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

Abstract

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 $$\sim $$ ∼ 1-4% to $$\sim $$ ∼ 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.

Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila

“…3389/fmicb.2024.1369263 Frontiers in Microbiology 13 frontiersin.org metagenome assemblies. Our analysis revealed the presence of several predominant phyla, including Proteobacteria, Cyanobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Spirochaetes, Chloroflexi, and Euryarchaeota, which is consistent with previous studies of diversity at the AD site (Espinosa-Asuar et al, 2022;Madrigal-Trejo et al, 2023).…”

“…These findings suggest that the groups analyzed, as well as other groups showing similar phylogenetic patterns, likely represent endemic groups. The observed clustering pattern could be related to oligotrophic conditions characterized by limited phosphorus availability reported at the site, as evidenced by a reported C:N:P ratio of 122:42:1 (Espinosa-Asuar et al, 2022;Medina-Chávez et al, 2023;Madrigal-Trejo et al, 2023).…”

“…This could have influenced the microbiological diversity at the AD site and in other ponds within the CCB. The studies by Madrigal-Trejo et al (2023), Cisneros-Martínez et al (2023) and Wolaver et al (2012) have also observed The diversity of archaea at the AD site can be attributed to the salinity conditions present in the environment. The Euryarchaeota is the most predominant, as observed in other places with high salinity (Fernández et al, 2014;Wang et al, 2022).…”

Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico

“…It has been shown that AD harbors a great diversity of bacteria on a short spatial scale [ 9 ] and is one of the most diverse archaeal communities in the world [ 8 ]. Such diversity includes sulfate-reducing Proteobacteria and extreme halophilic Euryarchaeota [ 42 ]. In addition, a highly diverse viral community has recently been described where haloarchaeaviruses constitute an essential part [ 10 ].…”

Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico

“…It has been shown that Archaean Domes harbors a great diversity of bacteria on a short spatial scale [17] and is one of the most diverse archaeal communities in the world [16]. Such diversity includes sulfate-reducing Proteobacteria and extreme halophilic Euryarchaeota [35]. In addition, a highly diverse viral community has recently been described where haloarchaeaviruses constitute an essential part [18].…”