Microbial indicators of environmental perturbations in coral reef ecosystems

Glasl, Bettina, Bourne, David G., Frade, Pedro R., Thomas, Torsten, Schaffelke, Britta, and Webster, Nicole S. (2019) Microbial indicators of environmental perturbations in coral reef ecosystems. Microbiome, 7. 94.

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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.

Item ID: 61788
Item Type: Article (Research - C1)
ISSN: 2049-2618
Keywords: coral reef, coral reef microbiomes, machine learning, microbial baselines, microbial indicators, microbial monitoring
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Copyright Information: © 2019 The Author(s).
Additional Information:

A version of this publication was included as Chapter 4 of the following PhD thesis: Glasl, Bettina (2019) Microbial indicators for environmental stress and ecosystem health assessments. PhD thesis, James Cook University, which is available Open Access in ResearchOnline@JCU. Please see the Related URLs for access.

Funders: Australian Government National Collaborative Research Infrastructure Strategy (NCRIS), Advance Queensland PhD Scholarship, Great Barrier Reef Marine Park Authority (GBRMPA), National Environmental Science Program
Projects and Grants: NCRIS Marine Microbes and Biomes of Australian Soil Environments projects, GBRMPA Management Award
Date Deposited: 19 May 2020 22:07
FoR Codes: 31 BIOLOGICAL SCIENCES > 3107 Microbiology > 310703 Microbial ecology @ 100%
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