Comparative metagenomics of two microbial mats at Cuatro Ciénegas Basin II: community structure and composition in oligotrophic environments

Abstract

Microbial mats are self-sustained, functionally complex ecosystems that make good models for the understanding of past and present microbial ecosystems as well as putative extraterrestrial ecosystems. Ecological theory suggests that the composition of these communities might be affected by nutrient availability and disturbance frequency. We characterized two microbial mats from two contrasting environments in the oligotrophic Cuatro Ciénegas Basin: a permanent green pool and a red desiccation pond. We analyzed their taxonomic structure and composition by means of 16S rRNA clone libraries and metagenomics and inferred their metabolic role by the analysis of functional traits in the most abundant organisms. Both mats showed a high diversity with metabolically diverse members and strongly differed in structure and composition. The green mat had a higher species richness and evenness than the red mat, which was dominated by a lineage of Pseudomonas. Autotrophs were abundant in the green mat, and heterotrophs were abundant in the red mat. When comparing with other mats and stromatolites, we found that taxonomic composition was not shared at species level but at order level, which suggests environmental filtering for phylogenetically conserved functional traits with random selection of particular organisms. The highest diversity and composition similarity was observed among systems from stable environments, which suggests that disturbance regimes might affect diversity more strongly than nutrient availability, since oligotrophy does not appear to prevent the establishment of complex and diverse microbial mat communities. These results are discussed in light of the search for extraterrestrial life.

FIG. 1.

Schematic map depicting the geographic origin of the metagenomic data sets analyzed in this study.

FIG. 2.

Consensus phylogenetic tree of 16S rRNA gene clone libraries from the green and red microbial mats reconstructed by Maximum Likelihood with 1000 bootstraps. The outer rings represent the relative abundance of each OTU clustered at 97% of the green (green bars) and red (red bars) mats. Black points on the branches indicate clades present in >80% of the phylogenies. Color key for bacterial phyla are given clockwise from top to bottom.

FIG. 3.

(a) Phylogenetic tree of the Pseudomonas subclade reconstructed by maximum likelihood. OTUs containing sequences from this study are typed in boldface, and reference sequences are in italics. The abundance bars represent the number of sequences contained in each OTU at 98% identity. Bars are colored as follows: green mat (green), red mat (red), red mat 2 (orange). (b) Venn diagram depicting the number of shared and unique OTUs between libraries. Color images available online at www.liebertpub.com/ast

FIG. 4.

Principal component analysis ordination plot of the Cuatro Ciénegas metagenomes using the taxon-abundance matrix constructed with deduced protein markers in the green (GP) and red (RP) microbial mats and Pozas Azules (PA) and Río Mesquites (RM) stromatolites. The names of the top 14 genera most greatly contributing to the principal components are indicated. Color images available online at www.liebertonline.com/ast

FIG. 5.

(a) Estimated rarefaction curves for the 16S rRNA gene clone libraries, with OTUs clustered at 97% identity. (b) Renyi's entropy profile for the four Cuatro Ciénegas metagenomes. Profiles were calculated with the taxon-abundance matrix constructed with protein marker analyses. Green mat (GP), red mat (RP), Río Mesquites (RM), and Pozas Azules (PA). Color images available online at www.liebertonline.com/ast

FIG. 6.

Relative abundance distributions of the most abundant orders by means of the all-reads metagenomic complement approach. Abundant taxa are considered as those comprising 75% of the total annotated reads in each metagenome. Green mat, outer circle; Pozas Azules, middle circle; Guerrero Negro, inner circle. The black line indicates where the cumulative proportion of the three samples reaches 70%, just after Myxococcales.