The degradation of exopolymeric substances (EPS) by heterotrophic bacteria, concomitant release of calcium ions and precipitation of carbonates were studied in a temperate mountain lake, Lac d'Ilay, Jura France. Phytoplankton blooms in this lake produced large amounts of exopolymeric substances (EPS; 1.8–3.0 mg L⁻¹), probably inhibiting CaCO₃ precipitation by binding Ca²⁺ as shown by the saturation index of calcite and aragonite remaining well below 1. EPS settled to the sediments, where additional polymeric substances were produced by the benthic community. The total amount of EPS decreased downcore from ca 50 μg/g dry sediment near the surface to ca 1.5 μg/g dry sediment at the bottom (120 cm depth). A decrease in acidity, protein and sugar content, and calcium-binding capacity of EPS with depth coincided with active calcite precipitation. Aerobic and anaerobic EPS-degrading heterotrophic enrichments were obtained from the top, middle and bottom of the core. Doubling times of aerobic cultures from the top were six times shorter than those of cultures obtained from the bottom of the core, but anaerobic growth rates were similar across all enrichments. Aerobic turnover rates of organic compounds decreased by a factor of 4–5 from top to bottom; anaerobic rates were similar at all depths, except for the turnover of polymers, which was negligible at the surface compared to rates at the middle and bottom. All enrichments released calcium when grown on EPS. Growth on calcium-saturated EPS in anaerobic cultures obtained from the bottom of the core was the slowest, but still released 26% of the Ca in 20 days. This release during EPS degradation explained an increase in free calcium ions with depth reported in a previous study and may account for a large fraction of the carbonate mud. This suggests that sediments should be considered as an important source of biogenic carbonates.

The interplay between microbial activity and mineral precipitation in extreme environments plays a critical role in shaping sedimentary textures and influencing biosignature preservation. This study explores coupled Mg silicate and carbonate precipitation in the marginal lakes of the Salar de Atacama, Northern Chile, expanding previous findings from the Salar de Llamara. Using field samples from the Aguas de Quelana and Soncor sectors, sedimentary deposits classified as sediments, unlithified microbial mats and lithified microbial buildups are each characterised by distinct microbial architectures and mineralisation processes. Detailed analyses conducted via scanning electron microscopy, energy dispersive spectroscopy (EDS) and X-ray diffraction identified minerals and mineral associations and revealed pathways of coupled Mg silicate–carbonate precipitation. Results indicate that organic matter production is followed by precipitation of amorphous to nanocrystalline Mg silicate. Aragonite then templates on and replaces Mg silicate and infills voids. Dense microbial colonies within high-viscosity extracellular polymeric substances (EPS) promote precipitation of welded Mg silicate (W-MS), conferring structural stability, while loosely organised EPS networks result in porous deposits of granular sediments. W-MS serves as a scaffolding that enhances preservation of morphological biosignatures. Overall, sedimentary product diversity reflects variations in microbial density and EPS organisation, suggesting that variations in initial microbial colony distribution and EPS determine the eventual sedimentary product. Our results also highlight the role of Mg silicate–carbonate precipitation in the formation of grainy sediments, expanding prior work on Mg silicate–carbonate coupling forming microbialites and unlithified microbial mats in the Atacama Desert. The data set presented here provides a robust analogue for interpreting ancient sedimentary systems and emphasises the significance of microbe–mineral interactions forming Mg silicate–carbonate deposits in extreme environments.

Microbialites accrete through microbe-environment interactions and incorporate elements like arsenic, creating enrichment patterns that can preserve evidence of ancient microbial activity. However, the effects of morphology, fabric, and accretion mechanism on arsenic incorporation in microbialites is poorly understood, complicating the use of arsenic enrichment patterns as a chemical biosignature. By analyzing arsenic concentrations in actively accreting microbialites with diverse architectures from Hamelin Pool, Australia, we document the effects of morphology, fabric, and accretion mechanism on arsenic enrichment patterns. Our results demonstrate that arsenic enrichment patterns originate from microbial activity, sedimentary inputs, and seawater chemistry, the proportions of which vary with changing aspects of microbialite morphogenesis. Here we show that initial microbialite architecture is a fundamental yet underexplored factor that controls the geochemical composition of microbialites through geological time.

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

Hamelin Pool, Shark Bay, Western Australia hosts the world's largest and most extensive assemblages of living marine microbialites, comparable in size and shape to ancient structures found throughout the fossil record. Documented here are the internal fabrics of modern microbialites collected throughout Hamelin Pool. Mesoscale and microscale observations of microbialite polished slabs and thin section scans, optical microscopy and scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy formed the basis for a fabric classification system that combines accretionary mat type with microfabric. Accretionary mat types included pustular, smooth, colloform, as well as ‘transitional’ mats that are a cross between pustular and smooth mats. Mapping of fabrics in 45 microbialite heads indicated bidirectional evolution. An upward progression of fabrics corresponded to changes in mat type as the head grew upward into shallower water. A downward evolution of microfabrics occurred as surface mats transitioned into the subsurface of the microbialite structure. Downward microfabric evolution occurred as a result of early taphonomic processes, and involved a progression from the original depositional architecture to subsequent stages of “Micritic Thickening”, and finally, “Cement Infilling”. The observed bidirectional evolution of microbialite microfabrics within Hamelin Pool offers a conceptual framework for the study of modern microbialites, not simply as the sole product of accretionary mat types but rather as the combined result of the activity of surface mats and their taphonomic evolution. Early taphonomic processes induce further lithification of the microbialites which may enhance preservation potential in the geological record.

Dissolved inorganic carbon (DIC) levels in freshwaters play a key role in the equilibrium of the carbon cycle between the atmosphere, water and living beings. Standard classical methods for DIC determination generally involve bulky and expensive equipment used in centralized laboratories, resulting in time-consuming processes that do not allow for adequate monitoring in the field. In order to address this challenge, we have developed a distance-based paper analytical device (PAD) for on-site determination of DIC in water. The portable, cost-effective and easy-to-use device was based on the miniaturization and integration of a classical acid-base colorimetric titration on a paper channel, enabling an accurate determination of DIC in less than 20 min. The length of the blue colored line in the detection channel after being filled with the sample was related to the DIC concentration in the sample. The reagent solution used to modify the titration channel was optimized so that DIC concentrations in the range 50–1000 mg L⁻¹ could be measured. The long-term stability of the paper-based device was also evaluated, demonstrating a working stability for more than 70 days after their fabrication, an important characteristic for in-the-field analysis. Finally, the PAD was validated with different water samples, i.e. tap water, commercial bottled drinking water and water samples from a mine, with excellent agreement between the results obtained from the PAD and the standard method. This demonstrates the high potential of the proposed paper analytical device to quantify DIC in situ by minimally-trained personnel without the need for peripheral equipment, which represents an important advance compared to the current limited analysis systems.

Manganese oxides occur in a wide range of environmental settings either as coatings on rocks, sediment, and soil particles, or as discrete grains. Although the production of biologically mediated Mn oxides is well established, relatively little is known about microbial-specific strategies for utilizing Mn in the environment and how these affect the morphology, structure, and chemistry of associated mineralizations. Defining such strategies and characterizing the associated mineral properties would contribute to a better understanding of their impact on the local environment and possibly facilitate evaluation of biogenicity in recent and past Mn accumulations. Here, we supplement field data from a Mn rock wall deposit in the Ytterby mine, Sweden, with data retrieved from culturing Mn oxidizers isolated from this site. Microscopic and spectroscopic techniques are used to characterize field site products and Mn precipitates generated by four isolated bacteria (Hydrogenophaga sp., Pedobacter sp., Rhizobium sp., and Nevskia sp.) and one fungal-bacterial co-culture (Cladosporium sp.—Hydrogenophaga sp. Rhizobium sp.—Nevskia sp.). Two of the isolates (Pedobacter sp. and Nevskia sp.) are previously unknown Mn oxidizers. At the field site, the onset of Mn oxide mineralization typically occurs in areas associated with globular wad-like particles and microbial traces. The particles serve as building blocks in the majority of the microstructures, either forming the base for further growth into laminated dendrites-botryoids or added as components to an existing structure. The most common nanoscale structures are networks of Mn oxide sheets structurally related to birnessite. The sheets are typically constructed of very few layers and elongated along the octahedral chains. In places, the sheets bend and curl under to give a scroll-like appearance. Culturing experiments show that growth conditions (biofilm or planktonic) affect the ability to oxidize Mn and that taxonomic affiliation influences crystallite size, structure, and average oxidation state as well as the onset location of Mn precipitation.

Microbial mats or biofilms are known to colonize a wide range of substrates in aquatic environments. These dense benthic communities efficiently recycle nutrients and often exhibit high tolerance to environmental stressors, characteristics that enable them to inhabit harsh ecological niches. In some special cases, floating biofilms form at the air-water interface residing on top of a hydrophobic microlayer. Here, we describe biofilms that reside at the air-air interface by forming gas bubbles (bubble biofilms) in the former Ytterby mine, Sweden. The bubbles are built by micrometer thick membrane-like biofilm that holds enough water to sustain microbial activity. Molecular identification shows that the biofilm communities are dominated by the neuston bacterium Nevskia. Gas bubbles contain mostly air with a slightly elevated concentration of carbon dioxide. Biofilm formation and development was monitored in situ using a time-lapse camera over one year, taking one image every second hour. The bubbles were stable over long periods of time (weeks, even months) and gas build-up occurred in pulses as if the bedrock suddenly exhaled. The result was however not a passive inflation of a dying biofilm becoming more fragile with time (as a result of overstretching of the organic material). To the contrary, microbial growth lead to a more robust, hydrophobic bubble biofilm that kept the bubbles inflated for extended periods (several weeks, and in some cases even months).

Microbe-mediated precipitation of Mn-oxides enriched in rare earth elements (REE) and other trace elements was discovered in tunnels leading to the main shaft of the Ytterby mine, Sweden. Defining the spatial distribution of microorganisms and elements in this ecosystem provide a better understanding of specific niches and parameters driving the emergence of these communities and associated mineral precipitates. Along with elemental analyses, high-throughput sequencing of the following four subsystems were conducted: (i) water seeping from a rock fracture into the tunnel, (ii) Mn-oxides and associated biofilm; referred to as the Ytterby Black Substance (YBS) biofilm (iii) biofilm forming bubbles on the Mn-oxides; referred to as the bubble biofilm and (iv) fracture water that has passed through the biofilms. Each subsystem hosts a specific collection of microorganisms. Differentially abundant bacteria in the YBS biofilm were identified within the Rhizobiales (e.g. Pedomicrobium), PLTA13 Gammaproteobacteria, Pirellulaceae, Hyphomonadaceae, Blastocatellia and Nitrospira. These taxa, likely driving the Mn-oxide production, were not detected in the fracture water. This biofilm binds Mn, REE and other trace elements in an efficient, dynamic process, as indicated by substantial depletion of these metals from the fracture water as it passes through the Mn deposit zone. Microbe-mediated oxidation of Mn(II) and formation of Mn(III/IV)-oxides can thus have considerable local environmental impact by removing metals from aquatic environments.

Arsenic-consuming microbes of the hypersaline Laguna La Brava in Chile may be an analogue for early life during the anoxic conditions of the Archean, according to geochemical and metagenomic analyses of the extant microbial mats The earliest evidence of life captured in lithified microbial mats (microbialites) predates the onset of oxygen production and yet, modern oxygenic mats are often studied as analogs based on their morphological similarity and their sedimentological and biogeochemical context. Despite their structural similarity to fossil microbialites, the presence of oxygen in most modern microbial mats disqualifies them as appropriate models for understanding early Earth conditions. Here we describe the geochemistry, element cycling and lithification potential of microbial mats that thrive under permanently anoxic conditions in arsenic laden, sulfidic waters feeding Laguna La Brava, a hypersaline lake in the Salar de Atacama of northern Chile. We propose that these anoxygenic, arsenosulfidic, phototrophic mats are a link to the Archean because of their distinctive metabolic adaptations to a reducing environment with extreme conditions of high UV, vast temperature fluctuations, and alkaline water inputs from combined meteoric and volcanic origin, reminiscent of early Earth.