PONE-D-24-28640Cryptic genetic structure of the coral host is the primary driver of holobiont assembly in massive PoritesPLOS ONE

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This research was supported by NSF DGE-2137420 to C.B.S, NSF grant IOS-1755277 to M. V. M., funding from the University of Texas Department of Integrative Biology to C.B.S, and funding from the International Women’s Fishing Association to C.B.S.

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Reviewer #1: The presented study provides an overview of cryptic lineages in massive Porites spp. on Orpheus and Pelorus Islands on the Great Barrier Reef, Australia. Cryptic diversity is large in corals in general, but specifically in massive Porites as other studies have found. The paper presented here expands on these previous studies and shows that the genetic structure of the host was the main driver of symbiont and microbial associations. They further disentangle the drivers reef site and size class (small, i.e. <30cm and large, i.e. >2m) on the associated microbes, where the microbiome was shaped by reef site and size class and the symbiont community was unaffected by both. In light of growing restauration efforts and other techniques to mitigate the impact of climate change on coral reefs, this study adds onto the relevant literature identifying cryptic diversity in corals and provides a framework for understanding holobiont flexibility in light of environmental change. The paper is well-written, the methodology is thorough and the conclusions drawn are comprehensible. I would advise to accept this manuscript with minor changes.

Minor issues are provided in the attached file.

Reviewer #2: The ms presented by Scott et al. is a well written and data rich study that investigates factors responsible for prokaryotic and algal microbiome composition of Porites spp. corals. There has been relatively little focus to dissect detailed microbial and algal strain diversity in relationship to fine scale host genetics. In that respect, the study is timely and interesting to the coral community and beyond. The methodology looks sound to me, the presentations are generally clear.

My main concern is the notion of "cryptic genetic structure" that already appears in the title. My understanding is that the authors study a species complex, genus Porites, where the existence of several species is an acknowledged fact. Being not a coral expert, I assume that these species are morphologically so plastic and /or similar that non-genetic taxonomy will not work. This is also rightly acknowledged by the authors in line 366.

By means of Rad-seq /SNP calling they are able to resolve them to species level which is an interesting finding in and among itself.

If so, it is rather (the difficult to determine) taxonomic affiliation to a species within a genus that determines the composition of algal and prokaryotic symbionts. As such, the entire data set would also be interesting data worthwhile to report, but with a changed interpretation /implication. As it stands now, the title implies (to me) within-species genetic structure.

Along the same lines, in order to benchmark the differences among the host genetic clusters (aka cryptic species?) it would be great to quantify /date the divergence among coral hosts, maybe with some mitochondrial genetic clock? This way, the data would become comparable to other such studies that look at the effects of host genotypic /species affiliation for microbial community assembly.

Finally, can any specific inference be made as to the level of species-affiliated genomic divergence vs. within species genetic structure, based on the data of the host? I note that there are two levels of clustering that the authors describe, but this is not picked up later in the ms. Maybe the combined sample size is too low here?

Further suggestions, in the order of appearance

L58: the study results do not really present anything on the role of the associated microbial community for holobiont adaptation /resilience, so a different intro lead would be more appropriate for the paper

L88: This reads awkward, as the data presented are also not long term, but deal with a single survey

L99: an overview on the "site * colony size * replicate sample" combinations would be nice, and also the absolute spatial distances at all scales.

Fig 4. Here, the community composition patterns look like rather uniform among host groups. This might partly be a result of the "binning" of the color coding. But this is confusing as the diagram in its present form suggests hardly any structure. This figure should convey as much qualitative differentiation as possible to explain the clear MDS clustering in later analyses.

As a suggestion, is it possible to look at a heat map for each individual sample clustered (i) by microbial /algal composition (ii) by host genetics? Such a diagram could convey everyting at a glance.

L363: I would present a STRUCTURE graph also with 10 clusters, as you repeatedly refer to that optimal cluster number rather than 5 (as in Fig 2).

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Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-24-28640_Comments_to_Authors.docx

https://doi.org/10.1371/journal.pone.0328479.r002

Genetic clustering within massive Porites species complex is the primary driver of holobiont assembly

PONE-D-24-28640R1

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PONE-D-24-28640R1

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