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

A Biofilm Channel Origin for Vermiform Microstructure in Carbonate Microbialites

A three-dimensional tubular fabric known as "vermiform microstructure" in Phanerozoic and Neoproterozoic carbonate microbialites has been hypothesized to represent the body fossil of nonspicular keratose demosponges. If correct, this interpretation extends the sponge body fossil record and origin of animals to ~890 Ma. However, the veracity of the keratose sponge interpretation for vermiform microstructure remains in question, and the origin of the tubular fabric is enigmatic. Here we compare exceptionally well-preserved microbialite textures from the Upper Triassic to channel networks created by modern microbial biofilms. We demonstrate that anastomosing channel networks of similar size and geometries are produced by microbial biofilms in the absence of sponges, suggesting the origin for vermiform microstructure in ancient carbonates is not unique to sponges and perhaps best interpreted conservatively as likely microbial in origin. We present a taphonomic model of early biofilm lithification in seawater with anomalously high carbonate saturation necessary to preserve delicate microbial textures. This work has implications for the understanding of three-dimensional biofilm architecture that goes beyond the current micro-scale observations available from living biofilm experiments and suggests that biofilm channel networks have an extensive fossil record.

Microbialite Accretion and Growth: Lessons from Shark Bay and the Bahamas

Microbialites provide geological evidence of one of Earth's oldest ecosystems, potentially recording long-standing interactions between coevolving life and the environment. Here, we focus on microbialite accretion and growth and consider how environmental and microbial forces that characterize living ecosystems in Shark Bay and the Bahamas interact to form an initial microbialite architecture, which in turn establishes distinct evolutionary pathways. A conceptual three-dimensional model is developed for microbialite accretion that emphasizes the importance of a dynamic balance between extrinsic and intrinsic factors in determining the initial architecture. We then explore how early taphonomic and diagenetic processes modify the initial architecture, culminating in various styles of preservation in the rock record. The timing of lithification of microbial products is critical in determining growth patterns and preservation potential. Study results have shown that all microbialites are not created equal; the unique evolutionary history of an individual microbialite matters.

Structure and function of Shark Bay microbial communities following tropical cyclone Olwyn: A metatranscriptomic and organic geochemical perspective

Shark Bay, Western Australia, is episodically impacted by tropical cyclones. During 2015, the region was hit by a category 3 cyclone, "severe tropical cyclone Olywn," leading to the formation of a black sludge in an intertidal zone harboring microbial mats and microbialites. Upon returning to the impacted site 12 months later, the black sludge deposit was still recognizable between the microbialite columns and mucilaginous cobbles near the shoreline in the impacted area. Metatranscriptomic and organic geochemical analyses were carried out on the cyclone-derived materials and impacted microbial mat communities to unravel the structure, function, and potential preservation of these deposits following a tropical cyclone. It was found that samples derived from the black sludge contained low relative abundances of cyanobacteria but had higher proportions of heterotrophic and anaerobic microorganisms (e.g., methanogens and sulfate-reducing bacteria). Increased metabolic activity by these microorganisms (e.g., sulfate reduction and organic matter degradation) is thought to drive calcium carbonate precipitation and helps in mat preservation. Comparison of the aliphatic biomarker by gas chromatography-mass spectrometry (GC-MS) analyses showed that C₂₅  highly branched isoprenoid (HBI) alkenes were significantly higher in the cyclone-derived materials attributed to the relocation of subtidal sediments containing HBI-producing diatom communities by the tropical cyclone. Raney nickel desulfurization of the polar fraction extracted from a mucilaginous cobble revealed sulfur-bound hopanoids and a series of benzohopanes. The presence of these compounds could be indicative of microbial matter that has been influenced by the tropical cyclone which may have caused elevated levels of water column anoxia promoting increased sulfurization of the organic matter to occur.

Carbonate facies-specific stable isotope data record climate, hydrology, and microbial communities in Great Salt Lake, UT

Organic and inorganic stable isotopes of lacustrine carbonate sediments are commonly used in reconstructions of ancient terrestrial ecosystems and environments. Microbial activity and local hydrological inputs can alter porewater chemistry (e.g., pH, alkalinity) and isotopic composition (e.g., δ¹⁸ O_water , δ¹³ C_DIC ), which in turn has the potential to impact the stable isotopic compositions recorded and preserved in lithified carbonate. The fingerprint these syngenetic processes have on lacustrine carbonate facies is yet unknown, however, and thus, reconstructions based on stable isotopes may misinterpret diagenetic records as broader climate signals. Here, we characterize geochemical and stable isotopic variability of carbonate minerals, organic matter, and water within one modern lake that has known microbial influences (e.g., microbial mats and microbialite carbonate) and combine these data with the context provided by 16S rRNA amplicon sequencing community profiles. Specifically, we measure oxygen, carbon, and clumped isotopic compositions of carbonate sediments (δ¹⁸ O_carb , δ¹³ C_carb , ∆₄₇ ), as well as carbon isotopic compositions of bulk organic matter (δ¹³ C_org ) and dissolved inorganic carbon (DIC; δ¹³ C_DIC ) of lake and porewater in Great Salt Lake, Utah from five sites and three seasons. We find that facies equivalent to ooid grainstones provide time-averaged records of lake chemistry that reflect minimal alteration by microbial activity, whereas microbialite, intraclasts, and carbonate mud show greater alteration by local microbial influence and hydrology. Further, we find at least one occurrence of ∆₄₇ isotopic disequilibrium likely driven by local microbial metabolism during authigenic carbonate precipitation. The remainder of the carbonate materials (primarily ooids, grain coatings, mud, and intraclasts) yield clumped isotope temperatures (T(∆₄₇ )), δ¹⁸ O_carb , and calculated δ¹⁸ O_water in isotopic equilibrium with ambient water and temperature at the time and site of carbonate precipitation. Our findings suggest that it is possible and necessary to leverage diverse carbonate facies across one sedimentary horizon to reconstruct regional hydroclimate and evaporation-precipitation balance, as well as identify microbially mediated carbonate formation.

The Record of Environmental and Microbial Signatures in Ancient Microbialites: The Terminal Carbonate Complex from the Neogene Basins of Southeastern Spain

The Messinian microbialites of the Terminal Carbonate Complex (TCC) from the Neogene basins of southeastern Spain show both diversified morphologies and an excellent preservation of primary microbial microstructures. Their stratigraphic architecture, fabric (micro-, meso-, and macro-fabric), and mineralogical composition were investigated in eight localities from three sedimentary basins of southeastern Spain: The Sorbas and Bajo Segura basins and the Agua Amarga depression. Two recurrent microbialite associations were distinguished. Laterally linked low relief stromatolites predominated in Microbialite Association 1 (MA1), which probably formed in low energy lagoons or lakes with fluctuating normal marine to hypersaline water. The microfabrics of MA1 reflected the predominance of microbially induced/influenced precipitation of carbonates and locally (Ca)-Mg-Al silicates. Microbialite Association 2 (MA2) developed in high energy wave and tidal influenced foreshore to shoreface, in normal marine to hypersaline water. High-relief buildups surrounded by mobile sediment (e.g., ooids or pellets) dominated in this environment. MA2 microbialites showed a significant proportion of thrombolitic mesofabric. Grain-rich microfabrics indicated that trapping and binding played a significant role in their accretion, together with microbially induced/influenced carbonate precipitation. The stratigraphic distribution of MA1 and MA2 was strongly influenced by water level changes, the morphology and nature of the substratum, and exposure to waves. MA1 favorably developed in protected areas during third to fourth order early transgression and regression phases. MA2 mostly formed during the late transgressions and early regressions in high energy coastal areas, often corresponding to fossil coral reefs. Platform scale syn-sedimentary gypsum deformation and dissolution enhanced microbial carbonate production, microbialites being thicker and more extended in zones of maximum deformation/dissolution. Microbial microstructures (e.g., microbial peloids) and microfossils were preserved in the microbialites. Dolomite microspheres and filaments showed many morphological similarities with some of the cyanobacteria observed in modern open marine and hypersaline microbialites. Dolomite potentially replaced a metastable carbonate phase during early diagenesis, possibly in close relationship with extracellular polymeric substances (EPS) degradation. Double-layered microspheres locally showed an inner coating made of (Ca)-Mg-Al silicates and carbonates. This mineral coating could have formed around coccoid cyanobacteria and indicated an elevated pH in the upper part of the microbial mats and a potential dissolution of diatoms as a source of silica. Massive primary dolomite production in TCC microbialites may have resulted from enhanced sulfate reduction possibly linked to the dissolving gypsum that would have provided large amounts of sulfate-rich brines to microbial mats. Our results open new perspectives for the interpretation of ancient microbialites associated with major evaporite deposits, from microbe to carbonate platform scales.

Microbial Origin of the Organic Matter Preserved in the Cayo Coco Lagoonal Network, Cuba

The southern part of the tropical Cayo Coco Island (Cuba) hosts a complex, highly evaporative and marine-fed lagoonal network. In the easternmost lagoon of this network, hypersaline conditions favour the development of complex sedimentary microbial ecosystems within the water column at the bottom water-sediment interface and on the shore. Some of these ecosystems are producing microbial mats and biofilms with variable mineralisation rates, depending on their location. Since the mineralisation of these microbial deposits is rare, the sedimentary record does not provide a direct window on the evolution of these ecosystems or their distribution through space and time. However, microbial deposits also produce copious amounts of organic matter, which may be used to decipher any microbial-related origin within the sedimentary record. Microbial mats and biofilms were identified as the potential source of organic material in addition to the surrounding mangrove, soils and suspended particulate matter (SPM). The origin and evolution of the sedimentary organic matter preserved within the lagoonal sediments has been analysed using geochemical parameters such as elemental (TOC, TN and [C/N]atomic ratio) and isotopic (δ13Corg and δ15NTN) signals on four sedimentary cores retrieved from different locations in the lagoon and compared with the geochemical signatures of the potential sources. Despite the high potential for organic matter accumulation in the studied lagoon, the TOC and TN downcore values in sediments that were analysed (i.e., micritic muds and bioclastic sands) remain very low compared to the sediment-water interface. The relative contributions of the different potential sources of organic matter were estimated using [C/N]atomic ratios and δ13Corg values. The δ15NTN signature was discarded as a source signature as it records synsedimentary, early diagenetic, secondary evolution of the nitrogen signal associated with OM remineralisation (i.e., denitrification). Finally, among the microbial deposits, the slime recognised in the permanently submersed zone of the waterbody appears to be the main contributor to the organic matter preserved within the sediments of the lagoon. SPM, mainly composed of microbial-rich particles, also contribute and cannot be ruled out as a source.

Instant Attraction: Clay Authigenesis in Fossil Fungal Biofilms

Clay authigenesis associated with the activity of microorganisms is an important process for biofilm preservation and may provide clues to the formation of biominerals on the ancient Earth. Fossilization of fungal biofilms attached to vesicles or cracks in igneous rock, is characterized by fungal-induced clay mineralization and can be tracked in deep rock and deep time, from late Paleoproterozoic (2.4 Ga), to the present. Here we briefly review the current data on clay mineralization by fossil fungal biofilms from oceanic and continental subsurface igneous rock. The aim of this study was to compare the nature of subsurface fungal clays from different igneous settings to evaluate the importance of host rock and ambient redox conditions for clay speciation related to fossil microorganisms. Our study suggests that the most common type of authigenic clay associated with pristine fossil fungal biofilms in both oxic (basaltic) and anoxic (granitic) settings are montmorillonite-like smectites and confirms a significant role of fungal biofilms in the cycling of elements between host rock, ocean and secondary precipitates. The presence of life in the deep subsurface may thus prove more significant than host rock geochemistry in directing the precipitation of authigenic clays in the igneous crust, the extent of which remains to be fully understood.

Biotic–Abiotic Influences on Modern Ca–Si-Rich Hydrothermal Spring Mounds of the Pastos Grandes Volcanic Caldera (Bolivia)

The lacustrine-to-palustrine Pastos Grandes Laguna (Bolivia) is located in a volcanic caldera fed by active hot springs, with a carbonate crust extending over 40 km2. An integrated approach based on geology and hydrochemistry was used to characterize La Salsa, one of its hydrothermal systems, composed of a flat mound with a hydrothermal discharge. The mound is composed of carbonate–diatom aggregates, forming muds that accumulate and undergo slight swelling. The discharge area along the hydrothermal pathway exhibits several facies and microfabrics, with considerable biological activity and microbialite development. Both the downstream evolution of carbonate and silica content in sediments and the distribution of microbialites can be linked to changes in biotic-abiotic processes occurring along the pathway. The spatial distribution of microbialites and their morphologies are related to hydrodynamic conditions, the nature of the substrate on which they grow and, to a lesser extent, to the accommodation space available. The evolution of the physicochemical properties of the water and biological activity mainly impact mineral precipitation but also affect microbialite morphologies and microstructures. This atypical Si- and Ca-rich hydrothermal system therefore provides insights into the diversity of environmental, chemical, and biotic factors controlling mineralization, which also responds to independent thermodynamic controls.

The Role of the Substrate on the Mineralization Potential of Microbial Mats in A Modern Freshwater River (Paris Basin, France)

The relationship between environmental conditions and the development, mineralization and preservation of modern tufa microbialites was investigated in a 1.1 km long freshwater stream in Villiers-le-Bâcle, a tributary of Mérantaise river. Detailed mapping of the tufa microbialite distribution combined with sedimentological, petrographical and mineralogical analyses were coupled with chemical measurements. Six organosedimentary structures were identified; their distribution appears heterogeneous along the stream and responds to physicochemical conditions of water and specific biological components (e.g., microorganism, exopolymeric substance). Two of the organosedimentary structures show evidence of mineralization and only one is lithified. Based on field observations and in-situ deployment of mineralization markers (bricks), three zones with increasing mineralization intensities are defined, ranging from no mineralization to thick mineralized crusts forming riverine tufa. Both biotic and abiotic processes were proposed for the tufa microbialite formation. We explained changes in mineralization intensities by the specific physicochemical conditions (e.g., calcite saturation index (SIcalc) and partial pressure of CO2 (pCO2) and a closed proximity of the cyanobacterial biofilm and carbonates precipitates. The physical and chemical composition of substrate impact development of microbial communities, mineralization potential of tufa microbialite. Even though the physicochemical and biological conditions were optimal for mineral precipitation, the potential of lithification depended on the presence of a suitable (physical and chemical) substrate.

Mineralized microbialites as archives of environmental evolution, Laguna Negra, Catamarca Province, Argentina

Environmental fluctuations are recorded in a variety of sedimentary archives of lacustrine depositional systems. Geochemical signals recovered from bottom sediments in closed-basin lakes are among the most sensitive paleoenvironmental indicators and are commonly used in reconstructing lake evolution. Microbialites (i.e., organosedimentary deposits accreted through microbial trapping and binding of detrital sediment or in situ mineral precipitation on organics [Palaios, 2, 1987, 241]), however, have been largely overlooked as paleoenvironmental repositories. Here, we investigate concentrically laminated mineralized microbialites from Laguna Negra, a high-altitude (4,100 m above sea level) hypersaline, closed-basin lake in northwestern Argentina, and explore the potential for recovery of environmental signals from these unique sedimentary archives. Spatial heterogeneity in hydrological regime helps define zones inside Laguna Negra, each with their own morphologically distinct microbialite type. Most notably, platey microbialites (in Zone 3A) are precipitated by evaporative concentration processes, while discoidal oncolites (in Zone 3C) are interpreted result from fluid mixing and biologically mediated nucleation. This spatial heterogeneity is reflected in petrographically distinct carbonate fabrics: micritic, botryoidal, and isopachous. Fabric type is interpreted to reflect a combination of physical and biological influences during mineralization, and paired C-isotope measurement of carbonate and organic matter supports ecological differences as a dominant control on C-isotopic evolution between zones. Laminae of Laguna Negra microbialites preserve a range of δ¹³ C_carb from +5.75‰ to +18.25‰ and δ¹⁸ O_carb from -2.04‰ to +9.28‰. Temporal trends of lower carbon and oxygen isotopic compositions suggest that the influence of CO₂ degassing associated with evaporation has decreased over time. Combined, these results indicate that microbialite archives can provide data that aid in interpretation of both lake paleohydrology and paleoenvironmental change.

Microterracettes in Sabkha Oum Dba (Western Sahara, Morocco): Physical and Biological Interactions in the Formation of a Surface Micromorphology

Small-scale terracing (microterracettes) is a surface geomorphic feature that recurs under a range of environmental settings, such as those existing in high to low temperature geothermal springs and evaporitic environments, through the single or combined action of physicochemical agents and microbiological processes. Such morphology can also be observed in a confined sector of the Sabkha Oum Dba, which is an inland sabkha of the Western Sahara (Morocco), where field and laboratory investigations revealed that they primarily depend on the accumulation of naviculoid diatoms. Through their biofilm production ability, these benthic diatoms are able to stabilize surface morphologies and make organic alveolar frameworks where the precipitation of low Mg calcite occurs in areas subjected to active oxygenic photosynthesis. Because microterracettes arise in a specific set of environmental conditions, they have environmental significance and, thanks to a high fossilization potential due to mineral precipitation, they can be an effective source of biomorphological and chemical evidence for life. The relationship with aqueous environments, considered to be widespread on Mars especially during a period of intense hydrologic activity as in the late Noachian and Hesperian periods, make the understanding of surficial processes useful (such as the formation of microterracettes) whose formation is frequent in terrestrial analogues for martian environments, such as ephemeral saline continental lakes (sabkhas) and related to the products of bacterial and eukaryotic life, as in the case of biofilms, in search for similar life forms beyond Earth.

A microbial role in the construction of Mono Lake carbonate chimneys?

Lacustrine carbonate chimneys are striking, metre-scale constructions. If these were bioinfluenced constructions, they could be priority targets in the search for early and extraterrestrial microbial life. However, there are questions over whether such chimneys are built on a geobiological framework or are solely abiotic geomorphological features produced by mixing of lake and spring waters. Here, we use correlative microscopy to show that microbes were living around Pleistocene Mono Lake carbonate chimneys during their growth. A plausible interpretation, in line with some recent works by others on other lacustrine carbonates, is that benthic cyanobacteria and their associated extracellular organic material (EOM) formed tubular biofilms around rising sublacustrine spring vent waters, binding calcium ions and trapping and binding detrital silicate sediment. Decay of these biofilms would locally have increased calcium and carbonate ion activity, inducing calcite precipitation on and around the biofilms. Early manganese carbonate mineralisation was directly associated with cell walls, potentially related to microbial activity though the precise mechanism remains to be elucidated. Much of the calcite crystal growth was likely abiotic, and no strong evidence for either authigenic silicate growth or a clay mineral precursor framework was observed. Nevertheless, it seems likely that the biofilms provided initial sites for calcite nucleation and encouraged the primary organised crystal growth. We suggest that the nano-, micro- and macroscale fabrics of these Pleistocene Mono Lake chimneys were affected by the presence of centimetre-thick tubular and vertically stacked calcifying microbial mats. Such carbonate chimneys represent a promising macroscale target in the exploration for ancient or extraterrestrial life.

Snapshot of an early Paleoproterozoic ecosystem: Two diverse microfossil communities from the Turee Creek Group, Western Australia

Eighteen microfossil morphotypes from two distinct facies of black chert from a deep-water setting of the c. 2.4 Ga Turee Creek Group, Western Australia, are reported here. A primarily in situ, deep-water benthic community preserved in nodular black chert occurs as a tangled network of a variety of long filamentous microfossils, unicells of one size distribution and fine filamentous rosettes, together with relatively large spherical aggregates of cells interpreted as in-fallen, likely planktonic, forms. Bedded black cherts, in contrast, preserve microfossils primarily within, but also between, rounded clasts of organic material that are coated by thin, convoluted carbonaceous films interpreted as preserved extracellular polymeric substance (EPS). Microfossils preserved within the clasts include a wide range of unicells, both much smaller and larger than those in the nodular black chert, along with relatively short, often degraded filaments, four types of star-shaped rosettes and umbrella-like rosettes. Large, complexly branching filamentous microfossils are found between the clasts. The grainstone clasts in the bedded black chert are interpreted as transported from shallower water, and the contained microfossils thus likely represent a phototrophic community. Combined, the two black chert facies provide a snapshot of a microbial ecosystem spanning shallow to deeper-water environments, and an insight into the diversity of life present during the rise in atmospheric oxygen. The preserved microfossils include two new, distinct morphologies previously unknown from the geological record, as well as a number of microfossils from the bedded black chert that are morphologically similar to-but 400-500 Ma older than-type specimens from the c. 1.88 Ga Gunflint Iron Formation. Thus, the Turee Creek Group microfossil assemblage creates a substantial reference point in the sparse fossil record of the earliest Paleoproterozoic and demonstrates that microbial life diversified quite rapidly after the end of the Archean.

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.

Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico

Laguna Bacalar is a sulfate-rich freshwater lake on the Yucatan Peninsula that hosts large microbialites. High sulfate concentrations distinguish Laguna Bacalar from other freshwater microbialite sites such as Pavilion Lake and Alchichica, Mexico, as well as from other aqueous features on the Yucatan Peninsula. While cyanobacterial populations have been described here previously, this study offers a more complete characterization of the microbial populations and corresponding biogeochemical cycling using a three-pronged geobiological approach of microscopy, high-throughput DNA sequencing, and lipid biomarker analyses. We identify and compare diverse microbial communities of Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria that vary with location along a bank-to-bank transect across the lake, within microbialites, and within a neighboring mangrove root agglomeration. In particular, sulfate-reducing bacteria are extremely common and diverse, constituting 7%-19% of phylogenetic diversity within the microbialites, and are hypothesized to significantly influence carbonate precipitation. In contrast, Cyanobacteria account for less than 1% of phylogenetic diversity. The distribution of lipid biomarkers reflects these changes in microbial ecology, providing meaningful biosignatures for the microbes in this system. Polysaturated short-chain fatty acids characteristic of cyanobacteria account for <3% of total abundance in Laguna Bacalar microbialites. By contrast, even short-chain and monounsaturated short-chain fatty acids attributable to both Cyanobacteria and many other organisms including types of Alphaproteobacteria and Gammaproteobacteria constitute 43%-69% and 17%-25%, respectively, of total abundance in microbialites. While cyanobacteria are the largest and most visible microbes within these microbialites and dominate the mangrove root agglomeration, it is clear that their smaller, metabolically diverse associates are responsible for significant biogeochemical cycling in this microbialite system.

Evidence of oxygenic phototrophy in ancient phosphatic stromatolites from the Paleoproterozoic Vindhyan and Aravalli Supergroups, India

Fossil microbiotas are rare in the early rock record, limiting the type of ecological information extractable from ancient microbialites. In the absence of body fossils, emphasis may instead be given to microbially derived features, such as microbialite growth patterns, microbial mat morphologies, and the presence of fossilized gas bubbles in lithified mats. The metabolic affinity of micro-organisms associated with phosphatization may reveal important clues to the nature and accretion of apatite-rich microbialites. Stromatolites from the 1.6 Ga Chitrakoot Formation (Semri Group, Vindhyan Supergroup) in central India contain abundant fossilized bubbles interspersed within fine-grained in situ-precipitated apatite mats with average δ¹³ C_org indicative of carbon fixation by the Calvin cycle. In addition, the mats hold a synsedimentary fossil biota characteristic of cyanobacterial and rhodophyte morphotypes. Phosphatic oncoid cone-like stromatolites from the Paleoproterozoic Aravalli Supergroup (Jhamarkotra Formation) comprise abundant mineralized bubbles enmeshed within tufted filamentous mat fabrics. Construction of these tufts is considered to be the result of filamentous bacteria gliding within microbial mats, and as fossilized bubbles within pristine mat laminae can be used as a proxy for oxygenic phototrophy, this provides a strong indication for cyanobacterial activity in the Aravalli mounds. We suggest that the activity of oxygenic phototrophs may have been significant for the formation of apatite in both Vindhyan and Aravalli stromatolites, mainly by concentrating phosphate and creating steep diurnal redox gradients within mat pore spaces, promoting apatite precipitation. The presence in the Indian stromatolites of alternating apatite-carbonate lamina may result from local variations in pH and oxygen levels caused by photosynthesis-respiration in the mats. Altogether, this study presents new insights into the ecology of ancient phosphatic stromatolites and warrants further exploration into the role of oxygen-producing biotas in the formation of Paleoproterozoic shallow-basin phosphorites.

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.

Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems

Microbial cells (i.e., bacteria, archaea, microeukaryotes) in oceans secrete a diverse array of large molecules, collectively called extracellular polymeric substances (EPSs) or simply exopolymers. These secretions facilitate attachment to surfaces that lead to the formation of structured 'biofilm' communities. In open-water environments, they also lead to formation of organic colloids, and larger aggregations of cells, called 'marine snow.' Secretion of EPS is now recognized as a fundamental microbial adaptation, occurring under many environmental conditions, and one that influences many ocean processes. This relatively recent realization has revolutionized our understanding of microbial impacts on ocean systems. EPS occur in a range of molecular sizes, conformations and physical/chemical properties, and polysaccharides, proteins, lipids, and even nucleic acids are actively secreted components. Interestingly, however, the physical ultrastructure of how individual EPS interact with each other is poorly understood. Together, the EPS matrix molecules form a three-dimensional architecture from which cells may localize extracellular activities and conduct cooperative/antagonistic interactions that cannot be accomplished efficiently by free-living cells. EPS alter optical signatures of sediments and seawater, and are involved in biogeomineral precipitation and the construction of microbial macrostructures, and horizontal-transfers of genetic information. In the water-column, they contribute to the formation of marine snow, transparent exopolymer particles (TEPs), sea-surface microlayer biofilm, and marine oil snow. Excessive production of EPS occurs during later-stages of phytoplankton blooms as an excess metabolic by product and releases a carbon pool that transitions among dissolved-, colloidal-, and gel-states. Some EPS are highly labile carbon forms, while other forms appear quite refractory to degradation. Emerging studies suggest that EPS contribute to efficient trophic-transfer of environmental contaminants, and may provide a protective refugia for pathogenic cells within marine systems; one that enhances their survival/persistence. Finally, these secretions are prominent in 'extreme' environments ranging from sea-ice communities to hypersaline systems to the high-temperatures/pressures of hydrothermal-vent systems. This overview summarizes some of the roles of exopolymer in oceans.

Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes

The role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of putative niches in these systems. In the present study, high throughput amplicon sequencing was undertaken in conjunction with analysis of key biogeochemical properties of two mats (smooth and pustular) from Shark Bay, Australia. One-way analysis of similarity tests indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1%). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Pustular mats were enriched with Halobacteria and Parvarchaeota. Key metabolisms (bacterial and archaeal) were measured, and the rates of oxygen production/consumption and sulfate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic layers and was up to seven-fold higher in smooth than pustular mats. The finding of an abundance of anaerobic methanogens enriched at the surface where oxygen levels were highest, coupled with peak methane production in the oxic zone, suggests putative surface anoxic niches in these microbial mats.

Microbial and diagenetic steps leading to the mineralisation of Great Salt Lake microbialites

Microbialites are widespread in modern and fossil hypersaline environments, where they provide a unique sedimentary archive. Authigenic mineral precipitation in modern microbialites results from a complex interplay between microbial metabolisms, organic matrices and environmental parameters. Here, we combined mineralogical and microscopic analyses with measurements of metabolic activity in order to characterise the mineralisation of microbial mats forming microbialites in the Great Salt Lake (Utah, USA). Our results show that the mineralisation process takes place in three steps progressing along geochemical gradients produced through microbial activity. First, a poorly crystallized Mg-Si phase precipitates on alveolar extracellular organic matrix due to a rise of the pH in the zone of active oxygenic photosynthesis. Second, aragonite patches nucleate in close proximity to sulfate reduction hotspots, as a result of the degradation of cyanobacteria and extracellular organic matrix mediated by, among others, sulfate reducing bacteria. A final step consists of partial replacement of aragonite by dolomite, possibly in neutral to slightly acidic porewater. This might occur due to dissolution-precipitation reactions when the most recalcitrant part of the organic matrix is degraded. The mineralisation pathways proposed here provide pivotal insight for the interpretation of microbial processes in past hypersaline environments.

Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics

Microbialite-forming communities interact with the environment and influence the precipitation of calcium carbonate through their metabolic activity. The functional genes associated with these metabolic processes and their environmental interactions are therefore critical to microbialite formation. The microbiomes associated with microbialite-forming ecosystems are just now being elucidated and the extent of shared pathways and taxa across different environments is not fully known. In this study, we profiled the microbiome of microbial communities associated with lacustrine thrombolites located in Lake Clifton, Western Australia using metagenomic sequencing and compared it to the non-lithifying mats associated with surrounding sediments to determine whether differences in the mat microbiomes, particularly with respect to metabolic pathways and environmental interactions, may potentially contribute to thrombolite formation. Additionally, we used stable isotope biosignatures to delineate the dominant metabolism associated with calcium carbonate precipitation in the thrombolite build-ups. Results indicated that the microbial community associated with the Lake Clifton thrombolites was predominantly bacterial (98.4%) with Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria comprising the majority of annotated reads. Thrombolite-associated mats were enriched in photoautotrophic taxa and functional genes associated with photosynthesis. Observed δ¹³C values of thrombolite CaCO₃ were enriched by at least 3.5‰ compared to theoretical values in equilibrium with lake water DIC, which is consistent with the occurrence of photoautotrophic activity in thrombolite-associated microbial mats. In contrast, the microbiomes of microbial communities found on the sandy non-lithifying sediments of Lake Clifton represented distinct microbial communities that varied in taxa and functional capability and were enriched in heterotrophic taxa compared to the thrombolite-associated mats. This study provides new insight into the taxa and functional capabilities that differentiate potentially lithifying mats from other non-lithifying types and suggests that thrombolites are actively accreting and growing in limited areas of Lake Clifton.

Mineralogy and Microbial Diversity of the Microbialites in the Hypersaline Storr's Lake, the Bahamas

Microbialites found in the low-light-intensity, hypersaline waters of Storr's Lake (SL), San Salvador Island, the Bahamas, were investigated with respect to their morphology, mineralogy, and microbial diversity. Previously described microbialite morphologies, as well as a newly identified "multi-cuspate" morphology, were observed at various depths. Electron microscopy analysis revealed the presence of angular, blocky, and needle-shaped crystals with mineralized cyanobacterial filaments and remains of exopolymeric substances. X-ray diffraction studies confirmed the presence of both Mg-calcite and aragonite in the plateau-mushroom and pinnacle mound microbialites, whereas only Mg-calcite was identified in the other microbialite morphotypes. A comprehensive molecular analysis using barcoded pyrosequencing of five different microbial mat communities identified at least 12 dominant bacterial phyla. Cyanobacteria were generally low in abundance and ranged from ∼0.01% in the deeper pinnacle mounds to ∼3.2% in the shallow calcareous knobs. Other photosynthetic members included green nonsulfur bacteria of the phylum Chloroflexi and purple sulfur bacteria of the class Gammaproteobacteria. All mat types contained significant amounts of sulfate-reducing and dehalogenating bacteria. The low light intensity reaching the deeper microbialites, the lack of dominant cyanobacteria, and the abundance of sulfate reducers and Chloroflexi collectively suggest that sulfate reduction and anoxygenic photosynthetic processes influence the carbonate biomineralization process in these systems.

Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis

Modern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on understanding the taxonomic complexity and not fully elucidating the functional capabilities of these systems. Here, we begin to characterize the microbiome associated with stromatolites of Little Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct whole shotgun sequencing. The metagenomic analysis of the Little Darby stromatolites revealed many shared taxa and core pathways associated with biologically induced carbonate precipitation, suggesting functional convergence within Bahamian stromatolites. A comparison of the Little Darby stromatolites with other lithifying microbial ecosystems also revealed that although factors, such as geographic location and salinity, do drive some differences within the population, there are extensive similarities within the microbial populations. These results suggest that for stromatolite formation, 'who' is in the community is not as critical as metabolic activities and environmental interactions. Together, these analyses help improve our understanding of the similarities among lithifying ecosystems and provide an important first step in characterizing the shared microbiome of modern stromatolites.

Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats

Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism.

CaCO3 precipitation in multilayered cyanobacterial mats: clues to explain the alternation of micrite and sparite layers in calcareous stromatolites

Marine cyanobacterial mats were cultured on coastal sediments (Nivå Bay, Øresund, Denmark) for over three years in a closed system. Carbonate particles formed in two different modes in the mat: (i) through precipitation of submicrometer-sized grains of Mg calcite within the mucilage near the base of living cyanobacterial layers, and (ii) through precipitation of a variety of mixed Mg calcite/aragonite morphs in layers of degraded cyanobacteria dominated by purple sulfur bacteria. The d13C values were about 2‰ heavier in carbonates from the living cyanobacterial zones as compared to those generated in the purple bacterial zones. Saturation indices calculated with respect to calcite, aragonite, and dolomite inside the mats showed extremely high values across the mat profile. Such high values were caused by high pH and high carbonate alkalinity generated within the mats in conjunction with increased concentrations of calcium and magnesium that were presumably stored in sheaths and extracellular polymer substances (EPS) of the living cyanobacteria and liberated during their post-mortem degradation. The generated CaCO3 morphs were highly similar to morphs reported from heterotrophic bacterial cultures, and from bacterially decomposed cyanobacterial biomass emplaced in Ca-rich media. They are also similar to CaCO3 morphs precipitated from purely inorganic solutions. No metabolically (enzymatically) controlled formation of particular CaCO3 morphs by heterotrophic bacteria was observed in the studied mats. The apparent alternation of in vivo and post-mortem generated calcareous layers in the studied cyanobacterial mats may explain the alternation of fine-grained (micritic) and coarse-grained (sparitic) laminae observed in modern and fossil calcareous cyanobacterial microbialites as the result of a probably similar multilayered mat organization.

Changing microspatial patterns of sulfate-reducing microorganisms (SRM) during cycling of marine stromatolite mats

Microspatial arrangements of sulfate-reducing microorganisms (SRM) in surface microbial mats (~1.5 mm) forming open marine stromatolites were investigated. Previous research revealed three different mat types associated with these stromatolites, each with a unique petrographic signature. Here we focused on comparing "non-lithifying" (Type-1) and "lithifying" (Type-2) mats. Our results revealed three major trends: (1) Molecular typing using the dsrA probe revealed a shift in the SRM community composition between Type-1 and Type-2 mats. Fluorescence in-situ hybridization (FISH) coupled to confocal scanning-laser microscopy (CSLM)-based image analyses, and 35SO4(2-)-silver foil patterns showed that SRM were present in surfaces of both mat types, but in significantly (p < 0.05) higher abundances in Type-2 mats. Over 85% of SRM cells in the top 0.5 mm of Type-2 mats were contained in a dense 130 µm thick horizontal layer comprised of clusters of varying sizes; (2) Microspatial mapping revealed that locations of SRM and CaCO3 precipitation were significantly correlated (p < 0.05); (3) Extracts from Type-2 mats contained acylhomoserine-lactones (C4- ,C6- ,oxo-C6,C7- ,C8- ,C10- ,C12- , C14-AHLs) involved in cell-cell communication. Similar AHLs were produced by SRM mat-isolates. These trends suggest that development of a microspatially-organized SRM community is closely-associated with the hallmark transition of stromatolite surface mats from a non-lithifying to a lithifying state.