Interview with the author: Understanding reef bacterial responses to climate change

Climate change is causing dramatic changes to coral reefs and the eukaryotic life they provide habitat for, but what about the bacterial communities? In this interview with the author, Susana Carvalho from the Red Sea Research Center gives us a behind the scenes take on the paper she and colleagues published using autonomous reef monitoring structures (ARMS) to uncover insights into how bacterial communities respond to environmental stress.

See her bio here and the paper here.

An ARMS unit in action.  Photo credits:  Jessica Bouwmeester

What led to your interest in this topic / what was the motivation for this study? 

Coral reefs face unprecedented decline due to local pressures and climate change, making assessment of species diversity and responses to environmental change a priority. Despite the critical roles of bacteria in reef functioning, their communities remain largely overlooked, partially due to the lack of standardized tools and protocols. Fostered by the recently developed Autonomous Reef Monitoring Structures (ARMS), the team – already studying eukaryotes associated with ARMS – decided to expand the research to bacterial communities. This step was further motivated based on the knowledge previously gathered on the eukaryotic reef benthic communities as well as the fact that the Red Sea can be seen as a natural laboratory for ‘Future Oceans’ due to clear environmental gradients in sea surface temperature and salinity. 

What difficulties did you run into along the way? 

The biggest difficulties for this project were logistical and also the fact that it was an exploratory study. Firstly, the reefs which were studied were spread across 2000km of the Saudi Arabian coastline. This posed problems not only in getting permissions from a number of different agencies to visit the reefs but also in organising the logistics so equipment and people could undertake the sampling safely over such a wide spatial extent and across numerous years. Secondly, the nature of the experiment was exploratory, as very little knowledge is known about reefs in the Red Sea. While this makes the experiment vital to further knowledge it also complicates the ability to understand the trends observed as no prior knowledge is available.

What is the biggest or most surprising innovation highlighted in this study? 

While ARMS have previously been used to study the small cryptic eukaryotes (small-sized organisms that are hidden in the reef structure), they had not been utilised to study bacterial communities. For the first time, we employed ARMS to investigate structure and composition of bacterial reef communities across pronounced environmental gradients spanning 16 degrees of latitude. Using this standardized framework, we found that bacterial community structure and diversity aligned with environmental differences. We also found that the decrease in taxonomic diversity was not mirrored by a decrease in functional diversity, suggesting that resilience is not a direct function of taxonomic biodiversity. Importantly, the structure of ARMS devices feature crevices and light-/dark-exposed surfaces as well as exterior and interiors surfaces; in a word it displays many different microhabitats perfectly designed to sample a large diversity of bacteria. This is not possible using other sampling protocols (e.g. water sampling or sediment sampling). The current approach can be expanded to other regions allowing global questions such as the effect of climate change in coral reefs to be addressed and to build a standardized comparable ARMS-based database that allows for meta-analyses beyond the insight from single studies. 

Moving forward, what are the next steps in this area of research?

To fully understand how coral reef microbial communities are being affected by local and global stressors and how the functioning of the reef changes, long term time series are required. Thus, repeated sampling over a number of years is critical. Currently, we have 19 reefs along the Red Sea where ARMS are deployed and retrieved every two-years along with traditional reef surveys (photo-transects for benthos and fish visual censuses). To properly understand the function within the reef we also aim to undertake a metatranscriptomic analysis of the sessile community to see which genes are active. This would ideally be expanded to include manipulative experiments to understand how specific stressors affect not only the community composition but also the functional activity of the biological communities.

What would your message be for students about to start developing or using novel techniques in Molecular Ecology? 

First of all, we would recommend to consider fully the question/issue that they would like to address with these novel techniques. It should be taken in consideration whether the use of molecular tools will benefit the answering of the desired question in comparison with more traditional methods. While novel techniques can bring substantial improvements in understanding questions, such as the current study, sometimes improvements are just marginal, or can just be in cost and speed.

What have you learned about methods and resources development over the course of this project? 

The aim of this project was to characterize the taxonomic and functional diversity of coral reef-associated bacteria using ARMS. Whilst the team had previous experience working with bacterial taxonomic characterization, a ‘deep dive’ had to be undertaken to perform the functional analysis. These areas are rapidly developing with a wealth of new algorithms appearing in the literature. While there is no perfect approach, during the course of this project we learnt that one of the most crucial aspects when developing a new method is to understand both the benefits and the limitations of it. Only by gaining this understanding can you confidentially present your results and highlight the areas in which these techniques can be applied.

Describe the significance of this research for your scientific community in one sentence.

ARMS provide a standardized platform to investigate the response of coral reef-associated bacteria to environmental change, with current results suggesting that this research should be conducted from taxonomic and functional perspectives.

Describe the significance of this research for the general scientific community in one sentence.

This study lays the foundation for a holistic understanding of how reef communities respond to environmental changes and proposes a framework that, if applied worldwide, can be vital in providing answers to global questions such as the impacts of climate change on ecosystem diversity and functioning.

Citation: Pearman, JK, Aylagas, E, Voolstra, CR, Anlauf, H, Villalobos, R, Carvalho, S. Disentangling the complex microbial community of coral reefs using standardized Autonomous Reef Monitoring Structures (ARMS). Mol Ecol. 2019; 28: 3496– 3507.

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