Microbial lithification in marine stromatolites and hypersaline mats

Calcium dynamics in microbialite-forming exopolymer-rich mats on the atoll of Kiritimati, Republic of Kiribati, Central Pacific

Microbialite-forming microbial mats in a hypersaline lake on the atoll of Kiritimati were investigated with respect to microgradients, bulk water chemistry, and microbial community composition. O2, H2S, and pH microgradients show patterns as commonly observed for phototrophic mats with cyanobacteria-dominated primary production in upper layers, an intermediate purple layer with sulfide oxidation, and anaerobic bottom layers with sulfate reduction. Ca(2+) profiles, however, measured in daylight showed an increase of Ca(2+) with depth in the oxic zone, followed by a sharp decline and low concentrations in anaerobic mat layers. In contrast, dark measurements show a constant Ca(2+) concentration throughout the entire measured depth. This is explained by an oxygen-dependent heterotrophic decomposition of Ca(2+)-binding exopolymers. Strikingly, the daylight maximum in Ca(2+) and subsequent drop coincides with a major zone of aragonite and gypsum precipitation at the transition from the cyanobacterial layer to the purple sulfur bacterial layer. Therefore, we suggest that Ca(2+) binding exopolymers function as Ca(2+) shuttle by their passive downward transport through compression, triggering aragonite precipitation in the mats upon their aerobic microbial decomposition and secondary Ca(2+) release. This precipitation is mediated by phototrophic sulfide oxidizers whose action additionally leads to the precipitation of part of the available Ca(2+) as gypsum.

Assessment of the physicochemical conditions sediments in a polluted tidal flat colonized by microbial mats in Bahía Blanca Estuary (Argentina)

The aim of this work is to assess the physicochemical conditions of the supratidal sediments colonized by microbial mats at two sites from Rosales Harbor (Bahía Blanca Estuary, Argentina) close to sewage discharge. Both sites differed in the size grain. No differences in pH, Eh and temperature were observed. Moisture retention and chlorophyll a concentration were significantly different between sites and sediment layers. Heavy metals and organic matter content were significantly higher in SII. No statistical differences were found in porewater nutrients concentration, being higher in SI (except DSi). The presence of Escherichia coli in water and sediment (1000 CFU/100 mL - uncountable and 35-40 CFU g(-1) dw, respectively) evidenced microbial contamination in the study area. The relationships between the physicochemical parameters evaluated and the influence of the sewage discharge allow defining two different areas in the Rosales Harbor despite the proximity and the presence of microbial mats.

Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat

During a study of the anaerobic microbial community of a lithifying hypersaline microbial mat of Lake 21 on the Kiritimati atoll (Kiribati Republic, Central Pacific) strain L21-RPul-D2^T was isolated. The closest phylogenetic neighbor was Spirochaeta africana Z-7692^T that shared a 16S rRNA gene sequence identity value of 90% with the novel strain and thus was only distantly related. A comprehensive polyphasic study including determination of the complete genome sequence was initiated to characterize the novel isolate.

Cells of strain L21-RPul-D2^T had a size of 0.2 – 0.25 × 8–9 μm, were helical, motile, stained Gram-negative and produced an orange carotenoid-like pigment. Optimal conditions for growth were 35°C, a salinity of 50 g/l NaCl and a pH around 7.0. Preferred substrates for growth were carbohydrates and a few carboxylic acids. The novel strain had an obligate fermentative metabolism and produced ethanol, acetate, lactate, hydrogen and carbon dioxide during growth on glucose. Strain L21-RPul-D2^T was aerotolerant, but oxygen did not stimulate growth. Major cellular fatty acids were C_14:0, iso-C_15:0, C_16:0 and C_18:0. The major polar lipids were an unidentified aminolipid, phosphatidylglycerol, an unidentified phospholipid and two unidentified glycolipids. Whole-cell hydrolysates contained L-ornithine as diagnostic diamino acid of the cell wall peptidoglycan. The complete genome sequence was determined and annotated. The genome comprised one circular chromosome with a size of 3.78 Mbp that contained 3450 protein-coding genes and 50 RNA genes, including 2 operons of ribosomal RNA genes. The DNA G + C content was determined from the genome sequence as 51.9 mol%. There were no predicted genes encoding cytochromes or enzymes responsible for the biosynthesis of respiratory lipoquinones.

Based on significant differences to the uncultured type species of the genus Spirochaeta, S. plicatilis, as well as to any other phylogenetically related cultured species it is suggested to place strain L21-RPul-D2^T (=DSM 27196^T = JCM 18663^T) in a novel species and genus, for which the name Salinispira pacifica gen. nov., sp. nov. is proposed.

Adaptation, ecology, and evolution of the halophilic stromatolite archaeon Halococcus hamelinensis inferred through genome analyses

Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

Effect of carbonic anhydrase on silicate weathering and carbonate formation at present day CO₂ concentrations compared to primordial values

It is widely recognized that carbonic anhydrase (CA) participates in silicate weathering and carbonate formation. Nevertheless, it is still not known if the magnitude of the effect produced by CA on surface rock evolution changes or not. In this work, CA gene expression from Bacillus mucilaginosus and the effects of recombination protein on wollastonite dissolution and carbonate formation under different conditions are explored. Real-time fluorescent quantitative PCR was used to explore the correlation between CA gene expression and sufficiency or deficiency in calcium and CO₂ concentration. The results show that the expression of CA genes is negatively correlated with both CO₂ concentration and ease of obtaining soluble calcium. A pure form of the protein of interest (CA) is obtained by cloning, heterologous expression, and purification. The results from tests of the recombination protein on wollastonite dissolution and carbonate formation at different levels of CO₂ concentration show that the magnitudes of the effects of CA and CO₂ concentration are negatively correlated. These results suggest that the effects of microbial CA in relation to silicate weathering and carbonate formation may have increased importance at the modern atmospheric CO₂ concentration compared to 3 billion years ago.

Spatial variability in photosynthetic and heterotrophic activity drives localized δ13C org fluctuations and carbonate precipitation in hypersaline microbial mats

Modern laminated photosynthetic microbial mats are ideal environments to study how microbial activity creates and modifies carbon and sulfur isotopic signatures prior to lithification. Laminated microbial mats from a hypersaline lagoon (Guerrero Negro, Baja California, Mexico) maintained in a flume in a greenhouse at NASA Ames Research Center were sampled for δ(13) C of organic material and carbonate to assess the impact of carbon fixation (e.g., photosynthesis) and decomposition (e.g., bacterial respiration) on δ(13) C signatures. In the photic zone, the δ(13) C org signature records a complex relationship between the activities of cyanobacteria under variable conditions of CO2 limitation with a significant contribution from green sulfur bacteria using the reductive TCA cycle for carbon fixation. Carbonate is present in some layers of the mat, associated with high concentrations of bacteriochlorophyll e (characteristic of green sulfur bacteria) and exhibits δ(13) C signatures similar to DIC in the overlying water column (-2.0‰), with small but variable decreases consistent with localized heterotrophic activity from sulfate-reducing bacteria (SRB). Model results indicate respiration rates in the upper 12 mm of the mat alter in situ pH and HCO3- concentrations to create both phototrophic CO2 limitation and carbonate supersaturation, leading to local precipitation of carbonate minerals. The measured activity of SRB with depth suggests they variably contribute to decomposition in the mat dependent on organic substrate concentrations. Millimeter-scale variability in the δ(13) C org signature beneath the photic zone in the mat is a result of shifting dominance between cyanobacteria and green sulfur bacteria with the aggregate signature overprinted by heterotrophic reworking by SRB and methanogens. These observations highlight the impact of sedimentary microbial processes on δ(13) C org signatures; these processes need to be considered when attempting to relate observed isotopic signatures in ancient sedimentary strata to conditions in the overlying water column at the time of deposition and associated inferences about carbon cycling.

A mineralogical characterization of biogenic calcium carbonates precipitated by heterotrophic bacteria isolated from cryophilic polar regions

Precipitation of calcium carbonate (CaCO3(s) ) can be driven by microbial activity. Here, a systematic approach is used to identify the morphological and mineralogical characteristics of CaCO3(s) precipitated during the heterotrophic growth of micro-organisms isolated from polar environments. Focus was placed on establishing mineralogical features that are common in bioliths formed during heterotrophic activity, while in parallel identifying features that are specific to bioliths precipitated by certain microbial phylotypes. Twenty microbial isolates that precipitated macroscopic CaCO3(s) when grown on B4 media supplemented with calcium acetate or calcium citrate were identified. A multimethod approach, including scanning electron microscopy, high-resolution transmission electron microscopy, and micro-X-ray diffraction (μ-XRD), was used to characterize CaCO3(s) precipitates. Scanning and transmission electron microscopy showed that complete CaCO3(s) crystal encrustation of Arthrobacter sp. cells was common, while encrustation of Rhodococcus sp. cells did not occur. Several euhedral and anhedral mineral formations including disphenoid-like epitaxial plates, rhomboid-like aggregates with epitaxial rhombs, and spherulite aggregates were observed. While phylotype could not be linked to specific mineral formations, isolates tended to precipitate either euhedral or anhedral minerals, but not both. Three anhydrous CaCO3(s) polymorphs (calcite, aragonite, and vaterite) were identified by μ-XRD, and calcite and aragonite were also identified based on TEM lattice-fringe d value measurements. The presence of certain polymorphs was not indicative of biogenic origin, although several mineralogical features such as crystal-encrusted bacterial cells, or casts of bacterial cells embedded in mesocrystals are an indication of biogenic origin. In addition, some features such as the formation of vaterite and bacterial entombment appear to be linked to certain phylotypes. Identifying phylotypes consistent with certain mineralogical features is the first step toward discovering a link between these crystal features and the precise underlying molecular biology of the organism precipitating them.

Millennial-scale ocean acidification and late Quaternary decline of cryptic bacterial crusts in tropical reefs

Ocean acidification by atmospheric carbon dioxide has increased almost continuously since the last glacial maximum (LGM), 21,000 years ago. It is expected to impair tropical reef development, but effects on reefs at the present day and in the recent past have proved difficult to evaluate. We present evidence that acidification has already significantly reduced the formation of calcified bacterial crusts in tropical reefs. Unlike major reef builders such as coralline algae and corals that more closely control their calcification, bacterial calcification is very sensitive to ambient changes in carbonate chemistry. Bacterial crusts in reef cavities have declined in thickness over the past 14,000 years with largest reduction occurring 12,000-10,000 years ago. We interpret this as an early effect of deglacial ocean acidification on reef calcification and infer that similar crusts were likely to have been thicker when seawater carbonate saturation was increased during earlier glacial intervals, and thinner during interglacials. These changes in crust thickness could have substantially affected reef development over glacial cycles, as rigid crusts significantly strengthen framework and their reduction would have increased the susceptibility of reefs to biological and physical erosion. Bacterial crust decline reveals previously unrecognized millennial-scale acidification effects on tropical reefs. This directs attention to the role of crusts in reef formation and the ability of bioinduced calcification to reflect changes in seawater chemistry. It also provides a long-term context for assessing anticipated anthropogenic effects.

16S rDNA-based analysis reveals cosmopolitan occurrence but limited diversity of two cyanobacterial lineages with contrasted patterns of intracellular carbonate mineralization

Cyanobacteria are mainly thought to induce carbonate precipitation extracellularly via their photosynthetic activity combined with the nucleation potential of exopolymeric substances. The discovery in microbialites of the alkaline lake Alchichica (Mexico) of Candidatus Gloeomargarita lithophora, a cyanobacterium forming large amounts of intracellular Mg-Ca-Sr-Ba carbonate spherules, showed that intracellular biomineralization in cyanobacteria is also possible. A second cyanobacterium isolated from the same environment, Candidatus Synechococcus calcipolaris G9, has been recently shown to also form intracellular calcium carbonates at the cell poles, a capability shared by all cultured species of the Thermosynechococcus clade, to which it belongs. To explore the diversity of these two distant cyanobacterial lineages representing two different patterns of intracellular calcification, we designed specific primers against their 16S rRNA genes and looked for their occurrence in a wide variety of samples. We identified the presence of members of the Gloeomargarita and Thermosynechococcus/S. calcipolaris lineages in microbialites collected from Lake Alchichica and three other neighboring Mexican lakes. The two clades also occurred in karstic areas and in some thermophilic or hypersaline microbial mats collected in South America and/or Southern Europe. Surprisingly, the within-group diversity in the two clades was low, especially within the S. calcipolaris clade, with all 16S rRNA gene sequences retrieved sharing more than 97% identity. This suggests that these clades are composed of a limited number of operational taxonomic units (OTUs) with cosmopolitan distribution. Moreover, scanning electron microscopy coupled with energy dispersive x-ray spectrometry showed the presence of intracellularly calcifying Gloeomargarita-like cyanobacteria in fresh samples where this clade was relatively abundant, suggesting that these cyanobacteria do precipitate carbonates intracellularly under natural conditions.

Prokaryote populations of extant microbialites along a depth gradient in Pavilion Lake, British Columbia, Canada

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.

Functional gene diversity of oolitic sands from Great Bahama Bank

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.

Commensal symbiosis between agglutinated polychaetes and sulfate-reducing bacteria

Pendant bioconstructions occur within submerged caves in the Plemmirio Marine Protected Area in SE Sicily, Italy. These rigid structures, here termed biostalactites, were synsedimentarily lithified by clotted-peloidal microbial carbonate that has a high bacterial lipid biomarker content with abundant compounds derived from sulfate-reducing bacteria. The main framework builders are polychaete serpulid worms, mainly Protula with subordinate Semivermilia and Josephella. These polychaetes have lamellar and/or fibrillar wall structure. In contrast, small agglutinated terebellid tubes, which are a minor component of the biostalactites, are discontinuous and irregular with a peloidal micritic microfabric. The peloids, formed by bacterial sulfate reduction, appear to have been utilized by terebellids to construct tubes in an environment where other particulate sediment is scarce. We suggest that the bacteria obtained food from the worms in the form of fecal material and/or from the decaying tissue of surrounding organisms and that the worms obtained peloidal micrite with which to construct their tubes, either as grains and/or as tube encompassing biofilm. Peloidal worm tubes have rarely been reported in the recent but closely resemble examples in the geological record that extend back at least to the early Carboniferous. This suggests a long-lived commensal relationship between some polychaete worms and heterotrophic, especially sulfate-reducing, bacteria.

Lacustrine Nostoc (Nostocales) and associated microbiome generate a new type of modern clotted microbialite

Microbialites are mineral formations formed by microbial communities that are often dominated by cyanobacteria. Carbonate microbialites, known from Proterozoic times through the present, are recognized for sequestering globally significant amounts of inorganic carbon. Recent ecological work has focused on microbial communities dominated by cyanobacteria that produce microbial mats and laminate microbialites (stromatolites). However, the taxonomic composition and functions of microbial communities that generate distinctive clotted microbialites (thrombolites) are less well understood. Here, microscopy and deep shotgun sequencing were used to characterize the microbiome (microbial taxa and their genomes) associated with a single cyanobacterial host linked by 16S sequences to Nostoc commune Vaucher ex Bornet & Flahault, which dominates abundant littoral clotted microbialites in shallow, subpolar, freshwater Laguna Larga in southern Chile. Microscopy and energy-dispersive X-ray spectroscopy suggested the hypothesis that adherent hollow carbonate spheres typical of the clotted microbialite begin development on the rigid curved outer surfaces of the Nostoc balls. A surface biofilm included >50 nonoxygenic bacterial genera (taxa other than Nostoc) that indicate diverse ecological functions. The Laguna Larga Nostoc microbiome included the sulfate reducers Desulfomicrobium and Sulfospirillum and genes encoding all known proteins specific to sulfate reduction, a process known to facilitate carbonate deposition by increasing pH. Sequences indicating presence of nostocalean and other types of nifH, nostocalean sulfide:ferredoxin oxidoreductase (indicating anoxygenic photosynthesis), and biosynthetic pathways for the secondary products scytonemin, mycosporine, and microviridin toxin were identified. These results allow comparisons with microbiota and microbiomes of other algae and illuminate biogeochemical roles of ancient microbialites.

Community structure and activity of a highly dynamic and nutrient-limited hypersaline microbial mat in Um Alhool Sabkha, Qatar

The Um Alhool area in Qatar is a dynamic evaporative ecosystem that receives seawater from below as it is surrounded by sand dunes. We investigated the chemical composition, the microbial activity and biodiversity of the four main layers (L1–L4) in the photosynthetic mats. Chlorophyll a (Chl a) concentration and distribution (measured by HPLC and hyperspectral imaging, respectively), the phycocyanin distribution (scanned with hyperspectral imaging), oxygenic photosynthesis (determined by microsensor), and the abundance of photosynthetic microorganisms (from 16S and 18S rRNA sequencing) decreased with depth in the euphotic layer (L1). Incident irradiance exponentially attenuated in the same zone reaching 1% at 1.7-mm depth. Proteobacteria dominated all layers of the mat (24%–42% of the identified bacteria). Anoxygenic photosynthetic bacteria (dominated by Chloroflexus) were most abundant in the third red layer of the mat (L3), evidenced by the spectral signature of Bacteriochlorophyll as well as by sequencing. The deep, black layer (L4) was dominated by sulfate reducing bacteria belonging to the Deltaproteobacteria, which were responsible for high sulfate reduction rates (measured using ³⁵S tracer). Members of Halobacteria were the dominant Archaea in all layers of the mat (92%–97%), whereas Nematodes were the main Eukaryotes (up to 87%). Primary productivity rates of Um Alhool mat were similar to those of other hypersaline microbial mats. However, sulfate reduction rates were relatively low, indicating that oxygenic respiration contributes more to organic material degradation than sulfate reduction, because of bioturbation. Although Um Alhool hypersaline mat is a nutrient-limited ecosystem, it is interestingly dynamic and phylogenetically highly diverse. All its components work in a highly efficient and synchronized way to compensate for the lack of nutrient supply provided during regular inundation periods.

Characterizing microbial communities and processes in a modern stromatolite (Shark Bay) using lipid biomarkers and two-dimensional distributions of porewater solutes

Modern microbial mats are highly complex and dynamic ecosystems. Diffusive equilibration in thin films (DET) and diffusive gradients in thin films (DGT) samplers were deployed in a modern smooth microbial mat from Shark Bay in order to observe, for the first time, two-dimensional distributions of porewater solutes during day and night time. Two-dimensional sulfide and alkalinity distributions revealed a strong spatial heterogeneity and a minor contribution of sulfide to alkalinity. Phosphate distributions were also very heterogeneous, while iron(II) distributions were quite similar during day and night with a few hotspots of mobilization. Lipid biomarkers from the three successive layers of the mat were also analysed in order to characterize the microbial communities regulating analyte distributions. The major hydrocarbon products detected in all layers included n-alkanes and isoprenoids, whilst other important biomarkers included hopanoids. Phospholipid fatty acid profiles revealed a decrease in cyanobacterial markers with depth, whereas sulfate-reducing bacteria markers increased in abundance in accordance with rising sulfide concentrations with depth. Despite the general depth trends in community structure and physiochemical conditions within the mat, two-dimensional solute distributions showed considerable small-scale lateral variability, indicating that the distributions and activities of the microbial communities regulating these solute distributions were equally heterogeneous and complex.

Stromatolitic knobs in Storr's Lake (San Salvador, Bahamas): a model system for formation and alteration of laminae

The initial lamination in young, metabolically active Scytonema knobs developing in Storr's Lake (Bahamas) results from the iterative succession of two different stages of microbial growth at the top of this microbialite. Stage 1 is dominated by vertically oriented cyanobacterial filaments and is characterized by a high porosity of the fabric. Stage 2 shows a higher microbial density with the filaments oriented horizontally and with higher carbonate content. The more developed, dense microbial community associated with Stage 2 of the Scytonema knobs rapidly degrades extracellular organic matter (EOM) and coupled to this, precipitates carbonate. The initial nucleation forms high-Mg calcite nanospheroids that progressively replace the EOM. No precipitation is observed within the thick sheath of the Scytonema filaments, possibly because of strong cross-linking of calcium and EOM (forming EOM-Ca-EOM complexes), which renders Ca unavailable for carbonate nucleation (inhibition process). Eventually, organominerals precipitate and form an initial lamina through physicochemical and microbial processes, including high rates of photosynthetic activity that lead to (13) C-enriched DIC available for initial nucleation. As this lamina moves downward by the iterative production of new laminae at the top of the microbialite, increased heterotrophic activity further alters the initial mineral product at depth. Although some rare relic preservation of 'Stage 1-Stage 2' laminae in subfossil knobs exists, the very fine primary lamination is considerably altered and almost completely lost when the knobs develop into larger and more complex morphologies due to the increased accommodation space and related physicochemical and/or biological alteration. Despite considerable differences in microstructure, the emerging ecological model of community succession leading to laminae formation described here for the Scytonema knobs can be applied to the formation of coarse-grained, open marine stromatolites. Therefore, both fine- and coarse-grained extant stromatolites can be used as model systems to understand the formation of microbialites in the fossil record.

Metabolic potential of lithifying cyanobacteria-dominated thrombolitic mats

Thrombolites are unlaminated carbonate deposits formed by the metabolic activities of microbial mats and can serve as potential models for understanding the molecular mechanisms underlying the formation of lithifying communities. To assess the metabolic complexity of these ecosystems, high throughput DNA sequencing of a thrombolitic mat metagenome was coupled with phenotypic microarray analysis. Functional protein analysis of the thrombolite community metagenome delineated several of the major metabolic pathways that influence carbonate mineralization including cyanobacterial photosynthesis, sulfate reduction, sulfide oxidation, and aerobic heterotrophy. Spatial profiling of metabolite utilization within the thrombolite-forming microbial mats suggested that the top 5 mm contained a more metabolically diverse and active community than the deeper within the mat. This study provides evidence that despite the lack of mineral layering within the clotted thrombolite structure there is a vertical gradient of metabolic activity within the thrombolitic mat community. This metagenomic profiling also serves as a foundation for examining the active role individual functional groups of microbes play in coordinating metabolisms that lead to mineralization.

Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche

Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of hpnP, the gene encoding the C-2 hopanoid methylase. Here we show that hpnP copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial hpnP genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether hpnP presence might track with particular variables. We found hpnP to be significantly correlated with organisms, metabolisms and environments known to support plant-microbe interactions (P-value<10(-6)); in addition, we observed diverse hpnP types in closely packed microbial communities from other environments, including stromatolites, hot springs and hypersaline microbial mats. The common features of these niches indicate that 2-methylhopanoids are enriched in sessile microbial communities inhabiting environments low in oxygen and fixed nitrogen with high osmolarity. Our results support the earlier conclusion that 2-methylhopanoids are not reliable biomarkers for cyanobacteria or any other taxonomic group, and raise the new hypothesis that, instead, they are indicators of a specific environmental niche.

Lipid biomarkers in ooids from different locations and ages: evidence for a common bacterial flora

Ooids are one of the common constituents of ancient carbonate rocks, yet the role that microbial communities may or may not play in their formation remains unresolved. To search for evidence of microbial activity in modern and Holocene ooids, samples collected from intertidal waters, beaches and outcrops in the Bahamas and in Shark Bay in Western Australia were examined for their contents of lipid biomarkers. Modern samples from Cat and Andros islands in the Bahamas and from Carbla Beach in Hamelin Pool, Western Australia, showed abundant and notably similar distributions of hydrocarbons, fatty acids (FAs) and alcohols. A large fraction of these lipids were bound into the carbonate matrix and only released on acid dissolution, which suggests that these lipids were being incorporated continuously during ooid growth. The distributions of hydrocarbons, and their disparate carbon isotopic signatures, were consistent with mixed input from cyanobacteria together with small and variable amounts of vascular plant leaf wax [C27 -C35 ; δ(13) C -25 to -32‰Vienna Pee Dee Belemnite (VPDB)]. The FAs comprised a complex mixture of C12 -C18 normal and branched short-chain compounds with the predominant straight-chain components attributable to bacteria and/or cyanobacteria. Branched FA, especially 10-MeC16 and 10-MeC17 , together with the prevalence of elemental sulfur in the extracts, indicate an origin from sulfate-reducing bacteria. The iso- and anteiso-FA were quite variable in their (13) C contents suggesting that they come from organisms with diverse physiologies. Hydrogen isotopic compositions provide further insight into this issue. FAs in each sample show disparate δD values consistent with inputs from autotrophs and heterotrophs. The most enigmatic lipid assemblage is an homologous series of long-chain (C24 -C32 ) FA with pronounced even carbon number preference. Typically, such long-chain FA are thought to come from land plant leaf wax, but in this case, their (13) C-enriched isotopic signatures compared to co-occurring n-alkanes (e.g., Hamelin Pool TLE FA C24 -C32 ; δ(13) C -20 to -24.2‰ VPDB; TLE n-alkanes δ(13) C -24.1 to -26.2 -‰VPDB) indicate a microbial origin, possibly sulfate-reducing bacteria. Lastly, we identified homohopanoic acid and bishomohopanol as the primary degradation products of bacterial hopanoids. The distributions of lipids isolated from Holocene oolites from the Rice Bay Formation of Cat Island, Bahamas were very similar to the beach ooids described above and, in total, these modern and fossil biomarker data lead us to hypothesize that ooids are colonized by a defined microbial community and that these microbes possibly mediate calcification.

Physiologic and metagenomic attributes of the rhodoliths forming the largest CaCO3 bed in the South Atlantic Ocean

Rhodoliths are free-living coralline algae (Rhodophyta, Corallinales) that are ecologically important for the functioning of marine environments. They form extensive beds distributed worldwide, providing a habitat and nursery for benthic organisms and space for fisheries, and are an important source of calcium carbonate. The Abrolhos Bank, off eastern Brazil, harbors the world's largest continuous rhodolith bed (of ∼21,000 km(2)) and has one of the largest marine CaCO3 deposits (producing 25 megatons of CaCO3 per year). Nevertheless, there is a lack of information about the microbial diversity, photosynthetic potential and ecological interactions within the rhodolith holobiont. Herein, we performed an ecophysiologic and metagenomic analysis of the Abrolhos rhodoliths to understand their microbial composition and functional components. Rhodoliths contained a specific microbiome that displayed a significant enrichment in aerobic ammonia-oxidizing betaproteobacteria and dissimilative sulfate-reducing deltaproteobacteria. We also observed a significant contribution of bacterial guilds (that is, photolithoautotrophs, anaerobic heterotrophs, sulfide oxidizers, anoxygenic phototrophs and methanogens) in the rhodolith metagenome, suggested to have important roles in biomineralization. The increased hits in aromatic compounds, fatty acid and secondary metabolism subsystems hint at an important chemically mediated interaction in which a functional job partition among eukaryal, archaeal and bacterial groups allows the rhodolith holobiont to thrive in the global ocean. High rates of photosynthesis were measured for Abrolhos rhodoliths (52.16 μmol carbon m(-2 )s(-1)), allowing the entire Abrolhos rhodolith bed to produce 5.65 × 10(5) tons C per day. This estimate illustrates the great importance of the Abrolhos rhodolith beds for dissolved carbon production in the South Atlantic Ocean.

Active eukaryotes in microbialites from Highborne Cay, Bahamas, and Hamelin Pool (Shark Bay), Australia

Microbialites are organosedimentary structures that are formed through the interaction of benthic microbial communities and sediments and include mineral precipitation. These lithifying microbial mat structures include stromatolites and thrombolites. Exuma Sound in the Bahamas, and Hamelin Pool in Shark Bay, Western Australia, are two locations where significant stands of modern microbialites exist. Although prokaryotic diversity in these structures is reasonably well documented, little is known about the eukaryotic component of these communities and their potential to influence sedimentary fabrics through grazing, binding and burrowing activities. Accordingly, comparisons of eukaryotic communities in modern stromatolitic and thrombolitic mats can potentially provide insight into the coexistence of both laminated and clotted mat structures in close proximity to one another. Here we examine this possibility by comparing eukaryotic diversity based on Sanger and high-throughput pyrosequencing of small subunit ribosomal RNA (18S rRNA) genes. Analyses were based on total RNA extracts as template to minimize input from inactive or deceased organisms. Results identified diverse eukaryotic communities particularly stramenopiles, Alveolata, Metazoa, Amoebozoa and Rhizaria within different mat types at both locations, as well as abundant and diverse signatures of eukaryotes with <80% sequence similarity to sequences in GenBank. This suggests the presence of significant novel eukaryotic diversity, particularly in hypersaline Hamelin Pool. There was evidence of vertical structuring of protist populations and foraminiferal diversity was highest in bioturbated/clotted thrombolite mats of Highborne Cay.

Specific carbonate-microbe interactions in the modern microbialites of Lake Alchichica (Mexico)

The role of microorganisms in microbialite formation remains unresolved: do they induce mineral precipitation (microbes first) or do they colonize and/or entrap abiotic mineral precipitates (minerals first)? Does this role vary from one species to another? And what is the impact of mineral precipitation on microbial ecology? To explore potential biogenic carbonate precipitation, we studied cyanobacteria-carbonate assemblages in modern hydromagnesite-dominated microbialites from the alkaline Lake Alchichica (Mexico), by coupling three-dimensional imaging of molecular fluorescence emitted by microorganisms, using confocal laser scanning microscopy, and Raman scattering/spectrometry from the associated minerals at a microscale level. Both hydromagnesite and aragonite precipitate within a complex biofilm composed of photosynthetic and other microorganisms. Morphology and pigment-content analysis of dominant photosynthetic microorganisms revealed up to six different cyanobacterial morphotypes belonging to Oscillatoriales, Chroococcales, Nostocales and Pleurocapsales, as well as several diatoms and other eukaryotic microalgae. Interestingly, one of these morphotypes, Pleurocapsa-like, appeared specifically associated with aragonite minerals, the oldest parts of actively growing Pleurocapsa-like colonies being always aragonite-encrusted. We hypothesize that actively growing cells of Pleurocapsales modify local environmental conditions favoring aragonite precipitation at the expense of hydromagnesite, which precipitates at seemingly random locations within the biofilm. Therefore, at least part of the mineral precipitation in Alchichica microbialites is most likely biogenic and the type of biominerals formed depends on the nature of the phylogenetic lineage involved. This observation may provide clues to identify lineage-specific biosignatures in fossil stromatolites from modern to Precambrian times.

Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati atoll, Central Pacific

On the Kiritimati atoll, several lakes exhibit microbial mat-formation under different hydrochemical conditions. Some of these lakes trigger microbialite formation such as Lake 21, which is an evaporitic, hypersaline lake (salinity of approximately 170‰). Lake 21 is completely covered with a thick multilayered microbial mat. This mat is associated with the formation of decimeter-thick highly porous microbialites, which are composed of aragonite and gypsum crystals. We assessed the bacterial and archaeal community composition and its alteration along the vertical stratification by large-scale analysis of 16S rRNA gene sequences of the nine different mat layers. The surface layers are dominated by aerobic, phototrophic, and halotolerant microbes. The bacterial community of these layers harbored Cyanobacteria (Halothece cluster), which were accompanied with known phototrophic members of the Bacteroidetes and Alphaproteobacteria. In deeper anaerobic layers more diverse communities than in the upper layers were present. The deeper layers were dominated by Spirochaetes, sulfate-reducing bacteria (Deltaproteobacteria), Chloroflexi (Anaerolineae and Caldilineae), purple non-sulfur bacteria (Alphaproteobacteria), purple sulfur bacteria (Chromatiales), anaerobic Bacteroidetes (Marinilabiacae), Nitrospirae (OPB95), Planctomycetes and several candidate divisions. The archaeal community, including numerous uncultured taxonomic lineages, generally changed from Euryarchaeota (mainly Halobacteria and Thermoplasmata) to uncultured members of the Thaumarchaeota (mainly Marine Benthic Group B) with increasing depth.

Fungal communities of young and mature hypersaline microbial mats

Microbial mats are a laminated organic-sedimentary ecosystem, found in a wide range of habitats. Fluctuating diel and seasonal physicochemical gradients characterize these ecosystems, resulting in both strata and microenvironments that harbor specific microbial communities. This study was undertaken to compare two types of microbial mats across seasons to further understand the structure of fungal communities in hypersaline microbial mats and their seasonal dynamics. The structure and diversity of fungal communities was documented in young transient and mature hypersaline microbial mats from a tropical region (Puerto Rico) using one culture-dependent and three culture-independent molecular techniques based on the internal transcribed spacer (ITS) region of ribosomal DNA: terminal restriction fragment length polymorphism (TRFLP), denaturing gradient gel electrophoresis (DGGE) and clone libraries. Two microbial mats (one young and transient, one mature) were sampled in Nov 2007 (wet season), Jan 2008 (intermediate season) and Mar 2008 (dry season) in the Cabo Rojo Solar Salterns on the southwestern coast of Puerto Rico. Traditional and molecular techniques revealed strong spatial and temporal heterogeneities in both microbial mats. Higher abundance of isolates and phylotypes were observed during the wet season, and diversity decreased from the top (oxic) to the bottom (anoxic) layers in both seasons. Some of the species isolated belong to the genera Aspergillus, Cladosporium, Hortaea, Pichia and Wallemia, which often are isolated from hypersaline environments. The most abundant clones belong to Acremonium strictum and Cladosporium halotolerans, which were not isolated in pure culture. The differences observed using culture-based and molecular techniques demonstrates the need of combining methods to study the diversity of fungi in a given substrate.

Heterotrophic protists in hypersaline microbial mats and deep hypersaline basin water columns

Although hypersaline environments pose challenges to life because of the low water content (water activity), many such habitats appear to support eukaryotic microbes. This contribution presents brief reviews of our current knowledge on eukaryotes of water-column haloclines and brines from Deep Hypersaline Anoxic Basins (DHABs) of the Eastern Mediterranean, as well as shallow-water hypersaline microbial mats in solar salterns of Guerrero Negro, Mexico and benthic microbialite communities from Hamelin Pool, Shark Bay, Western Australia. New data on eukaryotic diversity from Shark Bay microbialites indicates eukaryotes are more diverse than previously reported. Although this comparison shows that eukaryotic communities in hypersaline habitats with varying physicochemical characteristics are unique, several groups are commonly found, including diverse alveolates, strameonopiles, and fungi, as well as radiolaria. Many eukaryote sequences (SSU) in both regions also have no close homologues in public databases, suggesting that these environments host unique microbial eukaryote assemblages with the potential to enhance our understanding of the capacity of eukaryotes to adapt to hypersaline conditions.

Microbial mats: an ecological niche for fungi

Fungi were documented in tropical hypersaline microbial mats and their role in the degradation of complex carbohydrates (exopolymeric substance - EPS) was explored. Fungal diversity is higher during the wet season with Acremonium, Aspergillus, Cladosporium, and Penicillium among the more common genera. Diversity is also higher in the oxic layer and in young and transient mats. Enrichments with xanthan (a model EPS) show that without antibiotics (full community) degradation is faster than enrichments with antibacterial (fungal community) and antifungal (bacterial community) agents, suggesting that degradation is performed by a consortium of organisms (bacteria and fungi). The combined evidence from all experiments indicates that bacteria carried out approximately two-third of the xanthan degradation. The pattern of degradation is similar between seasons and layers but degradation is faster in enrichments from the wet season. The research suggests that fungi thrive in these hypersaline consortia and may participate in the carbon cycle through the degradation of complex carbohydrates.

The discovery of stromatolites developing at 3570 m above sea level in a high-altitude volcanic lake Socompa, Argentinean Andes

We describe stromatolites forming at an altitude of 3570 m at the shore of a volcanic lake Socompa, Argentinean Andes. The water at the site of stromatolites formation is alkaline, hypersaline, rich in inorganic nutrients, very rich in arsenic, and warm (20-24°C) due to a hydrothermal input. The stromatolites do not lithify, but form broad, rounded and low-domed bioherms dominated by diatom frustules and aragonite micro-crystals agglutinated by extracellular substances. In comparison to other modern stromatolites, they harbour an atypical microbial community characterized by highly abundant representatives of Deinococcus-Thermus, Rhodobacteraceae, Desulfobacterales and Spirochaetes. Additionally, a high proportion of the sequences that could not be classified at phylum level showed less than 80% identity to the best hit in the NCBI database, suggesting the presence of novel distant lineages. The primary production in the stromatolites is generally high and likely dominated by Microcoleus sp. Through negative phototaxis, the location of these cyanobacteria in the stromatolites is controlled by UV light, which greatly influences their photosynthetic activity. Diatoms, dominated by Amphora sp., are abundant in the anoxic, sulfidic and essentially dark parts of the stromatolites. Although their origin in the stromatolites is unclear, they are possibly an important source of anaerobically degraded organic matter that induces in situ aragonite precipitation. To the best of our knowledge, this is so far the highest altitude with documented actively forming stromatolites. Their generally rich, diverse and to a large extent novel microbial community likely harbours valuable genetic and proteomic reserves, and thus deserves active protection. Furthermore, since the stromatolites flourish in an environment characterized by a multitude of extremes, including high exposure to UV radiation, they can be an excellent model system for studying microbial adaptations under conditions that, at least in part, resemble those during the early phase of life evolution on Earth.

Surface orientation affects the direction of cone growth by Leptolyngbya sp. strain C1, a likely architect of coniform structures Octopus Spring (Yellowstone National Park)

Laminated, microbially produced stromatolites within the rock record provide some of the earliest evidence for life on Earth. The chemical, physical, and biological factors that lead to the initiation of these organosedimentary structures and shape their morphology are unclear. Modern coniform structures with morphological features similar to stromatolites are found on the surface of cyanobacterial/microbial mats. They display a vertical element of growth, can have lamination, can be lithified, and observably grow with time. To begin to understand the microbial processes and interactions required for cone formation, we determined the phylogenetic composition of the microbial community of a coniform structure from a cyanobacterial mat at Octopus Spring, Yellowstone National Park, and reconstituted coniform structures in vitro. The 16S rRNA clone library from the coniform structure was dominated by Leptolyngbya sp. Other cyanobacteria and heterotrophic bacteria were present in much lower abundance. The same Leptolyngbya sp. identified in the clone library was also enriched in the laboratory and could produce cones in vitro. When coniform structures were cultivated in the laboratory, the initial incubation conditions were found to influence coniform morphology. In addition, both the angle of illumination and the orientation of the surface affected the angle of cone formation demonstrating how external factors can influence coniform, and likely, stromatolite morphology.

Millimeter-scale resolution of trace metal distributions in microbial mats from a hypersaline environment in Baja California, Mexico

Microbial mats from two ponds with different salinities from the saltern of Guerrero Negro (Mexico) points toward millimeter-scale coherent variations in trace metal (Me) concentrations (Cd, Co, Cu, Fe, Mn, Ni, Pb, Zn). Total, HCl-leachable and pyrite-associated Me showed a trend of increasing concentrations with increasing depth suggesting gradual addition of reactive Me probably as a result of metal sulfide precipitation at depth. The trends in Me profiles can be ascribed to the establishment and maintenance of microzones that promote geochemical processes, bacterial population distributions, and differential mass transport within the mats. Degrees of trace metal pyritization (1 ± 1% for Zn to 24 ± 7% for Cd) as well as metals associated with the pyrite fraction (<1.4-36 ± 18 nmol g(-1) for Zn and Mn, respectively) were low, as expected from a reactive Fe-limited system like Guerrero Negro. Calculated enrichment factors showed that Ni (2.6 ± 2.1), Co (5.5 ± 4.0), Pb (9.4 ± 7.4), and Cd (57 ± 39) were, on average, enriched in the microbial mats of Guerrero Negro. Natural enrichments of Cd, Pb, and Co in sediments along the coast of Baja California and metabolical requirements of Co and Ni by the predominant cyanobacteria in the Guerrero Negro mats may explain these enrichments. Metal characteristics in microbial mats could be advantageously used as biosignatures to identify their presence in the geological record or in other planetary systems.

Inside the alkalinity engine: the role of electron donors in the organomineralization potential of sulfate-reducing bacteria

Mineral precipitation in microbial mats may have been the key to their preservation as fossil stromatolites, potentially documenting evidence of the earliest life on Earth. Two factors that contribute to carbonate mineral precipitation are the saturation index (SI) and the presence of nucleation sites. Both of these can be influenced by micro-organisms, which can either alter SI through their metabolisms, or produce and consume organic substances such as extracellular polymeric substances (EPS) that can affect nucleation. It is the balance of individual metabolisms within the mat community that determines the pH and the dissolved inorganic carbon concentration, thereby potentially increasing the alkalinity and consequently the SI. Sulfate-reducing bacteria (SRB) are an important component of this 'alkalinity engine.' The activity of SRB often peaks in layers where CaCO(3) precipitates, and mineral precipitation has been demonstrated in SRB cultures; however, the effect of their metabolism on the alkalinity engine and actual contribution to mineral precipitation is the subject of controversy. Here, we show through culture experiments, theoretical calculations, and geochemical modeling studies that the pH, alkalinity, and organomineralization potential will vary depending on the type of electron donor. Specifically, hydrogen and formate can increase the pH, but electron donors like lactate and ethanol, and to a lesser extent glycolate, decrease the pH. The implication of this for the lithification of mats is that the combination of processes supplying electron donors and the utilization of these compounds by SRB may be critical to promoting mineral precipitation.

Microbialite genetic diversity and composition relate to environmental variables

Microbialites have played an important role in the early history of life on Earth. Their fossilized forms represent the oldest evidence of life on our planet dating back to 3500 Ma. Extant microbialites have been suggested to be highly productive and diverse communities with an evident role in the cycling of major elements, and in contributing to carbonate precipitation. Although their ecological and evolutionary importance has been recognized, the study of their genetic diversity is yet scanty. The main goal of this study was to analyse microbial genetic diversity of microbialites living in different types of environments throughout Mexico, including desert ponds, coastal lagoons and a crater-lake. We followed a pyrosequencing approach of hypervariable regions of the 16S rRNA gene. Results showed that microbialite communities were very diverse (H' = 6-7) and showed geographic variation in composition, as well as an environmental effect related to pH and conductivity, which together explained 33% of the genetic variation. All microbialites had similar proportions of major bacterial and archaeal phyla.

Metagenomic and metabolic profiling of nonlithifying and lithifying stromatolitic mats of Highborne Cay, The Bahamas

BACKGROUND

Stromatolites are laminated carbonate build-ups formed by the metabolic activity of microbial mats and represent one of the oldest known ecosystems on Earth. In this study, we examined a living stromatolite located within the Exuma Sound, The Bahamas and profiled the metagenome and metabolic potential underlying these complex microbial communities.

METHODOLOGY/PRINCIPAL FINDINGS

The metagenomes of the two dominant stromatolitic mat types, a nonlithifying (Type 1) and lithifying (Type 3) microbial mat, were partially sequenced and compared. This deep-sequencing approach was complemented by profiling the substrate utilization patterns of the mats using metabolic microarrays. Taxonomic assessment of the protein-encoding genes confirmed previous SSU rRNA analyses that bacteria dominate the metagenome of both mat types. Eukaryotes comprised less than 13% of the metagenomes and were rich in sequences associated with nematodes and heterotrophic protists. Comparative genomic analyses of the functional genes revealed extensive similarities in most of the subsystems between the nonlithifying and lithifying mat types. The one exception was an increase in the relative abundance of certain genes associated with carbohydrate metabolism in the lithifying Type 3 mats. Specifically, genes associated with the degradation of carbohydrates commonly found in exopolymeric substances, such as hexoses, deoxy- and acidic sugars were found. The genetic differences in carbohydrate metabolisms between the two mat types were confirmed using metabolic microarrays. Lithifying mats had a significant increase in diversity and utilization of carbon, nitrogen, phosphorus and sulfur substrates.

CONCLUSION/SIGNIFICANCE

The two stromatolitic mat types retained similar microbial communities, functional diversity and many genetic components within their metagenomes. However, there were major differences detected in the activity and genetic pathways of organic carbon utilization. These differences provide a strong link between the metagenome and the physiology of the mats, as well as new insights into the biological processes associated with carbonate precipitation in modern marine stromatolites.

The contribution of exopolysaccharides induced struvites accumulation to ammonium adsorption in aerobic granular sludge

Aerobic granular sludge from a lab-scale reactor with simultaneous nitrification/denitrification and enhanced biological phosphorus removal processes exhibited significant amount of ammonium adsorption (1.5 mg NH4+-N/g TSS at an ammonium concentration of 30 mg N/L). Potassium release accompanied ammonium adsorption, indicating an ion exchange process. The existence of potassium magnesium phosphate (K-struvite) as one of potassium sources in the granular sludge was studied by X-ray diffraction analysis (XRD). Artificially prepared K-struvite was indeed shown to adsorb ammonium. Alginate-like exopolysaccharides were isolated and their inducement for struvite formation was investigated as well. Potassium magnesium phosphate proved to be a major factor for ammonium adsorption on the granular sludge. Struvites (potassium/ammonium magnesium phosphate) accumulate in aerobic granular sludge due to inducing of precipitation by alginate-like exopolysaccharides.

Carbonate organo-mineral micro- and ultrastructures in sub-fossil stromatolites: Marion lake, South Australia

Sub-fossil stromatolites (5000-3000 years old) occur on the marginal flat surrounding Marion Lake (South Australia). A micrite/microsparite crystal fabric characterises these fine-grained, well-laminated stromatolites, which lack trapped grains. The internal lamination is characterised by a sub-millimetric alternation of porous and dense laminae. The microfabric of the laminae is ubiquitously composed of a fine (10-20 μm) peloidal texture, with many thinner aphanitic layers. Aggregates of very fine, low-Mg calcite and aragonite constitute both peloidal and aphanitic micrite, which is coated, respectively, by spherulitic and fringing acicular microspar. Micrite, with a high organic matter content, is formed of coalescing nanospheres grading into small polyhedrons, probably composed mainly of aragonite, with less calcite enriched in Mg, Sr, Na and S. Bacteria-like microfossils and relics of extracellular polymeric substance (EPS) occur abundantly within this micritic framework. The former consist of empty moulds and mineralised bodies of coccoid forms, whereas EPS relics consist of sheet-like or filamentous structures that appear both mineralised and more often still preserved as a C-enriched dehydrated substance that represents the main organic matter component of the deposit. Acicular crystals, which show a prismatic elongate shape, are composed of Mg-depleted aragonite that lacks fossils or organic relicts. Degrading EPS and micro-organisms appear gradually to be replaced and entombed by the nanospherical precipitates, implying the existence of processes of organo-mineralisation within an original syn-sedimentary microbial community. Succeeding micron-scale crystals merge to form isolated or connected micritic aggregates (the peloids), followed by the gradual formation of the acicular crystals as purely inorganic precipitates.

Unusual fungal niches

Fungi are found in all aerobic ecosystems, colonizing a diversity of substrates and performing a wide diversity of functions, some of which are not well understood. Many spices of fungi are cosmopolitan and generalists or habitats. Unusual fungal niches are habitats where extreme conditions would be expected to prevent the development of a mycobiota. In this review we describe five unusual fungal habitats in which fungi occupy poorly understood niches: Antarctic dry valleys, high Arctic glaciers, salt flats and salterns, hypersaline microbial mats and plant trichomes. Yeasts, black yeast-like fungi, melanized filamentous species as well as representatives of Aspergillus and Penicillium seem to be dominant among the mycobiota adapted to cold and saline niches. Plant trichomes appear to be a taxa. The advent of new sequencing technologies is helping to elucidate the microbial diversity in many ecosystems, but more studies are needed to document the functional role of fungi in the microbial communities thriving in these unusual environments.

Microbes and mass extinctions: paleoenvironmental distribution of microbialites during times of biotic crisis

Widespread development of microbialites characterizes the substrate and ecological response during the aftermath of two of the 'big five' mass extinctions of the Phanerozoic. This study reviews the microbial response recorded by macroscopic microbial structures to these events to examine how extinction mechanism may be linked to the style of microbialite development. Two main styles of response are recognized: (i) the expansion of microbialites into environments not previously occupied during the pre-extinction interval and (ii) increases in microbialite abundance and attainment of ecological dominance within environments occupied prior to the extinction. The Late Devonian biotic crisis contributed toward the decimation of platform margin reef taxa and was followed by increases in microbialite abundance in Famennian and earliest Carboniferous platform interior, margin, and slope settings. The end-Permian event records the suppression of infaunal activity and an elimination of metazoan-dominated reefs. The aftermath of this mass extinction is characterized by the expansion of microbialites into new environments including offshore and nearshore ramp, platform interior, and slope settings. The mass extinctions at the end of the Triassic and Cretaceous have not yet been associated with a macroscopic microbial response, although one has been suggested for the end-Ordovician event. The case for microbialites behaving as 'disaster forms' in the aftermath of mass extinctions accurately describes the response following the Late Devonian and end-Permian events, and this may be because each is marked by the reduction of reef communities in addition to a suppression of bioturbation related to the development of shallow-water anoxia.

Prokaryotic and eukaryotic community structure in field and cultured microbialites from the alkaline Lake Alchichica (Mexico)

The geomicrobiology of crater lake microbialites remains largely unknown despite their evolutionary interest due to their resemblance to some Archaean analogs in the dominance of in situ carbonate precipitation over accretion. Here, we studied the diversity of archaea, bacteria and protists in microbialites of the alkaline Lake Alchichica from both field samples collected along a depth gradient (0-14 m depth) and long-term-maintained laboratory aquaria. Using small subunit (SSU) rRNA gene libraries and fingerprinting methods, we detected a wide diversity of bacteria and protists contrasting with a minor fraction of archaea. Oxygenic photosynthesizers were dominated by cyanobacteria, green algae and diatoms. Cyanobacterial diversity varied with depth, Oscillatoriales dominating shallow and intermediate microbialites and Pleurocapsales the deepest samples. The early-branching Gloeobacterales represented significant proportions in aquaria microbialites. Anoxygenic photosynthesizers were also diverse, comprising members of Alphaproteobacteria and Chloroflexi. Although photosynthetic microorganisms dominated in biomass, heterotrophic lineages were more diverse. We detected members of up to 21 bacterial phyla or candidate divisions, including lineages possibly involved in microbialite formation, such as sulfate-reducing Deltaproteobacteria but also Firmicutes and very diverse taxa likely able to degrade complex polymeric substances, such as Planctomycetales, Bacteroidetes and Verrucomicrobia. Heterotrophic eukaryotes were dominated by Fungi (including members of the basal Rozellida or Cryptomycota), Choanoflagellida, Nucleariida, Amoebozoa, Alveolata and Stramenopiles. The diversity and relative abundance of many eukaryotic lineages suggest an unforeseen role for protists in microbialite ecology. Many lineages from lake microbialites were successfully maintained in aquaria. Interestingly, the diversity detected in aquarium microbialites was higher than in field samples, possibly due to more stable and favorable laboratory conditions. The maintenance of highly diverse natural microbialites in laboratory aquaria holds promise to study the role of different metabolisms in the formation of these structures under controlled conditions.

Biostrome communities and mercury and selenium bioaccumulation in the Great Salt Lake (Utah, USA)

The Great Salt Lake has a salinity near 150 g/L and is habitat for over 200 species of migratory birds. The diet of many of these birds is dependent on the food web of carbonaceous biostromes (stromatolites) that cover 260 km(2) of the lake's littoral zone. We investigated the biostrome community to understand their production processes and to assess whether they are a potential vector for bioconcentration of high mercury and selenium levels in the lake. The periphyton community of the biostromes was >99% colonial cyanobacteria. Periphyton chlorophyll levels averaged 900 mg m(-2) or nine times that of the lake's phytoplankton. Lake-wide estimates of chlorophyll suggest that their production is about 30% of that of the phytoplankton. Brine fly (Ephydra gracilis) larval densities on the biostromes increased from 7000 m(-2) in June to 20000m(-2) in December. Pupation and adult emergence halted in October and larvae of various instars overwintered at temperatures <5°C. Mean total dissolved and dissolved methyl mercury concentrations in water were 5.0 and 1.2 ηg L(-1). Total mercury concentrations in the periphyton, fly larvae, pupae, and adults were, respectively, 152, 189, 379 and 659 ηg g(-1) dry weight, suggesting that bioconcentration is only moderate in the short food web and through fly developmental stages. However, common goldeneye ducks (Bucephala clangula) that feed primarily on brine fly larvae at the Great Salt Lake had concentrations near 8000 ηg Hg g(-1) dry weight in muscle tissue. Data from a previous study indicated that selenium concentrations in periphyton, brine fly larvae and goldeneye liver tissue were high (1700, 1200 and 24,000 ηg g(-1), respectively) and Hg:Se molar ratios were <1.0 in all tissues, suggesting that the high mercury concentration in the ducks may be partially detoxified by combining with selenium. The study demonstrated that the high mercury levels in the Great Salt Lake are routed through the biostrome community resulting in invertebrate prey that may provide health risks for birds and humans that consume them.

Legacies of recent environmental change in the benthic communities of Lake Joyce, a perennially ice-covered Antarctic lake

Many Antarctic lakes provide habitat for extensive microbial mats that respond on various timescales to environmental change. Lake Joyce contains calcifying microbialites and provides a natural laboratory to constrain how environmental changes influence microbialite development. In Lake Joyce, depth-specific distributions of calcitic microbialites, organic carbon, photosynthetic pigments and photosynthetic potential cannot be explained by current growth conditions, but are a legacy of a 7-m lake level rise between 1973 and 2009. In the well-illuminated margins of the lake, photosynthetically active benthic communities colonised surfaces submerged for just a few years. However, observed increases in accumulated organic material with depth from 5 to 20 m (2-40 mg ash-free dry weight cm(-2)) and the presence of decimetre-scale calcite microbialites at 20-22 m depth, apparently related to in situ photosynthetic growth, are inconsistent with the current distributions of irradiance, photosynthetic pigments and mat photosynthetic potential (as revealed by pulse-amplitude-modulated fluorometry). The microbialites appeared photosynthetically active in 1986 and 1997, but were outside the depth zone where significant phototrophic growth was possible and were weakly photosynthetically competent in 2009. These complex microbial structures have persisted after growth has ceased, demonstrating how fluctuating environmental conditions and the hysteresis between environmental change, biological response and microbialite development can be important factors to consider when interpreting modern, and by inference ancient, microbially mediated structures.

Molecular biomineralization: toward an understanding of the biogenic origin of polymetallic nodules, seamount crusts, and hydrothermal vents

Polymetallic nodules and crusts, hydrothermal vents from the Deep Sea are economically interesting, since they contain alloying components, e.g., manganese or cobalt, that are used in the production of special steels; in addition, they contain rare metals applied for plasma screens, for magnets in hard disks, or in hybrid car motors. While hydrothermal vents can regenerate in weeks, polymetallic nodules and seamount crusts grow slowly. Even though the geochemical basis for the growth of the nodules and crusts has been well studied, the contribution of microorganisms to the formation of these minerals remained obscure. Recent HR-SEM (high-resolution scanning electron microscopy) analyses of nodules and crusts support their biogenic origin. Within the nodules, bacteria with surface S-layers are arranged on biofilm-like structures, around which Mn deposition starts. In crusts, coccoliths represent the dominant biologically formed structures that act as bio-seeds for an initial Mn deposition. In contrast, hydrothermal vents have apparently an abiogenic origin; however, their minerals are biogenically transformed by bacteria. In turn, strategies can now be developed for biotechnological enrichment as well as selective dissolution of metals from such concretions. We are convinced that the recent discoveries will considerably contribute to our understanding of the participation of organic matrices in the enrichment of those metals and will provide the basis for feasibility studies for biotechnological applications.

Extraction of high molecular weight DNA from microbial mats

Successful and accurate analysis and interpretation of metagenomic data is dependent upon the efficient extraction of high-quality, high molecular weight (HMW) community DNA. However, environmental mat samples often pose difficulties to obtaining large concentrations of high-quality, HMW DNA. Hypersaline microbial mats contain high amounts of extracellular polymeric substances (EPS)1 and salts that may inhibit downstream applications of extracted DNA. Direct and harsh methods are often used in DNA extraction from refractory samples. These methods are typically used because the EPS in mats, an adhesive matrix, binds DNA during direct lysis. As a result of harsher extraction methods, DNA becomes fragmented into small sizes. The DNA thus becomes inappropriate for large-insert vector cloning. In order to circumvent these limitations, we report an improved methodology to extract HMW DNA of good quality and quantity from hypersaline microbial mats. We employed an indirect method involving the separation of microbial cells from the background mat matrix through blending and differential centrifugation. A combination of mechanical and chemical procedures was used to extract and purify DNA from the extracted microbial cells. Our protocol yields approximately 2 μg of HMW DNA (35-50 kb) per gram of mat sample, with an A(260/280) ratio of 1.6. Furthermore, amplification of 16S rRNA genes suggests that the protocol is able to minimize or eliminate any inhibitory effects of contaminants. Our results provide an appropriate methodology for the extraction of HMW DNA from microbial mats for functional metagenomic studies and may be applicable to other environmental samples from which DNA extraction is challenging.

Comparative microbial diversity analyses of modern marine thrombolitic mats by barcoded pyrosequencing

Thrombolites are unlaminated carbonate structures that form as a result of the metabolic interactions of complex microbial mat communities. Thrombolites have a long geological history; however, little is known regarding the microbes associated with modern structures. In this study, we use a barcoded 16S rRNA gene-pyrosequencing approach coupled with morphological analysis to assess the bacterial, cyanobacterial and archaeal diversity associated with actively forming thrombolites found in Highborne Cay, Bahamas. Analyses revealed four distinct microbial mat communities referred to as black, beige, pink and button mats on the surfaces of the thrombolites. At a coarse phylogenetic resolution, the domain bacterial sequence libraries from the four mats were similar, with Proteobacteria and Cyanobacteria being the most abundant. At the finer resolution of the rRNA gene sequences, significant differences in community structure were observed, with dramatically different cyanobacterial communities. Of the four mat types, the button mats contained the highest diversity of Cyanobacteria, and were dominated by two sequence clusters with high similarity to the genus Dichothrix, an organism associated with the deposition of carbonate. Archaeal diversity was low, but varied in all mat types, and the archaeal community was predominately composed of members of the Thaumarchaeota and Euryarchaeota. The morphological and genetic data support the hypothesis that the four mat types are distinctive thrombolitic mat communities.

Exopolymeric substances (EPS) from Bacillus subtilis: polymers and genes encoding their synthesis

Bacterial exopolymeric substances (EPS) are molecules released in response to the physiological stress encountered in the natural environment. EPS are structural components of the extracellular matrix in which cells are embedded during biofilm development. The chemical nature and functions of these EPS are dependent on the genetic expression of the cells within each biofilm. Although some bacterial matrices have been characterized, understanding of the function of the EPS is relatively limited, particularly within the Bacillus genus. Similar gaps of knowledge exist with respect to the chemical composition and specific roles of the macromolecules secreted by Bacillus subtilis in its natural environment. In this review, the different EPS from B. subtilis were classified into four main functional categories: structural (neutral polymers), sorptive (charged polymers), surface-active and active polymers. In addition, current information regarding the genetic expression, production and function of the main polymers secreted by B. subtilis strains, particularly those related to biofilm formation and its architecture, has been compiled. Further characterization of these EPS from B. subtilis remains a challenge.