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Williams A. Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont. FEMS Microbiol Ecol 2024; 100:fiae058. [PMID: 38653719 PMCID: PMC11067971 DOI: 10.1093/femsec/fiae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/25/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024] Open
Abstract
Since their radiation in the Middle Triassic period ∼240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.
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Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
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Carrasco Flores D, Hotter V, Vuong T, Hou Y, Bando Y, Scherlach K, Burgunter-Delamare B, Hermenau R, Komor AJ, Aiyar P, Rose M, Sasso S, Arndt HD, Hertweck C, Mittag M. A mutualistic bacterium rescues a green alga from an antagonist. Proc Natl Acad Sci U S A 2024; 121:e2401632121. [PMID: 38568970 PMCID: PMC11009677 DOI: 10.1073/pnas.2401632121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
Photosynthetic protists, known as microalgae, are key contributors to primary production on Earth. Since early in evolution, they coexist with bacteria in nature, and their mode of interaction shapes ecosystems. We have recently shown that the bacterium Pseudomonas protegens acts algicidal on the microalga Chlamydomonas reinhardtii. It secretes a cyclic lipopeptide and a polyyne that deflagellate, blind, and lyse the algae [P. Aiyar et al., Nat. Commun. 8, 1756 (2017) and V. Hotter et al., Proc. Natl. Acad. Sci. U.S.A. 118, e2107695118 (2021)]. Here, we report about the bacterium Mycetocola lacteus, which establishes a mutualistic relationship with C. reinhardtii and acts as a helper. While M. lacteus enhances algal growth, it receives methionine as needed organic sulfur and the vitamins B1, B3, and B5 from the algae. In tripartite cultures with the alga and the antagonistic bacterium P. protegens, M. lacteus aids the algae in surviving the bacterial attack. By combining synthetic natural product chemistry with high-resolution mass spectrometry and an algal Ca2+ reporter line, we found that M. lacteus rescues the alga from the antagonistic bacterium by cleaving the ester bond of the cyclic lipopeptide involved. The resulting linearized seco acid does not trigger a cytosolic Ca2+ homeostasis imbalance that leads to algal deflagellation. Thus, the algae remain motile, can swim away from the antagonistic bacteria and survive the attack. All three involved genera cooccur in nature. Remarkably, related species of Pseudomonas and Mycetocola also act antagonistically against C. reinhardtii or as helper bacteria in tripartite cultures.
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Affiliation(s)
- David Carrasco Flores
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Vivien Hotter
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Trang Vuong
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Yu Hou
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Yuko Bando
- Institute for Organic Chemistry and Macromolecular Chemistry, Organic Chemistry, Friedrich Schiller University Jena, Jena07743, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
| | - Bertille Burgunter-Delamare
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Ron Hermenau
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
| | - Anna J. Komor
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
| | - Prasad Aiyar
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
| | - Magdalena Rose
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
- Institute of Biology, Plant Physiology, Leipzig University, Leipzig04103, Germany
| | - Severin Sasso
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
- Institute of Biology, Plant Physiology, Leipzig University, Leipzig04103, Germany
| | - Hans-Dieter Arndt
- Institute for Organic Chemistry and Macromolecular Chemistry, Organic Chemistry, Friedrich Schiller University Jena, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knöll Institute), Jena07745, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena 07743, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena07743, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, General Botany, Friedrich Schiller University Jena, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena 07743, Germany
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Cheng K, Li X, Tong M, Jong MC, Cai Z, Zheng H, Xiao B, Zhou J. Integrated metagenomic and metaproteomic analyses reveal bacterial micro-ecological mechanisms in coral bleaching. mSystems 2023; 8:e0050523. [PMID: 37882797 PMCID: PMC10734480 DOI: 10.1128/msystems.00505-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Coral reefs worldwide are facing rapid decline due to coral bleaching. However, knowledge of the physiological characteristics and molecular mechanisms of coral symbionts respond to stress is scarce. Here, metagenomic and metaproteomic approaches were utilized to shed light on the changes in the composition and functions of coral symbiotic bacteria during coral bleaching. The results demonstrated that coral bleaching significantly affected the composition of symbionts, with bacterial communities dominating in bleached corals. Through differential analyses of gene and protein expression, it becomes evident that symbionts experience functional disturbances in response to heat stress. These disturbances result in abnormal energy metabolism, which could potentially compromise the health and resilience of the symbionts. Furthermore, our findings highlighted the highly diverse microbial communities of coral symbionts, with beneficial bacteria providing critical services to corals in stress responses and pathogenic bacteria driving coral bleaching. This study provides comprehensive insights into the complex response mechanisms of coral symbionts under heat stress from the micro-ecological perspective and offers fundamental data for future monitoring of coral health.
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Affiliation(s)
- Keke Cheng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
| | - Xinyang Li
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
| | - Mengmeng Tong
- Ocean College, Zhejiang University, Zhoushan, Zhejiang, China
| | - Mui-Choo Jong
- Institute of Environment and Ecology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
| | - Huina Zheng
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China
| | - Baohua Xiao
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, China
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Lin Z, Zheng X, Chen J. Deciphering pH-dependent microbial taxa and functional gene co-occurrence in the coral Galaxea fascicularis. MICROBIAL ECOLOGY 2023; 86:1856-1868. [PMID: 36719456 DOI: 10.1007/s00248-023-02183-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
How the coral microbiome responds to oceanic pH changes due to anthropogenic climate change, including ocean acidification and deliberate artificial alkalization, remains an open question. Here, we applied a 16S profile and GeoChip approach to microbial taxonomic and gene functional landscapes in the coral Galaxea fascicularis under three pH levels (7.85, 8.15, and 8.45) and tested the influence of pH changes on the cell growth of several coral-associated strains and bacterial populations. Statistical analysis of GeoChip-based data suggested that both ocean acidification and alkalization destabilized functional cores related to aromatic degradation, carbon degradation, carbon fixation, stress response, and antibiotic biosynthesis in the microbiome, which are related to holobiont carbon cycling and health. The taxonomic analysis revealed that bacterial species richness was not significantly different among the three pH treatments, but the community compositions were significantly distinct. Acute seawater alkalization leads to an increase in pathogens as well as a stronger taxonomic shift than acidification, which is worth considering when using artificial ocean alkalization to protect coral ecosystems from ocean acidification. In addition, our co-occurrence network analysis reflected microbial community and functional shifts in response to pH change cues, which will further help to understand the functional ecological role of the microbiome in coral resilience.
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Affiliation(s)
- Zhenyue Lin
- Fujian Provincial Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
- Technology Innovation Center for Monitoring and Restoration Engineering of Ecological Fragile Zone in Southeast China, Ministry of Natural Resources, Fuzhou, 350001, China.
| | - Xinqing Zheng
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, 356015, China
| | - Jianming Chen
- Fujian Provincial Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
- Technology Innovation Center for Monitoring and Restoration Engineering of Ecological Fragile Zone in Southeast China, Ministry of Natural Resources, Fuzhou, 350001, China.
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Lin W, He Y, Li R, Mu C, Wang C, Shi C, Ye Y. Adaptive changes of swimming crab (Portunus trituberculatus) associated bacteria helping host against dibutyl phthalate toxification. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 324:121328. [PMID: 36828355 DOI: 10.1016/j.envpol.2023.121328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/17/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
The pollution of dibutyl phthalate (DBP) in aquatic environments is becoming an extensive environmental problem and detrimental to aquatic animals. Here, we quantified the response pattern of the bacterial community and metabolites of swimming crab (Portunus trituberculatus) juveniles exposed to 0.2, 2, and 10 mg/L DBP using 16 S rRNA gene amplicon sequencing coupled with metabolomic technique. The results showed that DBP changed the bacterial community compositions in a concentration-dependent pattern and decreased the Shannon index at the second developmental stage of the swimming crabs. The Rhodobacteraceae taxa were specifically enriched by crabs when challenged by 2 and 10 mg/L DBP, with an increased in Shannon index and enhanced drift in its assembly. Moreover, DBP changed the metabolic profiling of the swimming crab, highlighted by increased levels of lactate, valine, methionine, lysine, and phenylalanine in the 10 mg/L DBP-exposed crabs. Rhodobacteraceae presented the most considerable contribution to the metabolic potentials in phthalate and benzoate degradation, lactate production, and amino acid biosynthesis. Overall, our results indicated an adaptive change of crab-associated bacteria helped the host resist DBP stress. The findings extend our insights into the relationship between the microbiota and its host metabolism under DBP stress and reveal the potential microbiota modalities for DBP detoxification.
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Affiliation(s)
- Weichuan Lin
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Yimin He
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Ronghua Li
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, China
| | - Changkao Mu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, China
| | - Chunlin Wang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, China
| | - Ce Shi
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, 315832, China; Key Laboratory of Green Mariculture (Co-construction By Ministry and Province), Ministry of Agriculture and Rural, China
| | - Yangfang Ye
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315832, China.
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Zhang T, Wang X, Qu Y, Zhang X, Zhang Q, Yang D, Wang Q, Dong Z, Zhao J. Intestinal microbiota perturbations in the gastropod Trochus niloticus concurrently exposed to ocean acidification and environmentally relevant concentrations of sulfamethoxazole. CHEMOSPHERE 2023; 311:137115. [PMID: 36356817 DOI: 10.1016/j.chemosphere.2022.137115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Ocean acidification (OA) and antibiotic pollution pose severe threats to the fitness of keystone species in marine ecosystems. However, the combined effects of OA and antibiotic pollution on the intestinal microbiota of marine organisms are still not well known. In this study, we exposed the herbivorous gastropod Trochus niloticus, a keystone species to maintains the stability of coral reef ecosystems, to acidic seawater (pH 7.6) and/or sulfamethoxazole (SMX, 100 ng/L, 1000 ng/L) for 28 days and determined their impacts on (1) the accumulation of SMX in the intestine of T. niloticus; (2) the characteristics of the intestinal microbiota in T. niloticus; (3) the relative abundances of sulfonamide resistance genes (i.e., sul1 and sul2) and intI1 in the intestinal microbiota of T. niloticus. Our results show that OA exposure leads to dramatic microbiota dysbiosis in the intestine of T. niloticus, including changes in bacterial community diversity and structure, decreased abundances of dominant species, existences of characteristic taxa, and altered functional predictions. In addition, SMX exposure at environmentally relevant concentrations had little effect on the intestinal microbiota of T. niloticus, whether in isolation or in combination with OA. However, after exposure to the higher SMX concentration (1000 ng/L), the accumulation of SMX in the intestine of T. niloticus could induce an increase in the copies of sul2 in the intestinal microbiota. These results suggest that the intestinal health of T. niloticus might be affected by OA and SMX, which might lead to fitness loss of the keystone species in coral reef ecosystems.
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Affiliation(s)
- Tianyu Zhang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264117, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xin Wang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264117, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yi Qu
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264117, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xiaoli Zhang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264117, PR China
| | - Qianqian Zhang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264117, PR China
| | - Dinglong Yang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264117, PR China
| | - Qing Wang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264117, PR China
| | - Zhijun Dong
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264117, PR China
| | - Jianmin Zhao
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China; Muping Coastal Environmental Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264117, PR China; Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264117, PR China.
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Global change differentially modulates Caribbean coral physiology. PLoS One 2022; 17:e0273897. [PMID: 36054126 PMCID: PMC9439252 DOI: 10.1371/journal.pone.0273897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/17/2022] [Indexed: 11/19/2022] Open
Abstract
Global change driven by anthropogenic carbon emissions is altering ecosystems at unprecedented rates, especially coral reefs, whose symbiosis with algal symbionts is particularly vulnerable to increasing ocean temperatures and altered carbonate chemistry. Here, we assess the physiological responses of three Caribbean coral (animal host + algal symbiont) species from an inshore and offshore reef environment after exposure to simulated ocean warming (28, 31°C), acidification (300–3290 μatm), and the combination of stressors for 93 days. We used multidimensional analyses to assess how a variety of coral physiological parameters respond to ocean acidification and warming. Our results demonstrate reductions in coral health in Siderastrea siderea and Porites astreoides in response to projected ocean acidification, while future warming elicited severe declines in Pseudodiploria strigosa. Offshore S. siderea fragments exhibited higher physiological plasticity than inshore counterparts, suggesting that this offshore population was more susceptible to changing conditions. There were no plasticity differences in P. strigosa and P. astreoides between natal reef environments, however, temperature evoked stronger responses in both species. Interestingly, while each species exhibited unique physiological responses to ocean acidification and warming, when data from all three species are modelled together, convergent stress responses to these conditions are observed, highlighting the overall sensitivities of tropical corals to these stressors. Our results demonstrate that while ocean warming is a severe acute stressor that will have dire consequences for coral reefs globally, chronic exposure to acidification may also impact coral physiology to a greater extent in some species than previously assumed. Further, our study identifies S. siderea and P. astreoides as potential ‘winners’ on future Caribbean coral reefs due to their resilience under projected global change stressors, while P. strigosa will likely be a ‘loser’ due to their sensitivity to thermal stress events. Together, these species-specific responses to global change we observe will likely manifest in altered Caribbean reef assemblages in the future.
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