Isolation, differentiation and biodiversity of ureolytic bacteria of Qatari soil and their potential in microbially induced calcite precipitation (MICP) for soil stabilization

Yeast Diversity in Honey and Pollen Samples from Stingless Bees in the State of Bahia, Brazil: Use of the MALDI-TOF MS/Genbank Proteomic Technique

(1) Background: The identification of microorganisms includes traditional biochemical methods, molecular biology methods evaluating the conserved regions of rRNA, and the molecular biology of proteins (proteomics), such as MALDI-TOF MS mass spectrometry. This work aimed to identify the biodiversity of yeasts associated with stingless bee species' honey and pollen, Melipona scutellaris, Nannotrigona testaceicornes, and Tetragonisca angustula, from the region of São Gonçalo dos Campos-Bahia (BA) state, Brazil. (2) Methods: Cellular proteins were extracted from 2837 microbial isolates (pollen and honey) and identified via MALDI-TOF MS. The identified yeast species were also compared to the mass spectra of taxonomically well-characterized reference strains, available from the National Center of Biotechnology Information (NCBI) database. (3) Results: Nine yeast species were identified: Candida maltosa, Candida norvegica, Kazachstania telluris, Schizosaccharomyces pombe, Scheffersomyces insectosus, Meyerozyma guilliermondii, Brettanomyces bruxellensis, Kazachstania exigua, and Starmerella lactis-condensi. Nannotrigona testaceicornes pollen had the highest number of yeast colonies. The yeasts Brettanomyces bruxellensis and Kazachstania telluris showed high populations in the samples of Nannotrigona testaceicornes and Melipona scutellaris, respectively. This work shows that there is some sharing of the same species of yeast between honey and pollen from the same beehive. (4) Conclusions: A total of 71.84% of the identified species present a high level of confidence at the species level. Eight yeast species (Candida maltosa, Candida norvegica, Kazachstania telluris, Schizosaccharomyces pombe, Scheffersomyces insectosus, Meyerozyma guilliermondii, Kazachstania exigua, and Starmerella lactis-condensi) were found for the first time in the samples that the authors inspected. This contributes to the construction of new knowledge about the diversity of yeasts associated with stingless bee products, as well as to the possibility of the biotechnological application of some yeast species.

A review of biomineralization in healing concrete: Mechanism, biodiversity, and application

Concrete is the main ingredient in construction, but it inevitably fractures during its service life, requiring a large amount of cement and aggregate for maintenance. Concrete healing through biomineralization can repair cracks and improve the durability of concrete, which is conducive to saving raw materials and reducing carbon emissions. This paper reviews the biodiversity of microorganisms capable of precipitating mineralization to repair the concrete and their mineralization ability under different conditions. To better understand the mass transfer process of precipitates, two biomineralization mechanisms, microbially-controlled mineralization and microbially-induced mineralization, have been briefly described. The application of microorganisms in the field of healing concrete, comprising passive healing and intrinsic healing, is discussed. The key insight on the interaction between cementitious materials and microorganisms is the main approach for developing novel self-healing concrete in the future to improve the corrosion resistance of concrete. At the same time, the limitations and challenges are also pointed out.

Microbial induced carbonate precipitation for remediation of heavy metals, ions and radioactive elements: A comprehensive exploration of prospective applications in water and soil treatment

Improper disposal practices have caused environmental disruptions, possessing by heavy metal ions and radioactive elements in water and soil, where the innovative and sustainable remediation strategies are significantly imperative in last few decades. Microbially induced carbonate precipitation (MICP) has emerged as a pioneering technology for remediating contaminated soil and water. Generally, MICP employs urease-producing microorganisms to decompose urea (NH2CONH2) into ammonium (NH4+and carbon dioxide (CO2), thereby increasing pH levels and inducing carbonate precipitation (CO32-), and effectively removing remove contaminants. Nonetheless, the intricate mechanism underlying heavy metal mineralization poses a significant challenge, constraining its application in contaminants engineering, particularly in the context of prolonged heavy metal leaching over time and its efficacy in adverse environmental conditions. This review provides a comprehensive idea of recent development of MICP and its application in environmental engineering, examining metabolic pathways, mineral precipitation mechanisms, and environmental factors as well as providing future perspectives for commercial utilization. The use of ureolytic bacteria in MICP demonstrates cost-efficiency, environmental compatibility, and successful pollutant abatement over tradition bioremediation techniques, and bio-synthesis of nanoparticles. limitations such as large-scale application, elevated Ca2+levels in groundwater, and gradual contaminant release need to be overcome. The possible future research directions for MICP technology, emphasizing its potential in conventional remediation, CO2 sequestration, bio-material synthesis, and its role in reducing environmental impact for long-term economic benefits.

Insights in MICP dynamics in urease-positive Staphylococcus sp. H6 and Sporosarcina pasteurii bacterium

Microbially induced calcite precipitation (MICP) is an efficient and eco-friendly technique that has attracted significant interest for resolving various problems in the soil (erosion, improving structural integrity and water retention, etc.), remediation of heavy metals, production of self-healing concrete or restoration of different concrete structures. The success of most common MICP methods depends on microorganisms degrading urea which leads to the formation of CaCO3 crystals. While Sporosarcina pasteurii is a well-known microorganism for MICP, other soil abundant microorganisms, such as Staphylococcus bacteria have not been thoroughly studied for its efficiency in bioconsolidation though MICP is a very important proccess which can ensure soil quality and health. This study aimed to analyze MICP process at the surface level in Sporosarcina pasteurii and a newly screened Staphylococcus sp. H6 bacterium as well as show the possibility of this new microorganism to perform MICP. It was observed that Staphylococcus sp. H6 culture precipitated 157.35 ± 3.3 mM of Ca2+ ions from 200 mM, compared to 176 ± 4.8 mM precipitated by S. pasteurii. The bioconsolidation of sand particles was confirmed by Raman spectroscopy and XRD analysis, which indicated the formation of CaCO3 crystals for both Staphylococcus sp. H6 and S. pasteurii cells. The water-flow test suggested a significant reduction in water permeability in bioconsolidated sand samples for both Staphylococcus sp. H6 and S. pasteurii. Notably, this study provides the first evidence that CaCO3 precipitation occurs on the surface of Staphylococcus and S. pasteurii cells within the initial 15-30 min after exposure to the biocementation solution. Furthermore, Atomic force microscopy (AFM) indicated rapid changes in cell roughness, with bacterial cells becoming completely coated with CaCO3 crystals after 90 min incubation with a biocementation solution. To our knowledge, this is the first time where atomic force microscopy was used to visualize the dynamic of MICP on cell surface.

Identification of coastal pesticide pollutants as potent inhibitors of Bacillus pasteurii urease mediated calcium carbonate precipitation: a computational approach

Microbially induced calcite precipitation (MICP) through urease enzyme has attained a lot of recognition in various fields of civil engineering and geotechnology for stabilizing the strength of soil and various concrete materials. The activity of urease has been found to be affected by various factors like temperature, substrate concentrations, pH of the medium, presence of inhibitors, etc. Through this study, the outcome of the interaction of pesticides (commonly found in Indian coastal regions) on Bacillus pasteurii urease, a major organism reported for MICP studies has been investigated in silico. The results from the study revealed that the enzyme has higher interactions of -4.1, -3.2, and -3.4 kJ/mol with common pesticides like dichloro diphenyl dichloro ethane(DDD), dichloro diphenyl trichloroe thane (DDT), and methyl parathion of organochlorides and organophosphates class. From the molecular dynamics simulation analysis, complex 1 (DDD -receptor) has been found to have the highest and more compact structure followed by methyl parathion -receptor. Prime MM-GBSA analysis also revealed the highest binding energy of -27.8 kcal/mol with the protein and DDD. Thus, it can be inferred from the current study that pesticides, particularly, DDD, DDT, and methyl parathion present in the coastal areas may have an impact on urease. This interaction can result in the inhibition of the urease activity of B. pasteurii, thus preventing the biomineralization process. This study would be the first report on the computational approach to understanding the interaction of prominent pesticides on the coastal region and B. pasteurii urease.Communicated by Ramaswamy H. Sarma.

A Study on Bio-Stabilisation of Sub-Standard Soil by Indigenous Soil Urease-Producing Bacteria

Sub-standard soils are of great concern worldwide due to diverse economic losses and the possibility of severe environmental hazards ranging from catastrophic landslides, building collapse, and erosion to loss of lives and properties. This study explored the potential of urease-producing bacteria, <i>Bacillus cereus</i> and <i>Bacillus paramycoides</i>, to stabilise sub-standard soil bio-stabilisation. The maximum urease activity measured by <i>B. cereus</i> and <i>B. paramycoides</i> was 665 U/mL and 620 U/mL, respectively. <i>B. cereus</i> and <i>B. paramycoides</i> precipitated 943 ± 57 mg/L and 793 ± 51 mg/L of CaCO₃ at an optical density (425 nm) of 1.01 and 1.09 and pH 8.83 and 8.59, respectively, after 96 hours of incubation. SEM microstructural analysis of the precipitated CaCO₃ revealed crystals of various sizes (2.0–23.0 µm) with different morphologies. XRD analysis confirmed that the precipitated CaCO₃ comprised calcite and aragonite crystals. SEM analysis of the microstructure of organic and sandy clay soils treated with <i>B. cereus</i> and <i>B. paramycoides</i> showed the formation of bio-precipitated calcium carbonate deposits on the soil particles (biocementing soil grains), with <i>B. cereus</i> precipitating more CaCO₃ crystals with a better biocementing effect compared to <i>B. paramycoides</i>. Overall, the experimental results attributed CaCO₃ formation to bacterial-associated processes, suggesting that soil ureolytic bacteria are potentially useful to stabilise sub-standard soil.

Optimization of biocementation responses by artificial neural network and random forest in comparison to response surface methodology

In this article, the optimization of the specific urease activity (SUA) and the calcium carbonate (CaCO₃) using microbially induced calcite precipitation (MICP) was compared to optimization using three algorithms based on machine learning: random forest regressor, artificial neural networks (ANNs), and multivariate linear regression. This study applied the techniques in two existing response surface method (RSM) experiments involving MICP technique. Random forest-based models and artificial neural network-based models were submitted through the optimization of hyperparameters via cross-validation technique and grid search, to select the best-optimized model. For this study, the random forest-based algorithm is aimed at having the best performance of 0.9381 and 0.9463 in comparison to the original r² of 0.9021 and 0.8530, respectively. This study is aimed at exploring the capability of using machine learning-based models in small datasets for the purpose of optimization of experimental variables in MICP technique and the meaningfulness of the models by their specificities in the small experimental datasets applied to experimental designs. This study is aimed at exploring the capability of using machine learning-based models in small datasets for experimental variable optimization in MICP technique. The use of these techniques can create prerogatives to scale and mitigate costs in future experiments associated to the field.

Use of bacterial binder in repair mortar for micro-crack remediation

Micro-cracks are one of the types of stone deterioration which can propagate and lead to surface detachments and larger cracks in the long run. The present study developed a sustainable and environmentally friendly infill material-biological mortar (BM), as an alternative to conventional approaches. Using a biomineralization approach, this BM was explicitly designed for healing micro-cracks (less than 2 mm) in historic travertines. To this end, the mortar was prepared using a calcifying Bacillus sp. isolated from thermal spring water resources in Pamukkale Travertines (Denizli), stone powder gathered from travertine quarries in the vicinity, and a triggering solution specifically designed to set off calcium carbonate precipitation reaction. After setup, BM was applied to micro-cracks of artificially aged test stones for testing. Scanning electron microscopy revealed calcium carbonate-coated Bacillus sp. bodies in the BM matrix, optical microscopy showed secondary calcite minerals throughout the BM applied micro-cracks, and stereomicroscopy and nanoindentation analyses demonstrated bonding of BM with stone due to microbial calcification activities. Furthermore, BM and original material contact showed a continuous and coherent structure in all samples. Within this context, BM could be considered a promising and alternative approach for the remediation of micro-cracks of historic stones. KEY POINTS: A binder was produced by the MICP of Bacillus sp. Pamukkale. Physical, mineralogical, and nanomechanical characterization demonstrated microbial calcite precipitates in BM. A significant bond was determined between the grains and matrix of BM due to Bacillus sp. calcite production activities.

Evidencing the role of carbonic anhydrase in the formation of carbonate minerals by bacterial strains isolated from extreme environments in Qatar

Calcium carbonate, one of the most abundant minerals in the geological records is considered as primary source of the carbon reservoir. The role of microorganisms in the biotic precipitation of calcium carbonate has been extensively investigated, especially at extreme life conditions. In Qatar, Sabkhas which are microbial ecosystems housing biomineralizing bacteria, have been carefully studied as unique sites of microbial dolomite formation. Dolomite (CaMg(CO₃)₂ is an important carbonate mineral forming oil reservoir rocks; however, dolomite is rarely formed in modern environments. The enzyme carbonic anhydrase is present in many living organisms, performs interconversion between CO₂ and the bicarbonate ion. Thus, carbonic anhydrase is expected to accelerate both carbonate rock dissolution and CO₂ uptake at the same time, serving as carbonite source to carbonites-forming bacteria. This study gathered cross-linked data on the potential role of the carbonic anhydrase excreted by mineral-forming bacteria, isolated from two different extreme environments in Qatar. Dohat Faishakh Sabkha, is a hypersaline coastal Sabkha, from where various strains of the bacterium Virgibacillus were isolated. Virgibacillus can -not only-mediate carbonate mineral formation, but also contributes to magnesium incorporation into the carbonate minerals, leading to the formation of high magnesium calcite. The latter is considered as precursor for dolomite formation. In addition, bacterial strains isolated from marine sediments, surrounding coral reef in Qatar sea, would provide additional knowledge on the role of carbonic anhydrase in mineral formation. Here, the quantification of the two mostly described activities of carbonic anhydrase; esterase and hydration reactions were performed. Mineral-forming strains were shown to exhibit high activities as opposed to the non-forming minerals, which confirms the relation between the presence of active carbonic anhydrase combined with elevated metabolic activity and the biomineralizing potential of the bacterial strains. The highest specific intracellular carbonic anhydrase activity; as both esterase and hydration (i.e., 66 ± 3 and 583000 ± 39000 WAU/10⁸ cells respectively), was evidenced in mineral-forming strains as opposed to non-mineral forming strains (i.e., 6 ±. 0.5 and 1223 ± 61 WAU/10⁸cells) respectively. These findings would contribute to the understanding of the mechanism of microbially mediated carbonate precipitation. This role may be both in capturing CO₂ as source of carbonate, and partial solubilization of the formed minerals allowing incorporation of Mg instead of calcium, before catalyzing again the formation of more deposition of carbonates.

Interaction between indigenous hydrocarbon-degrading bacteria in reconstituted mixtures for remediation of weathered oil in soil

It has been demonstrated that biostimulation is necessary to investigate the interactions between indigenous bacteria and establish an approach for the bioremediation of soils contaminated with weathered oil. This was achieved by adjusting the carbon (C)/nitrogen (N)/phosphorus (P) ratio to 100/10/1 combined with the application of 0.8 mL/kg Tween-80. In addition, three indigenous bacteria isolated from the same soil were introduced solely or combined concomitantly with stimulation. Removal of n-alkanes and the ratios of n-heptadecane to pristane and n-octadecane to phytane were taken to indicate their biodegradation performance over a period of 16 weeks. One strain of Pseudomonas aeruginosa D7S1 improved the efficiency of the process of stimulation. However, another Pseudomonas aeruginosa, D5D1, inhibited the overall process when combined with other bacteria. One strain of Bacillus licheniformis D1D2 did not affect the process significantly. The Fourier transform infrared analysis of the residual hydrocarbons supported the conclusions pertaining to the biodegradation processes when probing the modifications in densities and stretching. The indigenous bacteria cannot mutually benefit from their metabolisms for bioremediation if augmented artificially. However, the strain Pseudomonas. aeruginosa D7S1 was able to perform better alone than in a consortium of indigenous bacteria.

Immobilization of heavy metals by microbially induced carbonate precipitation using hydrocarbon-degrading ureolytic bacteria

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Heavy metal toxicity to hydrocarbon-degrading ureolytic bacteria is Cd > Ni > Cr > Cu > Zn.

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The ureolytic bacteria can tolerate heavy metals and co-precipitate heavy metals.

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The precipitated minerals shifted between calcite and brushite depending on the heavy metal.

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The immobilization of heavy metals resulted in removal efficiency reaching 100%.

Crude oil contamination introduces multiple threats to human health and the environment, most of which are from toxic heavy metals. Heavy metals cause significant threats because of their persistence, toxicity, and bio-accumulation. Biomineralization, performed through many microbial processes, can lead to the immobilization of heavy metals in formed minerals. The potential of the microbially carbonate-induced precipitation (MICP) in removal by biomineralization of several heavy metals was investigated. A collection of diverse 11 bacterial strains exhibited ureolytic activity and tolerance to heavy metals when growing in Luria-Bertani (LB) and urea medium. Determination of the minimum inhibitory concentrations (MIC) revealed that heavy metal toxicity was arranged as Cd > Ni > Cr > Cu > Zn. Three hydrocarbon-degrading bacterial strains (two of Pseudomonas aeruginosa and one of Providencia rettgeri) exhibited the highest tolerance (MIC > 5 mM) to Cu, Cr, Zn, and Ni, whereas Cd exerted significantly higher toxicity with MIC <1 mM. At all MICP conditions, different proportions of calcium carbonate (calcite) and calcium phosphate (brushite) were formed. Pseudomonas aeruginosa strains (QZ5 and QZ9) exhibited the highest removal efficiency of Cr (100%), whereas Providencia rettgeri strain (QZ2) showed 100% removal of Zn. Heavy metal complexes were found as well. Cd removal was evidenced by the formation of cadmium phosphate induced by Providencia rettgeri bacterial activity. Our study confirmed that hydrocarbon-degrading ureolytic bacteria not only can tolerate heavy metal toxicity but also have the capability to co-precipitate heavy metals. These findings indicate an effective and novel biological approach to bioremediate petroleum hydrocarbons and immobilize multiple heavy metals with mineral formation. This is of high importance for ecological restoration via stabilization of soil and alleviation of heavy metal toxicity.

Research status and development of microbial induced calcium carbonate mineralization technology

In nature, biomineralization is a common phenomenon, which can be further divided into authigenic and artificially induced mineralization. In recent years, artificially induced mineralization technology has been gradually extended to major engineering fields. Therefore, by elaborating the reaction mechanism and bacteria of mineralization process, and summarized various molecular dynamics equations involved in the mineralization process, including microbial and nutrient transport equations, microbial adsorption equations, growth equations, urea hydrolysis equations, and precipitation equations. Because of the environmental adaptation stage of microorganisms in sandy soil, their reaction rate in sandy soil environment is slower than that in solution environment, the influencing factors are more different, in general, including substrate concentration, temperature, pH, particle size and grouting method. Based on the characteristics of microbial mineralization such as strong cementation ability, fast, efficient, and easy to control, there are good prospects for application in sandy soil curing, building improvement, heavy metal fixation, oil reservoir dissection, and CO₂ capture. Finally, it is discussed and summarized the problems and future development directions on the road of commercialization of microbial induced calcium carbonate precipitation technology from laboratory to field application.

Relationship between Bacterial Contribution and Self-Healing Effect of Cement-Based Materials

The civil research community has been attracted to self-healing bacterial-based concrete as a potential solution in the economy 4.0 era. This concept provides more sustainable material with a longer lifetime due to the reduction of crack appearance and the need for anthropogenic impact. Regardless of the achievements in this field, the gap in the understanding of the importance of the bacterial role in self-healing concrete remains. Therefore, understanding the bacterial life cycle in the self-healing effect of cement-based materials and selecting the most important relationship between bacterial contribution, self-healing effect, and material characteristics through the process of microbiologically (bacterially) induced carbonate precipitation is just the initial phase for potential applications in real environmental conditions. The concept of this study offers the possibility to recognize the importance of the bacterial life cycle in terms of application in extreme conditions of cement-based materials and maintaining bacterial roles during the self-healing effect.

Application of MALDI-TOF MS for identification of environmental bacteria: A review

Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.

Multiple fouling dynamics, interactions and synergistic effects in brackish surface water distribution systems

Dissolved salts, colloidal particles, and active microorganisms in brackish surface water distribution systems (BSWD) cause multiple fouling, poses potential threat to the environmental pollution, and raising technical and economic issues as well. So far, the co-occurrence and interactions of multiple fouling remains largely unknown. Multiple fouling behaviors were assessed in agriculture BSWD under different nitrogen (N) fertilizers. X-ray diffraction, Rietveld refinement analysis, 16S rRNA, and microbial network analysis were conducted to determine the fouling characteristics. Statistical analysis was applied to reveal the relative contributions and interaction of multiple fouling. Our results demonstrated, multiple fouling of precipitates, particulates and biofoulings were co-occurred. Fouling growth was largely attributed to the strong interactions of different fouling. The binary interactions of precipitates - particulates contributed 51.1%, and ternary interactions of precipitates - particulates - biofouling contributed 25.4% to explain the decline of system performance, while the contribution of each single type fouling was minimal. Thereby indicating the significant role of calcium silica, biomineralization and bio-silicates in fouling. The lower acid N fertilizer broken the interaction of multiple fouling by increasing the precipitate crystal parameters and repulsive forces amongst particulates, as well as destroyed microbial interactions in biofouling. Overall, this study open frontier for multiple fouling in-depth profiling and antifouling guidance for effective utilization of BSWD.

Comprehensive Profiling of Microbiologically Induced CaCO3 Precipitation by Ureolytic Bacillus Isolates from Alkaline Soils

Microbiologically induced CaCO3 precipitation (MICP) is a well-known bio-based solution with application in environmental, geotechnical, and civil engineering. The significance of the MICP has increased explorations of process efficiency and specificity via natural bacterial isolates. In this study, comprehensive profiling of five soil ureolytic Bacillus strains was performed through a newly formed procedure that involved six steps from selection and identification, through kinetic study, to the characterization of the obtained precipitates, for the first time. To shorten the whole selection procedure of 43 bioagents with the MICP potential, Standard Score Analysis was performed and five selected bacteria were identified as Bacillus muralis, B. lentus, B. simplex, B. firmus, and B. licheniformis by the MALDI-TOF mass spectrometry. Despite following the targeted activity, kinetic studies were included important aspects of ureolysis and the MICP such as cell concentration, pH profiling, and reduction in calcium ion concentration. At the final step, characterization of the obtained precipitates was performed using FTIR, XRD, Raman, DTA/TGA, and SEM analysis. Although all tested strains showed significant potential in terms of precipitation of calcite or calcite and vaterite phase, the main differences in the MICP behavior can be observed at the bacterial strain level. B. licheniformis showed favorable behavior compared to the reference Sporosarcina pasteurii DSM 33.

Ground improvement using chemical methods: A review

Ground improvement will be critically important in the present and future geotechnical practice for designing the structures in weak soil. This paper presents a review of the recent development in ground improvement techniques, especially chemical stabilisers. Various available chemical stabilisers are identified and compared with other available methods. Though the use of chemicals provides an excellent alternative to the traditional methods, they still lack proper understanding regarding their use, handling, application, and long-term effect on the environment. Various chemical stabilisers and their applicability conditions are summarised in the present paper. Insight of biochemical, electrochemical, inorganic, and organic stabilisers is presented with future scope of these methods along with the potential areas where a lot of efforts is needed to industrialise these methods are also discussed briefly. A need for developing a more environmentally friendly and safe method was felt while reviewing these methods. Lack of a large amount of data is a major concern for lesser use of these methods industrially. A lot of laboratory and field experiments should be conducted in different conditions to ensure safe results from chemical stabilisers.

Potential for native hydrocarbon-degrading bacteria to remediate highly weathered oil-polluted soils in Qatar through self-purification and bioaugmentation in biopiles

Petroleum-derived contamination events constitute a unique environmental issue in the arid areas because of the weathering processes, accentuated due to harsh conditions and representing the main origin of failure of bioremediation applications. The industrial area of Dukhan and the AlZubara coast represent wethered oily-sites as an appropriate model due to the extreme weather, which characterizes Qatar. Indigenous bacteria would be highly adapted and when re-introduced or stimulated would conduct to the remediation of these sites. An appropriate approach to bioremediating-weathered oil was investigated in these two areas. Systematic soil sampling was performed, and the soil samples were analyzed. The results clearly showed the harsh chemical compositions (high salinity and contents of total petroleum components contents in the range of the oil organics). By implementation of a procedure of isolation of highly adapted bacteria, few hydrocarbon-degrading bacteria were isolated in the objective of selecting those for further application. Their identification by ribotyping showed dominance of Bacillus and Virgibacillus in AlZubara site, and Bacillus and Pseudomonas in Dukhan site. All bacterial strains were highly tolerant to 10 % diesel and showed potential of removal of 20 %-85 % of C 10 to C 36 hydrocarbons. This potential was confirmed by determination of the n-heptadecane/pristane and n-octadecane/phytane ratios, indicating in turn their potential to bioremediate oil. This was demonstrated by comparison of the self-remediation to bioaugmentation using two selected Bacillus and Pseudomonas strains using Dukhan soil in biopiles. These strains when biostimulted in such a soil increased the removal of total petroleum components to 53 % compared to 30 % with self-purification, after 90 d. The results indicated that highly adapted endogenous bacteria might be used to bioremediate highly weathered oil-contaminated soil under harsh conditions.

Functionalization of reverse osmosis membrane with graphene oxide and polyacrylic acid to control biofouling and mineral scaling

The polyamide reverse osmosis (RO) membrane was modified with graphene oxide (GO), followed by polymerization of acrylic acid (used as an antiscalant) for the reduction of both biofouling and mineral scaling. After functionalization, the water contact angle reduced from 41.7 ± 4.5° for unmodified RO membrane to 24.4 ± 1.3° for the modified RO membranes, which showed that membrane hydrophilicity was significantly enhanced, in addition to the improvement in surface smoothness. The modified membranes were tested for their anti-scaling and anti-biofouling characteristics. When the mineral scaling test was performed using CaSO₄ solution as feedwater, the permeate flux was reduced by only 3% as compared to the unmodified RO membrane which encountered up to 22% decline in flux by the end of the experiment. After the scaling test, the membrane surface was characterized by Scanning electron microscopy - energy-dispersive X-ray spectroscopy, Fourier transform infrared, and X-ray diffraction techniques. The results showed that the unmodified RO membrane was fully covered with gypsum precipitates. Whereas, the precipitates were detected only at the highly saturated zones of the water channel i.e. towards the exit of water flow. Additionally, the anti-bacterial test was performed through bacteriostasis rate determination, which showed that the modified membranes inhibited the growth of nearly 95% of the bacterial cells. Further experiments were also performed to investigate the inhibition of both scaling and biofouling by modified RO membranes. Thus, it was found that the polymer-modified GO coated RO membranes were able to diminish both gypsum scaling and biofilm formation demonstrating their potential to control different types of membrane fouling.

Microbially induced calcite precipitation in calcareous soils by endogenous Bacillus cereus, at high pH and harsh weather

Microbially induced calcite precipitation (MICP) improves the physical properties of soils by increasing the solid content, decreasing the pore sizes and improving the rigidity of the particle-to-particle contact ending with a better mechanical and geotechnical performances of the soils. First, the physical characteristics of soils in Qatar showed similar grain size distributions with most falling in the category of fine particles (30 μm-1 μm), which is appropriate for MICP processes. MICP is ensured by the ureolytic activity of urease producing bacteria. However, Qatari soils are characterized with high carbonate contents exceeding 20%, high alkalinity and fluctuations of temperature and aeration. Although such properties can cause calcite dissolution as reported in literature, two Qatari endogenous B. cereus strains, QBB4 and QBB5, were shown able to adapt to the harsh conditions and induce mineral formations by MICP. Their optimal potentials was at wide ranges of temperature from 30 °C to 42 °C and pH from 7.0 to 8.0. Using Qatari bacteria in liquid cultures and at syringe level at laboratory conditions, as well as in plots at field conditions, 16% CaCO₃ increase in minerals formation was obtained, leading to 7% increase of soils stability. Increase of carbonate contents was also shown by an increase in the stability of aggregates to disintegration when incubated in water using a 0.25 mm sieve. MICP in Qatari soils is feasible using B. cereus QBB4, as this is an endogenous bacterium that tolerates harsh conditions, high alkalinity and calcium contents. The performance of these bacterial strains was achieved with clear formation of aragonite, feldspars and quartz in the calcareous soils.

The use of principle component analysis and MALDI-TOF MS for the differentiation of mineral forming Virgibacillus and Bacillus species isolated from sabkhas

Occurrence of mineral forming and other bacteria in mats is well demonstrated. However, their high diversity shown by ribotyping has not been explained, although it could explain the diversity of formed minerals. Common biomarkers as well as phylogenic relationships are useful tools for clustering the isolates and the prediction of their potential role in the natural niche. In this study, a combination of MALDI-TOF MS with PCA was shown to be a powerful tool to categorize 35 mineral forming bacterial isolates isolated from Dohat Faishakh sabkha, northwest of Qatar (23 from decaying mats and 12 from living ones). The 23 strains from decaying mats belong to the Virgibacillus genus as identified by ribotyping and are shown to be highly involved in the formation of protodolomite and a diversity of minerals. They were used as internal references for the categorization of sabkha bacteria. Combination of the isolation of bacteria on selective mineral forming media, their MALDI TOF MS protein profiling and PCA analysis established their relationship in a phylloproteomic dendrogram based on protein biomarkers including m/z 4905, 3265, 5240, 6430, 7765, and 9815. PCA analysis clustered the studied isolates into 3 major clusters, showing strong correspondence to the 3 phylloproteomic groups that were established by the dendrogram. Both clustering analysis means have evidently demonstrated a relationship between known Virgibacillus strains and other related bacteria based on profiling of their synthesized proteins. Thus, larger populations of bacteria in mats can be easily screened for their potential to exhibit certain activities, which is of ecological, environmental and biotechnological significance.

Occurrence of mineral forming and other bacteria in mats is well demonstrated.

Microbially Induced Carbonate Precipitation Using Microorganisms Enriched from Calcareous Materials in Marine Environments and Their Metabolites

Microbially induced Ca-carbonate precipitation (MICP) in general, refers to a process in which the urease secreted by microbes hydrolyzes urea to ammonium and carbon dioxide. The main objectives of this study were to identify the environmental factors (e.g., microbial growth, cell/metabolite presences, and calcium sources) that control Ca-carbonate formation and to investigate the mineralogical characteristics of the Ca-carbonate precipitated using ureolytic microorganisms cultured in marine environments. The two types of carbonate-forming microorganisms (CFMs), mixed cultures hydrolyzing urea, were enriched from calcareous materials in marine environments. The experiments using a CFM, Sporosarcina pasteurii, was also used for comparison. All the microbes were cultured aerobically in D-1 growth media that included urea. To investigate the effect of microbial growth states on Ca-carbonate precipitation, Ca-acetate was injected into the media before (i.e., lag phase) and after (i.e., stationary phase) microbial growth, and into the soluble microbial products (SMP) solution, respectively. XRD, FT-IR, and SEM-EDS analyses were used for mineralogical characterization of the precipitated Ca-carbonates. Results indicated that the Ca-carbonates, vaterite and/or calcite, precipitated under all the experimental conditions. The fastest precipitation of Ca-carbonates occurred in the SMP solution and formed calcite (size = 5–15 μm). When the concentrations of added Ca-acetate were varied from 0 to 0.5 M, the highest amounts of calcite, 22.8 g/L, were produced when 0.3 M Ca-acetate was injected. Therefore, the environmental factors (e.g., microbial growth, cell/metabolite presences, and calcium sources) could have an effect the rate of formation of Ca-carbonate and the types of carbonate minerals formed. Moreover, the use of cell-free SMP solution is expected to be applicable to Ca-carbonate precipitation in an environment where microbial growth is unfavorable.

Identification and overcome of limitations of weathered oil hydrocarbons bioremediation by an adapted Bacillus sorensis strain

Because of the high production of oil and gas in Qatar, the likelihood of oil spill occurrence is most probably susceptible to happen. Contaminated soil treatment is very expensive. Cost effective mechanisms are investigated to treat this threatening issue. For that reason, bioremediation and biotechnology tools are introduced to help accelerate and remove the pollution caused by the contamination process. This paper demonstrated the importance of optimising the treatment conditions to the indigenous bacterial strain to obtain the highest biodegradation efficiency rates. The usage of biopile system technology was used with biostimulation and bioaugmentation processes. The indigenous Bacillus sonorensis (B. sonorensis) D1 bacterium played a crucial role in the biodegradation process when introduced to optimized conditions; carbon/nitrogen/phosphorus (C/N/P) (100/10/1), temperature (37 °C), surfactant tween 80 (0.12% (v/w)), and moisture (10%). Gas chromatography (mass spectrometry/flame ionization detector) (GC- (MS/FID)), Fourier transform infrared (FTIR), and colony-forming unit (CFU) analyses were performed. The diesel range organics (DRO) and polycyclic aromatic hydrocarbons (PAH) removal (%) of the weathered oil contaminated soil reached, after 160 days, 39.2% and 32.4% simultaneously when ammonium nitrate was used as a nitrogen source. Whereas urea inhibited the oil degradation process and caused the pH to rise to 9.55.

Potential of mercury-tolerant bacteria for bio-uptake of mercury leached from discarded fluorescent lamps

In this study, ten bacterial strains were found to be mercury resistant after their isolation from Qatari coastal sediments. Tolerance was found to be up to 100-150 ppm for five strains. Those strains had optimum growth conditions at salinity level of 10 ppm NaCl and pH 7-8. Starting from a concentration 7.9 ppm of mercury extracted from fluorescent lamps and after 6 days of incubation at 37 °C, two isolated strains HA6 (Bacillus spp.) and HA9 (Acinetobacter sp.) showed 96.7% and 98.9% of mercury bio-uptake efficiency, respectively. Other strains were capable of removing more than 60% of extracted mercury.

Isolation, identification and biodiversity of antiscalant degrading seawater bacteria using MALDI-TOF-MS and multivariate analysis

Seawater reverse osmosis (SWRO) is a commonly used desalination technique owing to its lesser environmental and economic impacts as compared to thermal desalination techniques. Antiscalants are used in SWRO to reduce membrane scaling caused by the supersaturation of salts present in feed water. However, to remain effective in reducing membrane scaling, antiscalants should be highly stable and resistant to biological degradation by seawater microorganisms. In this research, several bacteria from Qatar's seawater were isolated and screened for their ability to use antiscalants as a carbon and energy source. The biodiversity of antiscalant degrading seawater bacteria was demonstrated through combining the techniques of MALDI-TOF MS and principle component analysis. It was found that the bacteria isolated from Qatar's seawater such as H. aquamarina, H. elongata, P. fragi, P. stutzeri and others can degrade antiscalants and use them as a carbon and energy source. It was observed that the growth rates varied based on the type of antiscalant and the bacteria used. Among the tested strains, H. aquamarina, which is also known for its potential to cause biofouling, demonstrated the highest growth rates in antiscalants media. Thus, it was concluded that there is wide variety of bacteria in Qatar's seawater that can biodegrade the antiscalants; reducing their efficiency to combat membrane scaling. Since, these antiscalants will be used as a source of carbon and energy, microbial growth will increase resulting in enhanced membrane biofouling in SWRO.

Effects of different calcium sources on the mineralization and sand curing of CaCO3 by carbonic anhydrase-producing bacteria

The deposition and dissolution of calcium carbonate can be affected by the action of biological factors, such as microbial-induced carbonate precipitation (MICP).