the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 17 Oct 2024
Microbial communities inhabiting 600-year-old sediments in the Inka-Coya Lake located in the Atacama Desert
Abstract. Lacustrine sediments are natural archives for the surrounding area's biogeochemical dynamics; in particular, the isolation and extreme conditions in which desert lakes are located make them ideal study models for studying perturbations in the ecosystem. Specifically, Inka-Coya Lake is in the Atacama Desert, where the presence of metals and metalloids associated with the active geological activity and local mining industry is a crucial driver for the biological dynamics in this ecosystem, as have been suggested for macroinvertebrates and plankton communities in the lake. In this study, we aimed to characterize the microbial communities that inhabit deep lacustrine sediments and their interaction with the surrounding environment. The results show that the microbial community from lacustrine sediments contains over 70 % unclassified organisms, highlighting this ecosystem's microbial taxonomic novelty. Our results indicate that the microbial communities cluster in three distinct zones: a superficial community, an intermediate and mixed community, and a more specialized anaerobic community in the deeper sediments. The microbial composition is dominated by chemoheterotrophic bacteria strongly associated with methane metabolism. Additionally, there is statistical evidence of strong correlations between particular taxa such as Sulfurimonadaceae, Metanoregulaceae, and Ktedonobacteroceae with elements like Cu, As, Fe, Ni, and V, and magnetic properties of the surrounding environment. Further detailed studies of the metabolic repertoire of these communities are necessary to understand the complex dynamics between microbial life and geochemical composition in this fragile and extreme environment.
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Status: open (until 04 Dec 2024)
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RC1: 'Comment on egusphere-2024-3035', Anonymous Referee #1, 01 Nov 2024
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Summary
Pardo-Esté et al. provide a biogeochemical and microbiological survey of a single sediment core (LIC-SHC03) from Inka-Coya lake, located in the Atacama Desert. The authors provide a time model that, they propose, resolves a local anthropogenic impact sequence generated by copper mining. The authors highlight that a large amounts of the microbial community, inferred by 16S rRNA gene sequences, belong to unclassified organisms and proffer statistical correlations between certain elements and sequence representatives related to chemoheterotrophic lineages. Overall, the study is due to the site and context is novel and provides a valuable contribution to environmental impact assessments associate with copper mining broadly and anthropogenic effects on relatively isolated lake ecosystems specifically.
General Comments/Suggestions
The writing contains numerous grammatical errors and may benefit from additional revisions by an additional number of native English speakers. I’ve done my best to highlight some of those instances, but many such issues remain. The study’s strength would largely benefit from additional details about the precautions the authors undertook during the molecular analysis step (details below). The taxonomy-based functional prediction approach (PICRUSt2), as noted in the methods, is tenuous at best. Thus, the tone of certain parts of the discussion needs to reflect this potential interpretative vulnerability.
Specific Comments/Suggestions/Questions
L34-37: A bit of a run-on sentence, please revise for clarity.
L58: What do the authors mean by “perform”; perhaps live or thrive may be better choices here?
L82: Do the authors mean assembly instead of assemble?
L82-85, L117-122: Are there other well established sedimentation rate models in other lakes of the region? Do you they match your independently determined rates?
L144: How exactly were the 5g of sediment collected for molecular analysis? Where these frozen split cores? Mini-cores with syringe? Specific precautions for prevent cross-contamination (top to bottom sequence) or external contaminants (subsampled in laminar flow hood)? Please expand on the specific extend of aseptic technique used.
L145: How was the DNA integrity, quantity, and quality ultimately determined? (ABS ratios?, smear gel?, what were the concentrations found for your samples?).
L149: was there a specific reason to not use the new version of the Earth Microbiome Primers (Parada et al.) given that the revised primer may be better able to capture Archaea?
L151: Where there any blanks sequences along with this analysis. If so, how were those sequences treated?
L159: Is this relative abundance normalized in any way before rank visualization in ggplot2? (Rarefied?). Please explain.
L163: Can the authors clarify the “phylogenetic diversity” metric?
L164: Did the authors perform any multiple testing correction following the non-parametric Wilcoxon test (e.g.: Pval adjustments Benjamini-Hochberg, etc.)?
L169: Any post-hoc multiple comparison corrections on your ANOVA test involving geochemical gradients to address potential type-1 error inflations (e.g.: Bonferroni, Tukey’s HSD?).
L174: Again, I think PICRUSt is a great hypothesis-generating approach, particularly for synoptic predictions of potential metabolisms within a single sample; however, statistical approaches described here, aiming to infer comparative differences across samples of taxonomically-inferred pathways and statistical differences between the estimates of these inferred pathways is tenuous operation. Perhaps this part of the methods would be a great part to explain this to the readership? I believe that would help the strength of the paper. Note: I see that the authors encourage further work with metagenomic methods in the discussion as well.
L277-279: Do the authors mean “communities living in depths greater than a meter”?
L284: change “microorganisms assemblage” to “microbial assemblages”.
L311: Can you specify the “lower taxonomic rank”.
L318: Do the authors mean viability rather than endurance?
L320: This may be an uncharacterized species of the genus since this based on a 16S rRNA gene study rather than culture, isolation, and characterization as would be necessary to make the statement as is. Please reframe to address this.
L332: Does your figure 4 show a high abundance of this methanogenic lineage as these other studies? It looks like, if you got it in your cores, it is much less prevalent correct?
L337: Perhaps chance “special” to “predicted” here.
L338: A metabolic approximation is not physiological evidence. Please re-write this to address this.
L340: Please note that in many other subsurface environments (terrestrial, marine from my experience) as deeper layers are sample lower percentages of 16S rRNA gene lineages are able to be identified (have close relatives) at the genus level. Thus, this observation falls in line with similar underexplored environments (Orca Basin, for example). This means that the deep community of this lake may not have an increased amount of “microbial dark matter” relative to any other under explored environment (most of the habitable space on Earth). I’d encourage to authors to re-contextualize their observation mentioned here accordingly.
L369: Did the authors observe any classic magneto-tactic lineages in their data?
L375: This reads a bit ambiguous. Can the authors explicitly state the need for shot-gun metagenomics.
L380: What do the authors suggest by resistance (a term often misconstrued in microbiology to mean antimicrobial resistance): perhaps detoxification and/or adaptations? To what environmental insult specifically?
L389: Change function to “predicted function”.
L396: No sure what authors mean by the “higher area” of studied sediments? Please disambiguate as surficial/interface, mid-core, and bottom core consistently throughout text to avoid reader confusion.
Citation: https://doi.org/10.5194/egusphere-2024-3035-RC1 -
RC2: 'Comment on egusphere-2024-3035', Anonymous Referee #2, 17 Nov 2024
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The authors studied the microbial community compositions and their response to the environment in sediments of Inka Coya Lake located in the Atacama Desert. They found that the microbial community in lake sediments contained over 70% of unclassified organisms, highlighting the novelty of microbial taxonomy in this ecosystem; Microbial communities assemble in three different regions: surface communities, intermediate and mixed communities, and anaerobic communities found exclusively in deep sediments. The microbial composition consists mainly of chemically heterotrophic bacteria, which are closely linked to methane metabolism; There is a strong correlation between certain subgroups (such as Sulfurimonadaceae, Metanoregulaceae, and Kdonobacteroceae) and elements such as Cu, As, Fe, Ni, and V, as well as the magnetic properties of the environment. These results are worth publishing. However, the authors must revise their manuscript thoroughly in the following aspects before it can be accepted:
Abstract
Line16-20: Authors should briefly explain the scientific problem or scientific knowledge gap that this article aims to address, rather than highlighting the characteristics of Inka Coya Lake here.
Line 28-30: Authors should tell readers what significance and/implications of their results are, rather than what to do in the future.
Due to the word limit of the abstract, it is not appropriate to use a large amount of text here to introduce the background information on the lake. A standard abstract should include the following parts: the scientific problem or scientific knowledge gap to be solved, the sample (research object) of the study, the research methods, the main research results, and the scientific significance of these research results. However, there should be no inferential sentences in the abstract. Therefore, the authors need to rewrite this abstract.
Introduction:
The author should provide the necessary scientific hypotheses or the scientific problem you are solving, which is currently missing. This does not conform to the logic of a scientific paper.
Results:
I didn't understand why the author provided data on the age of sediment core. The absence of core age data does not affect readers' understanding of the composition of the microbial community in the sediment core and its response to environmental factors. My understanding is that sediment core age data should be linked to human activities and the resulting environmental changes. However, this part of the data is not presented in the manuscript. Otherwise, the sediment core age testing method and associated result data can be deleted.
Line 192: Figure 2, If authors compare different indices of diversity, it is necessary to explain in detail the mathematical and ecological differences between the indices, because they appear to express the same meanings.
Line 232: Figure 6, authors should put a time scale on this graph instead of just showing the depth coordinates. In addition, if the author wants to discuss the response of the microbiome to heavy metal (such as the first part of the discussion section), it is best to show the picture of the metal element and the microbiome under the same depth/time scale, and mark the location of important nodes (such as human activities, climate events, etc.) for easy understanding.
Discussion:
In the discussion, the author should provide answers to the scientific hypotheses or questions raised in the previous introduction, thus ensuring coherence between the two. Currently in the discussion there is no author's viewpoint or conclusion, but only a repetition of the previous results.
Line 343: It is suggested that the authors use statistical methods to further quantify the effects of different elements on the composition of microbial communities and discuss the differences between different depth regions. Because As, Sb, V, Mo, Mi, Fe and Cu have great differences in physical and chemical properties, biological activity and biological toxicity, it is not appropriate to generalize.
Supplementary:
Line 408: The subgraph showing MetaCyC is missing the mark "C"
Citation: https://doi.org/10.5194/egusphere-2024-3035-RC2
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