The stratified microbial community at Laguna Figueroa,Baja California,Mexico: A possible model for prephanerozoic laminated microbial communities preserved in cherts

The microbial mat community of the evaporite flat at North Pond, Laguna Figueroa (Baja California, Mexico) was actively involved in the production of laminated sediments prior to 1978. Heavy rains in 1979 and 1980 flooded the mat with 1 and 3 meters of meteoric water respectively. The flooding deposited up to 10 cm of silicoclastic sediment over theMicrocoleus-dominated mat and resulted in the cessation of laminated sediment deposition. In 1982, the surface had been recolonized by species of cyanobacteria (Spirulina, Oscillatoria) and purple photosynthetic bacteria (Chromatium, Thiocapsa). The silicoclastic sediments and residual evaporites, which overlaid the laminated sediment, had been reworked into an anaerobic, sulfide-rich mud and contained well preserved sheaths of filamentous and coccoid bacteria.     

The stratified microbial community at Laguna Figueroa, Baja California, Mexico: a possible model for prephanerozoic laminated microbial communities preserved in cherts

The microbial mat community of the evaporite flat at North Pond, Laguna Figueroa (Baja California, Mexico) was actively involved in the production of laminated sediments prior to 1978. Heavy rains in 1979 and 1980 flooded the mat with 1 and 3 meters of meteoric water respectively. The flooding deposited up to 10 cm of silicoclastic sediment over the Microcoleus-dominated mat and resulted in the cessation of laminated sediment deposition. In 1982, the surface had been recolonized by species of cyanobacteria (Spirulina, Oscillatoria) and purple photosynthetic bacteria (Chromatium, Thiocapsa). The silicoclastic sediments and residual evaporites, which overlaid the laminated sediment, had been reworked into an anaerobic, sulfide-rich mud and contained well preserved sheaths of filamentous and coccoid bacteria. The Swaziland Sequence in the Barberton mountain land (which includes the Onverwacht and Fig Tree Group as well as the Swartkoppie zone between them) contains laminated sediments and carbon-rich chert. Structurally preserved microfossils have been found in the smooth black chert but not in the laminae. We concur with others who suggested that the laminated sediments from the Swaziland Sequence were deposited by an active stratified microbial community. However, we propose that these organisms which were preserved were originally buried in the associated sulfide-rich muds and were subsequently silicified.     

Infrared Spectroscopic Biosignatures from Hidden Cave,New Mexico: Possible Applications for Remote Life Detection

Subsurface environments are known to support and preserve diverse microbial communities. Giant pool fingers from Hidden Cave, New Mexico consist of mm-scale dark micritic calcite layers alternating with clear dogtooth spar crystals and contain morphological and geochemical evidence of past microbial communities. We used Fourier Transform infrared spectroscopy to identify fatty acids, proteins, PO₂-carrying compounds, and polysaccharides spatially related to morphological fossil filaments throughout the surface micritic laminations and central pool finger regions. These biomolecular signatures are important components that contribute to the biosignature suite under development that identify microbial involvement in carbonate precipitation on Earth and remotely.     

Factors determining soil microbial biomass and nutrient immobilization in desert soils

We examined the 10-day response of soil microbial biomass-N to additions of carbon (dextrose) and nitrogen (NH₄NO₃) to water-amended soils in a factorial experiment in four plant communities of the Chihuahuan desert of New Mexico (U.S.A.). In each site, microbial biomass-N and soil carbohydrates increased and extractable soil N decreased in response to watering alone. Fertilization with N increased microbial biomass-N in grassland soils; whereas, fertilization with C increased microbial biomass-N and decreased extractable N and P in all communities dominated by shrubs, which have invaded large areas of grassland in the Chihuahuan desert during the last 100 years. Our results support the hypothesis that the control of soil microbial biomass shifts from N to C when the ratio of C to N decreases during desertification.     

Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites,under natural conditions and methanogenic microcosm experiments

Extremophiles - Bacterial and archaeal community structure of five microbial communities, developing at different salinities in Baja California Sur, Mexico, were characterized by 16S rRNA...     

Diversity and distribution in hypersaline microbial mats of bacteria related to Chloroflexus spp

Filamentous bacteria containing bacteriochlorophylls c and a were enriched from hypersaline microbial mats. Based on phylogenetic analyses of 16S rRNA gene sequences, these organisms form a previously undescribed lineage distantly related to Chloroflexus spp. We developed and tested a set of PCR primers for the specific amplification of 16S rRNA genes from filamentous phototrophic bacteria within the kingdom of "green nonsulfur bacteria." PCR products recovered from microbial mats in a saltern in Guerrero Negro, Mexico, were subjected to cloning or denaturing gradient gel electrophoresis and then sequenced. We found evidence of a high diversity of bacteria related to Chloroflexus which exhibit different distributions along a gradient of salinity from 5.5 to 16%.     

Microbial endemism: does phosphorus limitation enhance speciation?

There is increasing evidence for the existence of unique ecosystems that are dominated by locally adapted microbiota which harbour distinct lineages and biological capabilities, much like the macrobiota of Darwin's Galapagos Islands. As a primary example of such a system, we highlight key discoveries from the Cuatro Ciénegas basin in Mexico. We argue that high microbial endemism requires a combination of geographical isolation, long-term continuity and mechanisms for reducing the intensity of horizontal gene transfer (HGT). We also propose that strong phosphorus limitation has an important role in microbial diversification by reducing the intensity of HGT.     

Paleoecology of Neoproterozoic hypersaline environments: Biomarker evidence for haloarchaea,methanogens, and cyanobacteria

While numerous studies have examined modern hypersaline ecosystems, their equivalents in the geologic past, particularly in the Precambrian, are poorly understood. In this study, biomarkers from ~820 million year (Ma)‐old evaporites from the Gillen Formation of the mid‐Neoproterozoic Bitter Springs Group, central Australia, are investigated to elucidate the antiquity and paleoecology of halophiles. The sediments were composed of alternating laminae of dolomitized microbial mats and up to 90% anhydrite. Solvent extraction of these samples yielded thermally well‐preserved hydrocarbon biomarkers. The regularly branched C₂₅ isoprenoid 2,6,10,14,18‐pentamethylicosane, the tail‐to‐tail linked C₃₀ isoprenoid squalane, and breakdown products of the head‐to‐head linked C₄₀ isoprenoid biphytane, were particularly abundant in the most anhydrite‐rich sediments and mark the oldest current evidence for halophilic archaea. Linear correlations between isoprenoid concentrations (normalized to n‐alkanes) and the anhydrite/dolomite ratio reveal microbial consortia that fluctuated with changing salinity levels. Halophilic archaea were the dominant organisms during periods of high salinity and gypsum precipitation, while bacteria were prevalent during stages of carbonate formation. The irregularly branched C₂₅ isoprenoid 2,6,10,15,19‐pentamethylicosane (PMI), with a central tail‐to‐tail link, was also abundant during periods of elevated salinity, highlighting the activity of methanogens. By contrast, the irregularly branched C₂₀ isoprenoid 2,6,11,15‐tetramethylhexadecane (crocetane) was more common in dolomite‐rich facies, revealing that an alternate group of archaea was active during less saline periods. Elevated concentrations of isotopically depleted heptadecane (n‐C₁₇) revealed the presence of cyanobacteria under all salinity regimes. The combination of biomarkers in the mid‐Neoproterozoic Gillen Formation resembles lipid compositions from modern hypersaline cyanobacterial mats, pointing to a community composition that remained broadly constant since at least the Neoproterozoic. However, as a major contrast to most modern hypersaline environments, the Gillen evaporites did not yield any evidence for algae or other eukaryotes.     

Dispersed oil disrupts microbial pathways in pelagic food webs

Most of the studies of microbial processes in response to the Deepwater Horizon oil spill focused on the deep water plume, and not on the surface communities. The effects of the crude oil and the application of dispersants on the coastal microbial food web in the northern Gulf of Mexico have not been well characterized even though these regions support much of the fisheries production in the Gulf. A mesocosm experiment was carried out to determine how the microbial community off the coast of Alabama may have responded to the influx of surface oil and dispersants. While the addition of glucose or oil alone resulted in an increase in the biomass of ciliates, suggesting transfer of carbon to higher trophic levels was likely; a different effect was seen in the presence of dispersant. The addition of dispersant or dispersed oil resulted in an increase in the biomass of heterotrophic prokaryotes, but a significant inhibition of ciliates, suggesting a reduction in grazing and decrease in transfer of carbon to higher trophic levels. Similar patterns were observed in two separate experiments with different starting nutrient regimes and microbial communities suggesting that the addition of dispersant and dispersed oil to the northern Gulf of Mexico waters in 2010 may have reduced the flow of carbon to higher trophic levels, leading to a decrease in the production of zooplankton and fish on the Alabama shelf.     

Mathematical simulation of the diel O, S, and C biogeochemistry of a hypersaline microbial mat

The creation of a mathematical simulation model of photosynthetic microbial mats is important to our understanding of key biogeochemical cycles that may have altered the atmospheres and lithospheres of early Earth. A model is presented here as a tool to integrate empirical results from research on hypersaline mats from Baja California Sur (BCS), Mexico into a computational system that can be used to simulate biospheric inputs of trace gases to the atmosphere. The first version of our model, presented here, calculates fluxes and cycling of O(2), sulfide, and dissolved inorganic carbon (DIC) via abiotic components and via four major microbial guilds: cyanobacteria (CYA), sulfate reducing bacteria (SRB), purple sulfur bacteria (PSB) and colorless sulfur bacteria (CSB). We used generalized Monod-type equations that incorporate substrate and energy limits upon maximum rates of metabolic processes such as photosynthesis and sulfate reduction. We ran a simulation using temperature and irradiance inputs from data collected from a microbial mat in Guerrero Negro in BCS (Mexico). Model O(2), sulfide, and DIC concentration profiles and fluxes compared well with data collected in the field mats. There were some model-predicted features of biogeochemical cycling not observed in our actual measurements. For instance, large influxes and effluxes of DIC across the MBGC mat boundary may reveal previously unrecognized, but real, in situ limits on rates of biogeochemical processes. Some of the short-term variation in field-collected mat O(2) was not predicted by MBGC. This suggests a need both for more model sensitivity to small environmental fluctuations for the incorporation of a photorespiration function into the model.     

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in the United State history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety of metabolic genes involved in both aerobic and anaerobic hydrocarbon degradation were highly enriched in the plume compared with outside the plume, indicating a great potential for intrinsic bioremediation or natural attenuation in the deep sea. Various other microbial functional genes that are relevant to carbon, nitrogen, phosphorus, sulfur and iron cycling, metal resistance and bacteriophage replication were also enriched in the plume. Together, these results suggest that the indigenous marine microbial communities could have a significant role in biodegradation of oil spills in deep-sea environments.     

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

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.     

Impact of paleoclimate on the distribution of microbial communities in the subsurface sediment of the Dead Sea

A long sedimentary core has been recently retrieved from the Dead Sea Basin (DSB) within the framework of the ICDP‐sponsored Dead Sea Deep Drilling Project. Contrasting climatic intervals were evident by distinctive lithological facies such as laminated aragonitic muds and evaporites. A geomicrobiological investigation was conducted in representative sediments of this core. To identify the microbial assemblages present in the sediments and their evolution with changing depositional environments through time, the diversity of the 16S rRNA gene was analyzed in gypsum, aragonitic laminae, and halite samples. The subsurface microbial community was largely dominated by the Euryarchaeota phylum (Archaea). Within the latter, Halobacteriaceae members were ubiquitous, probably favored by their ‘high salt‐in’ osmotic adaptation which also makes them one of the rare inhabitants of the modern Dead Sea. Bacterial community members were scarce, emphasizing that the ‘low salt‐in’ strategy is less suitable in this environment. Substantial differences in assemblages are observed between aragonitic sediments and gypsum–halite ones, independently of the depth and salinity. The aragonite sample, deposited during humid periods when the lake was stratified, consists mostly of the archaeal MSBL1 and bacterial KB1 Candidate Divisions. This consortium probably relies on compatible solutes supplied from the lake by halotolerant species present in these more favorable periods. In contrast, members of the Halobacteriaceae were the sole habitants of the gypsum–halite sediments which result from a holomictic lake. Although the biomass is low, these variations in the observed subsurface microbial populations appear to be controlled by biological conditions in the water column at the time of sedimentation, and subsequently by the presence or absence of stratification and dilution in the lake. As the latter are controlled by climatic changes, our data suggest a relationship between local lacustrine subsurface microbial assemblages and large‐scale climatic variations over the Dead Sea Basin.     

Nitrogen Fixation in Microbial Mat and Stromatolite Communities from Cuatro Cienegas,Mexico

Nitrogen fixation (nitrogenase activity, NA) of a microbial mat and a living stromatolite from Cuatro Cienegas, Mexico, was examined over spring, summer, and winter of 2004. The goal of the study was to characterize the diazotrophic community through molecular analysis of the nifH gene and using inhibitors of sulfate reduction and oxygenic and anoxygenic photosynthesis. We also evaluated the role of ultraviolet radiation on the diazotrophic activity of the microbial communities. Both microbial communities showed patterns of NA with maximum rates during the day that decreased significantly with 3-3,4-dichlorophenyl-1′,1′-dimethylurea, suggesting the potential importance of heterocystous cyanobacteria. There is also evidence of NA by sulfur-reducing bacteria in both microbial communities suggested by the negative effect exerted by the addition of sodium molybdate. Elimination of infrared and ultraviolet radiation had no effect on NA. Both microbial communities had nifH sequences that related to group I, including cyanobacteria and purple sulfur and nonsulfur bacteria, as well as group II nitrogenases, including sulfur reducing and green sulfur bacteria.     

Gypsum whiskers in Messinian evaporites identified by μ-XRD<Superscript>2</Superscript>

The gypsum mineralogy of hair-like, so-called whisker crystals was determined by micro X-ray diffractometry equipped with a focusing X-ray optic and a two-dimensional detector (μ-XRD²). Gypsum whiskers typically form by efflorescence on surfaces that are in contact with water. The delicate whiskers studied here formed within a Messinian evaporite mostly consisting of anhydrite. They project from alabastrine gypsum into former cavities. The gypsum resulted from hydration of anhydrite. Whiskers were finally engulfed by biogenic, native sulphur, which filled the cavities in the course of microbial alteration of the host lithology. The sulphur protected the delicate whisker crystals from destruction, including a period of exposure to weathering on a dumping site of a former mine where the rocks have been sampled. To the best of our knowledge, this is the first report of gypsum whiskers in evaporites. More significantly, this study reveals that μ-XRD² has great potential for sedimentary petrology, allowing the in situ identification of minute mineral phases that cannot be identified with conventional techniques.     

Diversity and Distribution in Hypersaline Microbial Mats of Bacteria Related to Chloroflexus spp.

Filamentous bacteria containing bacteriochlorophylls c and a were enriched from hypersaline microbial mats. Based on phylogenetic analyses of 16S rRNA gene sequences, these organisms form a previously undescribed lineage distantly related to Chloroflexus spp. We developed and tested a set of PCR primers for the specific amplification of 16S rRNA genes from filamentous phototrophic bacteria within the kingdom of “green nonsulfur bacteria.” PCR products recovered from microbial mats in a saltern in Guerrero Negro, Mexico, were subjected to cloning or denaturing gradient gel electrophoresis and then sequenced. We found evidence of a high diversity of bacteria related to Chloroflexus which exhibit different distributions along a gradient of salinity from 5.5 to 16%.     

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.     

Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates.

Although there is significant interest in the potential interactions of microbes with gas hydrate, no direct physical association between them has been demonstrated. We examined several intact samples of naturally occurring gas hydrate from the Gulf of Mexico for evidence of microbes. All samples were collected from anaerobic hemipelagic mud within the gas hydrate stability zone, at water depths in the ca. 540- to 2,000-m range. The delta(13)C of hydrate-bound methane varied from -45.1 per thousand Peedee belemnite (PDB) to -74.7 per thousand PDB, reflecting different gas origins. Stable isotope composition data indicated microbial consumption of methane or propane in some of the samples. Evidence of the presence of microbes was initially determined by 4,6-diamidino 2-phenylindole dihydrochloride (DAPI) total direct counts of hydrate-associated sediments (mean = 1.5 x 10(9) cells g(-1)) and gas hydrate (mean = 1.0 x 10(6) cells ml(-1)). Small-subunit rRNA phylogenetic characterization was performed to assess the composition of the microbial community in one gas hydrate sample (AT425) that had no detectable associated sediment and showed evidence of microbial methane consumption. Bacteria were moderately diverse within AT425 and were dominated by gene sequences related to several groups of Proteobacteria, as well as Actinobacteria and low-G + C Firmicutes. In contrast, there was low diversity of Archaea, nearly all of which were related to methanogenic Archaea, with the majority specifically related to Methanosaeta spp. The results of this study suggest that there is a direct association between microbes and gas hydrate, a finding that may have significance for hydrocarbon flux into the Gulf of Mexico and for life in extreme environments.     

Ribosomal RNA gene fragments from fossilized cyanobacteria identified in primary gypsum from the late Miocene,Italy

Earth scientists have searched for signs of microscopic life in ancient samples of permafrost, ice, deep‐sea sediments, amber, salt and chert. Until now, evidence of cyanobacteria has not been reported in any studies of ancient DNA older than a few thousand years. Here, we investigate morphologically, biochemically and genetically primary evaporites deposited in situ during the late Miocene (Messinian) Salinity Crisis from the north‐eastern Apennines of Italy. The evaporites contain fossilized bacterial structures having identical morphological forms as modern microbes. We successfully extracted and amplified genetic material belonging to ancient cyanobacteria from gypsum crystals dating back to 5.910–5.816 Ma, when the Mediterranean became a giant hypersaline brine pool. This finding represents the oldest ancient cyanobacterial DNA to date. Our clone library and its phylogenetic comparison with present cyanobacterial populations point to a marine origin for the depositional basin. This investigation opens the possibility of including fossil cyanobacterial DNA into the palaeo‐reconstruction of various environments and could also be used to quantify the ecological importance of cyanobacteria through geological time. These genetic markers serve as biosignatures providing important clues about ancient life and begin a new discussion concerning the debate on the origin of late Miocene evaporites in the Mediterranean.