Marine holobiont in the high throughput sequencing era
A community perspective on the concept of marine holobionts: current status, challenges, and future directions
The concept of holobiont dates back to more than thirty years, it was primarily coined to hypothesize the importance of symbiotic associations to generate significant evolutionary novelties. Quickly adopted to describe the now well-studied system formed by zooxanthella associated corals, this concept expanded much further after the emergence of High-Throughput Sequencing and associated progresses in metabarcoding and metagenomics.
Holobionts – defined as the association between an individual host and its microbiota - are now increasingly described at sea and on land. The opinion article by Dittami et al.  provides a synthetic overview of marine holobionts. It retraces the history of the holobiont concept, recalls the main mechanisms underlying the association between hosts and microbial communities, highlights the influence of these symbioses on marine ecosystem functioning, and outlines current tools and future lines of research.
In particular, the article discusses some particularities of marine systems, such as the strong connectivity allowing an exchange of microorganisms and chemical signals between and within holobionts.
The authors advocate the need to bridge the gap between large scale exploration studies and smaller scale mechanistic studies, by conducting interdisciplinary research (combining physiology, biochemistry, ecology, experimentation and computational modeling) on some keystone holobionts.
Finally, one strength of the paper by Dittami et al.  is that it places the concept of the holobiont in an applied research framework. Several possible applications of knowledge on host-microbiota interactions are suggested, both in the field of aquaculture and that of monitoring the health of marine ecosystems. This article contains all the necessary elements for someone who would like to jump into the study of the holobionths in the marine world.
 Dittami SM, Arboleda E, Auguet J, Bigalke A, Briand E, Cardenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli E, Morganti T, Núñez Pons L, Prado S, Pintado J, Saha M, Selosse M, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. (2020). A community perspective on the concept of marine holobionts: current status, challenges, and future directions. Zenodo, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.5281/zenodo.3696771
Sophie Arnaud-Haond and Corinne Vacher (2020) Marine holobiont in the high throughput sequencing era. Peer Community in Ecology, 100045. 10.24072/pci.ecology.100045
Revision round #32020-01-09
Decision round #3
Dear Dr. Dittami,
We thank you for this revised version. Please receive our sincere apologizes for the long delay in revising it.
We feel the article is substantially improved with this new revision.
We believe there is room for a more significant contribution, would the consortium take side on the realistic and operational scale of boundaries to apply to the holobionts concept (lines 246->253) the way they discuss it in the rest of the paper. Would the consortium advocate its extension to extremely large scale of ecosystem, would they consider it pragmatic and useful considering the research and application axis they forecast ?
We also feel there is a need to clarify the fundamental questions raised considering the holobionts concept (lines 255->268).
We attach a version including comments and suggestions for editing. We still feel more detailed recommendations would be needed in the last section on new methods, to enhance the interest and the future use.
We however appreciate the long time now since first submission, and are willing to recommend your manuscript on receipt of the next version.
All the best,
Sophie Arnaud-Haond and Corinne Vacher
Revision round #22019-07-26
Decision round #2
Dear Dr. Dittami,
Thank you for your detailed response to the comments of the two reviewers. I have read the revised version of your article carefully and I think the revisions have improved the article. However, there is still room for improvement. For your paper to become a reference in the field of holobiont research, I think you should list the priority research questions and indicate the biological models and the techniques that are appropriate to answer them. The glossary and the figures should also be strengthened. My detailed comments are in the attached pdf. I hope that you will find these comments useful and invite you to re-submit your article to PCI Ecology after this second round of revisions.
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Revision round #12019-04-12
Decision round #1
Dear Dr. Dittami, Thank you for submitting your article to PCI Ecology. I have now received two reviews of your manuscript, which you will find below. Both reviewers greatly appreciated your work, which is an extremely comprehensive and well-written review. I invite you to take into account all their comments and submit a revised version to PCI Ecology. In particular, the two reviewers suggest that the section on the evolution of holobionts be strengthened and better integrated with the rest of the study. I also suggest that throughout the manuscript, what distinguishes marine holobionts from terrestrial holobionts in terms of functioning, study methods and challenges, should be better highlighted. Future lines of research could also be more clearly stated in the summary and conclusion, with an emphasis on those specific to marine holobionts. I hope that these comments will allow you to further improve the manuscript and look forward to receiving the revised version. Yours sincerely, Corinne Vacher