Horizon-scanning prioritises coastal microbiome research
C3 PhD student Valentina Hurtado McCormick reveals the story behind the Nature paper.
Ecologists and evolutionary biologists around the world now see natural environments differently thanks to the increasing evidence of the importance of microbes for ecosystem function. As a consequence, they have started studying these habitats at relatively smaller scales. This, with the accelerated accumulation of accessible but massive descriptive data sets on environmental microbiomes - with the potential to answer a multitude of research questions - has inevitably resulted in many more questions than answers. How and where should we even start to address these issues?
A workshop held at Deakin University in Melbourne (July 2017) was the beginning of an incredible collaborative experience for 23 specialists in the field of coastal microbiome research (including a number of current and former UTS Climate Change Cluster colleagues), all wondering what the future of coastal ecosystem research should be focused on when considering the substantial relevance of the myriad microorganisms that inhabit and live in association with animals and plants in the ocean.
Figure 1: Map of coastal marine microbiome study sites across the globe - approach: data mining.
The decision was made to use the horizon scan approach, combined with a comprehensive literature review (Figure 1), to evaluate the current state of the research and interrogate the topics that should be prioritised to ultimately unify the strategy of research on coastal marine holobionts. These include corals, macroalgae, seagrasses, mangroves, sponges and saltmarshes, which form the foundation of coastal ecosystems (Figure 2). Our approach resulted in 108 questions that were carefully debated over two years following the meeting to condense them in seven themes encompassing the microbiome, microbiome and host, and the relationships among microbiome, host and environment. Details of the approach, research themes and outlook of next steps are well described in our Nature Ecology and Evolution Perspectives paper, and although the list is broad and ambitious, we stress the importance of collaborative networks along with well-executed hypothesis-driven manipulative experiments to progress the definition and functional relationships between microbiomes and hosts.
Figure 2 - Six key holobionts form the foundation of coastal ecosystems: corals, macroalgae, seagrasses, mangroves (sponges and saltmarshes not shown here).
As an international doctoral candidate at UTS, the workshop was an excellent opportunity for me to be exposed to experts in my field of interest at the very beginning of my PhD journey. In addition, I was able to assess the status of the field when I was starting to write my thesis, which helped me to put my work in seagrasses into a more realistic, global context. Now, two years later I can attribute much of my understanding of the field to the large scale of this collaboration and the intellectual effort it took to work on the data and participate in the discussion of ideas presented in our paper.
My perspective has certainly broadened since the beginning of my PhD; however, contributing to this paper gave me a clear vision of the gaps of knowledge that we, as researchers, need to be currently focusing on. It also strengthened my technical skills and trained me into the networking that is inherently necessary to conduct the large-scale projects that might eventually fill these gaps. We hope that our synthesis of open questions in marine microbiome research (Figure 3) challenge the perspective of the readers, interrogates their research strategies and triggers many further discussions.
Figure 3 - The paper synthesised the top questions in marine microbiome research that need to be answered. Credit M.Palacios.
Publication details
A horizon scan of priorities for coastal marine microbiome research Stacey M. Trevathan-Tackett et al Nature Ecology & Evolution volume 3, pages1509–1520 (2019)
