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

The effect of barium ions on the biomineralization of calcium and magnesium ions is often overlooked when utilizing microbial-induced carbonate precipitation technology for removing barium, calcium, and magnesium ions from oilfield wastewater. In this study, Bacillus licheniformis was used to bio-precipitate calcium, magnesium, and barium ions. The effects of barium ions on the physiological and biochemical characteristics of bacteria, as well as the components of extracellular polymers and mineral characteristics, were also studied in systems containing coexisting barium, calcium, and magnesium ions. The results show that the increasing concentrations of barium ions decreased pH, carbonic anhydrase activity, and concentrations of bicarbonate and carbonate ions, while it increased the contents of humic acids, proteins, polysaccharides, and DNA in extracellular polymers in the systems containing all three types of ions. With increasing concentrations of barium ions, the content of magnesium within magnesium-rich calcite and the size of minerals precipitated decreased, while the full width at half maximum of magnesium-rich calcite, the content of O-C=O and N–C=O, and the diversity of protein secondary structures in the minerals increased in systems containing all three coexisting ions. Barium ions does inhibit the precipitation of calcium and magnesium ions, but the immobilized bacteria can mitigate the inhibitory effect. The precipitation ratios of calcium, magnesium, and barium ions reached 81–94%, 68–82%, and 90–97%. This research provides insights into the formation of barium-enriched carbonate minerals and offers improvements for treating oilfield wastewater. [ABSTRACT FROM AUTHOR]

Microbially induced manganese carbonate precipitation has been utilized for the treatment of wastewater containing manganese. In this study, Virgibacillus dokdonensis was used to remove manganese ions from an environment containing 5% NaCl. The results showed a significant decrease in carbonic anhydrase activity and concentrations of carbonate and bicarbonate ions with increasing manganese ion concentrations. However, the levels of humic acid analogues, polysaccharides, proteins, and DNA in EPS were significantly elevated compared to those in a manganese-free environment. The rhodochrosite exhibited a preferred growth orientation, abundant morphological features, organic elements including nitrogen, phosphorus, and sulfur, diverse protein secondary structures, as well as stable carbon isotopes displaying a stronger negative bias. The presence of manganese ions was found to enhance the levels of chemical bonds O–C=O and N–C=O in rhodochrosite. Additionally, manganese in rhodochrosite exhibited both + 2 and + 3 valence states. Rhodochrosite forms not only on the cell surface but also intracellularly. After being treated with free bacteria for 20 days, the removal efficiency of manganese ions ranged from 88.4 to 93.2%, and reached a remarkable 100% on the 10th day when using bacteria immobilized on activated carbon fiber that had been pre-cultured for three days. The removal efficiency of manganese ions was significantly enhanced under the action of pre-cultured immobilized bacteria compared to non-pre-cultured immobilized bacteria. This study contributes to a comprehensive understanding of the mineralization mechanism of rhodochrosite, thereby providing an economically and environmentally sustainable biological approach for treating wastewater containing manganese. [ABSTRACT FROM AUTHOR]

The discovery of cyanobacteria fossils in microbialite prompts the investigation of carbonate biomineralization using cyanobacteria. However, the impact of coexisting magnesium and iron in microbialite on carbonate biomineralization has been overlooked. Here, Synechocystis sp. PCC 6803 was used to induce calcium carbonate in the presence of coexisting magnesium and ferric ions. The findings demonstrate that cell concentration, pH, carbonic anhydrase activity, and carbonate and bicarbonate concentrations decreased with increasing concentrations of magnesium and calcium ions. Ferric ions yielded a contrasting effect. The levels of deoxyribonucleic acid, protein, polysaccharides, and humic substances in extracellular polymeric substances increased in the presence of separated or coexisting calcium, magnesium, and ferric ions. Magnesium ions inhibited calcium ion precipitation, whereas ferric ions exhibited the opposite effect. Protein secondary structures became more abundant and O-C=O and N-C=O contents increased with increasing ion concentrations by Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy analyses. Scanning electron microscopy revealed that ferric ions lead to rougher surfaces and incomplete rhombohedral structures of calcite, whereas magnesium ions promoted greater diversity in morphology. Magnesium ions enhanced the incorporation of ferric ions. This work aims to further understand the effect of magnesium and ferric ions on calcium carbonate biomineralization induced by cyanobacteria. [ABSTRACT FROM AUTHOR]

Dolomite (CaMg(CO3)2) precipitation is kinetically inhibited at surface temperatures and pressures. Experimental studies have demonstrated that microbial extracellular polymeric substances (EPS) as well as certain clay minerals may catalyse dolomite precipitation. However, the combined association of EPS with clay minerals and dolomite and their occurrence in the natural environment are not well documented. We investigated the mineral and textural associations within groundwater dolocrete profiles from arid northwest Australia. Microbial EPS is a site of nucleation for both dolomite and authigenic clay minerals in this Late Miocene to Pliocene dolocrete. Dolomite crystals are commonly encased in EPS alveolar structures, which have been mineralised by various clay minerals, including montmorillonite, trioctahedral smectite and palygorskite‐sepiolite. Observations of microbial microstructures and their association with minerals resemble textures documented in various lacustrine and marine microbialites, indicating that similar mineralisation processes may have occurred to form these dolocretes. EPS may attract and bind cations that concentrate to form the initial particles for mineral nucleation. The dolomite developed as nanocrystals, likely via a disordered precursor, which coalesced to form larger micritic crystal aggregates and rhombic crystals. Spheroidal dolomite textures, commonly with hollow cores, are also present and may reflect the mineralisation of a biofilm surrounding coccoid bacterial cells. Dolomite formation within an Mg‐clay matrix is also observed, more commonly within a shallow pedogenic horizon. The ability of the negatively charged surfaces of clay and EPS to bind and dewater Mg2+, as well as the slow diffusion of ions through a viscous clay or EPS matrix, may promote the incorporation of Mg2+ into the mineral and overcome the kinetic effects to allow disordered dolomite nucleation and its later growth. The results of this study show that the precipitation of clay and carbonate minerals in alkaline environments may be closely associated and can develop from the same initial amorphous Ca–Mg–Si‐rich matrix within EPS. The abundance of EPS preserved within the profiles is evidence of past microbial activity. Local fluctuations in chemistry, such as small increases in alkalinity, associated with the degradation of EPS or microbial activity, were likely important for both clay and dolomite formation. Groundwater environments may be important and hitherto understudied settings for microbially influenced mineralisation and for low‐temperature dolomite precipitation. [ABSTRACT FROM AUTHOR]

Oil in the Jarvis structure underlying the main Upper Jurassic reservoir at the Ettrick oilfield (Outer Moray Firth, UK northern North Sea) is present in Upper Permian (Zechstein) carbonates. The origin of this "Jarvis oil" is investigated in this paper using a multidisciplinary approach based on data from well‐logs and cores from wells 20/02‐2 and 20/02‐3. Reservoirs at the Jarvis structure consist of carbonates in the upper part of the Halibut Carbonate Formation (Ca2) and in the Carbonate Member of the Turbot Anhydrite Formation (Ca3). These carbonates are typical Zechstein dolomites composed of a range of facies from mudpackstones with storm beds deposited at moderate water depths to shoreface bioclastic‐oolitic packstones to shallow‐subtidal and intertidal microbial laminites. Interbedded anhydrites replace sabkha and lagoonal selenitic gypsum. Several shallowing‐upward units are recognised. Molecular analysis of the Jarvis oil, and comparisons with biomarker and other geochemical data from extracts of Zechstein cores and published data from different source rocks from the North Sea area, suggest that the oil was generated by marine, OM‐rich shales in the Upper Jurassic Kimmeridge Clay Formation. The oil was generated at peak oil window maturity and is characterised by high Pr/Ph, BNH/H and DBT/P ratios, and abundant C28 steranes and C28+29 monoaromatic and C26R + C27S triaromatic steroids. The molecular composition of organic material in extracts of core samples of Zechstein carbonates from wells in the Jarvis structure differs significantly from that of the Jarvis oil. Biomarkers such as BNH are absent in the core extracts, and there are different distributions and abundances of saturated and aromatic hydrocarbons, likely controlled by thermal maturity. [ABSTRACT FROM AUTHOR]

Microbially-induced calcium carbonate precipitation (MICP) has been studied extensively. However, the effect of different sources of magnesium ions on calcium carbonate biomineralization has rarely been examined. In this study, Lysinibacillus xylanilyticus DB1-12 bacteria isolated from petroleum samples were used to biomineralize calcium ions under the action of different sources of magnesium (magnesium chloride and magnesium sulfate). The results show that calcium ion precipitation ratios were much higher in MgSO4 group experiments than in the MgCl2 group (p < 0.01). The mineral phases in the MgCl2 group experiments were the same as those in MgSO4 group at each Mg/Ca ratio. Minerals with a 'twisted' shape were much more common in the MgSO4 group; the protein secondary structures hidden in minerals were much more abundant in the MgCl2 group, and the activation energy of biotic monohydrocalcite at a Mg/Ca ratio of 11 was also much higher in the MgCl2 group than in the MgSO4 group. The main reasons for these differences are closely related to the lower magnesium content and the more common protein secondary structures in the monohydrocalcite in the MgCl2 group. The shift of Mg1s XPS spectra suggests that the chemical interactions occurring on the monohydrocalcite surfaces in the MgCl2 group were different from those in the MgSO4 group. The δ13CPDB values of the biominerals in the MgSO4 group are in the range of −16.93 to −18.87‰, lower than those in the MgCl2 group (-15.77 to −18.69‰). The morphology of L. xylanilyticus DB1-12 became deformed and some rod-shaped protrusions developed on the cell surface during the process of biomineralization. This study not only contributes to the understanding of biomineralization mechanisms generally, but is also helpful in the interpretations of paleo-environmental conditions. [ABSTRACT FROM AUTHOR]