Microbialites, Stromatolites, and Thrombolites

Biofilms in modern CaCO3-supersaturated freshwater environments reveal viral proxies

Biofilms are mucilaginous-organic layers produced by microbial activity including viruses. Growing biofilms form microbial mats which enhance sediment stability by binding particles with extracellular polymeric substances and promoting growth through nutrient cycling and organic matter accumulation. They preferentially develop at the sediment-water interface of both marine and non-marine environments, and upon the growing surfaces of modern tufa and travertine. In this context, however, little is known about the factors, environmental or anthropogenic, which affect viral communities in freshwater spring settings. To explore this issue, geochemical and metagenomic data were subjected to multidimensional analyses (Principal Component Analysis, Classical Multidimensional Scaling, Partial Least Squares analysis and cluster analysis based on beta-diversity), and these show that viral composition is specific and dependent on environment. Indeed, waters precipitating tufa and travertine do vary in their geochemistry with their viruses showing distinct variability between sites. These differences between virus groups allow the formulation of a viral proxy, based on the Caudoviricetes/Megaviricetes ratio established on the most abundant groups of viruses. This ratio may be potentially used in analysing ancient DNA preserved in carbonate formations as an additional source of information on the microbiological community during sedimentation.

The eukaryome of modern microbialites reveals distinct colonization across aquatic ecosystems

Protists are less studied for their role and diversity in ecosystems. Notably, protists have played and still play an important role in microbialites. Microbialites, or lithified microbial mats, represent the oldest evidence of fossil biofilms (~3.5 Gyr). Modern microbialites may offer a unique proxy to study the potential role of protists within a geological context. We examined protist diversity in freshwater (Kelly and Pavilion Lake in British Columbia, Canada) and marine (Highborne Cay, Bahamas) to hypersaline (Shark Bay, Australia) microbialites to decipher their geomicrobiological role. The freshwater microbialite communities were clearly distinct from their marine and hypersaline counterparts. Chlorophytes had higher numerical abundance in freshwater microbialites; whereas pennate diatoms dominated numerically in marine microbialites. Despite the differences, protists across ecosystems may have adopted similar roles and functions. We suggest a consistent biogeochemical role of protists across microbialites globally; but that salinity may shape protist composition and evolution in these ecosystems.

Pyritic stromatolites from the Paleoarchean Dresser Formation, Pilbara Craton: Resolving biogenicity and hydrothermally influenced ecosystem dynamics

This study investigates the paleobiological significance of pyritic stromatolites from the 3.48 billion-year-old Dresser Formation, Pilbara Craton. By combining paleoenvironmental analyses with observations from well-preserved stromatolites in newly obtained drill cores, the research reveals stratiform and columnar to domal pyritic structures with wavy to wrinkly laminations and crest thickening, hosted within facies variably influenced by syn-depositional hydrothermal activity. The columnar and domal stromatolites occur in strata with clearly distinguishable primary depositional textures. Mineralogical variability and fine-scale interference textures between the microbialites and the enclosing sediment highlight interplays between microbial and depositional processes. The stromatolites consist of organomineralization - nanoporous pyrite and microspherulitic barite - hosting significant thermally mature organic matter (OM). This includes filamentous organic microstructures encased within nanoporous pyrite, resembling the extracellular polymeric substance (EPS) of microbes. These findings imply biogenicity and support the activity of microbial life in a volcano-sedimentary environment with hydrothermal activity and evaporative cycles. Coupled changes in stromatolite morphology and host facies suggest growth in diverse niches, from dynamic, hydrothermally influenced shallow-water environments to restricted brine pools strongly enriched inSO 4 2 - $$ {\mathrm{SO}}_4^{2-} $$ from seawater and hydrothermal activity. These observations, along with S stable isotope data indicating influence by S metabolisms, and accumulations of biologically significant metals and metalloids (Ni and As) within the microbialites, help constrain microbial processes. Columnar to domal stromatolites in dynamic, hydrothermally influenced shallow water deposits likely formed by microbial communities dominated by phototrophs. Stratiform pyritic structures within barite-rich strata may reflect the prevalence of chemotrophs near hydrothermal venting, where hydrothermal activity and microbial processes influenced barite precipitation. Rapid pyrite precipitation, a putative taphonomic process for preserving microbial remnants, is attributed to microbial sulfate reduction and reduced S sourced from hydrothermal activity. In conclusion, this research underscores the biogenicity of the Dresser stromatolites and advances our understanding of microbial ecosystems in Earth's early history.

Key energy metabolisms in modern living microbialites from hypersaline Andean lagoons of the Salar de Atacama, Chile

Microbialites are organosedimentary structures formed mainly due to the precipitation of carbonate minerals, although they can also incorporate siliceous, phosphate, ferric, and sulfate minerals. The minerals' precipitation occurs because of local chemical changes triggered by changes in pH and redox transformations catalyzed by the microbial energy metabolisms. Here, geochemistry, metagenomics, and bioinformatics tools reveal the key energy metabolisms of microbial mats, stromatolites and an endoevaporite distributed across four hypersaline lagoons from the Salar de Atacama. Chemoautotrophic and chemoheterotrophic microorganisms seem to coexist and influence microbialite formation. The microbialite types of each lagoon host unique microbial communities and metabolisms that influence their geochemistry. Among them, photosynthetic, carbon- and nitrogen- fixing and sulfate-reducing microorganisms appear to control the main biogeochemical cycles. Genes associated with non-conventional energy pathways identified in MAGs, such as hydrogen production/consumption, arsenic oxidation/reduction, manganese oxidation and selenium reduction, also contribute to support life in microbialites. The presence of genes encoding for enzymes associated with ureolytic processes in the Cyanobacteria phylum and Gammaproteobacteria class might induce carbonate precipitation in hypersaline environments, contributing to the microbialites formation. To the best of our knowledge, this is the first study characterizing metagenomically microbialites enriched in manganese and identifying metabolic pathways associated with manganese oxidation, selenium reduction, and ureolysis in this ecosystem, which suggests that the geochemistry and bioavailability of energy sources (As, Mn and Se) shapes the microbial metabolisms in the microbialites.

Nubecularia-coralline algal-serpulid-microbial bioherms of the Paratethys Sea-Distribution and paleoecological significance (upper Serravallian, upper Sarmatian, Middle Miocene)

Nubecularia bioherms represent unique bioconstructions that are restricted to the upper Serravallian of the Paratethys and have been reported since the 19th century. They occur in the Central Paratethys in the late Sarmatian and the Eastern Paratethys in the Bessarabian both regional stages of the respective Paratethyan areas. In this study, several locations in the Vienna and Styrian basins of the Central Paratethys were studied out of which four localities were documented in detail (Wolfsthal, Maustrenk, St. Margarethen-Zollhaus, Vienna-Ruzickagasse) to reconstruct their sedimentary setting, their internal composition, and their indications of environmental parameters. The detailed studies included logging of outcrop sections, petrographic, facies and biotic analyses of polished slabs and thin sections and also cathodoluminescence analyses. These concluded that these bioconstructions are not only composed of the foraminifer Nubecularia but represent a complex mixture and interrelationships of Nubecularia, serpulids and microbial carbonate. Four boundstone types can be differentiated: Nubecularia boundstone, Nubecularia-coralline algal boundstone, stromatolitic/thrombolitic boundstone and serpulid-nubeculariid-microbial boundstone. The first 3 types are characteristic of specific localities; the fourth type occurs in all studied locations and represents the terminal association on top of the three other types. The three basal boundstones are predominantly of columnar growth form irrespective of dominance of Nubecularia, coralline algae or microbial carbonate, and the terminal boundstone is widely irregularly organized. The general depositional environment is characterized by cross-bedded oolitic grainstones with abundant quartz grains, miliolid foraminifers and mollusks. Intercalated are microbial carbonates mostly stromatolites but also thrombolites. This indicates a general high water energy environment interrupted by more calm periods when the microbial carbonate was built. The 3 basal types of bioconstructions are interpreted to reflect decreasing food supply and/or oxygenation from Nubecularia over Nubecularia-coralline algal to stromatolitic/thrombolitic boundstone. The serpulid-nubeculariid-microbial boundstone reflects an internal succession with a decrease of the same parameters. Water depth is considered very shallow ranging from 0 to a few meters, and salinity was normal marine to hypersaline. The reconstructed paleoenvironment with dominating oolite shoals and seagrass meadows was not restricted to the Central Paratethys but extended over the entire Paratethys and represented the largest oolite facies area of the entire Cenozoic!

Microbial biosignatures in ancient deep-sea hydrothermal sulfides

Deep-sea hydrothermal systems provide ideal conditions for prebiotic reactions and ancient metabolic pathways and, therefore, might have played a pivotal role in the emergence of life. To understand this role better, it is paramount to examine fundamental interactions between hydrothermal processes, non-living matter, and microbial life in deep time. However, the distribution and diversity of microbial communities in ancient deep-sea hydrothermal systems are still poorly constrained, so evolutionary, and ecological relationships remain unclear. One important reason is an insufficient understanding of the formation of diagnostic microbial biosignatures in such settings and their preservation through geological time. This contribution centers around microbial biosignatures in Precambrian deep-sea hydrothermal sulfide deposits. Intending to provide a valuable resource for scientists from across the natural sciences whose research is concerned with the origins of life, we first introduce different types of biosignatures that can be preserved over geological timescales (rock fabrics and textures, microfossils, mineral precipitates, carbonaceous matter, trace metal, and isotope geochemical signatures). We then review selected reports of biosignatures from Precambrian deep-sea hydrothermal sulfide deposits and discuss their geobiological significance. Our survey highlights that Precambrian hydrothermal sulfide deposits potentially encode valuable information on environmental conditions, the presence and nature of microbial life, and the complex interactions between fluids, micro-organisms, and minerals. It further emphasizes that the geobiological interpretation of these records is challenging and requires the concerted application of analytical and experimental methods from various fields, including geology, mineralogy, geochemistry, and microbiology. Well-orchestrated multidisciplinary studies allow us to understand the formation and preservation of microbial biosignatures in deep-sea hydrothermal sulfide systems and thus help unravel the fundamental geobiology of ancient settings. This, in turn, is critical for reconstructing life's emergence and early evolution on Earth and the search for life elsewhere in the universe.

Bacterial community structure and metabolic potential in microbialite-forming mats from South Australian saline lakes

Microbialites are sedimentary rocks created in association with benthic microorganisms. While they harbour complex microbial communities, Cyanobacteria perform critical roles in sediment stabilisation and accretion. Microbialites have been described from permanent and ephemeral saline lakes in South Australia; however, the microbial communities that generate and inhabit these biogeological structures have not been studied in detail. To address this knowledge gap, we investigated the composition, diversity and metabolic potential of bacterial communities from different microbialite-forming mats and surrounding sediments in five South Australian saline coastal lakes using 16S rRNA gene sequencing and predictive metagenome analyses. While Proteobacteria and Bacteroidetes were the dominant phyla recovered from the mats and sediments, Cyanobacteria were significantly more abundant in the mat samples. Interestingly, at lower taxonomic levels, the mat communities were vastly different across the five lakes. Comparative analysis of putative mat and sediment metagenomes via PICRUSt2 revealed important metabolic pathways driving the process of carbonate precipitation, including cyanobacterial oxygenic photosynthesis, ureolysis and nitrogen fixation. These pathways were highly conserved across the five examined lakes, although they appeared to be performed by distinct groups of bacterial taxa found in each lake. Stress response, quorum sensing and circadian clock were other important pathways predicted by the in silico metagenome analysis. The enrichment of CRISPR/Cas and phage shock associated genes in these cyanobacteria-rich communities suggests that they may be under selective pressure from viral infection. Together, these results highlight that a very stable ecosystem function is maintained by distinctly different communities in microbialite-forming mats in the five South Australian lakes and reinforce the concept that 'who' is in the community is not as critical as their net metabolic capacity.

Microbialites show a distinct cyanobacterial phylogenetic structure and functional redundancy in Bacalar lagoon and Cenote Azul sinkhole, Yucatan peninsula, Mexico

Cyanobacterial components of microbialites from two geographically close systems, the Bacalar lagoon (BL) and the Cenote Azul sinkhole (CA) in Quintana Roo, Mexico, were characterized. BL and CA systems were studied along a longitudinal gradient (north to south) and a depth gradient (5 to 30 m), respectively. Microscopic observations, 16S rRNA amplicon sequencing, and shotgun metagenomics were used to characterize Cyanobacteria. Both systems showed similar metabolic/functional profiles but harbored completely different cyanobacterial taxa. BL was dominated by Nostocales, including a population of previously undescribed Chakia sp., while CA was dominated by an unknown taxon of Chroococcales, comprising 70% of relative abundance through all depths. Interestingly, cyanobacterial assemblages in microbialites exhibited phylogenetic overdispersion in most of the BL sites, while CA sites exhibited phylogenetic clustering, these differences were attributed to depth/light conditions and possibly different times of geological formation for BL and CA systems.

The Large Dendritic Morphologies in the Antoniadi Crater (Mars) and Their Potential Astrobiological Significance

Mars has held large amounts of running and standing water throughout its history, as evidenced by numerous morphologies attributed to rivers, outflow channels, lakes, and possibly an ocean. This work examines the crater Antoniadi located in the Syrtis Major quadrangle. Some parts of the central area of the crater exhibit giant polygonal mud cracks, typical of endured lake bottom, on top of which a dark, tens of kilometers-long network of dendritic (i.e., arborescent) morphologies emerges, at first resembling the remnant of river networks. The network, which is composed of tabular sub-units, is in relief overlying hardened mud, a puzzling feature that, in principle, could be explained as landscape inversion resulting from stronger erosion of the lake bottom compared to the endured crust of the riverine sediments. However, the polygonal mud cracks have pristine boundaries, which indicate limited erosion. Furthermore, the orientation of part of the network is the opposite of what the flow of water would entail. Further analyses indicate the similarity of the dendrites with controlled diffusion processes rather than with the river network, and the presence of morphologies incompatible with river, alluvial, or underground sapping processes, such as overlapping of branches belonging to different dendrites or growth along fault lines. An alternative explanation worth exploring due to its potential astrobiological importance is that the network is the product of ancient reef-building microbialites on the shallow Antoniadi lake, which enjoyed the fortunate presence of a heat source supplied by the Syrtis Major volcano. The comparison with the terrestrial examples and the dating of the bottom of the crater (formed at 3.8 Ga and subjected to a resurfacing event at 3.6 Ga attributed to the lacustrine drape) contribute to reinforcing (but cannot definitely prove) the scenario of microbialitic origin for dendrites. Thus, the present analysis based on the images available from the orbiters cannot be considered proof of the presence of microbialites in ancient Mars. It is concluded that the Antoniadi crater could be an interesting target for the research of past Martian life in future landing missions.

Potential role for microbial ureolysis in the rapid formation of carbonate tufa mounds

Modern carbonate tufa towers in the alkaline (~pH 9.5) Big Soda Lake (BSL), Nevada, exhibit rapid precipitation rates (exceeding 3 cm/year) and host diverse microbial communities. Geochemical indicators reveal that carbonate precipitation is, in part, promoted by the mixing of calcium-rich groundwater and carbonate-rich lake water, such that a microbial role for carbonate precipitation is unknown. Here, we characterize the BSL microbial communities and evaluate their potential effects on carbonate precipitation that may influence fast carbonate precipitation rates of the active tufa mounds of BSL. Small subunit rRNA gene surveys indicate a diverse microbial community living endolithically, in interior voids, and on tufa surfaces. Metagenomic DNA sequencing shows that genes associated with metabolisms that are capable of increasing carbonate saturation (e.g., photosynthesis, ureolysis, and bicarbonate transport) are abundant. Enzyme activity assays revealed that urease and carbonic anhydrase, two microbial enzymes that promote carbonate precipitation, are active in situ in BSL tufa biofilms, and urease also increased calcium carbonate precipitation rates in laboratory incubation analyses. We propose that, although BSL tufas form partially as a result of water mixing, tufa-inhabiting microbiota promote rapid carbonate authigenesis via ureolysis, and potentially via bicarbonate dehydration and CO₂ outgassing by carbonic anhydrase. Microbially induced calcium carbonate precipitation in BSL tufas may generate signatures preserved in the carbonate microfabric, such as stromatolitic layers, which could serve as models for developing potential biosignatures on Earth and elsewhere.

Lithifying and Non-Lithifying Microbial Ecosystems in the Wetlands and Salt Flats of the Central Andes

The wetlands and salt flats of the Central Andes region are unique extreme environments as they are located in high-altitude saline deserts, largely influenced by volcanic activity. Environmental factors, such as ultraviolet (UV) radiation, arsenic content, high salinity, low dissolved oxygen content, extreme daily temperature fluctuation, and oligotrophic conditions, resemble the early Earth and potentially extraterrestrial conditions. The discovery of modern microbialites and microbial mats in the Central Andes during the past decade has increased the interest in this area as an early Earth analog. In this work, we review the current state of knowledge of Central Andes region environments found within lakes, small ponds or puquios, and salt flats of Argentina, Chile, and Bolivia, many of them harboring a diverse range of microbial communities that we have termed Andean Microbial Ecosystems (AMEs). We have integrated the data recovered from all the known AMEs and compared their biogeochemistry and microbial diversity to achieve a better understanding of them and, consequently, facilitate their protection.

Metazoan activity facilitates passive sediment trapping in modern supratidal microbialites: Revealed using µ-CT-scanning and microscopy

Microbialites are formed through two processes, the trapping and binding of sediment grains and mineral precipitation. Sediment trapping and binding result in coarse sandy textures, whereas fine micritic textures are produced by mineral precipitation. Although well-studied modern microbialites (e.g. Bahamas and Shark Bay) are formed through the former process, purely trapped-and-bound examples are rare throughout the geologic record and limited to shallow-marine environments. Through the use of conventional microscopy and 3D micro-computed tomography (µ-CT) scanning, this study found that South African coastal microbialites have a primarily mineral precipitated texture, although detrital material is included sporadically. Furthermore, these modern microbialites exhibit both micritic and fibrous layering with high porosity. The novel use of 3D microtomography rotational scans has revealed that microbialites are extensively burrowed by metazoan activity and was also able to distinguish the occurrence and distribution of heavy minerals and detrital shell material in the samples. Some of the detrital grains appeared to be accidental/random inclusions, while in other cases the metazoan burrows provided space for the accumulation of sediment once abandoned. In both cases, sediment was incorporated as a product of intermittent accumulation, rather than systematic trapping and binding. The microfabric texture of South African microbialites is therefore a function of both biological (e.g. microbially mediated precipitation) and environmental (e.g. sporadic sediment deposition and inorganic cementation) influence. Overall, the findings presented here highlight the importance of these systems regarding microbialite formation, ichnology and taphonomy.

Acid Mine Drainage as Energizing Microbial Niches for the Formation of Iron Stromatolites: The Tintillo River in Southwest Spain

The Iberian Pyrite Belt in southwest Spain hosts some of the largest and diverse extreme acidic environments with textural variation across rapidly changing biogeochemical gradients at multiple scales. After almost three decades of studies, mostly focused on molecular evolution and metagenomics, there is an increasing awareness of the multidisciplinary potential of these types of settings, especially for astrobiology. Since modern automatized exploration on extraterrestrial surfaces is essentially based on the morphological recognition of biosignatures, a macroscopic characterization of such sedimentary extreme environments and how they look is crucial to identify life properties, but it is a perspective that most molecular approaches frequently miss. Although acid mine drainage (AMD) systems are toxic and contaminated, they offer at the same time the bioengineering tools for natural remediation strategies. This work presents a biosedimentological characterization of the clastic iron stromatolites in the Tintillo river. They occur as laminated terraced iron formations that are the most distinctive sedimentary facies at the Tintillo river, which is polluted by AMD. Iron stromatolites originate from fluvial abiotic factors that interact with biological zonation. The authigenic precipitation of schwertmannite and jarosite results from microbial-mineral interactions between mineral and organic matrices. The Tintillo iron stromatolites are composed of bacterial filaments and diatoms as Nitzschia aurariae, Pinnularia aljustrelica, Stauroneis kriegeri, and Fragilaria sp. Furthermore, the active biosorption and bioleaching of sulfur are suggested by the black and white coloration of microbial filaments inside stromatolites. AMD systems are hazardous due to physical, chemical, and biological agents, but they also provide biogeochemical sources with which to infer past geochemical conditions on Earth and inform exploration efforts on extraterrestrial surfaces in the future.

A 571 million-year-old alkaline volcanic lake photosynthesizing microbial community, the Anti-atlas, Morocco

The Ediacaran period coincides with the emergence of ancestral animal lineages and cyanobacteria capable of thriving in nutrient deficient oceans which together with photosynthetic eukaryotic dominance, culminated in the rapid oxygenation of the Ediacaran atmosphere. However, ecological evidence for the colonization of the Ediacaran terrestrial biosphere by photosynthetic communities and their contribution to the oxygenation of the biosphere at this time is very sparse. Here, we expand the repertoire of Ediacaran habitable environments to a specific microbial community that thrived in an extreme alkaline volcanic lake 571 Myr ago in the Anti-atlas of Morocco. The microbial fabrics preserve evidence of primary growth structures, comprised of two main microbialitic units, with the lower section consisting of irregular and patchy thrombolytic mesoclots associated with composite microbialitic domes. Calcirudite interbeds, dominated by wave-rippled sandy calcarenites and stromatoclasts, fill the interdome troughs and seal the dome tops. A meter-thick epiclastic stromatolite bed grading upwards from a dominantly flat to wavy laminated base, transitions into low convex laminae consisting of decimeter to meter-thick dome-shaped stromatolitic columns, overlies the thrombolitic and composite microbialitic facies. Microbialitic beds constructed during periods of limited clastic input, and underlain by coarse-grained microbialite-derived clasts and by the wave-rippled calcarenites, suggest high-energy events associated with lake expansion. High-resolution microscopy revealed spherulitic aggregates and structures reminiscent of coccoidal microbial cell casts and mineralized extra-polymeric substances (EPS). The primary fabrics and multistage diagenetic features, represented by active carbonate production, photosynthesizing microbial communities, photosynthetic gas bubbles, gas escape structures, and tufted mats, suggest specialized oxygenic photosynthesizers thriving in alkaline volcanic lakes, contributed toward oxygen variability in the Ediacaran terrestrial biosphere.

Microbially induced chromium isotope fractionation and trace elements behavior in lower Cambrian microbialites from the Jaíba Member, Bambuí Basin, Brazil

In east-central Brazil, the Ediacaran-Cambrian Bambuí Basin has the potential to provide a record of unique geochemical responses of Earth's ocean and atmosphere evolution during this key time interval. From this perspective, we studied an interval of the upper Bambuí Basin using sedimentologic, stratigraphic, and chemostratigraphic tools. The lower Cambrian Jaíba Member of the uppermost Serra da Saudade Formation is an interval of up to 60 m-thick of carbonate rocks disposed into two shallowing upward trends. Inner to outer ramp and high-energy shoal deposits are described, in which laminated microbialites are the prevailing sedimentary facies. REE + Y data suggest contamination by iron (oxy)hydroxides that are dissociated from the riverine detritic flux. Sedimentary iron enrichment may be related to the settling of iron nanoparticles in coastal environments, diagenetic iron mobilization, or both. MREE enrichment is caused by microbial degradation of organic matter in the iron reduction zone during the anoxic early-diagenetic stage. Chromium isotopes yielded negatively fractionated values (δ⁵³ Cr = -0.69 to -0.27‰), probably resulting from biotic and abiotic reduction of dissolved Cr(VI) to light and less toxic Cr(III) within pores of microbial mats. The δ⁵³ Cr data of the Jaíba microbialite are thus a product of metabolic reactions in microbial mats and do not reflect seawater signal. The isotopic offset from seawater is feasible from molecular diffusion of Cr into pore water and reduction reactions occurring deep inside the mat, although the exact mechanism and consequences are not yet fully understood due to the poor preservation of metabolic reactions in the geological record. Our study suggests that Cr isotopes can be used to reconstruct Cr and other metals cycling within ancient microbial mats, and that caution should be taken when using past microbialites to infer seawater Cr records and redox state of the atmosphere and ocean.

The microbiome of modern microbialites in Bacalar Lagoon, Mexico

Microbialites are highly diverse microbial communities that represent modern examples of the oldest life forms, stromatolites (dated >3.7 Ga). Bacalar Lagoon, in Mexico, harbors the largest freshwater microbialite occurrences of the world; yet diverse anthropogenic activities are changing the oligotrophic conditions of the lagoon. The objective of this work was to perform a spatial exploration of the microbialites of Bacalar Lagoon, analyze their prokaryote diversity, following a high throughput sequencing approach of the V4 region of the 16S rDNA, and correlate to the environmental parameters that influence the structure of these communities. The results indicate the presence of microbialites throughout the periphery of the lagoon. The microbiome of the microbialites is composed primarily of Proteobacteria (40-80%), Cyanobacteria (1-11%), Bacteroidetes (7-8%), Chloroflexi (8-14%), Firmicutes (1-23%), Planctomycetes (1-8%), and Verrucomicrobia (1-4%). Phylogenetic distance analyses suggests two distinct groups of microbialites associated with regions in the lagoon that have differences in their environmental parameters, including soluble reactive silicate (in the north), bicarbonates and available forms of nitrogen (ammonium, nitrates and nitrites) (in the south). These microbialite groups had differences in their microbiome composition associated to strong anthropogenic pressure on water quality (agriculture, landfill leachate, lack of water treatment infrastructure and intensive tourism), which were related to a loss of microbial diversity.

Microbially influenced lacustrine carbonates: A comparison of Late Quaternary Lahontan tufa and modern thrombolite from Fayetteville Green Lake, NY

Carbonate microbialites in lakes can serve as valuable indicators of past environments, so long as the biogenicity and depositional setting of the microbialite can be accurately determined. Late Pleistocene to Early Holocene frondose draping tufa deposits from Winnemucca Dry Lake (Nevada, USA), a subbasin of pluvial Lake Lahontan, were examined in outcrop, petrographically, and geochemically to determine whether microbially induced precipitation is a dominant control on deposition. These observations were compared to modern, actively accumulating microbialites from Fayetteville Green Lake (New York, USA) using similar methods. In addition, preserved microbial DNA was extracted from the Lahontan tufa and sequenced to provide a more complete picture of the microbial communities. Tufas are texturally and geochemically similar to modern thrombolitic microbialites from Fayetteville Green Lake, and the stable isotopic composition of organic C, N, inorganic C, and O supports deposition associated with a lacustrine microbial mat environment dominated by photosynthetic processes. DNA extraction and sequencing indicate that photosynthetic microbial builders were present during tufa deposition, primarily Chloroflexi and Proteobacteria with minor abundances of Cyanobacteria and Acidobacteria. Based on the sequencing results, the depositional environment of the tufas can be constrained to the photic zone of the lake, contrasting with some previous interpretations that put tufa formation in deeper waters. Additionally, the presence of a number of mesothermophilic phyla, including Deinococcus-Thermus, indicates that thermal groundwater may have played a role in tufa deposition at sites not previously associated with groundwater influx. The interpretation of frondose tufas as microbially influenced deposits provides new context to interpretations of lake level and past environments in the Lahontan lake basins.

Facies selectivity of benthic invertebrates in a Permian/Triassic boundary microbialite succession: Implications for the "microbialite refuge" hypothesis

Thrombolite and stromatolite habitats are becoming increasingly recognized as important refuges for invertebrates during Phanerozoic Oceanic Anoxic Events (OAEs); it is posited that oxygenic photosynthesis by cyanobacteria in these microbialites provided a refuge from anoxic conditions (i.e., the "microbialite refuge" hypothesis). Here, we test this hypothesis by investigating the distribution of ~34, 500 benthic invertebrate fossils found in ~100 samples from a microbialite succession that developed following the latest Permian mass extinction event on the Great Bank of Guizhou (South China), representing microbial (stromatolites and thrombolites) and non-microbial facies. The stromatolites were the least taxonomically diverse facies, and the thrombolites also recorded significantly lower diversities when compared to the non-microbial facies. Based on the distribution and ornamentation of the bioclasts within the thrombolites and stromatolites, the bioclasts are inferred to have been transported and concentrated in the non-microbial fabrics, that is, cavities around the microbial framework. Therefore, many of the identified metazoans from the post-extinction microbialites are not observed to have been living within a microbial mat. Furthermore, the lifestyle of many of the taxa identified from the microbialites was not suited for, or even amenable to, life within a benthic microbial mat. The high diversity of oxygen-dependent metazoans in the non-microbial facies on the Great Bank of Guizhou, and inferences from geochemical records, suggests that the microbialites and benthic communities developed in oxygenated environments, which disproves that the microbes were the source of the oxygenation. Instead, we posit that microbialite successions represent a taphonomic window for exceptional preservation of the biota, similar to a Konzentrat-Lagerstätte, which has allowed for diverse fossil assemblages to be preserved during intervals of poor preservation.

Formation of stromatolite lamina at the interface of oxygenic-anoxygenic photosynthesis

In modern stromatolites, mineralization results from a complex interplay between microbial metabolisms, the organic matrix, and environmental parameters. Here, we combined biogeochemical, mineralogical, and microscopic analyses with measurements of metabolic activity to characterize the mineralization processes and products in an emergent (<18 months) hypersaline microbial mat. While the nucleation of Mg silicates is ubiquitous in the mat, the initial formation of a Ca-Mg carbonate lamina depends on (i) the creation of a high-pH interface combined with a major change in properties of the exopolymeric substances at the interface of the oxygenic and anoxygenic photoautotrophic layers and (ii) the synergy between two major players of sulfur cycle, purple sulfur bacteria, and sulfate-reducing bacteria. The repetition of this process over time combined with upward growth of the mat is a possible pathway leading to the formation of a stromatolite.

Stromatolites on the rise in peat-bound karstic wetlands

Stromatolites are the oldest evidence for life on Earth, but modern living examples are rare and predominantly occur in shallow marine or (hyper-) saline lacustrine environments, subject to exotic physico-chemical conditions. Here we report the discovery of living freshwater stromatolites in cool-temperate karstic wetlands in the Giblin River catchment of the UNESCO-listed Tasmanian Wilderness World Heritage Area, Australia. These stromatolites colonize the slopes of karstic spring mounds which create mildly alkaline (pH of 7.0-7.9) enclaves within an otherwise uniformly acidic organosol terrain. The freshwater emerging from the springs is Ca-HCO3 dominated and water temperatures show no evidence of geothermal heating. Using 16 S rRNA gene clone library analysis we revealed that the bacterial community is dominated by Cyanobacteria, Alphaproteobacteria and an unusually high proportion of Chloroflexi, followed by Armatimonadetes and Planctomycetes, and is therefore unique compared to other living examples. Macroinvertebrates are sparse and snails in particular are disadvantaged by the development of debilitating accumulations of carbonate on their shells, corroborating evidence that stromatolites flourish under conditions where predation by metazoans is suppressed. Our findings constitute a novel habitat for stromatolites because cool-temperate freshwater wetlands are not a conventional stromatolite niche, suggesting that stromatolites may be more common than previously thought.

Microbialite Biosignature Analysis by Mesoscale X-ray Fluorescence (μXRF) Mapping

As part of its biosignature detection package, the Mars 2020 rover will carry PIXL, the Planetary Instrument for X-ray Lithochemistry, a spatially resolved X-ray fluorescence (μXRF) spectrometer. Understanding the types of biosignatures detectable by μXRF and the rock types μXRF is most effective at analyzing is therefore an important goal in preparation for in situ Mars 2020 science and sample selection. We tested mesoscale chemical mapping for biosignature interpretation in microbialites. In particular, we used μXRF to identify spatial distributions and associations between various elements ("fluorescence microfacies") to infer the physical, biological, and chemical processes that produced the observed compositional distributions. As a test case, elemental distributions from μXRF scans of stromatolites from the Mesoarchean Nsuze Group (2.98 Ga) were analyzed. We included five fluorescence microfacies: laminated dolostone, laminated chert, clotted dolostone and chert, stromatolite clast breccia, and cavity fill. Laminated dolostone was formed primarily by microbial mats that trapped and bound loose sediment and likely precipitated carbonate mud at a shallow depth below the mat surface. Laminated chert was produced by the secondary silicification of microbial mats. Clotted dolostone and chert grew as cauliform, cryptically laminated mounds similar to younger thrombolites and was likely formed by a combination of mat growth and patchy precipitation of early-formed carbonate. Stromatolite clast breccias formed as lag deposits filling erosional scours and interstromatolite spaces. Cavities were filled by microquartz, Mn-rich dolomite, and partially dolomitized calcite. Overall, we concluded that μXRF is effective for inferring genetic processes and identifying biosignatures in compositionally heterogeneous rocks. Key Words: Stromatolites-Biosignatures-Spectroscopy-Archean. Astrobiology 17, 1161-1172.

Microbialite response to an anthropogenic salinity gradient in Great Salt Lake, Utah

A railroad causeway across Great Salt Lake, Utah (GSL), has restricted water flow since its construction in 1959, resulting in a more saline North Arm (NA; 24%-31% salinity) and a less saline South Arm (SA; 11%-14% salinity). Here, we characterized microbial carbonates collected from the SA and the NA to evaluate the effect of increased salinity on community composition and abundance and to determine whether the communities present in the NA are still actively precipitating carbonate or if they are remnant features from prior to causeway construction. SSU rRNA gene abundances associated with the NA microbialite were three orders of magnitude lower than those associated with the SA microbialite, indicating that the latter community is more productive. SSU rRNA gene sequencing and functional gene microarray analyses indicated that SA and NA microbialite communities are distinct. In particular, abundant sequences affiliated with photoautotrophic taxa including cyanobacteria and diatoms that may drive carbonate precipitation and thus still actively form microbialites were identified in the SA microbialite; sequences affiliated with photoautotrophic taxa were in low abundance in the NA microbialite. SA and NA microbialites comprise smooth prismatic aragonite crystals. However, the SA microbialite also contained micritic aragonite, which can be formed as a result of biological activity. Collectively, these observations suggest that NA microbialites are likely to be remnant features from prior to causeway construction and indicate a strong decrease in the ability of NA microbialite communities to actively precipitate carbonate minerals. Moreover, the results suggest a role for cyanobacteria and diatoms in carbonate precipitation and microbialite formation in the SA of GSL.

Lateral Comparative Investigation of Stromatolites: Astrobiological Implications and Assessment of Scales of Control

The processes that govern the formation of stromatolites--structures that may represent macroscopic manifestation of microbial processes and a clear target for astrobiological investigation--occur at various scales (local versus regional), yet determining their relative importance remains a challenge, particularly for ancient deposits and/or if similar deposits are discovered elsewhere in the Solar System. We build upon the traditional multiscale level approach of investigation (micro-, meso-, macro-, mega-) by including a lateral comparative investigational component of fine- to large-scale features to determine the relative significance of local and/or nonlocal controls on stromatolite morphology, and in the process, help constrain the dominant influences on microbialite formation. In one example of lateral comparative investigation, lacustrine microbialites from the Miocene Barstow Formation (California) display two main mesofabrics: (1) micritic bands that drastically change in thickness and cannot directly be traced between adjacent decimeter-scale subunits and (2) sparry fibrous layers that are strikingly consistent across subunits, suggesting the formation of sparry fibrous layers was influenced by a process larger than the length scale between the subunits (likely lake chemistry). Microbialites from the uppermost Triassic Cotham Member, United Kingdom, occur as meter-scale mounds and contain a characteristic succession of laminated and dendrolitic mesofabrics. The same succession of laminated/dendrolitic couplets can be traced, not only from mound to mound, but over 100 km, indicating a regional-scale influence on very small structures (microns to centimeters) that would otherwise not be apparent without the lateral comparative approach, and demonstrating that the scale of the feature does not necessarily scale with the scope of the process. Thus, the combination of lateral comparative investigations and multiscale analyses can provide an effective approach for evaluating the dominant controls on stromatolite texture and morphology throughout the rock record and potentially on other planets via rover-scale analyses (e.g., Mars).

Biomarker Analysis of Samples Visually Identified as Microbial in the Eocene Green River Formation: An Analogue for Mars

One of the major exploration targets for current and future Mars missions are lithofacies suggestive of biotic activity. Although such lithofacies are not confirmation of biotic activity, they provide a way to identify samples for further analyses. To test the efficacy of this approach, we identified carbonate samples from the Eocene Green River Formation as "microbial" or "non-microbial" based on the macroscale morphology of their laminations. These samples were then crushed and analyzed by gas chromatography/mass spectroscopy (GC/MS) to determine their lipid biomarker composition. GC/MS analysis revealed that carbonates visually identified as "microbial" contained a higher concentration of more diverse biomarkers than those identified as "non-microbial," suggesting that this could be a viable detection strategy for selecting samples for further analysis or caching on Mars.

Grain trapping by filamentous cyanobacterial and algal mats: implications for stromatolite microfabrics through time

Archean and Proterozoic stromatolites are sparry or fine-grained and finely laminated; coarse-grained stromatolites, such as many found in modern marine systems, do not appear until quite late in the fossil record. The cause of this textural change and its relevance to understanding the evolutionary history of stromatolites is unclear. Cyanobacteria are typically considered the dominant stromatolite builders through time, but studies demonstrating the trapping and binding abilities of cyanobacterial mats are limited. With this in mind, we conducted experiments to test the grain trapping and binding capabilities of filamentous cyanobacterial mats and trapping in larger filamentous algal mats in order to better understand grain size trends in stromatolites. Mats were cut into squares, inclined in saltwater tanks at angles from 0 to 75° (approximating the angle of lamina in typical stromatolites), and grains of various sizes (fine sand, coarse sand, and fine pebbles) were delivered to their surface. Trapping of grains by the cyanobacterial mats depended strongly on (i) how far filaments protruded from the sediment surface, (ii) grain size, and (iii) the mat's incline angle. The cyanobacterial mats were much more effective at trapping fine grains beyond the abiotic slide angle than larger grains. In addition, the cyanobacterial mats actively bound grains of all sizes over time. In contrast, the much larger algal mats trapped medium and coarse grains at all angles. Our experiments suggest that (i) the presence of detrital grains beyond the abiotic slide angle can be considered a biosignature in ancient stromatolites where biogenicity is in question, and, (ii) where coarse grains are present within stromatolite laminae at angles beyond the abiotic angle of slide (e.g., most modern marine stromatolites), typical cyanobacterial-type mats are probably not solely responsible for the construction, giving insight into the evolution of stromatolite microfabrics through time.

Carbonate fabrics in the modern microbialites of Pavilion Lake: two suites of microfabrics that reflect variation in microbial community morphology, growth habit, and lithification

Modern microbialites in Pavilion Lake, BC, provide an analog for ancient non-stromatolitic microbialites that formed from in situ mineralization. Because Pavilion microbialites are mineralizing under the influence of microbial communities, they provide insights into how biological processes influence microbialite microfabrics and mesostructures. Hemispherical nodules and micrite-microbial crusts are two mesostructures within Pavilion microbialites that are directly associated with photosynthetic communities. Both filamentous cyanobacteria in hemispherical nodules and branching filamentous green algae in micrite-microbial crusts were associated with calcite precipitation at microbialite surfaces and with characteristic microfabrics in the lithified microbialite. Hemispherical nodules formed at microbialite surfaces when calcite precipitated around filamentous cyanobacteria with a radial growth habit. The radial filament pattern was preserved within the microbialite to varying degrees. Some subsurface nodules contained well-defined filaments, whereas others contained only dispersed organic inclusions. Variation in filament preservation is interpreted to reflect differences in timing and amount of carbonate precipitation relative to heterotrophic decay, with more defined filaments reflecting greater lithification prior to degradation than more diffuse filaments. Micrite-microbial crusts produce the second suite of microfabrics and form in association with filamentous green algae oriented perpendicular to the microbialite surface. Some crusts include calcified filaments, whereas others contained voids that reflect the filamentous community in shape, size, and distribution. Pavilion microbialites demonstrate that microfabric variation can reflect differences in lithification processes and microbial metabolisms as well as microbial community morphology and organization. Even when the morphology of individual filaments or cells is not well preserved, the microbial growth habit can be captured in mesoscale microbialite structures. These results suggest that when petrographic preservation is extremely good, ancient microbialite growth structures and microfabrics can be interpreted in the context of variation in community organization, community composition, and lithification history. Even in the absence of distinct microbial microfabrics, mesostructures can capture microbial community morphology.

Carbonate build-ups in lacustrine, hydrothermal and fluvial settings: comparing depositional geometry, fabric types and geochemical signature

Carbonate build-ups in lakes, hydrothermal and fluvial settings are characterized by distinctive geometry, spatial distribution, fabrics and geochemical signature but also by some comparable features. Lake margin bioherms form continuous belts for hundreds of metres to kilometres, subparallel to shorelines. Sublacustrine spring mounds are spaced at hundreds of metres to kilometres and aligned along faults. Hydrothermal travertine mounds and aprons with planar clinoforms or terraced slopes are controlled by faults, thermal water discharge and substrate topography. Fluvial tufa barrages, cascades and terraced slopes are controlled by climate, vegetation and substrate gradient. The wide spectrum of carbonate microfabrics ranges from clotted peloidal micrite and laminated boundstone to crystalline dendrite cementstone. Non-marine carbonate microfabrics cannot be linked to specific depositional environments, and are not deterministic proxies for the interpretation of build-up architecture. Microfabric associations can be indicative, but not exclusive, of specific depositional environments and geometry. Stable isotope geochemistry is a useful tool to distinguish between hydrothermal, karstic freshwater and evaporative lake carbonates. Carbonate precipitation results from a continuum of abiotic and biologically influenced/induced processes in settings where carbonate supersaturation is largely driven by physico-chemical mechanisms and microbial biofilms, even if acting as passive low-energy surface sites for nucleation, are widely present.

An abiotic model for the development of textures in some South Atlantic early Cretaceous lacustrine carbonates

The cyclic distribution of various types of carbonates and Mg-clays in early Cretaceous rift-sag phase lacustrine carbonates from the subsurface of the South Atlantic provides an insight into how evolving lake chemistries in highly alkaline settings control facies development. The typically subdecametre scale symmetrical and asymmetrical cyclothems exhibit three main components: mud-grade laminated carbonates, millimetre-diameter spherulites with evidence of having been in a matrix of Mg-silicates, and millimetre–centimetre calcitic shrub-like growths. The laminites contain conspicuous numbers of ostracods and vertebrate remains and were produced by short-lived pluvial events, causing expansion of shallow lakes. Later evaporation triggered Mg-silicate precipitation and calcite nucleation within gels to produce spherulitic textures. When the rate of gel precipitation decreased or ceased, calcite growth, now less inhibited, produced shrub-like calcites resembling those produced abiotically in modern travertines, although still with some evidence of the former presence of some Mg-silicates. Physical reworking of these sediments led to the dispersion of the gels and the concentration of detrital carbonate components. Despite earlier proposals, evidence of microbial processes producing carbonates in these Cretaceous lake deposits is rare and the application of facies models based on modern and ancient microbialite analogues maybe be misplaced.

Deep-water microbialites of the Mesoproterozoic Dismal Lakes Group: microbial growth, lithification, and implications for coniform stromatolites

Offshore facies of the Mesoproterozoic Sulky Formation, Dismal Lakes Group, arctic Canada, preserve microbialites with unusual morphology. These microbialites grew in water depths greater than several tens of meters and correlate with high-relief conical stromatolites of the more proximal September Lake reef complex. The gross morphology of these microbial facies consists of ridge-like vertical supports draped by concave-upward, subhorizontal elements, resulting in tent-shaped cuspate microbialites with substantial primary void space. Morphological and petrographic analyses suggest a model wherein penecontemporaneous upward growth of ridge elements and development of subhorizontal draping elements initially resulted in a buoyantly supported, unlithified microbial form. Lithification began via precipitation within organic elements during microbialite growth. Mineralization either stabilized or facilitated collapse of initially neutrally buoyant microbialite forms. Microbial structures and breccias were then further stabilized by precipitation of marine herringbone cement. During late-stage diagenesis, remaining void space was occluded by ferroan dolomite cement. Cuspate microbialites are most similar to those found in offshore facies of Neoarchean carbonate platforms and to unlithified, buoyantly supported microbial mats in modern ice-covered Antarctic lakes. We suggest that such unusual microbialite morphologies are a product of the interaction between motile and non-motile communities under nutrient-limiting conditions, followed by early lithification, which served to preserve the resultant microbial form. The presence of marine herringbone cement, commonly associated with high dissolved inorganic carbon (DIC), low O2 conditions, also suggests growth in association with reducing environments at or near the seafloor or in conjunction with a geochemical interface. Predominance of coniform stromatolite forms in the Proterozoic--across a variety of depositional environments--may thus reflect a combination of heterogeneous nutrient distribution, potentially driven by variable redox conditions, and an elevated carbonate saturation state, which permits preservation of these unusual microbialite forms.

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.

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.