Effects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove

de Santana, Carolina Oliveira; Spealman, Pieter; Melo, Vânia Maria Maciel; Gresham, David; de Jesus, Taíse Bomfim; Chinalia, Fabio Alexandre

doi:https://doi.org/10.5194/bg-18-2259-2021

Articles | Volume 18, issue 7

https://doi.org/10.5194/bg-18-2259-2021

© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.

https://doi.org/10.5194/bg-18-2259-2021

© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.

Articles | Volume 18, issue 7

Research article

|

06 Apr 2021

Research article |

| 06 Apr 2021

Effects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove

Carolina Oliveira de Santana, Pieter Spealman, Vânia Maria Maciel Melo, David Gresham, Taíse Bomfim de Jesus, and Fabio Alexandre Chinalia

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Final revised paper (published on 06 Apr 2021)
Supplement to the final revised paper
Preprint (discussion started on 08 Jul 2020)
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Interactive discussion

Status: closed

AC: Author comment | RC: Referee comment | SC: Short comment | EC: Editor comment

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- Supplement

RC1: 'Manuscript needs a lot more work', Anonymous Referee #1, 17 Sep 2020
- AC1: 'Response to Reviewer One', David Gresham, 10 Nov 2020
RC2: 'Differential analysis of prokaryotic communities from pristine mangrove tidal zone sediments reveal distinct structures and functional profiles', Anonymous Referee #2, 20 Oct 2020
- AC2: 'Response to Reviewer Two', David Gresham, 10 Nov 2020

Peer-review completion

AR: Author's response | RR: Referee report | ED: Editor decision

ED: Reconsider after major revisions (17 Nov 2020) by Denise Akob

AR by David Gresham on behalf of the Authors (22 Dec 2020) Author's response Author's tracked changes Manuscript

ED: Referee Nomination & Report Request started (05 Jan 2021) by Denise Akob

RR by Anonymous Referee #2 (12 Jan 2021)

RR by Anonymous Referee #3 (05 Feb 2021)

Suggestions for revision or reasons for rejection

Review: Biogeosciences “Tidal influences on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove”

The authors present a study that is highlighting differences in community composition in the sediment of mangroves across different tidal zones. Apart from focusing on the community composition the authors also try to predict community functioning by predicting functions from 16S rRNA gene sequences via Picrust2. In the updated version of the manuscript the limitations of predicting functions based on taxonomic affiliation are better addressed than in the original manuscript. However, some critical points of the manuscript need to be revised and addressed.

Comments

Abstract and Introduction
- The abstract would benefit from some sharpening and highlighting actual findings, such as abundant taxa discovered and how that differs from other studies in mangroves that discovered much greater diversity in mangrove sediments (see e.g. Zhou et al., 2017, Zhang et al. 2021.

- The introduction seems to have improved significantly compare to the original version of the manuscript. However, it could still need some sharpening. Especially the explanation of study site, aim and hypotheses could be brought more “to the point” to become clearer to the reader.
Results
- Figure 2: I find this way of plotting the abundance data very hard to read compared to a normal stacked bar chart. E.g. finding the abundances of Bathyarchaeia is almost impossible. For the main text a simple stacked bar chart on phylum level might be easier to read and interpret.

- under 3.3. the enrichment of specific taxa and their potential function across zones is highlighted. This paragraph would benefit greatly if the connections between tidal zone, dominant taxa and function would become more clear and easier to understand. At this point the text is hard to read with numerous pathway codes and repetitions. Figure 5 does support the reader in understanding the text, however also here highlighting the different predicted functions more clearly could be helpful.

- What about archaeal taxa found in the sediment?

Discussion
- How does the community composition, especially in the sublittoral zone, compare to other environments such as shallow marine sediments in coastal areas?

- Studies that have performed metagenome sequencing on mangrove sediments are more suitable to predict functions. How to the findings of this study compare to those of other studies (e.g. Zhang et al., 2021). Trying for highlight differences and similarities would certainly benefit the manuscript.

- Recent studies using metagenomics on mangroves, but also other environments have shown, that especially yet uncultivated microorganisms are often being not detected by primer sets frequently used for amplicon sequencing (Eloe-Fadrosh et al., 2016). However, these microbes are often dominant parts of the microbial community. Could key players in mangrove sediments have been overlooked?

Minor comments:
- the correct term is “16S rRNA gene amplicon sequencing”

- Supplemental table 1: change “metagenomics method” to just “Method”. DGGE, T-RFLP and amplicon sequencing are not metagenomics! More recent metagenomic studies are completely missing from this table as well as being ignored in the manuscript.

- Figure 1: stay consistent between capital and lower-case letters in figure and figure legend (e.g. (a) vs (A))

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ED: Reconsider after major revisions (10 Feb 2021) by Denise Akob

AR by David Gresham on behalf of the Authors (23 Feb 2021) Author's response Author's tracked changes Manuscript

ED: Publish subject to technical corrections (26 Feb 2021) by Denise Akob

AR by David Gresham on behalf of the Authors (27 Feb 2021) Author's response Manuscript

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Short summary

This study highlights the influence of tidal zonation on the prokaryotic sediment communities of a pristine mangrove forest. We observed that the variability in environmental factors between tidal zones results in differences in structure, diversity, and the potential function of prokaryotic populations. This suggests that further work is needed in determining the role tidal microhabitat biodiversity has in mangroves.