A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment

Microbial mats are complex ecological assemblages that have been present in the rock record since the Precambrian and can still be found in extant marginalized environments. These structures are considered highly stable ecosystems. In this study, we evaluate the ecological stability of dome-forming microbial mats in a modern, water-level fluctuating, hypersaline pond located in the Cuatro Ciénegas Basin, Mexico. We conducted metagenomic sampling of the site from 2016 to 2019 and detected 2250 genera of Bacteria and Archaea, with only <20 belonging to the abundant taxa (>1%). The microbial community was dominated by Proteobacteria, Euryarchaeota, Bacteroidetes, Firmicutes, and Cyanobacteria, and was compositionally sensitive to disturbances, leading to high taxonomic replacement even at the phylum level, with a significant increase in Archaea from \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sim $$\end{document}∼1-4% to \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sim $$\end{document}∼33% throughout the 2016-2019 study period. Although a core community represented most of the microbial community (>75%), relative abundances shifted significantly between samples, as demonstrated by changes in the abundance of Coleofasciculus from 10.2% in 2017 to 0.05% in 2019. Although functional differences between seasons were subtle, co-occurrence networks suggest differential ecological interactions between the seasons, with the addition of a new module during the rainy season and the potential shift in hub taxa. Functional composition was slightly more similar between samples, but basic processes such as carbohydrate, amino acid, and nucleic acid metabolisms were widely distributed among samples. Major carbon fixation processes included sulfur oxidation, nitrogen fixation, and photosynthesis (both oxygenic and anoxygenic), as well as the Wood-Ljundgahl and Calvin cycles. Supplementary Information The online version contains supplementary material available at 10.1007/s00248-023-02231-9.

2 m 1 cm 1 cm 10 cm 15 cm 5 cm 5 cm 3 cm 20 cm 30 cm 30 cm 5 cm Fig. S2: Microbially Induced Sedimentary Structures (MISS) found at the Archean Domes system.Gas dome structures are the most distinctive feature during both a) rainy, and b) dry seasons.c) During the dry season, most gas domes are uncollapsed and retain their shape.d) Small sized gas dome alongside milimiter sized blisters.e) Potential gas duct exposed during sampling (arrow).f ) Polygonal, meter-sized shrinkage cracks; angular intersections between cracks can be observed (arrows).g-h) Shrinkage cracks with instances of rolled-up structures (black arrows) and mat chips (white arrow).i-j) Elongated petee structures.k) Small-scale reticulated mat surface.l) Cauliflower shaped nodules at the edge of the pond.m) Trapped and, n) disrupted milimeter-sized gas bubbles.Fig. S16: Core composition at the genus level.Each of the 250 genera that constitute the core is shown in order to emphasize the changes in relative abundance for each sample.-2019- 7,799,883,462 588,197,199 7,211,686,263 500 1,142.20 142,626 Wet-2019 7,744,171,739 621,571,725 7,122,600, 7,744,171,739 621,571,725 7,122,600, Fig. S3 (continued) Fig.S5: Resistance genes found at the Archean Domes.Through all samples, most resistance genes are associated to alkaline and salt response genes.The gray line shows the mean normalized abundance of stress response genes for each sample.Selected GO terms for each category are shown in TableS9.
The Archean Domes community based on their relative abundance at genus level.Abundant taxa comprise most of the whole community, in contrast to moderate and rare taxa abundance.
Relative abundance of the Archean Domes core community at the genus level.Abundant taxa comprise most of the core, in contrast to moderate and rare taxa abundance.Core taxonomic and functional details.a) Core composition at phylum level.The number of genera for each phylum appears next to each bar.b) Core functions under a PCoA ordination method.Roughly, there appears to be a seasonal pattern with a close association between two dry and rainy season samples, although the rainy sample from 2019 and the dry sample from 2017 does not group with any other sample.c) Function composition for core genera.Overall, similar relative abundances between samples can be appreciated.

Table S2 :
Carbon, nitrogen, and phosphorus content for dry and rainy 2019 samples (March 2019 and September 2019, respectively).Sediment pH and Grain size analysis are also shown.

Table S4 :
Raw reads and quality control (QC) metadata for each shotgun metagenome studied.

Table S5 :
Metagenome assembly metadata for each sample.Minimum, average, and maximum contig length is also shown

Table S6 :
Metagenome assembly metadata for sequences not initially assembled.

Table S7 :
Taxonomic annotation (CAT) metadata for each sample and relative abundances for each superkingdom.

Table S8 :
Relative abundances for each superkingdom based on ribosomal-protein annotation.Selected ribosomal-protein families for this taxonomic annotation are described in the main text.

Table S9 :
Selected GO terms for specific resistance mechanisms.UniProt amino acid sequences tagged with one or more of the specified GO terms were downloaded for further analysis.