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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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Darolt JC, Bento FDMM, Merlin BL, Peña L, Cônsoli FL, Wulff NA. The Genome of " Candidatus Liberibacter asiaticus" Is Highly Transcribed When Infecting the Gut of Diaphorina citri. Front Microbiol 2021; 12:687725. [PMID: 34322103 PMCID: PMC8312247 DOI: 10.3389/fmicb.2021.687725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/04/2021] [Indexed: 11/13/2022] Open
Abstract
The Asian citrus psyllid, Diaphorina citri, is the vector of the bacterium "Candidatus Liberibacter asiaticus" (Las), associated with the devastating, worldwide citrus disease huanglongbing. In order to explore the molecular interactions of this bacterium with D. citri during the vector acquisition process, cDNA libraries were sequenced on an Illumina platform, obtained from the gut of adult psyllids confined in healthy (H) and in Las-infected young shoots (Las) for different periods of times (I = 1/2 days, II = 3/4 days, and III = 5/6 days). In each sampling time, three biological replicates were collected, containing 100 guts each, totaling 18 libraries depleted in ribosomal RNA. Reads were quality-filtered and mapped against the Chinese JXGC Las strain and the Floridian strain UF506 for the analysis of the activity of Las genome and SC1, SC2, and type 3 (P-JXGC-3) prophages of the studied Las strain. Gene activity was considered only if reads of at least two replicates for each acquisition access period mapped against the selected genomes, which resulted in coverages of 44.4, 79.9, and 94.5% of the JXGC predicted coding sequences in Las I, Las II, and Las III, respectively. These genes indicate an active metabolism and increased expression according to the feeding time in the following functional categories: energy production, amino acid metabolism, signal translation, cell wall, and replication and repair of genetic material. Pilins were among the most highly expressed genes regardless of the acquisition time, while only a few genes from cluster I of flagella were not expressed. Furthermore, the prophage region had a greater coverage of reads for SC1 and P-JXGC-3 prophages and low coverage in SC2 and no indication of activity for the lysis cycle. This research presents the first descriptive analysis of Las transcriptome in the initial steps of the D. citri gut colonization, where 95% of Las genes were active.
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Affiliation(s)
- Josiane Cecília Darolt
- Instituto de Química, Universidade Estadual Paulista “Julio de Mesquita Filho” – UNESP, Araraquara, Brazil
- Departamento de Pesquisa & Desenvolvimento, Fundo de Defesa da Citricultura – Fundecitrus, Araraquara, Brazil
| | - Flavia de Moura Manoel Bento
- Laboratório de Interações em Insetos, Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil
| | - Bruna Laís Merlin
- Laboratório de Interações em Insetos, Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil
| | - Leandro Peña
- Departamento de Pesquisa & Desenvolvimento, Fundo de Defesa da Citricultura – Fundecitrus, Araraquara, Brazil
- Instituto de Biologia Molecular y Celular de Plantas – Consejo Superior de Investigaciones Científicas, Universidade Politécnica de Valencia, Valencia, Spain
| | - Fernando Luis Cônsoli
- Laboratório de Interações em Insetos, Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil
| | - Nelson Arno Wulff
- Instituto de Química, Universidade Estadual Paulista “Julio de Mesquita Filho” – UNESP, Araraquara, Brazil
- Departamento de Pesquisa & Desenvolvimento, Fundo de Defesa da Citricultura – Fundecitrus, Araraquara, Brazil
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Mohamed AR, Andrade N, Moya A, Chan CX, Negri AP, Bourne DG, Ying H, Ball EE, Miller DJ. Dual RNA-sequencing analyses of a coral and its native symbiont during the establishment of symbiosis. Mol Ecol 2020; 29:3921-3937. [PMID: 32853430 DOI: 10.1111/mec.15612] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022]
Abstract
Despite the ecological significance of the mutualistic relationship between Symbiodiniaceae and reef-building corals, the molecular interactions during establishment of this relationship are not well understood. This is particularly true of the transcriptional changes that occur in the symbiont. In the current study, a dual RNA-sequencing approach was used to better understand transcriptional changes on both sides of the coral-symbiont interaction during the colonization of Acropora tenuis by a compatible Symbiodiniaceae strain (Cladocopium goreaui; ITS2 type C1). Comparison of transcript levels of the in hospite symbiont 3, 12, 48 and 72 hr after exposure to those of the same strain in culture revealed that extensive and generalized down-regulation of symbiont gene expression occurred during the infection process. Included in this "symbiosis-derived transcriptional repression" were a range of stress response and immune-related genes. In contrast, a suite of symbiont genes implicated in metabolism was upregulated in the symbiotic state. The coral data support the hypothesis that immune-suppression and arrest of phagosome maturation play important roles during the establishment of compatible symbioses, and additionally imply the involvement of some SCRiP family members in the colonization process. Consistent with previous ecological studies, the transcriptomic data suggest that active translocation of metabolites to the host may begin early in the colonization process, and thus that the mutualistic relationship can be established at the larval stage. This dual RNA-sequencing study provides insights into the transcriptomic remodelling that occurs in C. goreaui during transition to a symbiotic lifestyle and the novel coral genes implicated in symbiosis.
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Affiliation(s)
- Amin R Mohamed
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Qld, Australia.,Zoology Department, Faculty of Science, Benha University, Benha, Egypt.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, AIMS@JCU, Australian Institute of Marine Science, James Cook University, Townsville, Qld, Australia
| | - Natalia Andrade
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
| | - Aurelie Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
| | - Andrew P Negri
- Australian Institute of Marine Science, Townsville, Qld, Australia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Qld, Australia.,Department of Marine Ecosystems and Impacts, James Cook University, Townsville, Qld, Australia
| | - Hua Ying
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia
| | - Eldon E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
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