Bioprecipitation of Calcium Carbonate Crystals by Bacteria Isolated from Saline Environments Grown in Culture Media Amended with Seawater and Real Brine

Molecular study of Enterobacteriaceae bacterium isolated from dishwashers

The Enterobacteriaceae family is considered one of the medically essential families in which there is a continuous change in classification, and new species are added to it. In this study, we obtained a novel strain registered in the NCBI under Enterobacteriaceae bacterium strain PRL 4-2, with the accession number MW540823, and the isolate considered unclassified Enterobacteriaceae. The isolate was obtained from dishwashers, which is a mine for many new species and strains due to the unique environmental conditions of this habitat, fluctuation in temperature, use of high temperatures, utilization of cleaning materials as well as humidity and the presence of organic materials, especially in case of neglect of cleaning. The isolate was characterized by its slow growth on culture media and its ability to form biofilms and possess some virulence factors. Its resistance to antibiotics was also studied, as it showed resistance to the antibiotics used in this study. The oddness for this strain is that it showed a different diagnosis when using VITEK (The VITEK 2 system has everything healthcare laboratories need for fast, accurate microbial identification and antibiotic susceptibility testing.) compared to diagnosis using 16S rRNA. As for the taxonomic tree, the closest species was Enterobacter sp. Strain 188. This study supplements a few other studies of this novel species, isolated from different environments. These researches can be integrated to give an itinerary for other studies on the new species and their different capabilities. Keywords. Enterobacteriaceae bacterium, dishwasher, Enterobacteriaceae bacterium PRL-2, Enterobacter sp., biofilm.

New Biocalcifying Marine Bacterial Strains Isolated from Calcareous Deposits and Immediate Surroundings

Marine bacterial biomineralisation by CaCO3 precipitation provides natural limestone structures, like beachrocks and stromatolites. Calcareous deposits can also be abiotically formed in seawater at the surface of steel grids under cathodic polarisation. In this work, we showed that this mineral-rich alkaline environment harbours bacteria belonging to different genera able to induce CaCO3 precipitation. We previously isolated 14 biocalcifying marine bacteria from electrochemically formed calcareous deposits and their immediate environment. By microscopy and µ-Raman spectroscopy, these bacterial strains were shown to produce calcite-type CaCO3. Identification by 16S rDNA sequencing provided between 98.5 and 100% identity with genera Pseudoalteromonas, Pseudidiomarina, Epibacterium, Virgibacillus, Planococcus, and Bhargavaea. All 14 strains produced carbonic anhydrase, and six were urease positive. Both proteins are major enzymes involved in the biocalcification process. However, this does not preclude that one or more other metabolisms could also be involved in the process. In the presence of urea, Virgibacillus halodenitrificans CD6 exhibited the most efficient precipitation of CaCO3. However, the urease pathway has the disadvantage of producing ammonia, a toxic molecule. We showed herein that different marine bacteria could induce CaCO3 precipitation without urea. These bacteria could then be used for eco-friendly applications, e.g., the formation of bio-cements to strengthen dikes and delay coastal erosion.

Isolation of alkaliphilic calcifying bacteria and their feasibility for enhanced CaCO3 precipitation in bio-based cementitious composites

Microbially induced calcite precipitation (MICP), secreted through biological metabolic activity, secured an imperative position in remedial measures within the construction industry subsequent to ecological, environmental and economical returns. However, this contemporary recurrent healing system is susceptible to microbial depletion in the highly alkaline cementitious environment. Therefore, researchers are probing for alkali resistant calcifying microbes. In the present study, alkaliphilic microbes were isolated from different soil sources and screened for probable CaCO3 precipitation. Non-ureolytic pathway (oxidation of organic carbon) was adopted for calcite precipitation to eliminate the production of toxic ammonia. For this purpose, calcium lactate Ca(C3 H5 O3 )2 and calcium acetate Ca(CH3 COO)2 were used as CaCO3 precipitation precursors. The quantification protocol for precipitated CaCO3 was established to select potent microbial species for implementation in the alkaline cementitious systems as more than 50% of isolates were able to precipitate CaCO3 . Results suggested 80% of potent calcifying strains isolated in this study, portrayed higher calcite precipitation at pH 10 when compared to pH 7. Ten superlative morphologically distinct isolates capable of CaCO3 production were identified by 16SrRNA sequencing. Sequenced microbes were identified as species of Bacillus, Arthrobacter, Planococcus, Chryseomicrobium and Corynebacterium. Further, microstructure of precipitated CaCO3 was inspected through scanning electron microscopy (SEM), X-ray diffraction (XRD) and thermal gravimetric (TG) analysis. Then, the selected microbes were investigated in the cementitious mortar to rule out any detrimental effects on mechanical properties. These strains showed maximum of 36% increase in compressive strength and 96% increase in flexural strength. Bacillus, Arthrobacter, Corynebacterium and Planococcus genera have been reported as CaCO3 producers but isolated strains have not yet been investigated in conjunction with cementitious mortar. Moreover, species of Chryseomicrobium and Glutamicibacter were reported first time as calcifying strains.

Bacteria-induced mineral precipitation: a mechanistic review

Micro-organisms contribute to Earth's mineral deposits through a process known as bacteria-induced mineral precipitation (BIMP). It is a complex phenomenon that can occur as a result of a variety of physiological activities that influence the supersaturation state and nucleation catalysis of mineral precipitation in the environment. There is a good understanding of BIMP induced by bacterial metabolism through the control of metal redox states and enzyme-mediated reactions such as ureolysis. However, other forms of BIMP often cannot be attributed to a single pathway but rather appear to be a passive result of bacterial activity, where minerals form as a result of metabolic by-products and surface interactions within the surrounding environment. BIMP from such processes has formed the basis of many new innovative biotechnologies, such as soil consolidation, heavy metal remediation, restoration of historic buildings and even self-healing concrete. However, these applications to date have primarily incorporated BIMP-capable bacteria sampled from the environment, while detailed investigations of the underpinning mechanisms have been lagging behind. This review covers our current mechanistic understanding of bacterial activities that indirectly influence BIMP and highlights the complexity and connectivity between the different cellular and metabolic processes involved. Ultimately, detailed insights will facilitate the rational design of application-specific BIMP technologies and deepen our understanding of how bacteria are shaping our world.

Biodeteriogens Characterization and Molecular Analyses of Diverse Funeral Accessories from XVII Century

A historical crypt offers us a particular view of the conditions of some buried materials (in this case textiles) and the various biogenic phenomena to which they were subjected over the centuries. In addition, significant knowledge can come by studying the DNA of buried objects which allows the recognition of materials, but also to reveal some practice of the funeral ceremony. In this study, the deteriorating microbial communities colonizing various funeral textile items were identified and characterized using microscopic observation, cultivation, polymerase chain reaction (PCR) and sequencing, hydrolytic tests; and culture-independent analysis (high-throughput sequencing, MinION platform). Different PCR assays and consequent sequencing of amplicons were employed to recognize the animal origin of bodice reinforcements and the type of plant used to embellish the young girl. The analysis of ancient DNA (aDNA from animal and plant) was also completed by the application of high-throughput sequencing through Illumina platform. The combination of all these techniques permitted the identification of a complex microbiota composed by dangerous degradative microorganisms able to hydrolyze various organic substrates such as fibroin, keratin, and cellulose. Bacteria responsible for metal corrosion and bio-mineralization, and entomopathogenic and phytopathogenic fungi. The analysis of aDNA identified the animal component used in bodice manufacturing, the plant utilized as ornament and probably the season of this fatal event.

Physicochemical Parameters Affecting the Distribution and Diversity of the Water Column Microbial Community in the High-Altitude Andean Lake System of La Brava and La Punta

Due to the low incidence of precipitation attributed to climate change, many high-altitude Andean lakes (HAALs) and lagoons distributed along the central Andes in South America may soon disappear. This includes La Brava–La Punta, a brackish lake system located south of the Salar de Atacama within a hyper-arid and halophytic biome in the Atacama Desert. Variations in the physicochemical parameters of the water column can induce changes in microbial community composition, which we aimed to determine. Sixteen sampling points across La Brava–La Punta were studied to assess the influence of water physicochemical properties on the aquatic microbial community, determined via 16S rRNA gene analysis. Parameters such as pH and the concentrations of silica, magnesium, calcium, salinity, and dissolved oxygen showed a more homogenous pattern in La Punta samples, whereas those from La Brava had greater variability; pH and total silica were significantly different between La Brava and La Punta. The predominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The genera Psychroflexus (36.85%), Thiomicrospira (12.48%), and Pseudomonas (7.81%) were more abundant in La Brava, while Pseudospirillum (20.73%) and Roseovarius (17.20%) were more abundant in La Punta. Among the parameters, pH was the only statistically significant factor influencing the diversity within La Brava lake. These results complement the known microbial diversity and composition in the HAALs of the Atacama Desert.

Effect of simulated acid rain on the stability of calcium carbonate immobilized by microbial carbonate precipitation

The stability of carbonate products resulting from microbially induced carbonate precipitation (MICP) under acid rain is under question. The present study investigated the stability of CaCO₃ precipitated by MICP in soil under simulated acid rain (SAR). Soils were treated continuously for two months with four SAR pH levels: 3.5, 4.5, 5.5, and 7.0. During SAR, biostimulation using nutrient broth containing urea and calcium chloride was adopted to ensure CaCO₃ precipitation. At the end of treatments, soil samples from top and bottom layers were analyzed for bacterial diversity by Illumina MiSeq sequencing, Fourier transform infrared (FTIR) spectroscopy for identification of chemical functional groups related to calcite precipitation, and X-ray diffraction (XRD) for identification of the main crystalline phases. The analysis identified several ureolytic bacteria mainly from Arthrobacter and Sporosarcina genera in SAR-treated soils accelerated with biostimulation, and urease quantities of greater than 300 mg NH₄⁺ per kg soil at all pH levels. The precipitation of CaCO₃ was pronounced and its stability was maintained even when the pH was as low as 3.5. The results obtained in this study are helpful to the scientific community to ensure the immobilization of heavy metals with microbial carbonate precipitation in soil under acid rain.

Aerobic and anaerobic removal of lead and mercury via calcium carbonate precipitation mediated by statistically optimized nitrate reductases

The nonbiodegradability nature of heavy metals renders them resident in food chain and subsequently, destructing the entire ecosystem. Therefore, this study aimed to employ nitrate reduction-driven calcium carbonate precipitation in remediation of lead and mercury aerobically and anaerobically by Proteus mirabilis 10B, for the first time. Initially, Plackett-Burman design was employed to screen of 16 independent variables for their significances on periplasmic (NAP) and membrane-bound (NAR) nitrate reductases. The levels for five significant variables and their interaction effects were further optimized by central composite design. The maximum activities of NAP and NAR recorded 2450 and 3050 U/mL by 2-fold enhancement, comparing with non-optimized medium. Under aerobic and anaerobic optimized remediation conditions, the changes in media chemistry revealed positive correlation among bacterial growth, nitrate reductase activity, pH, NO₃^- and NO₂^- consumption and removal of Ca²⁺, Pb²⁺ and Hg²⁺. Subsequently, the remediated precipitates were subjected to mineralogical analysis; energy dispersive X-ray patterns exhibited characteristic peaks of C, O and Ca in addition to Pb and Hg. Scanning electron microscope depicted the presence of bacterial imprints and protrusions on rough and smooth surface bioliths. However, X-ray diffraction indicated entrapment of PbCO₃, Pb₂O, CaPbO₃, Hg and Hg₂O in calcite lattice. Interestingly, such approach is feasible, efficient, cost-effective and ecofriendly for heavy metals remediation.

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.

Enhanced biomass and lipid production of Neochloris oleoabundans under high light conditions by anisotropic nature of light-splitting CaCO3 crystal

The aim of this work was to study the anisotropic effect of crystalline CaCO₃ nanoparticles (CN)-driven multiple refraction/scattering from the CN-coated agglomerated cells on the rate of photosynthesis and the product yield under high light conditions in the freshwater microalgae Neochloris oleoabundans. The CN-coating via biomineralization significantly improved the biomass and lipid production of N. oleoabundans during second stage of autotrophic induction by sustaining relatively high rate of photosynthesis at high irradiance using the multiple-splitting effect of the anisotropic polymorphism. The CN were successfully produced, adsorbed and grown on the external cells under conditions of mild alkalinity (pH 7.5-8.0), mild CaCl₂ concentration (0.05 M) and under nitrogen starvation with strong light (400 µE m^-2 s^-1). Consequently, lipid content and productivity of N. oleoabundans cells cultured with 0.05 M CaCl₂ increased by 18.4% and 31.5%, respectively, compared to the cells cultured with 0.05 M CaCl₂ and acetazolamide to inhibit calcification.

Bio-Precipitation of Calcium and Magnesium Ions through Extracellular and Intracellular Process Induced by Bacillus Licheniformis SRB2

Removal of calcium and magnesium ions through biomineralization induced by bacteria has been proven to be an effective and environmentally friendly method to improve water quality, but the process and mechanism are far from fully understood. In this study, a newly isolated probiotic Bacillus licheniformis SRB2 (GenBank: KM884945.1) was used to induce the bio-precipitation of calcium and magnesium at various Mg/Ca molar ratios (0, 6, 8, 10, and 12) in medium with 30 g L−1 sodium chloride. Due to the increasing pH and HCO3− and CO32− concentrations caused by NH3 and carbonic anhydrase, about 98% Ca2+ and 50% Mg2+ were precipitated in 12 days. The pathways of bio-precipitation include extracellular and intracellular processes. Biominerals with more negative δ13C values (−16‰ to −18‰) were formed including calcite, vaterite, monohydrocalcite, and nesquehonite with preferred orientation. The nucleation on extracellular polymeric substances was controlled by the negatively charged amino acids and organic functional groups. The intracellular amorphous inclusions containing calcium and magnesium also contributed to the bio-precipitation. This study reveals the process and mechanism of microbial desalination for the removal of calcium and magnesium, and provides some references to explain the formation of the nesquehonite and other carbonate minerals in a natural and ancient earth surface environment.

Microbial Mg-rich Carbonates in an Extreme Alkaline Lake (Las Eras, Central Spain)

This paper provides strong evidence for the contribution of the phylum Firmicutes in mediating the primary precipitation of Mg-rich carbonates (hydromagnesite, dolomite, magnesite, and nesquehonite) in recent microbialites from a highly alkaline and ephemeral inland lake (Las Eras, Central Spain). The carbonate mineral precipitation occurs sequentially as the microbial mats decay. Scanning electron microscopy (SEM) provided solid proof that hydromagnesite nucleation is initiated on the exopolymeric substances (EPS) and the microbial cells associated to the microbial mat degradation areas. The progressive mineralization of the EPS and bacterial cells by hydromagnesite plate-like crystals on their surface, results in the entombment of the bacteria and formation of radiating aggregates of hydromagnesite crystals. The hydrous phases, mostly hydromagnesite, were produced at a high percentage in the first stages of the microbial degradation of organic matter. When the availability of organic substrates declines, the heterotrophs tend to reduce their number and metabolic activity, remain dormant. At this stage, the anhydrous phases, dolomite and magnesite, nucleate on bacterial nanoglobules and/or collapsed cells. Evidence for the sequential formation of the Mg-rich carbonates trough the decay of organic matter by a fermentative EPS-forming bacterium isolated from the microbialites, Desemzia incerta, is drawn through a comparative analysis of carbonate formation in both natural and experimental settings. This study will help to constrain potential mechanisms of carbonate formation in natural systems, which are of fundamental importance not only for understanding modern environments but also as a window into the geologic past of Earth and potentially Mars.

Bioprospecting of Ureolytic Bacteria From Laguna Salada for Biomineralization Applications

The processes of biomineralization, mediated by ureolytic bacteria, possess a wide range of technological applications, such as the formation of biocements and remediation of water and soil environments. For this reason, the bioprospecting of new ureolytic bacteria is interesting for its application to these technologies, particularly for water treatment. This study demonstrates the isolation, selection, and identification of halotolerant ureolytic bacteria from Laguna Salada (inland from Atacama Desert) and the evaluation of their ability to precipitate calcium carbonate crystals in freshwater in the presence of calcium ions, as well as the ability to induce the precipitation of crystals from different ions present in seawater. Twenty-four halotolerant ureolytic bacteria whose molecular identification gives between 99 and 100% identity with species of the genus Bacillus, Porphyrobacter, Pseudomonas, Salinivibrio, and Halomonas were isolated. When cultivated in freshwater, urea, and calcium chloride, all species are able to biomineralize calcium carbonate in different concentrations. In seawater, the strains that biomineralize the highest concentration of calcium carbonate correspond to Bacillus subtilis and Halomonas sp. SEM–EDX and XRD analyses determined that both bacteria induce the formation of 9–33% halite (NaCl), 31–66% monohydrocalcite (CaCO₃ × H₂O), and 24–27% struvite (MgNH₄PO₄ × 6H₂O). Additionally, B.subtilis induces the formation of 7% anhydrite (CaSO₄). In seawater, B.subtilis and Halomonas sp. were able to precipitate both calcium (96–97%) and magnesium (63–67%) ions over 14 days of testing. Ion removal assays with B.subtilis immobilized in beads indicate a direct relationship between the urea concentration and a greater removal of ions with similar rates to free cells. These results demonstrate that the biomineralization mediated by bacterial urea hydrolysis is feasible in both freshwater and seawater, and we propose its application as a new technology in improving water quality for industrial uses.

Biofouling Formation and Bacterial Community Structure in Hybrid Moving Bed Biofilm Reactor-Membrane Bioreactors: Influence of Salinity Concentration

Two pilot-scale hybrid moving bed biofilm reactor-membrane bioreactors were operated in parallel for the treatment of salinity-amended urban wastewater under 6 hours of hydraulic retention time and 2500 mg L−1 total solids concentration. Two salinity conditions were tested: the constant salinity of 6.5 mS cm−1 electric conductivity (3.6 g L−1 NaCl) and the tidal-like variable salinity with maximum 6.5 mS cm−1 electric conductivity. An investigation was developed on the biofouling produced on the ultrafiltration membrane surface evaluating its bacterial community structure and its potential function in the fouling processes. The results showed that biofouling was clearly affected by salinity scenarios in terms of α-diversity and β-diversity and bacterial community structure, which confirms lower bacterial diversity under variable salinity conditions with Rhodanobacter and Dyella as dominant phylotypes. Microorganisms identified as bio-mineral formers belonged to genera Bacillus, Citrobacter, and Brevibacterium. These findings will be of help for the prevention and control of biofouling in saline wastewater treatment systems.

Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations

The ability of Halomonas maura to bioprecipitate carbonate and sulphate crystals in solid media at different manganese concentrations has been demonstrated in this study for the first time. The precipitated minerals were studied by X-ray diffraction, scanning and transmission electron microscopy, and energy-dispersive X-ray spectroscopy. The precipitated minerals were different based on the manganese concentration present in the medium and the incubation time. In the absence of manganese, H. maura formed pseudokutnahorite crystals; in the presence of manganese, the concentration in the culture medium determined the precipitation carbonates, such as rhodochrosite and dolomites. However, in the presence of low concentrations of manganese chloride (MnCl₂) (5 g/l), kutnohorite crystals were also formed. Finally, when H. maura was grown in the presence of manganese, small amounts of sulphate crystals (such as bassanite and gypsum) were detected. Our study of the precipitated minerals showed an active role of H. maura in the biomineralisation process, but the geochemical conditions, and the manganese concentrations in particular, were clearly influential.