Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites

Abstract

Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at macroscale, and suggest a potential causal link. Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.

Evidence of high Ca uptake by cyanobacteria forming intracellular CaCO3 and impact on their growth

“…Moreover, cyanobacteria of the Chroococcales order, to which Gloeocapsa sp. PCC 7428 belong, have been proposed more generally to be particularly efficient at precipitating Ca‐carbonates (e.g., Saghaï et al., ). Overall, the present survey of a large number of cyanobacterial strains supports the idea that Gloeocapsa sp.…”

Comparative metagenomics unveils functions and genome features of microbialite‐associated communities along a depth gradient

“…First, AL‐W could harbor higher phylogenetic diversity. Although this does not appear to be the case in terms of large taxa (Saghaï et al ., ; see below), the internal diversity within phylogenetic lineages might be higher. Second, eukaryotes, having longer genomes, could be more relatively abundant in AL‐W.…”

“…Second, eukaryotes, having longer genomes, could be more relatively abundant in AL‐W. Indeed, based on the presence of SSU rRNA genes, eukaryotes appear to be on average twice as abundant (10–15% of total rRNA genes) as they are in AL‐N samples (3–8%) (Saghaï et al ., ). Finally, eukaryotic genomes in AL‐W (largely dominated by diatoms) might be bigger than those of AL‐N samples (largely dominated by green algae) (Saghaï et al ., ).…”

“…S2A). This may be partly due to the increasing proportions of Pleurocapsales with depth (Saghaï et al ., ), since contigs affiliating to Pleurocapsales (see below) show 38% GC content (average/median values). The GC content distribution in Alchichica metagenomes diverged from that of other microbialites and mat metagenomes.…”

“…Lake Alchichica, an alkaline crater lake at pH ∼ 9 located at high altitude (2300 m above sea level), harbors actively growing microbialites, which are mostly composed of hydromagnesite [Mg 5 (CO 3 ) 4 (OH) 2 .4(H 2 O)] and aragonite (CaCO 3 ) (Kaźmierczak et al ., ). Previous surveys of prokaryotic and eukaryotic diversity (Couradeau et al ., ; Saghaï et al ., ) revealed a wide diversity of largely dominant bacteria (85–95% total rRNA genes), whereas eukaryotes were fairly diverse, displaying moderate abundance (5–15%), and archaea exhibited poor diversity and extremely low (0.02–0.3%) relative abundances (Saghaï et al ., ). Cyanobacteria performing a new form of intracellular biomineralization were isolated from these microbialites (Couradeau et al ., ).…”