Junde Dong
- CAS 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.
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, People's Republic of China.
- Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China, Sea Institute of Oceanology , Chinese Academy of Sciences, Shantou, 515041, People's Republic of China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 511458, China.
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Tomaszewski T, Ali MA, Caetano-Anollés K, Caetano-Anollés G. Seasonal effects decouple SARS-CoV-2 haplotypes worldwide. F1000Res 2023; 12:267. [PMID: 37069849 PMCID: PMC10105261 DOI: 10.12688/f1000research.131522.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Background: Variants of concern (VOCs) have been replacing each other during the still rampant COVID-19 pandemic. As a result, SARS-CoV-2 populations have evolved increasingly intricate constellations of mutations that often enhance transmissibility, disease severity, and other epidemiological characteristics. The origin and evolution of these constellations remain puzzling. Methods: Here we study the evolution of VOCs at the proteome level by analyzing about 12 million genomic sequences retrieved from GISAID on July 23, 2022. A total 183,276 mutations were identified and filtered with a relevancy heuristic. The prevalence of haplotypes and free-standing mutations was then tracked monthly in various latitude corridors of the world. Results: A chronology of 22 haplotypes defined three phases driven by protein flexibility-rigidity, environmental sensing, and immune escape. A network of haplotypes illustrated the recruitment and coalescence of mutations into major VOC constellations and seasonal effects of decoupling and loss. Protein interaction networks mediated by haplotypes predicted communications impacting the structure and function of proteins, showing the increasingly central role of molecular interactions involving the spike (S), nucleocapsid (N), and membrane (M) proteins. Haplotype markers either affected fusogenic regions while spreading along the sequence of the S-protein or clustered around binding domains. Modeling of protein structure with AlphaFold2 showed that VOC Omicron and one of its haplotypes were major contributors to the distortion of the M-protein endodomain, which behaves as a receptor of other structural proteins during virion assembly. Remarkably, VOC constellations acted cooperatively to balance the more extreme effects of individual haplotypes. Conclusions: Our study uncovers seasonal patterns of emergence and diversification occurring amid a highly dynamic evolutionary landscape of bursts and waves. The mapping of genetically-linked mutations to structures that sense environmental change with powerful ab initio modeling tools demonstrates the potential of deep-learning for COVID-19 predictive intelligence and therapeutic intervention.
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Affiliation(s)
- Tre Tomaszewski
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Muhammad Asif Ali
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | | | - Gustavo Caetano-Anollés
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- C. R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
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Tomaszewski T, Gurtler V, Caetano-Anollés K, Caetano-Anollés G. The emergence of SARS-CoV-2 variants of concern in Australia by haplotype coalescence reveals a continental link to COVID-19 seasonality. METHODS IN MICROBIOLOGY 2022; 50:233-268. [PMID: 38013929 PMCID: PMC9110064 DOI: 10.1016/bs.mim.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
SARS-CoV-2 continues to evolve, even after implementation of public-wide vaccination, as can be observed by an increasing number of mutations over time. Compared to responses by the United States and European countries, the disease mitigation strategies employed by the Australian government have been swift and effective. This provides a unique opportunity to study the emergence of variants of concern (VOCs) at many latitude levels in a country that has been able to control infection for the majority of the pandemic. In the present study, we explored the occurrence and accumulation of major mutations typical of VOCs in different regions of Australia and the effects that latitude has on the establishment of VOC-induced disease. We also studied the constellation of mutations characteristic of VOCs to determine if the mutation sets acted as haplotypes. Our goal was to explore processes behind the emergence of VOCs as the viral disease progresses towards becoming endemic. Most reported COVID-19 cases were in largest cities located within a -30°S to - 50°S latitude corridor previously identified to be associated with seasonal behavior. Accumulation plots of individual amino acid variants of major VOCs showed that the first major haplotypes reported worldwide were also present in Australia. A classification of accumulation plots revealed the existence of 18 additional haplotypes associated with VOCs alpha, delta and omicron. Core mutant constellations for these VOCs and curve overlaps for variants in each set of haplotypes demonstrated significant decoupling patterns, suggesting processes of emergence. Finally, construction of a "haplotype network" that describes the viral population landscape of Australia throughout the COVID-19 pandemic revealed significant and unanticipated seasonal patterns of emergence and diversification. These results provide a unique window into our evolutionary understanding of a human pathogen of great significance. They may guide future research into mitigation and prediction strategies for future VOCs.
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Affiliation(s)
- Tre Tomaszewski
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | | | | | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
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Tang J, Cai W, Yan Z, Zhang K, Zhou Z, Zhao J, Lin S. Interactive effects of acidification and copper exposure on the reproduction and metabolism of coral endosymbiont Cladocopium goreaui. MARINE POLLUTION BULLETIN 2022; 177:113508. [PMID: 35259567 DOI: 10.1016/j.marpolbul.2022.113508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/13/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Ocean acidification resulting from increased CO2 and pollution from land-sourced toxicants such as copper have been linked to coral cover declines in coastal reef ecosystems. The impacts of ocean acidification and copper pollution on corals have been intensively investigated, whereas research on their effects on coral endosymbiont Symbiodiniaceae is limited. In this study, reproduction, photosynthetic parameters, nutrient accumulation and metabolome of Symbiodiniaceae Cladocopium goreaui were investigated after a weeklong treatment with acute CO2-induced acidification and copper ion. Acidification promoted algal reproduction through increased nutrients assimilation, upregulated citrate cycle and biomolecular biosynthesis pathway, while copper exposure repressed algal reproduction through toxic effects. The combined acidification and copper exposure caused the same decline in algal reproduction as copper exposure alone, but the upregulation of pentose phosphate pathway and the downregulation of aromatic amino acid biosynthesis. These results suggest that copper pollution could override the positive effects of acidification on the symbiodiniacean reproduction.
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Affiliation(s)
- Jia Tang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
| | - Wenqi Cai
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan University, Haikou, Hainan, China
| | - Zhicong Yan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan University, Haikou, Hainan, China
| | - Kaidian Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan University, Haikou, Hainan, China
| | - Zhi Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan University, Haikou, Hainan, China.
| | - Jianmin Zhao
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China.
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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Dimos B, Emery M, Beavers K, MacKnight N, Brandt M, Demuth J, Mydlarz L. Adaptive Variation in Homolog Number Within Transcript Families Promotes Expression Divergence in Reef-Building Coral. Mol Ecol 2022; 31:2594-2610. [PMID: 35229964 DOI: 10.1111/mec.16414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 02/10/2022] [Accepted: 02/22/2022] [Indexed: 11/30/2022]
Abstract
Gene expression, especially in multi-species experiments, is used to gain insight into the genetic basis of how organisms adapt and respond to changing environments. However, evolutionary processes which can influence gene expression patterns between species such as the presence of paralogs which arise from gene duplication events are rarely accounted for. Paralogous transcripts can alter the transcriptional output of a gene and thus exclusion of these transcripts can obscure important biological differences between species. To address this issue, we investigated how differences in transcript family size is associated with divergent gene expression patterns in five species of Caribbean reef-building corals. We demonstrate that transcript families that are rapidly evolving in terms of size have increased levels of expression divergence. Additionally, these rapidly evolving transcript families are enriched for multiple biological processes, with genes involved in the coral innate immune system demonstrating pronounced variation in homolog number between species. Overall, this investigation demonstrates the importance of incorporating paralogous transcripts when comparing gene expression across species by influencing both transcriptional output and the number of transcripts within biological processes. As this investigation was based on transcriptome assemblies, additional insights into the relationship between gene duplications and expression patterns will likely emergence once more genome assemblies are available for study.
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Affiliation(s)
- Bradford Dimos
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Madison Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Kelsey Beavers
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Nicholas MacKnight
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Marilyn Brandt
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, US Virgin Islands, 00802, USA
| | - Jeffery Demuth
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Laura Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
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Caetano-Anollés K, Hernandez N, Mughal F, Tomaszewski T, Caetano-Anollés G. The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike. METHODS IN MICROBIOLOGY 2021; 50:27-81. [PMID: 38620818 PMCID: PMC8590929 DOI: 10.1016/bs.mim.2021.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Seasonal behaviour is an attribute of many viral diseases. Like other 'winter' RNA viruses, infections caused by the causative agent of COVID-19, SARS-CoV-2, appear to exhibit significant seasonal changes. Here we discuss the seasonal behaviour of COVID-19, emerging viral phenotypes, viral evolution, and how the mutational landscape of the virus affects the seasonal attributes of the disease. We propose that the multiple seasonal drivers behind infectious disease spread (and the spread of COVID-19 specifically) are in 'trade-off' relationships and can be better described within a framework of a 'triangle of viral persistence' modulated by the environment, physiology, and behaviour. This 'trade-off' exists as one trait cannot increase without a decrease in another. We also propose that molecular components of the virus can act as sensors of environment and physiology, and could represent molecular culprits of seasonality. We searched for flexible protein structures capable of being modulated by the environment and identified a galectin-like fold within the N-terminal domain of the spike protein of SARS-CoV-2 as a potential candidate. Tracking the prevalence of mutations in this structure resulted in the identification of a hemisphere-dependent seasonal pattern driven by mutational bursts. We propose that the galectin-like structure is a frequent target of mutations because it helps the virus evade or modulate the physiological responses of the host to further its spread and survival. The flexible regions of the N-terminal domain should now become a focus for mitigation through vaccines and therapeutics and for prediction and informed public health decision making.
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Affiliation(s)
| | - Nicolas Hernandez
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Tre Tomaszewski
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
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