Breitbart M, Hoare A, Nitti A, Siefert J, Haynes M, Dinsdale E et al.. Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Cienegas, Mexico. Environ Microbiol 11: 16-34

College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
Environmental Microbiology (Impact Factor: 6.2). 10/2008; 11(1):16-34. DOI: 10.1111/j.1462-2920.2008.01725.x
Source: PubMed


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.

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    • "The major Level 1 subsystems in ADS were carbohydrates, protein metabolism, amino acids and derivatives, besides clustering-based subsystem (Table S8). Several other studies also suggested similar major subsystems in the various ecosystems , including grassland (Delmont et al. 2012), kimchi (Jung et al. 2011), marine, fresh water and microbialite (Breitbart et al. 2009). Principal component analysis (PCA) (Fig. 4) was carried out based on the Level 1 subsystems distribution to compare five different environmental samples, including ADS, AS, oceans, human faeces and soil (Table S11). "
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    ABSTRACT: This study applied Illumina high-throughput sequencing to explore the microbial communities and functions in anaerobic digestion sludge (ADS) from two wastewater treatment plants based on a metagenomic view. Taxonomic analysis using SILVA SSU database indicated that Proteobacteria (9.52-13.50 %), Bacteroidetes (7.18 %-10.65 %) and Firmicutes (7.53 %-9.46 %) were the most abundant phyla in the ADS. Differences of microbial communities between the two types of ADS were identified. Genera of Methanosaeta and Methanosarcina were the major methanogens. Functional analysis by SEED subsystems showed that the basic metabolic functions of metagenomes in the four ADS samples had no significant difference among them, but they were different from other microbial communities from activated sludge, human faeces, ocean and soil. Abundances of genes in methanogenesis pathway were also quantified using a methanogenesis genes database extracted from KEGG. Results showed that acetotrophic was the major methanogenic pathway in the anaerobic sludge digestion.
    Applied Microbiology and Biotechnology 03/2014; 98(12). DOI:10.1007/s00253-014-5648-0 · 3.34 Impact Factor
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    • "According to Diaz et al. (2013), oolitic communities are characterized by the ubiquitous presence of particleattached bacteria and EPS producers/degraders (e.g., sulfate reducers and lineages within Proteobacteria, Planctomycetes , Bacteroidetes, Cyanobacteria), all of which can combine to create steep redox gradients to facilitate anaerobic metabolism in an otherwise oxygenated environment (Paerl & Prufert, 1987). A similar mechanism has been reported for microbialite systems, where copious amount of EPS secreted by micro-organisms (e.g., sulfate reducers, cyanobacteria) induce steep/redox gradients (Breitbart et al., 2009). Measurements of EPS abundance associated with oolitic grains provide further evidence for the ubiquitous presence of EPS biofilm and associated communities. "
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    ABSTRACT: Despite the importance of oolitic depositional systems as indicators of climate and reservoirs of inorganic C, little is known about the microbial functional diversity, structure, composition, and potential metabolic processes leading to precipitation of carbonates. To fill this gap, we assess the metabolic gene carriage and extracellular polymeric substance (EPS) development in microbial communities associated with oolitic carbonate sediments from the Bahamas Archipelago. Oolitic sediments ranging from high-energy ‘active’ to lower energy ‘non-active’ and ‘microbially stabilized’ environments were examined as they represent contrasting depositional settings, mostly influenced by tidal flows and wave-generated currents. Functional gene analysis, which employed a microarray-based gene technology, detected a total of 12 432 of 95 847 distinct gene probes, including a large number of metabolic processes previously linked to mineral precipitation. Among these, gene-encoding enzymes for denitrification, sulfate reduction, ammonification, and oxygenic/anoxygenic photosynthesis were abundant. In addition, a broad diversity of genes was related to organic carbon degradation, and N2 fixation implying these communities has metabolic plasticity that enables survival under oligotrophic conditions. Differences in functional genes were detected among the environments, with higher diversity associated with non-active and microbially stabilized environments in comparison with the active environment. EPS showed a gradient increase from active to microbially stabilized communities, and when combined with functional gene analysis, which revealed genes encoding EPS-degrading enzymes (chitinases, glucoamylase, amylases), supports a putative role of EPS-mediated microbial calcium carbonate precipitation. We propose that carbonate precipitation in marine oolitic biofilms is spatially and temporally controlled by a complex consortium of microbes with diverse physiologies, including photosynthesizers, heterotrophs, denitrifiers, sulfate reducers, and ammonifiers.
    Geobiology 03/2014; 12(3). DOI:10.1111/gbi.12079 · 3.83 Impact Factor
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    • "The direction of deviation of the d 13 C of carbonate minerals from the predicted equilibrium abiotic values provides insight into dominant metabolic processes. Biosignatures of heterotrophic influences on carbonate precipitation have been detected in some marine (e.g., Andres et al., 2006) and freshwater microbialite systems (e.g., Breitbart et al., 2009; Bonilla-Rosso et al., 2012; Peimbert et al., 2012). Phototrophic influence on carbonate precipitation, as reflected in 13 C-enriched d 13 C values, has also been identified in lacustrine systems (Hollander & Mckenzie, 1991; Thompson et al., 1997). "
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    ABSTRACT: Pavilion Lake in British Columbia, Canada, is home to modern-day microbialites that are actively growing at multiple depths within the lake. While microbialite morphology changes with depth and previous isotopic investigations suggested a biological role in the formation of these carbonate structures, little is known about their microbial communities. Microbialite samples acquired through the Pavilion Lake Research Project (PLRP) were first investigated for phototrophic populations using Cyanobacteria-specific primers and 16S rRNA gene cloning. These data were expounded on by high-throughput tagged sequencing analyses of the general bacteria population. These molecular analyses show that the microbial communities of Pavilion Lake microbialites are diverse compared to non-lithifying microbial mats also found in the lake. Phototrophs and heterotrophs were detected, including species from the recently described Chloroacidobacteria genus, a photoheterotroph that has not been previously observed in microbialite systems. Phototrophs were shown as the most influential contributors to community differences above and below 25 meters, and corresponding shifts in heterotrophic populations were observed at this interface as well. The isotopic composition of carbonate also mirrored this shift in community states. Comparisons to previous studies indicated this population shift may be a consequence of changes in lake chemistry at this depth. Microbial community composition did not correlate with changing microbialite morphology with depth, suggesting something other than community changes may be a key to observed variations in microbialite structure.
    Geobiology 03/2014; 2(3). DOI:10.1111/gbi.12082 · 3.83 Impact Factor
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