Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico

Abstract

Ancient biologically mediated sedimentary carbonate deposits, including stromatolites and other microbialites, provide insight into environmental conditions on early Earth. The primary limitation to interpreting these records is our lack of understanding regarding microbial processes and the preservation of geochemical signatures in contemporary microbialite systems. Using a combination of metagenomic sequencing and isotopic analyses, this study describes the identity, metabolic potential and chemical processes of microbial communities from living microbialites from Cuatro Ciénegas, Mexico. Metagenomic sequencing revealed a diverse, redox-dependent microbial community associated with the microbialites. The microbialite community is distinct from other marine and freshwater microbial communities, and demonstrates extensive environmental adaptation. The microbialite metagenomes contain a large number of genes involved in the production of exopolymeric substances and the formation of biofilms, creating a complex, spatially structured environment. In addition to the spatial complexity of the biofilm, microbial activity is tightly controlled by sensory and regulatory systems, which allow for coordination of autotrophic and heterotrophic processes. Isotopic measurements of the intracrystalline organic matter demonstrate the importance of heterotrophic respiration of photoautotrophic biomass in the precipitation of calcium carbonate. The genomic and stable isotopic data presented here significantly enhance our evolving knowledge of contemporary biomineralization processes, and are directly applicable to studies of ancient microbialites.

Metabolic potential of lithifying cyanobacteria-dominated thrombolitic mats

“…Cyanobacteria have long been known to dominate microbialite forming communities (e.g., Reid et al 2000;Breitbart et al 2009;Myshrall et al 2010;Santos et al 2010;Foster and Green 2011;Khodadad and Foster 2012). The metagenomic sequencing of the thrombolitic mats reinforces this concept and shows that the majority of the recovered reads from the Bahamian thrombolitic mats were derived from cyanobacteria.…”

“…Amplicon libraries of the 16S rRNA gene amplicon studies have previously shown the presence of several sulfate-reducing bacteria (SRB) mostly associated with the Desulfovibrionales in the thrombolitic mats (Mobberley et al 2012;Myshrall et al 2010). The metagenomic survey of the top 9 mm of the thrombolitic mats, however, showed that the relative abundance of dissimilatory sulfate reduction genes was low compared to metagenomic studies of other microbialite forming communities (Breitbart et al 2009;Khodadad and Foster 2012). Additionally, most of the recovered genes in thrombolitic mats were similar to Desulfobacterales, although a few genes associated with Desulfovibrionales were detected ( Table 2).…”

“…The thrombolitic metagenome also contained many bacterial organic substrate degradation pathways that have also been recovered from other microbialite forming systems (Breitbart et al 2009;Khodadad and Foster 2012) and were primarily derived from the phyla Proteobacteria, Bacteroidetes, and Planctomycetes. Additionally, genes were recovered from lactate and mixed acid fermentation pathways from a variety of bacteria with most reads sharing similarity to cyanobacteria.…”

“…Comparisons were made using SEED subsystems with the following parameters: minimum E value of 10 −5 and minimum identity of 60 %. The following publically available datasets were used in this analysis (citation and MG-RAST IDs given): thrombolitic mat replicates (this study); non-lithifying (Type 1) and lithifying (Type 3) Highborne Cay stromatolitic mats (Khodadad and Foster 2012;4449590.3, 4449591.3), Cuatro Ciénegas lithifying oncolites (layered spherical microbialites) and thrombolites (Breitbart et al 2009;44440060.4, 4440067.3), Cuatro Ciénegas non-lithifying mats (Peimbert et al 2012;4442466.3, 4441363.3), Guerrero Negro hypersaline mats (Kunin et al 2008;4440964.3-4440972.3), Octopus Springs mat, Yellowstone National Park (Bhaya et al 2007;4443749.3), and a Global Ocean Sampling Sargasso Sea water column sample served as an outgroup (Rusch et al 2007;4441570.3). Multivariate analysis of the metagenomes functional subsystems was performed within the R statistical program (R Development Core Team 2010) using the random forest (version 4.6-2; Liaw and Weiner 2002) and bpca (version 1.0-10; Faria and Demetrio 2008) as previously described (Dinsdale et al 2013).…”

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

“…Such efforts have traditionally been hampered by the diversity and as-yetuncultivated status of many SRMs, but these studies have recently been transformed by the development of large-scale genome sequencing and associated metagenomic technologies, such as functional gene arrays. The new techniques have been used to characterize SRMs in various environments, such as fresh water 89 , deep-sea sediments and vents 90,91 , a gold mine 31 , symbionts 92,93 , animal microbiomes [94][95][96] and groundwater 97 . Owing to space limitations, this section focuses primarily on representative extreme environments and in particular on heavy-metal-contaminated groundwater.…”