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

Reduced greenhouse gas emissions from particulate organic matter degradation in iron-enriched sediments

Iron (Fe) plays an important role in the biogeochemical cycling of carbon and nutrients in aquatic systems. Reactive Fe phases can interact with organic carbon and facilitate the removal of carbon from the biogeochemical cycle; however, this important ecosystem function is often strongly controlled by Fe availability. Due to pollution from lignite mining in the Lusatian province in Northeast Germany, large amounts of iron and sulfate are released into the fluvial-lacustrine system of the Spree River. It was hypothesized that the input of freshly precipitated iron oxyhydroxides from mining areas (e.g., ferrihydrite) alter the biodegradation of particulate organic matter (POM) in downstream lacustrine sediments. To investigate the Fe-dependent degradation of POM, slurries mimicking iron-polluted sediments (85 mg Fe per g, 116 mg Fe per g, and 149 mg Fe per g dry weight) were incubated with plankton or leaf POM under anoxic and oxic headspace conditions, and CO2 and CH4 emissions, water chemistry, and stable isotopes of dissolved inorganic carbon were measured. The experiments revealed that (i) with an increasing Fe content, the CO2 and CH4 emissions were gradually reduced, (ii) CO2 and CH4 production was higher during plankton degradation than during leaf decomposition, and (iii) under oxic conditions, CO2 production was higher and CH4 production was lower when compared to the treatments under anoxic conditions. These findings demonstrate that while benthic mineralization of fresh POM typically releases greenhouse gases into the water column, the availability of iron oxyhydroxides can contribute to reduced greenhouse gas emissions from sediments. This is of considerable relevance for future carbon budgets of similar mining-affected, iron-polluted fluvial-lacustrine river systems.

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.

Aragonite crystallization in a sulfate-rich hypersaline wetland under dry Mediterranean climate (Laguna Honda, eastern Guadalquivir basin, S Spain)

This research investigates the influence of water composition, the presence of seasonal algal mats, detrital inputs and the activity of microorganisms on the crystallization of aragonite in the sediments deposited in the hypersaline Laguna Honda wetland (S of Spain). The high alkaline and hypersaline waters (pH > 9.2 and C.E. > 70 mS/cm) of the wetland lake are rich in SO42- (>24,000 mg/l), Cl- (>21,000 mg/l), Na+ (>11,000 mg/l) Mg2+ (>8400 mg/l) and Ca2+ (>1000 mg/l), and are supersaturated for dolomite, calcite and aragonite. Sediments have lower pH values than column waters, oscillating from 8.54 in the low Eh (up to -80.9 mV) central deep sediments and 6.33 in the shallower higher Eh (around -13.6 mV) shore sediments. Erosion of the surrounding olive groves soils produced detrital silicates rich sediments with concretions of carbonate or sulfate. Aragonite (up to 19 %) and pyrite (up to 13 %) are mainly concentrated in the organic matter rich samples from the upper part of the sediment cores, whereas gypsum is preferably concentrated in low organic matter content samples. Mineral crusts containing a MgAl silicate phase, epsomite, halite and gypsum are precipitated on the floating algal mats covering the wetland waters. Floating algal mats deposit increased the organic matter content of the upper sediments which promoted the presence of fermentative microorganisms, sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) communities and variations of Eh that influence the authigenesis of carbonate and S-bearing minerals. Replacement of poorly crystalline MgSi phases infilling algal cells by aragonite was favored in the organic matter rich sediments with low Eh values and important SRB communities that promoted sulfate bioreduction processes to form pyrite. Aragonite precipitation was favored by the increase of carbonate and bicarbonate concentration produced by the SRB oxidation of organic matter, the CO2 degassing by high summer temperatures and the CO2 uptake by photosynthesis of the algal mats.

Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat

In this study, the microbial ecology, potential environmental adaptive mechanisms, and the potential evolutionary interlinking of genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. The community composition based on unique genes comprised bacteria (98.01%), archaea (1.81%), eukarya (0.07%) and viruses (0.11%). A gene-focused analysis of bacteria archaea, eukarya and viruses showed a vertical partition of the community. The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment were detected, such as UV radiation, multidrug resistance, oxidative stress, heavy metals, salinity and desiccation. Those genes were found in bacterial, archaeal and viral lineages with 6477, 44, and 1 genes, respectively. The evolutionary histories of those genes were studied using phylogenetic analysis, showing an interlinking between domains in GN mat.

The Characterization of Microbiome and Interactions on Weathered Rocks in a Subsurface Karst Cave, Central China

Karst caves are a natural oligotrophic subsurface biosphere widely distributed in southern China. Despite the progress in bacterial and fungal diversity, the knowledge about interactions between bacteria, fungi, and minerals is still limited in caves. Hence, for the first time, we investigated the interaction between bacteria and fungi living on weathered rocks in the Heshang Cave via high-throughput sequencing of 16S rRNA and ITS1 genes, and co-occurrence analysis. The mineral compositions of weathered rocks were analyzed by X-ray diffraction. Bacterial communities were dominated by Actinobacteria (33.68%), followed by Alphaproteobacteria (8.78%), and Planctomycetia (8.73%). In contrast, fungal communities were dominated by Sordariomycetes (21.08%) and Dothideomycetes (14.06%). Mineral substrata, particularly phosphorus-bearing minerals, significantly impacted bacterial (hydroxyapatite) and fungal (fluorapatite) communities as indicated by the redundancy analysis. In comparison with fungi, the development of bacterial communities was more controlled by the environmental selection indicated by the overwhelming contribution of deterministic processes. Co-occurrence network analysis showed that all nodes were positively linked, indicating ubiquitous cooperation within bacterial groups and fungal groups, as well as between bacteria and fungi under oligotrophic conditions in the subsurface biosphere. In total, 19 bacterial ASVs and 34 fungal OTUs were identified as keystone taxa, suggesting the fundamental role of fungi in maintaining the microbial ecosystem on weathered rocks. Ascomycota was most dominant in keystone taxa, accounting for 26.42%, followed by Actinobacteria in bacteria (24.53%). Collectively, our results confirmed the highly diverse bacterial and fungal communities on weathered rocks, and their close cooperation to sustain the subsurface ecosystem. Phosphorus-bearing minerals were of significance in shaping epipetreous bacterial and fungal communities. These observations provide new knowledge about microbial interactions between bacteria, fungi, and minerals in the subterranean biosphere.

Microbe-mediated transformation of metal sulfides: Mechanisms and environmental significance

Microorganisms play a key role in the natural circulation of various constituent elements of metal sulfides. Some microorganisms (such as Thiobacillus ferrooxidans) can promote the oxidation of metal sulfides to increase the release of heavy metals. However, other microorganisms (such as Desulfovibrio vulgaris) can transform heavy metals into metal sulfides crystals. Therefore, insight into the metal sulfides transformation mediated by microorganisms is of great significance to environmental protection. In this review, first, we discuss the mechanism and influencing factors of microorganisms transforming heavy metals into metal sulfides crystals in different environments. Then, we explore three microbe-mediated transformation forms of heavy metals to metal sulfides and their environmental applications: (1) transformation to metal sulfides precipitation for metal resource recovery; (2) transformation to metal sulfides nanoparticles (NPs) for pollutant treatment; (3) transformation to "metal sulfides-microbe" biohybrid system for clean energy production and pollutant remediation. Finally, we further provide critical views on the application of microbe-mediated metal sulfides transformation in the environmental field and discuss the need for future research.

Mineral Paragenesis Precipitating in Salt Flat Pools of Continental Environments Replicated in Microbial Mat Microcosms without Evaporation

Mineral precipitation can be observed in natural environments, such as lagoons, rivers, springs, and soils. The primary precipitation process has long been believed to be abiotic due to evaporation, leading to phase supersaturation. However, biotic interactions of microbial metabolism, organic compounds, and dissolved ions leading to mineral precipitation has been shown in laboratory studies using single-organism culture. The increase in pH inducing calcium carbonate precipitation due to oxygenic photosynthesis by Cyanobacteria and the release of ions due to organic matter decomposition by Firmicutes-inducing magnesium carbonate precipitation are recognized examples. As microbes do not live as pure cultures in natural environments but form complex communities, such pure culture lab studies do not reflect natural conditions. In this study, we grew natural complex microbial communities in microcosm conditions using filtered brine as water column and two types of natural gypsum substrates, and we replenished incubations to avoid evaporation. We monitored microbial communities through optical microscopy and analyzed mineral paragenesis in association with and without microbes, using different analytical techniques, such X-ray diffraction, and optical and field emission scanning electron microscopies. To detect changes throughout the experiment, small amounts of water column brine were extracted for physicochemial determinations. We were able to detect mineral paragenesis, avoiding evaporation, including major phases of chemical sedimentary rocks, such as gypsum, calcium carbonate, and some silicates in association to microbes. In addition, we evidenced that the use of natural substrates positively impacts growth of microbial communities, promoting the development of more biomass. This study can be seen as the first attempt and proof of concept of differentiating biotic and abiotic participation in evaporitic deposits, as they can form mineral paragenesis without evaporation. Future studies with microcosm experiments using microbial mats will be needed to establish mineral precipitation induced by micro-organisms and their extracellular polymeric substances (EPS), specifically to replicate mineral paragenesis sedimented from natural brines.

Sodium molybdate does not inhibit sulfate-reducing bacteria but increases shell growth in the Pacific oyster Magallana gigas

Recent work on microbe-host interactions has revealed an important nexus between the environment, microbiome, and host fitness. Marine invertebrates that build carbonate skeletons are of particular interest in this regard because of predicted effects of ocean acidification on calcified organisms, and the potential of microbes to buffer these impacts. Here we investigate the role of sulfate-reducing bacteria, a group well known to affect carbonate chemistry, in Pacific oyster (Magallana gigas) shell formation. We reared oyster larvae to 51 days post fertilization and exposed organisms to control and sodium molybdate conditions, the latter of which is thought to inhibit bacterial sulfate reduction. Contrary to expectations, we found that sodium molybdate did not uniformly inhibit sulfate-reducing bacteria in oysters, and oysters exposed to molybdate grew larger shells over the experimental period. Additionally, we show that microbiome composition, host gene expression, and shell size were distinct between treatments earlier in ontogeny, but became more similar by the end of the experiment. Although additional testing is required to fully elucidate the mechanisms, our work provides preliminary evidence that M. gigas is capable of regulating microbiome dysbiosis caused by environmental perturbations, which is reflected in shell development.

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.

Denitrification Biokinetics: Towards Optimization for Industrial Applications

Denitrification is a microbial process that converts nitrate (NO₃^–) to N₂ and can play an important role in industrial applications such as souring control and microbially enhanced oil recovery (MEOR). The effectiveness of using NO₃^– in souring control depends on the partial reduction of NO₃^– to nitrite (NO₂^–) and/or N₂O while in MEOR complete reduction of NO₃^– to N₂ is desired. Thauera has been reported as a dominant taxon in such applications, but the impact of NO₃^– and NO₂^– concentrations, and pH on the kinetics of denitrification by this bacterium is not known. With the goal of better understanding the effects of such parameters on applications such as souring and MEOR, three strains of Thauera (K172, NS1 and TK001) were used to study denitrification kinetics when using acetate as an electron donor. At low initial NO₃^– concentrations (∼1 mmol L^–1) and at pH 7.5, complete NO₃^– reduction by all strains was indicated by non-detectable NO₃^– concentrations and near-complete recovery (> 97%) of the initial NO₃-N as N₂ after 14 days of incubation. The relative rate of denitrification by NS1 was low, 0.071 mmol L^–1 d^–1, compared to that of K172 (0.431 mmol L^–1 d^–1) and TK001 (0.429 mmol L^–1 d^–1). Transient accumulation of up to 0.74 mmol L^–1 NO₂^– was observed in cultures of NS1 only. Increased initial NO₃^– concentrations resulted in the accumulation of elevated concentrations of NO₂^– and N₂O, particularly in incubations with K172 and NS1. Strain TK001 had the most extensive NO₃^– reduction under high initial NO₃^– concentrations, but still had only ∼78% of the initial NO₃-N recovered as N₂ after 90 days of incubation. As denitrification proceeded, increased pH substantially reduced denitrification rates when values exceeded ∼ 9. The rate and extent of NO₃^– reduction were also affected by NO₂^– accumulation, particularly in incubations with K172, where up to more than a 2-fold rate decrease was observed. The decrease in rate was associated with decreased transcript abundances of denitrification genes (nirS and nosZ) required to produce enzymes for reduction of NO₂^– and N₂O. Conversely, high pH also contributed to the delayed expression of these gene transcripts rather than their abundances in strains NS1 and TK001. Increased NO₂^– concentrations, N₂O levels and high pH appeared to cause higher stress on NS1 than on K172 and TK001 for N₂ production. Collectively, these results indicate that increased pH can alter the kinetics of denitrification by Thauera strains used in this study, suggesting that liming could be a way to achieve partial denitrification to promote NO₂^– and N₂O production (e.g., for souring control) while pH buffering would be desirable for achieving complete denitrification to N₂ (e.g., for gas-mediated MEOR).

Prokaryotic diversity and biogeochemical characteristics of field living and laboratory cultured stromatolites from the hypersaline Laguna Interna, Salar de Atacama (Chile)

Stromatolites are organo-sedimentary structures found principally in seas and saline lakes that contain sheets of sediments and minerals formed by layers of microbial communities, which trap sediments and induce the precipitation of minerals.A living stromatolite from the alkaline Laguna Interna in the Salar de Atacama was collected and one of the fragments was deposited in an experimental aquarium for 18 months. We used Illumina sequencing of PCR-amplified V4 regions of 16S rRNA genes from total extracted DNA to identify the microbial populations. The chemical structure was studied using X-Ray Diffraction (XRD) and bench chemical methods. We found that members belonging to the Proteobacteria, Planctomycetes, Chloroflexi and Bacteroidetes phyla dominated the bacterial communities of the living and aquarium cultured samples. The potential metabolic functionality of the prokaryotic community reveals that sulfur, nitrogen, methane and carbon fixation metabolism functions are present in the samples. This study is the first to provide new insights into the prokaryotic community composition from this unusual aquatic desert site. Further studies will be helpful to obtain a better understanding of the biotic and abiotic mechanisms residing in stromatolites from Laguna Interna, as well as to have better knowledge about the formation of these biosignatures.

A Review of Methods to Determine Viability, Vitality, and Metabolic Rates in Microbiology

Viability and metabolic assays are commonly used as proxies to assess the overall metabolism of microorganisms. The variety of these assays combined with little information provided by some assay kits or online protocols often leads to mistakes or poor interpretation of the results. In addition, the use of some of these assays is restricted to simple systems (mostly pure cultures), and care must be taken in their application to environmental samples. In this review, the necessary data are compiled to understand the reactions or measurements performed in many of the assays commonly used in various aspects of microbiology. Also, their relationships to each other, as metabolism links many of these assays, resulting in correlations between measured values and parameters, are discussed. Finally, the limitations of these assays are discussed.

Spherulitic microbialites from modern hypersaline lakes, Rottnest Island, Western Australia

Fibrous-radiating carbonate spherulites spatially associated with poorly crystalline Mg-Si substances have formed within conical microbialites in modern hypersaline lakes on Rottnest Island, Western Australia. Two spherulitic fabrics can be distinguished based on compositional and textural differences. The oldest (lowermost) fabric comprises variably intergrown aragonitic spherulites 100-500 μm wide, containing micritic nuclei with coccoid cell molds in various stages of cell division. Spherulite matrices contain aggregates of individual nanospheres 150-200 nm wide, composed of a poorly crystalline Mg-Si phase, locally containing cell molds with similar dimensions to those within spherulite nuclei. The younger (upper) fabric comprises sub-polyhedral networks of mineralized EPS composed of an Mg-Si substance. The polyhedrons contain aragonite-replaced coccoid cells, voids, and polyhedral spherulites 8-12 μm wide with a morphology determined by fossil EPS, interpreted to have been produced by coccoid cyanobacteria. These spherulites are composed of high-Mg calcite, inferred to have formed in association with heterotrophic bacteria. Stable isotope data, textural relationships, and geochemical modeling are consistent with cyanobacterial oxygenic photosynthesis influencing the precipitation of Mg-Si substances and aragonitic spherulites by locally increasing the pH. The morphology of the polyhedral spherulites suggests the former presence of EPS and that faceted spherulites with similar dimensions in the geological record may represent biosignatures. The Rottnest Island conical microbialites demonstrate an intimate association between microbial features and processes and spherulitic fabrics, potentially providing insights into texturally and compositionally similar features in the geological record.

Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient

Microbialites are usually carbonate-rich sedimentary rocks formed by the interplay of phylogenetically and metabolically complex microbial communities with their physicochemical environment. Yet, the biotic and abiotic determinants of microbialite formation remain poorly constrained. Here, we analysed the structure of prokaryotic and eukaryotic communities associated with microbialites occurring in several crater lakes of the Trans-Mexican volcanic belt along an alkalinity gradient. Microbialite size and community structure correlated with lake physicochemical parameters, notably alkalinity. Although microbial community composition varied across lake microbialites, major taxa-associated functions appeared quite stable with both, oxygenic and anoxygenic photosynthesis and, to less extent, sulphate reduction, as major putative carbonatogenic processes. Despite interlake microbialite community differences, we identified a microbial core of 247 operational taxonomic units conserved across lake microbialites, suggesting a prominent ecological role in microbialite formation. This core mostly encompassed Cyanobacteria and their typical associated taxa (Bacteroidetes, Planctomycetes) and diverse anoxygenic photosynthetic bacteria, notably Chloroflexi, Alphaproteobacteria (Rhodobacteriales, Rhodospirilalles), Gammaproteobacteria (Chromatiaceae) and minor proportions of Chlorobi. The conserved core represented up to 40% (relative abundance) of the total community in lakes Alchichica and Atexcac, displaying the highest alkalinities and the most conspicuous microbialites. Core microbialite communities associated with carbonatogenesis might be relevant for inorganic carbon sequestration purposes.

A comparative metagenomic study reveals microbial diversity and their role in the biogeochemical cycling of Pangong lake

The environment of a high altitude brackish water lake presents an unprecedented reservoir for the microbial community with adaptability towards surviving stressful conditions. Pangong lake is a high altitude brackish water lake of the Himalayas situated in the eastern part of Ladakh (Indian Tibet), at the height of 4250 m above the sea level. Shotgun metagenomics sequencing of Pangong Lake sediments was performed to examine the taxonomic diversity and functional adaptations of the resident psychrophilic and psychrotolerant microbial communities of the lake (September; a temperature of ±10 °C). Proteobacteria was the most prominent phylum, and Methylophaga, Halomonas, and Marinobacter were mainly abundant at the genus level. Enzyme pathways responsible for methane metabolism, nitrogen metabolism, sulfur reduction, benzoate, and xylene degradation appeared to be complete in the metagenomic dataset. Stress response genes responsible for adaption to pH, cold, salt tolerance, osmotic stress, and oxidative stress were also found in abundance in the metagenome. We compared the Pangong lake metagenome sample to sediments and water samples from three different aquatic habitats, namely saline lake, freshwater lakes and marine ecosystem using MG-RAST server against RefSeq and Subsystem databases. The Pangong lake microbial community contains six unique genera. Regression analysis using metagenome samples suggested that Pangong lake was most closely related to the Trophic South Pacific Ocean (R² = 0.971) and Socompa lake ecosystem (R² = 0.991) at phylum and functional level II, respectively. Our study signifies that the functional metabolic potentiality of Pangong lake is strongly influenced by the taxonomic structure and environmental conditions. We are reporting the metagenome of the sediment sample of the Pangong lake, which unveils the microbial diversity and their functional potential.

Between a Rock and a Soft Place: The Role of Viruses in Lithification of Modern Microbial Mats

Stromatolites are geobiological systems formed by complex microbial communities, and fossilized stromatolites provide a record of some of the oldest life on Earth. Microbial mats are precursors of extant stromatolites; however, the mechanisms of transition from mat to stromatolite are controversial and are still not well understood. To fully recognize the profound impact that these ecosystems have had on the evolution of the biosphere requires an understanding of modern lithification mechanisms and how they relate to the geological record. We propose here viral mechanisms in carbonate precipitation, leading to stromatolite formation, whereby viruses directly or indirectly impact microbial metabolisms that govern the transition from microbial mat to stromatolite. Finding a tangible link between host-virus interactions and changes in biogeochemical processes will provide tools to interpret mineral biosignatures through geologic time, including those on Earth and beyond.

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.

Influence of temperature, salinity and Mg2+:Ca2+ ratio on microbially-mediated formation of Mg-rich carbonates by Virgibacillus strains isolated from a sabkha environment

Studies have demonstrated that microbes facilitate the incorporation of Mg²⁺ into carbonate minerals, leading to the formation of potential dolomite precursors. Most microbes that are capable of mediating Mg-rich carbonates have been isolated from evaporitic environments in which temperature and salinity are higher than those of average marine environments. However, how such physicochemical factors affect and concur with microbial activity influencing mineral precipitation remains poorly constrained. Here, we report the results of laboratory precipitation experiments using two mineral-forming Virgibacillus strains and one non-mineral-forming strain of Bacillus licheniformis, all isolated from the Dohat Faishakh sabkha in Qatar. They were grown under different combinations of temperature (20°, 30°, 40 °C), salinity (3.5, 7.5, 10 NaCl %w/v), and Mg²⁺:Ca²⁺ ratios (1:1, 6:1 and 12:1). Our results show that the incorporation of Mg²⁺ into the carbonate minerals is significantly affected by all of the three tested factors. With a Mg²⁺:Ca²⁺ ratio of 1, no Mg-rich carbonates formed during the experiments. With a Mg²⁺:Ca²⁺ ratios of 6 and 12, multivariate analysis indicates that temperature has the highest impact followed by salinity and Mg²⁺:Ca²⁺ ratio. The outcome of this study suggests that warm and saline environments are particularly favourable for microbially mediated formation of Mg-rich carbonates and provides new insight for interpreting ancient dolomite formations.

Carbon isotopic composition of lipid biomarkers from an endoevaporitic gypsum crust microbial mat reveals cycling of mineralized organic carbon

Microbial mats that inhabit gypsum deposits in ponds at Guerrero Negro, Baja California Sur, Mexico, developed distinct pigmented horizons that provided an opportunity to examine the fixation and flow of carbon through a trophic structure and, in conjunction with previous phylogenetic analyses, to assess the diagenetic fates of molecular δ¹³ C biosignatures. The δ¹³ C values of individual biomarker lipids, total carbon, and total organic carbon (TOC) were determined for each of the following horizons: tan-orange (TO) at the surface, green (G), purple (P), and olive-black (OB) at the bottom. δ¹³ C of individual fatty acids from intact polar lipids (IPFA) in TO were similar to δ¹³ C of dissolved inorganic carbon (DIC) in the overlying water column, indicating limited discrimination by cyanobacteria during CO₂ fixation. δ¹³ C_TOC of the underlying G was 3‰ greater than that of TO. The most δ¹³ C-depleted acetogenic lipids in the upper horizons were the cyanobacterial biomarkers C₁₇ n-alkanes and polyunsaturated fatty acids. Bishomohopanol was 4 to 7‰ enriched, relative to alkanes and intact polar fatty acids (IPFA), respectively. Acyclic C₂₀ isoprenoids were depleted by 14‰ relative to bishomohopanol. Significantly, ∆[δ¹³ C_TOC  - δ¹³ C_∑IPFA ] increased from 6.9‰ in TO to 14.7‰ in OB. This major trend might indicate that ¹³ C-enriched residual organic matter accumulated at depth. The permanently anoxic P horizon was dominated by anoxygenic phototrophs and sulfate-reducing bacteria. P hosted an active sulfur-dependent microbial community. IPFA and bishomohopanol were ¹³ C-depleted relative to upper crust by 7 and 4‰, respectively, and C₂₀ isoprenoids were somewhat ¹³ C-enriched. Synthesis of alkanes in P was evidenced only by ¹³ C-depleted n-octadecane and 8-methylhexadecane. In OB, the marked increase of total inorganic carbon δ¹³ C (δ¹³ C_TIC ) of >6‰ perhaps indicated terminal mineralization. This δ¹³ C_TIC increase is consistent with degradation of the osmolyte glycine betaine by methylotrophic methanogens and loss of ¹³ C-depleted methane from the mat.

Carbonate Precipitation in Mixed Cyanobacterial Biofilms Forming Freshwater Microbial Tufa

: Mixed cyanobacteria-dominated biofilms, enriched from a tributary of the Mérantaise (France) were used to conduct laboratory experiments in order to understand the relationship between the morphology of carbonate precipitates and the biological activity (e.g., cyanobacterial exopolymeric substances (EPS) production, photosynthetic pH increases). DNA sequencing data showed that the enriched biofilm was composed predominantly of two types of filamentous cyanobacteria that belonged to the Oscillatoriaceae and Phormidiaceae families, respectively. Microscopic analysis also indicated the presence of some coccoid cyanobacteria resembling Gloeocapsa. Analysis of carbonate precipitates in experimental biofilms showed three main morphologies: micro-peloids with different shapes of mesocrystals associated with Oscillatoriaceae filaments and theirs EPS, lamellae of carbonate formed directly on Phormidiaceae filaments, and rhombic sparite crystals wrapped in EPS. All crystals were identified by FT-IR spectroscopy as calcite. Similar structures as those that formed in laboratory conditions were observed in the microbial-tufa deposits collected in the stream. Microscopic and spectroscopic analysis of laboratory and natural samples indicated a close proximity of the cyanobacterial EPS and precipitated carbonates in both. Based on the laboratory experiments, we conclude that the microbial tufa in the stream is in an early stage of formation.

Sulfate-Reducing Bacteria That Produce Exopolymers Thrive in the Calcifying Zone of a Hypersaline Cyanobacterial Mat

Calcifying microbial mats in hypersaline environments are important model systems for the study of the earliest ecosystems on Earth that started to appear more than three billion years ago and have been preserved in the fossil record as laminated lithified structures known as stromatolites. It is believed that sulfate-reducing bacteria play a pivotal role in the lithification process by increasing the saturation index of calcium minerals within the mat. Strain L21-Syr-AB^T was isolated from anoxic samples of a several centimeters-thick microbialite-forming cyanobacterial mat of a hypersaline lake on the Kiritimati Atoll (Kiribati, Central Pacific). The novel isolate was assigned to the family Desulfovibrionaceae within the Deltaproteobacteria. Available 16S rRNA-based population surveys obtained from discrete layers of the mat indicate that the occurrence of a species-level clade represented by strain L21-Syr-AB^T is restricted to a specific layer of the suboxic zone, which is characterized by the presence of aragonitic spherulites. To elucidate a possible function of this sulfate-reducing bacterium in the mineral formation within the mat a comprehensive phenotypic characterization was combined with the results of a comparative genome analysis. Among the determined traits of strain L21-Syr-AB^T, several features were identified that could play a role in the precipitation of calcium carbonate: (i) the potential deacetylation of polysaccharides and consumption of substrates such as lactate and sulfate could mobilize free calcium; (ii) under conditions that favor the utilization of formate and hydrogen, the alkalinity engine within the mat is stimulated, thereby increasing the availability of carbonate; (iii) the production of extracellular polysaccharides could provide nucleation sites for calcium mineralization. In addition, our data suggest the proposal of the novel species and genus Desulfohalovibrio reitneri represented by the type strain L21-Syr-AB^T (=DSM 26903^T = JCM 18662^T).

Carbon Sequestration in Biogenic Magnesite and Other Magnesium Carbonate Minerals

The stability and longevity of carbonate minerals make them an ideal sink for surplus atmospheric carbon dioxide. Biogenic magnesium carbonate mineral precipitation from the magnesium-rich tailings generated by many mining operations could offset net mining greenhouse gas emissions, while simultaneously giving value to mine waste products. In this investigation, cyanobacteria in a wetland bioreactor enabled the precipitation of magnesite (MgCO₃), hydromagnesite [Mg₅(CO₃)₄(OH)₂·4H₂O], and dypingite [Mg₅(CO₃)₄(OH)₂·5H₂O] from a synthetic wastewater comparable in chemistry to what is produced by acid leaching of ultramafic mine tailings. These precipitates occurred as micrometer-scale mineral grains and microcrystalline carbonate coatings that entombed filamentous cyanobacteria. This provides the first laboratory demonstration of low temperature, biogenic magnesite precipitation for carbon sequestration purposes. These findings demonstrate the importance of extracellular polymeric substances in microbially enabled carbonate mineral nucleation. Fluid composition was monitored to determine carbon sequestration rates. The results demonstrate that up to 238 t of CO₂ could be stored per hectare of wetland/year if this method of carbon dioxide sequestration was implemented at an ultramafic mine tailing storage facility. The abundance of tailings available for carbonation and the anticipated global implementation of carbon pricing make this method of mineral carbonation worth further investigation.

Thermodesulfobium sp. strain 3baa, an acidophilic sulfate reducing bacterium forming biofilms triggered by mineral precipitation

Sulfate reducing prokaryotes are promising candidates for the remediation of acidic metal-rich waste waters. However, only few acidophilic species have been described to date. Chemolithoautotrophic strain 3baa was isolated from sediments of an acidic mine pit lake. Based on its 16S-rRNA gene sequence it belongs to the genus Thermodesulfobium. It was identified as an acidophile growing in artificial pore water medium in the range of pH 2.6-6.6. Though the highest sulfate reduction rates were obtained at the lower end of this range, elongated cells and extended lag phases demonstrated acid stress. Sulfate reduction at low pH was accompanied by the formation of mineral precipitates strongly adhering to solid surfaces. A structural investigation by laser scanning microscopy, electron microscopy and X-ray microanalysis revealed the formation of Al hydroxides and Fe sulfides which were densely populated by cells. Al hydroxides precipitated first, enabling initial cell attachment. Colonization of solid surfaces coincided with increased sulfate reducing activity indicating more favourable growth conditions within biofilms compared with free-living cells. These findings point out the importance of cell-mineral interaction for biofilm formation and contribute to our understanding how sulfate reducing prokaryotes thrive in both natural and engineered systems at low pH.

Environmental and Biological Influences on Carbonate Precipitation Within Hot Spring Microbial Mats in Little Hot Creek, CA

Microbial mats are found in a variety of modern environments, with evidence for their presence as old as the Archean. There is much debate about the rates and conditions of processes that eventually lithify and preserve mats as microbialites. Here, we apply novel tracer experiments to quantify both mat biomass addition and the formation of CaCO3. Microbial mats from Little Hot Creek (LHC), California, contain calcium carbonate that formed within multiple mat layers, and thus constitute a good test case to investigate the relationship between the rate of microbial mat growth and carbonate precipitation. The laminated LHC mats were divided into four layers via color and fabric, and waters within and above the mat were collected to determine their carbonate saturation states. Samples of the microbial mat were also collected for 16S rRNA analysis of microbial communities in each layer. Rates of carbonate precipitation and carbon fixation were measured in the laboratory by incubating homogenized samples from each mat layer with δ13C-labeled HCO3- for 24 h. Comparing these rates with those from experimental controls, poisoned with NaN3 and HgCl2, allowed for differences in biogenic and abiogenic precipitation to be determined. Carbon fixation rates were highest in the top layer of the mat (0.17% new organic carbon/day), which also contained the most phototrophs. Isotope-labeled carbonate was precipitated in all four layers of living and poisoned mat samples. In the top layer, the precipitation rate in living mat samples was negligible although abiotic precipitation occurred. In contrast, the bottom three layers exhibited biologically enhanced carbonate precipitation. The lack of correlation between rates of carbon fixation and biogenic carbonate precipitation suggests that processes other than autotrophy may play more significant roles in the preservation of mats as microbialites.

Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes

The functional metagenomic potential of Shark Bay microbial mats was examined for the first time at a millimeter scale, employing shotgun sequencing of communities via the Illumina NextSeq 500 platform in conjunction with defined chemical analyses. A detailed functional metagenomic profile has elucidated key pathways and facilitated inference of critical microbial interactions. In addition, 87 medium-to-high-quality metagenome-assembled genomes (MAG) were assembled, including potentially novel bins under the deep-branching archaeal Asgard group (Thorarchaetoa and Lokiarchaeota). A range of pathways involved in carbon, nitrogen, sulfur, and phosphorus cycles were identified in mat metagenomes, with the Wood-Ljungdahl pathway over-represented and inferred as a major carbon fixation mode. The top five sets of genes were affiliated to sulfate assimilation (cysNC cysNCD, sat), methanogenesis (hdrABC), Wood-Ljungdahl pathways (cooS, coxSML), phosphate transport (pstB), and copper efflux (copA). Polyhydroxyalkanoate (PHA) synthase genes were over-represented at the surface, with PHA serving as a potential storage of fixed carbon. Sulfur metabolism genes were highly represented, in particular complete sets of genes responsible for both assimilatory and dissimilatory sulfate reduction. Pathways of environmental adaptation (UV, hypersalinity, oxidative stress, and heavy metal resistance) were also delineated, as well as putative viral defensive mechanisms (core genes of the CRISPR, BREX, and DISARM systems). This study provides new metagenome-based models of how biogeochemical cycles and adaptive responses may be partitioned in the microbial mats of Shark Bay.

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.

Symbiodinium-Induced Formation of Microbialites: Mechanistic Insights From in Vitro Experiments and the Prospect of Its Occurrence in Nature

Dinoflagellates in the genus Symbiodinium exhibit a variety of life styles, ranging from mutualistic endosymbioses with animal and protist hosts to free-living life styles. In culture, Symbiodinium spp. and naturally associated bacteria are known to form calcifying biofilms that produce so-called symbiolites, i.e., aragonitic microbialites that incorporate Symbiodinium as endolithic cells. In this study, we investigated (i) how algal growth and the combined physiological activity of these bacterial-algal associations affect the physicochemical macroenvironment in culture and the microenvironment within bacterial-algal biofilms, and (ii) how these interactions induce the formation of symbiolites. In batch culture, calcification typically commenced when Symbiodinium spp. growth approached stationary phase and when photosynthetic activity and its influence on pH and the carbonate system of the culture medium had already subsided, indicating that symbiolite formation is not simply a function of photosynthetic activity in the bulk medium. Physical disturbance of bacteria-algal biofilms, via repeated detaching and dispersing of the developing biofilm, generally impeded symbiolite formation, suggesting that the structural integrity of biofilms plays an important role in generating conditions conducive to calcification. Microsensor measurements of pH and O₂ revealed a biofilm microenvironment characterized by high photosynthetic rates and by dynamic changes in photosynthesis and respiration with light intensity and culture age. Ca²⁺ microsensor measurements confirmed the significance of the biofilm microenvironment in inducing calcification, as photosynthesis within the biofilm induced calcification without the influence of batch culture medium and under environmentally relevant flow conditions. Furthermore, first quantitative data on calcification from 26 calcifying cultures enabled a first broad comparison of Symbiodinium-induced bacterial-algal calcification with other calcification processes. Our findings support the idea that symbiolite formation is a typical, photosynthesis-induced, bacterial-algal calcification process that is likely to occur under natural conditions.

Mineralisation of filamentous cyanobacteria in Lake Thetis stromatolites, Western Australia

Stromatolites are cited as some of the earliest evidence for life on Earth, but problems remain in reconciling the paucity of microfossils in ancient carbonate examples with the abundance of microbes that help construct modern analogues. Here, we trace the mineralisation pathway of filamentous cyanobacteria within stromatolites from Lake Thetis, Western Australia, providing new insights into microfossil preservation in carbonate stromatolites. Lake Thetis cyanobacteria exhibit a spectrum of mineralisation processes that include early precipitation of Mg-silicates, largely controlled by the morphochemical features of the cyanobacteria, followed by aragonite formation that is inferred to be driven by heterotrophic activity. Fossilised cyanobacteria with high-quality morphological preservation are characterised by a significant volume of authigenic Mg-silicates, which have preferentially nucleated in/on extracellular organic material and on cell walls, and now replicate the region once occupied by the cyanobacterial sheath. In such specimens, aragonite is restricted to the outer sheath margin and parts of the cell interior. Cyanobacteria that display more significant degradation appear to possess a higher ratio of aragonite to Mg-silicate. In these specimens, aragonite forms micronodules in the sheath zone and is spatially associated with the inferred remains of heterotrophic bacteria. Aragonite also occurs as an advancing front from the outer margin of the sheath where it is commonly intergrown with Mg-silicates. Where there is no evidence of Mg-silicates within filaments, the fidelity of microfossil preservation is poor. In these cases, individual filaments may no longer be visible under light microscopy, and little organic material remains, but filament traces remain detectable using electron microscopy due to variations in aragonite texture. These data provide further evidence that authigenic silicate minerals play a crucial role in the fossilisation of micro-organisms; in their absence, carbonate crystal growth potentially mediated by heterotrophic microbial decay may largely obliterate morphological evidence for life within stromatolites, although mineralogical traces may still be detectable using electron microscopy.

Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems in Natural and in Vitro Biomineralization Conditions

Natural mineral formations are a window into important processes leading to carbon storage and mineralized carbonate structures formed through abiotic and biotic processes. In the current study, we made an attempt to undertake a comprehensive approach to characterize the mineralogical, mechanical, and microbial properties of different kinds of speleothems from karstic caves; with an aim to understand the bio-geo-chemical processes in speleothem structures and their impact on nanomechanical properties. We also investigated the biomineralization abilities of speleothem surface associated microbial communities in vitro. Mineralogical profiling using techniques such as X-ray powder Diffraction (XRD) and Tescan Integrated Mineral Analyzer (TIMA) demonstrated that calcite was the dominant mineral in the majority of speleothems with Energy Dispersive X-ray Analysis (EDS) indicating a few variations in the elemental components. Differing proportions of polymorphs of calcium carbonate such as aragonite and vaterite were also recorded. Significant variations in trace metal content were recorded through Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Scanning Electron Microscopy (SEM) analysis revealed differences in morphological features of the crystals which varied from triangular prismatic shapes to etched spiky forms. Microbial imprints and associations were seen in a few sections. Analysis of the associated microbial diversity showed significant differences between various speleothems at Phylum level; although Proteobacteria and Actinobacteria were found to be the predominant groups. Genus level microbial associations showed a relationship with the geochemistry, mineralogical composition, and metal content of the speleothems. The assessment of nanomechanical properties measured by Nanoindentation revealed that the speleothems with a dominance of calcite were stronger than the speleothems with mixed calcium carbonate polymorphs and silica content. The in vitro metabolic activity of the microbial communities associated with the surfaces of the speleothems resulted in calcium carbonate crystal precipitation. Firmicutes and Proteobacteria dominated these populations, in contrast to the populations seen in natural systems. The precipitation of calcium carbonate crystals in vitro indicated that microbial metabolic activity may also play an important role in the synthesis and dissociation of biominerals in the natural environment. Our study provides novel evidence of the close relationship between mineralogy, microbial ecology, geochemistry, and nanomechanical properties of natural formations.

Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems at La Brava, a hypersaline lake at Salar de Atacama, Chile

Benthic microbial ecosystems of Laguna La Brava, Salar de Atacama, a high altitude hypersaline lake, were characterized in terms of bacterial and archaeal diversity, biogeochemistry, (including O₂ and sulfide depth profiles and mineralogy), and physicochemical characteristics. La Brava is one of several lakes in the Salar de Atacama where microbial communities are growing in extreme conditions, including high salinity, high solar insolation, and high levels of metals such as lithium, arsenic, magnesium, and calcium. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. In this study, the La Brava non-lithifying microbial mats, microbialites, and rhizome-associated concretions were compared to each other and their diversity was related to their environmental conditions. All the ecosystems revealed an unusual community where Euryarchaeota, Crenarchaeota, Acetothermia, Firmicutes and Planctomycetes were the most abundant groups, and cyanobacteria, typically an important primary producer in microbial mats, were relatively insignificant or absent. This suggests that other microorganisms, and possibly novel pathways unique to this system, are responsible for carbon fixation. Depth profiles of O₂ and sulfide showed active production and respiration. The mineralogy composition was calcium carbonate (as aragonite) and increased from mats to microbialites and rhizome-associated concretions. Halite was also present. Further analyses were performed on representative microbial mats and microbialites by layer. Different taxonomic compositions were observed in the upper layers, with Archaea dominating the non-lithifying mat, and Planctomycetes the microbialite. The bottom layers were similar, with Euryarchaeota, Crenarchaeota and Planctomycetes as dominant phyla. Sequences related to Cyanobacteria were very scarce. These systems may contain previously uncharacterized community metabolisms, some of which may be contributing to net mineral precipitation. Further work on these sites might reveal novel organisms and metabolisms of biotechnological interest.

Salinity stratification controlled productivity variation over 300 ky in the Bay of Bengal

The unique hydrographic setting of the Bay of Bengal (BoB) makes it an ideal tropical marine system to study the influence of regional and global forcings on productivity and [CO2aq] through the late quaternary. Enormous fresh water flux into the BoB and consequent salinity stratification significantly weaken the convective mixing and wind driven processes which are commonly responsible for transport of nutrients to the euphotic zone driving primary productivity. Here we present a high resolution organic carbon-CaCO3 MAR and δ13CTOC records for the last 300 ky from the BoB. The results show significant productivity variation at marine isotope sub-stages and millennial timescales. Colder sub-stages and stadials (Dansgard-Oeschger cycle) show a boost in productivity which may be attributed to thinning of low salinity cap, thereby facilitating efficient nutrient transport across the euphotic zone by the combination of wind driven processes (entrainment and upwelling), convective mixing and cold core eddies. The [CO2aq] was a net result of global pCO2 variation and regional processes. Our long term high-resolution data indicates a possibility of marked change in productivity/biogeochemistry of BOB in the future due to global warming, thus affecting the coastal economy.

Alkaline textile wastewater biotreatment: A sulfate-reducing granular sludge based lab-scale study

In this study the feasibility of treating dyeing wastewater with sulfate reducing granular sludge was explored, focusing on decolorization/degradation of azo dye (Procion Red HE-7B) and the performance of microbial consortia under alkaline conditions (pH=11). Efficiency of HE-7B degradation was influenced strongly by the chemical oxygen demand (COD) concentration which was examined in the range of 500-3000mg/L. COD removal efficiency was reduced at high COD concentration, while specific removal rate was enhanced to 17.5 mg-COD/gVSSh^-1. HE-7B removal was also improved at higher organic strength with more than 90% removal efficiency and a first-rate removal constant of 5.57h^-1 for dye degradation. Three dye-degradation metabolites were identified by HPLC-MS. The granular structure provided enhanced removal performance for HE-7B and COD in comparison to a near-identical floc SRB system and the key functional organisms were identified by high throughput sequencing. This study demonstrates an example of a niche application where SRB granules can be applied for high efficient and cost-effective treatment of a wastewater under adverse environmental conditions.

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.

A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses

Thrombolites are buildups of carbonate that exhibit a clotted internal structure formed through the interactions of microbial mats and their environment. Despite recent advances, we are only beginning to understand the microbial and molecular processes associated with their formation. In this study, a spatial profile of the microbial and metabolic diversity of thrombolite-forming mats of Highborne Cay, The Bahamas, was generated by using 16S rRNA gene sequencing and predictive metagenomic analyses. These molecular-based approaches were complemented with microelectrode profiling and in situ stable isotope analysis to examine the dominant taxa and metabolic activities within the thrombolite-forming communities. Analyses revealed three distinctive zones within the thrombolite-forming mats that exhibited stratified populations of bacteria and archaea. Predictive metagenomics also revealed vertical profiles of metabolic capabilities, such as photosynthesis and carboxylic and fatty acid synthesis within the mats that had not been previously observed. The carbonate precipitates within the thrombolite-forming mats exhibited isotopic geochemical signatures suggesting that the precipitation within the Bahamian thrombolites is photosynthetically induced. Together, this study provides the first look at the spatial organization of the microbial populations within Bahamian thrombolites and enables the distribution of microbes to be correlated with their activities within modern thrombolite systems. Key Words: Thrombolites-Microbial diversity-Metagenome-Stable isotopes-Microbialites. Astrobiology 17, 413-430.

Genomic and Transcriptomic Insights into Calcium Carbonate Biomineralization by Marine Actinobacterium Brevibacterium linens BS258

Calcium carbonate (CaCO3) biomineralization has been investigated due to its wide range of scientific and technological implications, however, the molecular mechanisms of this important geomicrobiological process are largely unknown. Here, a urease-positive marine actinobacterium Brevibacterium linens BS258 was demonstrated to effectively form CaCO3 precipitates. Surprisingly, this bacterium could also dissolve the formed CaCO3 with the increase of the Ca2+ concentration. To disclose the mechanisms of biomineralization, the genome of B. linens BS258 was further completely sequenced. Interestingly, the expression of three carbonic anhydrases was significantly up-regulated along with the increase of Ca2+ concentration and the extent of calcite dissolution. Moreover, transcriptome analyses revealed that increasing concentration of Ca2+ induced KEGG pathways including quorum sensing (QS) in B. linens BS258. Notably, most up-regulated genes related to QS were found to encode peptide/nickel ABC transporters, which suggested that nickel uptake and its associated urease stimulation were essential to boost CaCO3 biomineralization. Within the genome of B. linens BS258, there are both cadmium and lead resistance gene clusters. Therefore, the sequestration abilities of Cd2+ and Pb2+ by B. linens BS258 were checked. Consistently, Pb2+ and Cd2+ could be effectively sequestered with the precipitation of calcite by B. linens BS258. To our knowledge, this is the first study investigating the microbial CaCO3 biomineralization from both genomic and transcriptomic insights, which paves the way to disclose the relationships among bacterial metabolisms and the biomineralization.

Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes

Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (<0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines.

Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient

Modern microbialites are often used as analogs of Precambrian stromatolites; therefore, studying the metabolic interplay within their associated microbial communities can help formulating hypotheses on their formation and long-term preservation within the fossil record. We performed a comparative metagenomic analysis of microbialite samples collected at two sites and along a depth gradient in Lake Alchichica (Mexico). The community structure inferred from single-copy gene family identification and long-contig (>10 kb) assignation, consistently with previous rRNA gene surveys, showed a wide prokaryotic diversity dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Bacteroidetes, while eukaryotes were largely dominated by green algae or diatoms. Functional analyses based on RefSeq, COG and SEED assignations revealed the importance of housekeeping functions, with an overrepresentation of genes involved in carbohydrate metabolism, as compared with other metabolic capacities. The search for genes diagnostic of specific metabolic functions revealed the important involvement of Alphaproteobacteria in anoxygenic photosynthesis and sulfide oxidation, and Cyanobacteria in oxygenic photosynthesis and nitrogen fixation. Surprisingly, sulfate reduction appeared negligible. Comparative analyses suggested functional similarities among various microbial mat and microbialite metagenomes as compared with soil or oceans, but showed differences in microbial processes among microbialite types linked to local environmental conditions.

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.

Metagenomic Analysis Suggests Modern Freshwater Microbialites Harbor a Distinct Core Microbial Community

Modern microbialites are complex microbial communities that interface with abiotic factors to form carbonate-rich organosedimentary structures whose ancestors provide the earliest evidence of life. Past studies primarily on marine microbialites have inventoried diverse taxa and metabolic pathways, but it is unclear which of these are members of the microbialite community and which are introduced from adjacent environments. Here we control for these factors by sampling the surrounding water and nearby sediment, in addition to the microbialites and use a metagenomics approach to interrogate the microbial community. Our findings suggest that the Pavilion Lake microbialite community profile, metabolic potential and pathway distributions are distinct from those in the neighboring sediments and water. Based on RefSeq classification, members of the Proteobacteria (e.g., alpha and delta classes) were the dominant taxa in the microbialites, and possessed novel functional guilds associated with the metabolism of heavy metals, antibiotic resistance, primary alcohol biosynthesis and urea metabolism; the latter may help drive biomineralization. Urea metabolism within Pavilion Lake microbialites is a feature not previously associated in other microbialites. The microbialite communities were also significantly enriched for cyanobacteria and acidobacteria, which likely play an important role in biomineralization. Additional findings suggest that Pavilion Lake microbialites are under viral selection as genes associated with viral infection (e.g CRISPR-Cas, phage shock and phage excision) are abundant within the microbialite metagenomes. The morphology of Pavilion Lake microbialites changes dramatically with depth; yet, metagenomic data did not vary significantly by morphology or depth, indicating that microbialite morphology is altered by other factors, perhaps transcriptional differences or abiotic conditions. This work provides a comprehensive metagenomic perspective of the interactions and differences between microbialites and their surrounding environment, and reveals the distinct nature of these complex communities.

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.

Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential

Within the subarctic climate of Clinton Creek, Yukon, Canada, lies an abandoned and flooded open-pit asbestos mine that harbors rapidly growing microbialites. To understand their formation we completed a metagenomic community profile of the microbialites and their surrounding sediments. Assembled metagenomic data revealed that bacteria within the phylum Proteobacteria numerically dominated this system, although the relative abundances of taxa within the phylum varied among environments. Bacteria belonging to Alphaproteobacteria and Gammaproteobacteria were dominant in the microbialites and sediments, respectively. The microbialites were also home to many other groups associated with microbialite formation including filamentous cyanobacteria and dissimilatory sulfate-reducing Deltaproteobacteria, consistent with the idea of a shared global microbialite microbiome. Other members were present that are typically not associated with microbialites including Gemmatimonadetes and iron-oxidizing Betaproteobacteria, which participate in carbon metabolism and iron cycling. Compared to the sediments, the microbialite microbiome has significantly more genes associated with photosynthetic processes (e.g., photosystem II reaction centers, carotenoid, and chlorophyll biosynthesis) and carbon fixation (e.g., CO dehydrogenase). The Clinton Creek microbialite communities had strikingly similar functional potentials to non-lithifying microbial mats from the Canadian High Arctic and Antarctica, but are functionally distinct, from non-lithifying mats or biofilms from Yellowstone. Clinton Creek microbialites also share metabolic genes (R² < 0.750) with freshwater microbial mats from Cuatro Ciénegas, Mexico, but are more similar to polar Arctic mats (R² > 0.900). These metagenomic profiles from an anthropogenic microbialite-forming ecosystem provide context to microbialite formation on a human-relevant timescale.

Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites

Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at macroscale, and suggest a potential causal link. Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.

Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling

Microbialites are sedimentary deposits formed by the metabolic interactions of microbes and their environment. These lithifying microbial communities represent one of the oldest ecosystems on Earth, yet the molecular mechanisms underlying the function of these communities are poorly understood. In this study, we used comparative metagenomic and metatranscriptomic analyses to characterize the spatial organization of the thrombolites of Highborne Cay, The Bahamas, an actively forming microbialite system. At midday, there were differences in gene expression throughout the spatial profile of the thrombolitic mat with a high abundance of transcripts encoding genes required for photosynthesis, nitrogen fixation and exopolymeric substance production in the upper three mm of the mat. Transcripts associated with denitrification and sulfate reduction were in low abundance throughout the depth profile, suggesting these metabolisms were less active during midday. Comparative metagenomics of the Bahamian thrombolites with other known microbialite ecosystems from across the globe revealed that, despite many shared core pathways, the thrombolites represented genetically distinct communities. This study represents the first time the metatranscriptome of living microbialite has been characterized and offers a new molecular perspective on those microbial metabolisms, and their underlying genetic pathways, that influence the mechanisms of carbonate precipitation in lithifying microbial mat ecosystems.

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

Modern microbial mats are potential analogues of some of Earth's earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic next-generation sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.

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.

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

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

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

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

A greenhouse-scale photosynthetic microbial bioreactor for carbon sequestration in magnesium carbonate minerals

A cyanobacteria dominated consortium collected from an alkaline wetland located near Atlin, British Columbia, Canada accelerated the precipitation of platy hydromagnesite [Mg5(CO3)4(OH)2·4H2O] in a linear flow-through experimental model wetland. The concentration of magnesium decreased rapidly within 2 m of the inflow point of the 10-m-long (∼1.5 m(2)) bioreactor. The change in water chemistry was monitored over two months along the length of the channel. Carbonate mineralization was associated with extra-cellular polymeric substances in the nutrient-rich upstream portion of the bioreactor, while the lower part of the system, which lacked essential nutrients, did not exhibit any hydromagnesite precipitation. A mass balance calculation using the water chemistry data produced a carbon sequestration rate of 33.34 t of C/ha per year. Amendment of the nutrient deficiency would intuitively allow for increased carbonation activity. Optimization of this process will have application as a sustainable mining practice by mediating magnesium carbonate precipitation in ultramafic mine tailings storage facilities.