1
|
Lima LFO, Alker AT, Morris MM, Edwards RA, de Putron SJ, Dinsdale EA. Pre-Bleaching Coral Microbiome Is Enriched in Beneficial Taxa and Functions. Microorganisms 2024; 12:1005. [PMID: 38792833 PMCID: PMC11123844 DOI: 10.3390/microorganisms12051005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Coral reef health is tightly connected to the coral holobiont, which is the association between the coral animal and a diverse microbiome functioning as a unit. The coral holobiont depends on key services such as nitrogen and sulfur cycling mediated by the associated bacteria. However, these microbial services may be impaired in response to environmental changes, such as thermal stress. A perturbed microbiome may lead to coral bleaching and disease outbreaks, which have caused an unprecedented loss in coral cover worldwide, particularly correlated to a warming ocean. The response mechanisms of the coral holobiont under high temperatures are not completely understood, but the associated microbial community is a potential source of acquired heat-tolerance. Here we investigate the effects of increased temperature on the taxonomic and functional profiles of coral surface mucous layer (SML) microbiomes in relationship to coral-algal physiology. We used shotgun metagenomics in an experimental setting to understand the dynamics of microbial taxa and genes in the SML microbiome of the coral Pseudodiploria strigosa under heat treatment. The metagenomes of corals exposed to heat showed high similarity at the level of bacterial genera and functional genes related to nitrogen and sulfur metabolism and stress response. The coral SML microbiome responded to heat with an increase in the relative abundance of taxa with probiotic potential, and functional genes for nitrogen and sulfur acquisition. Coral-algal physiology significantly explained the variation in the microbiome at taxonomic and functional levels. These consistent and specific microbial taxa and gene functions that significantly increased in proportional abundance in corals exposed to heat are potentially beneficial to coral health and thermal resistance.
Collapse
Affiliation(s)
- Laís F. O. Lima
- Marine Biology, Scripps Institute of Oceanography, University of California San Diego, La Jolla, CA 92093, USA;
- San Diego State University, San Diego, CA 92182, USA
| | - Amanda T. Alker
- Innovative Genomics Institute, University of California, Berkeley, SA 5045, USA;
| | - Megan M. Morris
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA;
| | - Robert A. Edwards
- Flinders Accelerator Microbiome Exploration, Flinders University, Bedford Park, SA 5042, Australia;
| | | | - Elizabeth A. Dinsdale
- Flinders Accelerator Microbiome Exploration, Flinders University, Bedford Park, SA 5042, Australia;
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Xu M, Cheng K, Xiao B, Tong M, Cai Z, Jong MC, Chen G, Zhou J. Bacterial Communities Vary from Different Scleractinian Coral Species and between Bleached and Non-Bleached Corals. Microbiol Spectr 2023; 11:e0491022. [PMID: 37191552 PMCID: PMC10269541 DOI: 10.1128/spectrum.04910-22] [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: 11/30/2022] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Bleaching is one of the most relevant factors implicated in the integrity of coral reef ecosystems, with the increasing frequency and intensity of damaging events representing a serious threat to reef biodiversity. Here, we analyzed changes in coral-associated bacteria from three types of non-bleached and bleached scleractinian corals (Acropora digitifera, Galaxea fascicularis, and Porites pukoensis) in Hainan Luhuitou peninsula coastal areas. The community structure of symbiotic bacteria differed significantly among the three apparently healthy corals. The bleached corals had higher bacterial alpha diversity and some specific bacteria genera, including Ruegeria, Methyloceanibacter, Filomicrobium, Halioglobus, Rubripirellula, Rhodopirellula, Silicimonas, Blastopirellula, Sva0996 marine group, Woeseia, and unclassified_c_Gammaproteobacteria, were consistently increased in bleached groups. Network analysis revealed significantly different degrees of modularity between bleached and non-bleached groups at the bacterial genus level, and a higher proportion of links was dominated by positive co-occurrences. Functional prediction analysis illustrated that coral-associated bacteria remained relatively consistent in the bleached and non-bleached groups. Structure equation modeling revealed that the bacterial community diversity and function were directly influenced by host and environment factors. These findings suggested that coral-associated bacterial responses to bleaching occur in a host-dependent manner, informing novel strategies for restoring coral and aiding adaption to bleaching stress. IMPORTANCE Accumulating evidence indicates that coral-associated bacteria play an important role in the health of holobionts. However, the variability of the symbiotic bacterial community structure among coral species with different coral health statuses remains largely unknown. Here, we investigated three apparent non-bleached (healthy) and bleached coral species (sampled in situ), involving related symbiotic bacterial profiles, including composition, alpha diversity, network relationship, and potential function. Structural equation modeling analysis was used to analyze the relationship between coral status and abiotic and biotic factors. The bacterial community structure of different groups was shown to exhibit host-specific traits. Both host and environmental impacts had primary effects on coral-associated microbial communities. Future studies are needed to identify the mechanisms that mediate divergent microbial consortia.
Collapse
Affiliation(s)
- Meiting Xu
- School of Environment, Harbin Institute of Technology, Harbin, People’s Republic of China
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, Shandong Province, People’s Republic of China
| | - Keke Cheng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, People’s Republic of China
| | - Baohua Xiao
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, People’s Republic of China
| | - Mengmeng Tong
- Ocean College, Zhejiang University, Zhoushan, People’s Republic of China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, People’s Republic of China
| | - Mui-Choo Jong
- Institute of Environment and Ecology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, People’s Republic of China
| | - Guofu Chen
- School of Environment, Harbin Institute of Technology, Harbin, People’s Republic of China
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, Shandong Province, People’s Republic of China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, People’s Republic of China
| |
Collapse
|
4
|
Zhu W, Liu X, Zhang J, Zhao H, Li Z, Wang H, Chen R, Wang A, Li X. Response of coral bacterial composition and function to water quality variations under anthropogenic influence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 884:163837. [PMID: 37137368 DOI: 10.1016/j.scitotenv.2023.163837] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023]
Abstract
Microbial communities play key roles in the adaptation of corals living in adverse environments, as the microbiome flexibility can enhance environmental plasticity of coral holobiont. However, the ecological association of coral microbiome and related function to locally deteriorating water quality remains underexplored. In this work, we used 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) to investigate the seasonal changes of bacterial communities, particularly their functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycle, of the scleractinian coral Galaxea fascicularis from nearshore reefs exposed anthropogenic influence. We used nutrient concentrations as the indicator of anthropogenic activities in coastal reefs, and found a higher nutrient pressure in spring than summer. The bacterial diversity, community structure and dominant bacteria of coral shifted significantly due to seasonal variations dominated by nutrient concentrations. Additionally, the network structure and nutrient cycling gene profiles in summer under low nutrient stress was distinct from that under poor environmental conditions in spring, with lower network complexity and abundance of CNPS cycling genes in summer compared with spring. We further identified significant correlations between microbial community (taxonomic composition and co-occurrence network) and geochemical functions (abundance of multiple functional genes and functional community). Nutrient enrichment was proved to be the most important environmental fluctuation in controlling the diversity, community structure, interactional network and functional genes of the coral microbiome. These results highlight that seasonal shifts in coral-associated bacteria due to anthropogenic activities alter the functional potentials, and provide novel insight about the mechanisms of coral adaptation to locally deteriorating environments.
Collapse
Affiliation(s)
- Wentao Zhu
- College of Ecology and Environment, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiangbo Liu
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Junling Zhang
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - He Zhao
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Zhuoran Li
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Hao Wang
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Rouwen Chen
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Aimin Wang
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiubao Li
- College of Marine Science, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China.
| |
Collapse
|