Brad M. Bebout

The role of microbes in accretion, lamination and early lithification of modern marine stromatolites.

For three billion years, before the Cambrian diversification of life, laminated carbonate build-ups called stromatolites were widespread in shallow marine seas. These ancient structures are generally thought to be microbial in origin and potentially preserve evidence of the Earths earliest biosphere. Despite their evolutionary significance, little is known about stromatolite formation, especially the relative roles of microbial and environmental factors in stromatolite accretion. Here we show that growth of modern marine stromatolites represents a dynamic balance between sedimentation and intermittent lithification of cyanobacterial mats. Periods of rapid sediment accretion, during which stromatolite surfaces are dominated by pioneer communities of gliding filamentous cyanobacteria, alternate with hiatal intervals. These discontinuities in sedimentation are characterized by development of surface films of exopolymer and subsequent heterotrophic bacterial decomposition, forming thin crusts of microcrystalline carbonate. During prolonged hiatal periods, climax communities develop, which include endolithic coccoid cyanobacteria. These coccoids modify the sediment, forming thicker lithified laminae. Preservation of lithified layers at depth creates millimetre-scale lamination. This simple model of modern marine stromatolite growth may be applicable to ancient stromatolites.

Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat

ABSTRACT We applied nucleic acid-based molecular methods, combined with estimates of biomass (ATP), pigments, and microelectrode measurements of chemical gradients, to map microbial diversity vertically on a millimeter scale in a hypersaline microbial mat from Guerrero Negro, Baja California Sur, Mexico. To identify the constituents of the mat, small-subunit rRNA genes were amplified by PCR from community genomic DNA extracted from layers, cloned, and sequenced. Bacteria dominated the mat and displayed unexpected and unprecedented diversity. The majority (1,336) of the 1,586 bacterial 16S rRNA sequences generated were unique, representing 752 species (≥97% rRNA sequence identity) in 42 of the main bacterial phyla, including 15 novel candidate phyla. The diversity of the mat samples differentiated according to the chemical milieu defined by concentrations of O2 and H2S. Bacteria of the phylum Chloroflexi formed the majority of the biomass by percentage of bulk rRNA and of clones in rRNA gene libraries. This result contradicts the general belief that cyanobacteria dominate these communities. Although cyanobacteria constituted a large fraction of the biomass in the upper few millimeters (>80% of the total rRNA and photosynthetic pigments), Chloroflexi sequences were conspicuous throughout the mat. Filamentous Chloroflexi bacteria were identified by fluorescence in situ hybridization within the polysaccharide sheaths of the prominent cyanobacterium Microcoleus chthonoplastes, in addition to free living in the mat. The biological complexity of the mat far exceeds that observed in other polysaccharide-rich microbial ecosystems, such as the human and mouse distal guts, and suggests that positive feedbacks exist between chemical complexity and biological diversity.

Microscale observations of sulfate reduction: Correlation of microbial activity with lithified micritic laminae in modern marine stromatolites

We report for the first time micrometer-scale correlation of geologic and microbial processes in modern marine stromatolites. Precipitation of micritic laminae in these stromatolites was studied by comparing microstructure, as observed in petrographic thin sections, with microbial sulfatereduction activity. Two-dimensional mapping of sulfate-reduction rates was implemented by incubating a vertical section of a stromatolite face on silver foil coated with 35 SO 4 2– . Our results show that sulfate-reduction activity is high in zones of CaCO 3 precipitation and indicate that microbial activity produces lithified micritic laminae near the surface of the stromatolites. Similarities with micritic laminae in ancient stromatolites suggest that sulfate reduction may also have been an important mechanism of carbonate precipitation in these fossilized structures.

The role of microbial mats in the production of reduced gases on the early Earth

The advent of oxygenic photosynthesis on Earth may have increased global biological productivity by a factor of 100–1,000 (ref. 1), profoundly affecting both geochemical and biological evolution. Much of this new productivity probably occurred in microbial mats, which incorporate a range of photosynthetic and anaerobic microorganisms in extremely close physical proximity. The potential contribution of these systems to global biogeochemical change would have depended on the nature of the interactions among these mat microorganisms. Here we report that in modern, cyanobacteria-dominated mats from hypersaline environments in Guerrero Negro, Mexico, photosynthetic microorganisms generate H2 and CO—gases that provide a basis for direct chemical interactions with neighbouring chemotrophic and heterotrophic microbes. We also observe an unexpected flux of CH4, which is probably related to H2-based alteration of the redox potential within the mats. These fluxes would have been most important during the nearly 2-billion-year period during which photosynthetic mats contributed substantially to biological productivity—and hence, to biogeochemistry—on Earth. In particular, the large fluxes of H2 that we observe could, with subsequent escape to space, represent a potentially important mechanism for oxidation of the primitive oceans and atmosphere.

Sulfate reduction and methanogenesis in a Thioploca-dominated sediment off the coast of Chile

Continental shelf sediments of the central Chile upwelling area are dominated by the presence of dense mats of the filamentous, sulfur-depositing bacterium Thioploca spp. We examined rates and pathways of S and methane cycling in these sediments along a transect from the Bay of Concepcion to the continental slope. Sulfate reduction rates (170–4670 nmol cm−3 d−1) were equal to or exceeded rates reported for other subtidal marine sediments. Elemental S and pyrite were the dominant end-products of sulfate reduction in Thioploca mats on the continental shelf, whereas, in the highly-reducing, Beggiatoa-dominated sediments of the nearby Bay of Concepcion, acid-volatile S was the principal end-product. Dissolved organic C values were lowest at the stations with the highest sulfate reduction rates and increased offshore. Sediment porewater methane concentrations in all surface sediments were low (<12 nmol cm−3), and methane production rates at the station most dominated by Thioploca were extremely low ( <0.5 nmol cm−3 d−1). Low methane production rates and concentrations were matched by low methane oxidation rates (<0.1 nmol cm−3 d−1). Radio-tracer studies showed that methane production was almost exclusively from methylamines, substrates which are noncompetitive with sulfate reduction, rather than from acetate or CO2/H2. Bacterial MPN (most probable number) counts also indicated the presence of a methylotrophic population of methanogens. Surprisingly, high numbers of autotrophic acetogenic bacteria were found, suggesting that the bacterial population involved in anaerobic DOC degradation is more complex than expected. In spite of the high sulfate reduction rates, sulfide concentrations in the shelf and slope were low or undetectable (<0.5 μM), and sulfate concentrations were never depleted below bottom water levels down to depths of 25–30 cm. Calculations suggest that Thioploca were oxidizing a maximum of 35% of sulfide production—not enough to prevent sulfate depletion. Either other sulfide oxidizers were also present or transient hydrodynamic conditions coupled with bioturbation resulted in oxidation of the sediments.

MILLIMETER-SCALE GENETIC GRADIENTS AND COMMUNITY-LEVEL MOLECULAR CONVERGENCE IN A HYPERSALINE MICROBIAL MAT

To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter‐scale genetic gradients that were consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near‐identical and acid‐shifted isoelectric point profiles due to a molecular convergence of amino‐acid usage, indicating that hypersalinity enforces an overriding selective pressure on the mat community.

Salinity control of benthic microbial mat community production in a Bahamian hypersaline lagoon

The purpose of this study was to determine the production and N2 fixation responses of a hypersaline mat community following a reduction in salinity and nutrient enrichment. Cyanobateria-dominated microbial mat samples were collected from hypersaline Storrs Lake and normal seawater salinity Pigeon Creek and preincubated at ambient (90%.) and reduced (45%.) salinities following no nutrient as well as inorganic nutrient (NO3−, PO4−, trace metals) and dissolved organic carbon (DOC, as mannitol) enrichment. CO2 and N2 fixation rates were determined 2 and 4 days later. In addition, DOC (trace concentrations of 3H-labeled glucose and amino acids) uptake was measured in mats under normal and hypersaline conditions. A reduction in salinity from 90 to 45%. significantly enhanced CO2 and N2 fixation rates, but inorganic nutrient and DOC additions did not significantly enhance rates compared with the controls. Dissolved organic carbon/dissolved organic nitrogen (DON) uptake was not influenced over the entire range of salinities (45–90%.) used in this study. When salinity-induced osmotic stress was relieved, mats underwent enhanced primary production and nitrogen fixation. Abiotic stress, induced by hypersaline conditions in Bahamian lagoons, results in lower productivity of the microbial mat communities and this stress may outweigh the typical limiting factors regulating phototrophic community primary production.

Long-term manipulations of intact microbial mat communities in a greenhouse collaboratory: simulating earth's present and past field environments.

Photosynthetic microbial mat communities were obtained from marine hypersaline saltern ponds, maintained in a greenhouse facility, and examined for the effects of salinity variations. Because these microbial mats are considered to be useful analogs of ancient marine communities, they offer insights about evolutionary events during the >3 billion year time interval wherein mats co-evolved with Earths lithosphere and atmosphere. Although photosynthetic mats can be highly dynamic and exhibit extremely high activity, the mats in the present study have been maintained for >1 year with relatively minor changes. The major groups of microorganisms, as assayed using microscopic, genetic, and biomarker methodologies, are essentially the same as those in the original field samples. Field and greenhouse mats were similar with respect to rates of exchange of oxygen and dissolved inorganic carbon across the mat-water interface, both during the day and at night. Field and greenhouse mats exhibited similar rates of efflux of methane and hydrogen. Manipulations of salinity in the water overlying the mats produced changes in the community that strongly resemble those observed in the field. A collaboratory testbed and an array of automated features are being developed to support remote scientific experimentation with the assistance of intelligent software agents. This facility will permit teams of investigators the opportunity to explore ancient environmental conditions that are rare or absent today but that might have influenced the early evolution of these photosynthetic ecosystems.

Comparative ecology of H2 cycling in sedimentary and phototrophic ecosystems.

The simple biochemistry of H2 is critical to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. The sensitivity of each of these processes to H2 can be described collectively, through the quantitative language of thermodynamics. A necessary prerequisite is to understand the factors that, in turn, control H2 partial pressures. These factors are assessed for two distinctly different ecosystems. In anoxic sediments from Cape Lookout Bight (North Carolina, USA), H2 partial pressures are strictly maintained at low, steady-state levels by H2-consuming organisms, in a fashion that can be quantitatively predicted by simple thermodynamic calculations. In phototrophic microbial mats from Baja California (Mexico), H2 partial pressures are controlled by the activity of light-sensitive H2-producing organisms, and consequently fluctuate over orders of magnitude on a daily basis. The differences in H2 cycling can subsequently impact any of the H2-sensitive microbial processes in these systems. In one example, methanogenesis in Cape Lookout Bight sediments is completely suppressed through the efficient consumption of H2 by sulfate-reducing bacteria; in contrast, elevated levels of H2 prevail in the producer-controlled phototrophic system, and methanogenesis occurs readily in the presence of 40 mM sulfate.

Variation in sulfide tolerance of photosystem II in phylogenetically diverse cyanobacteria from sulfidic habitats

ABSTRACT Physiological and molecular phylogenetic approaches were used to investigate variation among 12 cyanobacterial strains in their tolerance of sulfide, an inhibitor of oxygenic photosynthesis. Cyanobacteria from sulfidic habitats were found to be phylogenetically diverse and exhibited an approximately 50-fold variation in photosystem II performance in the presence of sulfide. Whereas the degree of tolerance was positively correlated with sulfide levels in the environment, a strains phenotype could not be predicted from the tolerance of its closest relatives. These observations suggest that sulfide tolerance is a dynamic trait primarily shaped by environmental variation. Despite differences in absolute tolerance, similarities among strains in the effects of sulfide on chlorophyll fluorescence induction indicated a common mode of toxicity. Based on similarities with treatments known to disrupt the oxygen-evolving complex, it was concluded that sulfide toxicity resulted from inhibition of the donor side of photosystem II.