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Microbial indicators of environmental perturbations in coral reef ecosystems.
Microbiome. 2019 06 21; 7(1):94.M

Abstract

BACKGROUND

Coral reefs are facing unprecedented pressure on local and global scales. Sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. Although the fundamental contribution of microbes to the stability and functioning of coral reefs is widely recognised, it remains unclear how different reef microbiomes respond to environmental perturbations and whether microbiomes are sensitive enough to predict environmental anomalies that can lead to ecosystem stress. However, the lack of coral reef microbial baselines hinders our ability to study the link between shifts in microbiomes and ecosystem stress. In this study, we established a comprehensive microbial reference database for selected Great Barrier Reef sites to assess the diagnostic value of multiple free-living and host-associated reef microbiomes to infer the environmental state of coral reef ecosystems.

RESULTS

A comprehensive microbial reference database, originating from multiple coral reef microbiomes (i.e. seawater, sediment, corals, sponges and macroalgae), was generated by 16S rRNA gene sequencing for 381 samples collected over the course of 16 months. By coupling this database to environmental parameters, we showed that the seawater microbiome has the greatest diagnostic value to infer shifts in the surrounding reef environment. In fact, 56% of the observed compositional variation in the microbiome was explained by environmental parameters, and temporal successions in the seawater microbiome were characterised by uniform community assembly patterns. Host-associated microbiomes, in contrast, were five-times less responsive to the environment and their community assembly patterns were generally less uniform. By applying a suite of indicator value and machine learning approaches, we further showed that seawater microbial community data provide an accurate prediction of temperature and eutrophication state (i.e. chlorophyll concentration and turbidity).

CONCLUSION

Our results reveal that free-living microbial communities have a high potential to infer environmental parameters due to their environmental sensitivity and predictability. This highlights the diagnostic value of microorganisms and illustrates how long-term coral reef monitoring initiatives could be enhanced by incorporating assessments of microbial communities in seawater. We therefore recommend timely integration of microbial sampling into current coral reef monitoring initiatives.

Authors+Show Affiliations

Australian Institute of Marine Science, Townsville, QLD, Australia. b.glasl@aims.gov.au. College of Science and Engineering, James Cook University, Townsville, QLD, Australia. b.glasl@aims.gov.au. AIMS@JCU, Townsville, QLD, Australia. b.glasl@aims.gov.au.Australian Institute of Marine Science, Townsville, QLD, Australia. College of Science and Engineering, James Cook University, Townsville, QLD, Australia. AIMS@JCU, Townsville, QLD, Australia.Centre of Marine Science, University of Algarve, Faro, Portugal.Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia.Australian Institute of Marine Science, Townsville, QLD, Australia.Australian Institute of Marine Science, Townsville, QLD, Australia. AIMS@JCU, Townsville, QLD, Australia. Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

31227022

Citation

Glasl, Bettina, et al. "Microbial Indicators of Environmental Perturbations in Coral Reef Ecosystems." Microbiome, vol. 7, no. 1, 2019, p. 94.
Glasl B, Bourne DG, Frade PR, et al. Microbial indicators of environmental perturbations in coral reef ecosystems. Microbiome. 2019;7(1):94.
Glasl, B., Bourne, D. G., Frade, P. R., Thomas, T., Schaffelke, B., & Webster, N. S. (2019). Microbial indicators of environmental perturbations in coral reef ecosystems. Microbiome, 7(1), 94. https://doi.org/10.1186/s40168-019-0705-7
Glasl B, et al. Microbial Indicators of Environmental Perturbations in Coral Reef Ecosystems. Microbiome. 2019 06 21;7(1):94. PubMed PMID: 31227022.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Microbial indicators of environmental perturbations in coral reef ecosystems. AU - Glasl,Bettina, AU - Bourne,David G, AU - Frade,Pedro R, AU - Thomas,Torsten, AU - Schaffelke,Britta, AU - Webster,Nicole S, Y1 - 2019/06/21/ PY - 2019/01/30/received PY - 2019/05/28/accepted PY - 2019/6/23/entrez PY - 2019/6/23/pubmed PY - 2020/5/8/medline KW - Coral reef KW - Coral reef microbiomes KW - Machine learning KW - Microbial baselines KW - Microbial indicators KW - Microbial monitoring SP - 94 EP - 94 JF - Microbiome JO - Microbiome VL - 7 IS - 1 N2 - BACKGROUND: Coral reefs are facing unprecedented pressure on local and global scales. Sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. Although the fundamental contribution of microbes to the stability and functioning of coral reefs is widely recognised, it remains unclear how different reef microbiomes respond to environmental perturbations and whether microbiomes are sensitive enough to predict environmental anomalies that can lead to ecosystem stress. However, the lack of coral reef microbial baselines hinders our ability to study the link between shifts in microbiomes and ecosystem stress. In this study, we established a comprehensive microbial reference database for selected Great Barrier Reef sites to assess the diagnostic value of multiple free-living and host-associated reef microbiomes to infer the environmental state of coral reef ecosystems. RESULTS: A comprehensive microbial reference database, originating from multiple coral reef microbiomes (i.e. seawater, sediment, corals, sponges and macroalgae), was generated by 16S rRNA gene sequencing for 381 samples collected over the course of 16 months. By coupling this database to environmental parameters, we showed that the seawater microbiome has the greatest diagnostic value to infer shifts in the surrounding reef environment. In fact, 56% of the observed compositional variation in the microbiome was explained by environmental parameters, and temporal successions in the seawater microbiome were characterised by uniform community assembly patterns. Host-associated microbiomes, in contrast, were five-times less responsive to the environment and their community assembly patterns were generally less uniform. By applying a suite of indicator value and machine learning approaches, we further showed that seawater microbial community data provide an accurate prediction of temperature and eutrophication state (i.e. chlorophyll concentration and turbidity). CONCLUSION: Our results reveal that free-living microbial communities have a high potential to infer environmental parameters due to their environmental sensitivity and predictability. This highlights the diagnostic value of microorganisms and illustrates how long-term coral reef monitoring initiatives could be enhanced by incorporating assessments of microbial communities in seawater. We therefore recommend timely integration of microbial sampling into current coral reef monitoring initiatives. SN - 2049-2618 UR - https://www.unboundmedicine.com/medline/citation/31227022/Microbial_indicators_of_environmental_perturbations_in_coral_reef_ecosystems_ L2 - https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0705-7 DB - PRIME DP - Unbound Medicine ER -