Isolation and Potential Biocementation of Calcite Precipitation Inducing Bacteria from Colombian Buildings

Bhargavaea beijingensis a promising tool for bio-cementation, soil improvement, and mercury removal

Microbially Induced Calcite Precipitation (MICP) has emerged as a promising technique for bio-cementation, soil improvement, and heavy metal remediation. This study explores the potential of Bhargavaea beijingensis, a urease-producing bacterium, for these applications. Six ureolytic bacteria were isolated from calcareous bricks mine soil and screened for urease and calcite production. B. beijingensis exhibited the highest urease activity and calcite precipitation. Urease activity, calcite precipitation, sand solidification, heavy metal removal efficiency, and compressive strength were evaluated. It showed significant heavy metal removal efficiency, particularly highest for HgCl2. Mortar blocks treated with B. beijingensis or its crude enzyme exhibited improved compressive strength, suggesting its potential for bio-cementation. Crack remediation tests demonstrated successful crack healing in mortar blocks using the bacterium or its enzyme. This study identifies B. beijingensis as a novel and promising MICP agent with potential applications in bio-cementation, soil improvement, and heavy metal remediation. Hence, B. beijingensis diversified abilities prove superior performance compared to commonly used strains like Bacillus subtilis and Shewanella putrefaciens in bio-cementation applications. Its high urease activity, calcite precipitation, and heavy metal removal abilities make it a valuable candidate for sustainable and eco-friendly solutions in various fields.

Microbially Induced Calcium Carbonate Precipitation Using Lysinibacillus sp.: A Ureolytic Bacterium from Uttarakhand for Soil Stabilization

Microbially induced calcium carbonate precipitation (MICP) is a soil remediation method that has emerged as a viable and long-term solution for enhancing soil mechanical qualities. The technique of MICP that has been extensively researched is urea hydrolysis, which occurs naturally in the environment by urease-producing bacteria as part of their fundamental metabolic processes. The objectives of the current study include screening and identifying native ureolytic bacteria from soil in Uttarakhand, optimizing growth factors for increased urease activity, and calcite precipitation by the bacteria using response surface methodology. Additionally, it was assessed how well the isolated bacteria in the medium biomineralized when using synthetic media and cheaper alternatives such as cow urine and eggshell as sources of urea and Ca2+, respectively. The isolated strain identified as Lysinibacillus sp. was found to be the very active strain after soil samples were screened for ureolytic bacteria. It was discovered that optimization studies with values of pH 8, urea concentration (0.8 M), inoculum concentration (3%), and incubation time (48 h) yielded a higher activity of 33.7 U/mL (threefold increase), and a higher calcium carbonate precipitation (enzyme activity: 10.96 U/mL, pH: 8.92, soluble Ca2⁺: 25.53 mM and insoluble Ca2⁺: 0.856 g). The calcite precipitation in broth media supplemented with ready-made substrates and alternative sources demonstrated a similar result of increased pH and ammonia release. Thus, the current study successfully paves the way for several possibilities to stabilize the slopy soils prone to landslides and erosion in Uttarakhand and pinpoint an economic approach through biomineralization.

Comparison of calcium carbonate production by bacterial isolates from recycled aggregates

The new technology of microbially induced calcium carbonate precipitation (MICP) has been applied in construction materials as a strategy to enhance their properties. In pursuit of solutions that are more localized and tailored to the study's target, this work focused on isolating and selecting bacteria capable of producing CaCO3 for posterior application in concrete aggregates. First, eleven bacterial isolates were obtained from aggregates and identified as genera Bacillus, Lysinibacillus, Exiguobacterium, and Micrococcus. Then, the strains were compared based on the quantity and nature of calcium carbonate they produced using thermogravimetric analysis, X-ray diffraction, and scanning electron microscopy with energy dispersive spectroscopy. Bacillus sp. dominated the cultured isolates and, along with Lysinibacillus sp., exhibited the highest CaCO3 conversion (up to 80%). On the other hand, Exiguobacterium and Micrococcus genera showed the poor ability to MICP (21.3 and 20.3%, respectively). Calcite and vaterite were the dominant carbonate polymorphs, with varying proportions. Concrete aggregates have proven to be a source of microorganisms capable of producing stable calcium carbonates with a high conversion rate. This indicates the feasibility of using microorganisms derived from local sources for application in construction materials as a sustainable way to enhance their characteristics.

Potential use of two Serratia strains for cadmium remediation based on microbiologically induced carbonate precipitation and their cadmium resistance

Cadmium (Cd) presence and bioavailability in soils is a serious concern for cocoa producers. Cocoa plants can bioaccumulate Cd that can reach humans through the food chain, thus posing a threat to human health, as Cd is a highly toxic metal. Currently, microbiologically induced carbonate precipitation (MICP) by the ureolytic path has been proposed as an effective technique for Cd remediation. In this work, the Cd remediation potential and Cd resistance of two ureolytic bacteria, Serratia sp. strains 4.1a and 5b, were evaluated. The growth of both Serratia strains was inhibited at 4 mM Cd(II) in the culture medium, which is far higher than the Cd content that can be found in the soils targeted for remediation. Regarding removal efficiency, for an initial concentration of 0.15 mM Cd(II) in liquid medium, the maximum removal percentages for Serratia sp. 4.1.a and 5b were 99.3% and 99.57%, respectively. Their precipitates produced during Cd removal were identified as calcite by X-ray diffraction. Energy dispersive X-ray spectroscopy analysis showed that a portion of Cd was immobilized in this matrix. Finally, the presence of a partial gene from the czc operon, involved in Cd resistance, was observed in Serratia sp. 5b. The expression of this gene was found to be unaffected by the presence of Cd(II), and upregulated in the presence of urea. This work is one of the few to report the use of bacterial strains of the Serratia genus for Cd remediation by MICP, and apparently the first one to report differential expression of a Cd resistance gene due to the presence of urea.

Environmental Drivers of the Moonmilk Microbiome Diversity in Some Temperate and Tropical Caves

Moonmilk is a cave deposit that was used for medical and cosmetic purposes and has lately raised interest for its antimicrobial potential. We studied five moonmilk samples from four caves with different microclimatic conditions, two temperate in north-western and northern Romania (Ferice, Fața Apei, and Izvorul Tăușoarelor caves) and one tropical in Minas Gerais, Brazil (Nestor Cave). The physicochemical and mineralogical analyses confirmed the presence of calcite and dolomite as the main phase in the moonmilk. A 16S rRNA gene-based metabarcoding approach showed the most abundant bacteria phyla Proteobacteria, GAL15, Actinobacteriota, and Acidobacteriota. The investigated caves differed in the dominant orders of bacteria, with the highest distance between the Romanian and Nestor Cave samples. Climate and, implicitly, the soil microbiome can be responsible for some differences we found between all the samples. However, other factors can be involved in shaping the moonmilk microbiome, as differences were found between samples in the same cave (Ferice). In our five moonmilk samples, 1 phylum, 70 orders (~ 36%), and 252 genera (~ 47%) were unclassified, which hints at the great potential of cave microorganisms for future uses.

Isolation of urease-producing bacteria from cocoa farms soils in Santander, Colombia, for cadmium remediation

Cadmium (Cd) is a toxic heavy metal that causes serious health problems and is present in agriculturally important soils in Colombia, such as the ones used for cocoa farming. Recently, the use of ureolytic bacteria by the Microbiologically Induced Carbonate Precipitation (MICP) activity has been proposed as an alternative to mitigate the availability of Cd in contaminated soils. In this study, 12 urease-positive bacteria able to grow in the presence of Cd(II) were isolated and identified. Three were selected based on urease activity, precipitates formation and growth, with two belonging to the genus Serratia (codes 4.1a and 5b) and one to Acinetobacter (code 6a). These isolates exhibited low urease activity levels (3.09, 1.34 and 0.31 μmol mL-1 h-1, respectively), but could raise the pH to values close to 9.0 and to produce carbonate precipitates. It was shown that the presence of Cd affects the growth of the selected isolates. However, urease activity was not negatively influenced. In addition, the three isolates were observed to efficiently remove Cd from solution. The two Serratia isolates presented maximum removals of 99.70% and 99.62%, with initial 0.05 mM Cd(II) in the culture medium (supplemented with urea and Ca(II)) at 30 °C and 144 h of incubation. For the Acinetobacter isolate, the maximum removal was 91.23% at the same conditions. Thus, this study evidences the potential use of these bacteria for bioremediation treatments in samples contaminated with Cd, and it is one of the few reports that shows the high cadmium removal capacity of bacteria from the genus Serratia.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03495-1.

Pedosedimentary and microbial investigation of a karst sequence record

A 3-m thick sediment sequence, found in a limestone mine located in the south of Italy at a depth of ca. 25-30 m from the current ground level, was investigated. Samples from 5 layers were analysed by X-ray diffraction, elemental analysis, Inductively Coupled Plasma Mass Spectrometry and micromorphology. Microbial DNA was analysed by 16S rRNA gene metabarcoding. The main mineral compounds found in the 5 layers were calcite (70-80%) and clay minerals in layers #1 and #5, goethite (75%) and hematite in layer #2, manganese (66%) and iron oxides in layer #3, and almost exclusively goethite in layer #4. Micromorphology data allowed to shed light in understanding whether these sediments formed by subsequent weathering of carbonates and silicates or by migration of soil sediments from the surface, or also by the accumulation of shallow marine sediments occurring between the middle Pliocene and the lower Pleistocene, when the extreme western sector of this area underwent strong subsidence. From the microbiological point of view, upon the 16S rRNA gene analysis, these 5 layers appear to cluster in three groups. Overall, such a distribution suggests that, both in the top (#1) and in bottom layers (#4 and #5), different communities would have undergone in situ reproduction and colonization exploiting metabolically the substrate, whereas the two mid layers would have received bacterial convection by passive transport of percolating waters. At the same time, micromorphological data show that each layer preserved its distinct features to be related to the environmental condition at the time of deposition. The chemical, mineralogical and micromorphological features of the layers and the known physiology of the microbial taxa thereby encountered highlight the possible role of the latter in elucidating the occurrence of certain mineral species as well as the biogeochemistry of elements like Mn and Fe in sediment layers.

Isolation, Screening and Characterization of Ureolytic Bacteria from Cave Ornament

<b>Background and Objective:</b> Ureolytic bacteria are bacteria capable of hydrolyzing urea. In construction, these bacteria are known to help improve soil stability. One of the habitats of ureolytic bacteria is cave ornaments such as gourdam, flowstone, stalagmite and stalactite. This study aims to find isolates and characterization of ureolytic bacteria in cave ornaments. <b>Materials and Methods:</b> Urea-CaCl<sub>2</sub> was used as the isolation medium and urea agar medium was used as a qualitative urease test for cave ornament bacteria isolate. This study applied a survey method and tested for gram staining, spore staining, mannitol test, catalase test and lactose test for characterization. <b>Results:</b> There were 17 isolates positive for urease from 30 isolates from the isolates of cave ornament bacteria. The characteristics of 17 ureolytic bacteria isolates were 2 isolates gram-negative basil with negative lactose test and 1 isolate positive glucose and 1 isolate negative glucose. Total 15 isolates gram-positive basil with spore staining results, 14 isolates spore-positive with 2 isolates positive mannitol and 12 isolates negative mannitol and 1 isolate spore-negative with negative catalase. <b>Conclusion:</b> Total 17 ureolytic bacteria isolates were found from cave ornaments. Biochemical characterization showed 1 isolate of <i>Proteus</i> spp., 1 isolate of <i>Pseudomonas</i> spp, 2 isolates suspected of being <i>Bacillus megaterium</i> or <i>Bacillus subtilis</i>, 12 isolates of <i>Bacillus cereus</i> and 1 isolate of <i>Lactobacillus</i> spp.

Study of the Behavior of Structural Materials Treated with Bioconsolidant

In this article, the effectiveness of the bioconsolidation technique applied to degraded structural materials is illustrated as a new method of consolidation and conservation of the existing building heritage in a less invasive way. Satisfactory results have been obtained by an experimental campaign carried out through non-destructive diagnostic tests, static destructive mechanical tests, and microstructural analyses on a series of natural stone material specimens and artificial stone materials before and after the use of bioconsolidants. The consolidated specimens have been tested after three to four weeks after the application of the M3P nutritional solution on each specimen. The effect on the microstructure of this technique has also been observed using scanning electron microscope and optical photomicrograph, the formation of new calcium carbonate crystals promoting the structural consolidation of the materials under examination was observed in all the specimens analyzed.

Bioconservation of Historic Stone Buildings—An Updated Review

Cultural heritage buildings of stone construction require careful restorative actions to maintain them as close to the original condition as possible. This includes consolidation and cleaning of the structure. Traditional consolidants may have poor performance due to structural drawbacks such as low adhesion, poor penetration and flexibility. The requirement for organic consolidants to be dissolved in volatile organic compounds may pose environmental and human health risks. Traditional conservation treatments can be replaced by more environmentally acceptable, biologically-based, measures, including bioconsolidation using whole bacterial cells or cell biomolecules; the latter include plant or microbial biopolymers and bacterial cell walls. Biocleaning can employ microorganisms or their extracted enzymes to remove inorganic and organic surface deposits such as sulfate crusts, animal glues, biofilms and felt tip marker graffiti. This review seeks to provide updated information on the innovative bioconservation treatments that have been or are being developed.

Calcifying Bacteria Flexibility in Induction of CaCO3 Mineralization

Microbially induced CaCO₃ precipitation (MICP) is considered as an alternative green technology for cement self-healing and a basis for the development of new biomaterials. However, some issues about the role of bacteria in the induction of biogenic CaCO₃ crystal nucleation, growth and aggregation are still debatable. Our aims were to screen for ureolytic calcifying microorganisms and analyze their MICP abilities during their growth in urea-supplemented and urea-deficient media. Nine candidates showed a high level of urease specific activity, and a sharp increase in the urea-containing medium pH resulted in efficient CaCO₃ biomineralization. In the urea-deficient medium, all ureolytic bacteria also induced CaCO₃ precipitation although at lower pH values. Five strains (B. licheniformis DSMZ 8782, B. cereus 4b, S. epidermidis 4a, M. luteus BS52, M. luteus 6) were found to completely repair micro-cracks in the cement samples. Detailed studies of the most promising strain B. licheniformis DSMZ 8782 revealed a slower rate of the polymorph transformation in the urea-deficient medium than in urea-containing one. We suppose that a ureolytic microorganism retains its ability to induce CaCO₃ biomineralization regardless the origin of carbonate ions in a cell environment by switching between mechanisms of urea-degradation and metabolism of calcium organic salts.

Bacterial Diversity Evolution in Maya Plaster and Stone Following a Bio-Conservation Treatment

To overcome the limitations of traditional conservation treatments used for protection and consolidation of stone and lime mortars and plasters, mostly based on polymers or alkoxysilanes, a novel treatment based on the activation of indigenous carbonatogenic bacteria has been recently proposed and applied both in the laboratory and in situ. Despite very positive results, little is known regarding its effect on the evolution of the indigenous bacterial communities, specially under hot and humid tropical conditions where proliferation of microorganisms is favored, as it is the case of the Maya area. Here, we studied changes in bacterial diversity of severely degraded tuff stone and lime plaster at the archeological Maya site of Copan (Honduras) after treatment with the patented sterile M-3P nutritional solution. High-throughput sequencing by Illumina MiSeq technology shows significant changes in the bacterial population of the treated stones, enhancing the development of Arthrobacter, Micrococcaceae, Nocardioides, Fictibacillus, and Streptomyces, and, in one case, Rubrobacter (carved stone blocks at Structure 18). In the lime plaster, Arthrobacter, Fictibacillus, Bacillus, Agrococcus, and Microbacterium dominated after treatment. Most of these detected genera have been shown to promote calcium carbonate biomineralization, thus implying that the novel bio-conservation treatment would be effective. Remarkably, the treatment induced the reduction or complete disappearance of deleterious acid-producing bacteria such as Marmoricola or the phylum Acidobacteria. The outcome of this study demonstrates that such a bio-conservation treatment can safely and effectively be applied on temples, sculptures and stuccos of the Maya area and, likely, in other hot and humid environments.

Insights into the Current Trends in the Utilization of Bacteria for Microbially Induced Calcium Carbonate Precipitation

Nowadays, microbially induced calcium carbonate precipitation (MICP) has received great attention for its potential in construction and geotechnical applications. This technique has been used in biocementation of sand, consolidation of soil, production of self-healing concrete or mortar, and removal of heavy metal ions from water. The products of MICP often have enhanced strength, durability, and self-healing ability. Utilization of the MICP technique can also increase sustainability, especially in the construction industry where a huge portion of the materials used is not sustainable. The presence of bacteria is essential for MICP to occur. Bacteria promote the conversion of suitable compounds into carbonate ions, change the microenvironment to favor precipitation of calcium carbonate, and act as precipitation sites for calcium carbonate crystals. Many bacteria have been discovered and tested for MICP potential. This paper reviews the bacteria used for MICP in some of the most recent studies. Bacteria that can cause MICP include ureolytic bacteria, non-ureolytic bacteria, cyanobacteria, nitrate reducing bacteria, and sulfate reducing bacteria. The most studied bacterium for MICP over the years is Sporosarcina pasteurii. Other bacteria from Bacillus species are also frequently investigated. Several factors that affect MICP performance are bacterial strain, bacterial concentration, nutrient concentration, calcium source concentration, addition of other substances, and methods to distribute bacteria. Several suggestions for future studies such as CO₂ sequestration through MICP, cost reduction by using plant or animal wastes as media, and genetic modification of bacteria to enhance MICP have been put forward.

Differential colonization of microbial communities inhabiting Lede stone in the urban and rural environment

Air pollution is one of the main actors of stone deterioration. It influences not only the material itself but also prokaryotes colonizing rocks. Prokaryotes can affect rock substrates and biological colonization will most likely become relatively more important during the course of the 21st century. Therefore, it is necessary to understand the effects of air pollution on biological colonization and on the impact of this colonization on rock weathering. For this reason, we studied the prokaryotic community of Lede stone from two deteriorated monuments in Belgium: one in the urban and one in the rural environment. This research conducts 16S rRNA gene Next Generation Sequencing combined with an isolation campaign. It revealed diverse and complex prokaryotic communities with more specialized bacteria present in the urban environment, while archaea were barely detected. Some genera could cause biodeterioration but the isolates did not produce a significant amount of acid. Soluble salts analysis revealed an important effect of salts on the prokaryotic community. Colour measurements at least indicate that a main effect of prokaryotes might be on the aesthetics: In the countryside prokaryotic communities seemed to discolour Lede stone, while pollution most likely blackened building stones in the urban environment.

AISLAMIENTO E IDENTIFICACIÓN DE Lactobacillus spp. (LACTOBACILLACEAE) RESISTENTES A Cd(II) Y As(III) RECUPERADOS DE FERMENTO DE CACAO

El objetivo de este estudio fue aislar e identificar a partir de cacao fermentado en Caldas Colombia, bacterias con potencial de aplicación en procesos biotecnológicos, como la detoxificación de cadmio (Cd(II)) y arsénico (As(III)) en el organismo humano. En total se recuperaron 36 aislados de los cuales se recuperaron 11 en presencia de 1,0 mg/L de Cd(II) y 25 en presencia de 0,1 mg/L de As(III). Su identificación molecular determinó que la mayoría de los aislados son del género Lactobacillus. Los ensayos de crecimiento en presencia de diferentes concentraciones de los elementos evaluados permitió determinar que gran parte de los aislamientos presentan resistencia a mayores concentraciones de As(III) (300 mg/L) que de Cd(II) (10 mg/L). En ensayos de tolerancia a la acidez (pH 2,5) se encontró que la cepa tipo Lactobacillus plantarumJCM 1055, junto con los aislamientos nativos L. plantarumA19, A26 y C16, mostraron la mayor tolerancia, por lo que se seleccionaron para evaluar su tolerancia a condiciones de salinidad. Las bacterias evaluadas mostraron crecimiento en concentraciones de hasta 4 g/L de sales biliares. Se concluye que los L. plantarumevaluados en este trabajo tienen un gran potencial para futuros ensayos en los que se busque demostrar la disminución de la bioaccesibilidad de Cd(II) y As(III) en condiciones in vitro del sistema digestivo humano debido a su resistencia a altas concentraciones de estos elementos y su tolerancia a condiciones de acidez y salinidad. Esto, junto con el reconocido potencial probiótico que tienen estos microorganismos, permitirá a futuro su uso en procesos biológicos de mitigación de Cd(II) y As(III).

Microbial Diversity in Moonmilk of Baeg-nyong Cave, Korean CZO

The Baeg-nyong cave is a limestone cave which has been nominated as the first critical zone observatory (CZO) in South Korea. Moonmilk is a well-known speleothem composed of various carbonate minerals. To characterize moonmilk from the Baeg-nyong cave, we performed mineralogical analyses and applied high-throughput 16S rRNA gene sequencing to analyze the microbial communities, including bacteria and fungi, of dry and wet moonmilk samples. The results showed that the dry and wet moonmilk samples had different and atypical crystal structures, although they were predominantly composed of CaCO3. Furthermore, metagenomic data revealed that the dry and wet moonmilk samples collected from an oligotrophic environment had completely different bacterial communities when compared to the outside soil, and there was a difference in bacterial communities even between dry and wet moonmilk specimens. Fungal communities, however, did not differ significantly between dry and wet moonmilk samples. This study is the first metagenomic analysis of two different types of moonmilk with different physical properties and the first report on the microbial diversity of moonmilk from a cave in the first CZO in South Korea.

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.

Corn steep liquor as a nutritional source for biocementation and its impact on concrete structural properties

Microbial-induced carbonate precipitation (MICP) has a potential to improve the durability properties and remediate cracks in concrete. In the present study, the main emphasis is placed upon replacing the expensive laboratory nutrient broth (NB) with corn steep liquor (CSL), an industrial by-product, as an alternate nutrient medium during biocementation. The influence of organic nutrients (carbon and nitrogen content) of CSL and NB on the chemical and structural properties of concrete structures is studied. It has been observed that cement-setting properties were unaffected by CSL organic content, while NB medium influenced it. Carbon and nitrogen content in concrete structures was significantly lower in CSL-treated specimens than in NB-treated specimens. Decreased permeability and increased compressive strength were reported when NB is replaced with CSL in bacteria-treated specimens. The present study results suggest that CSL can be used as a replacement growth medium for MICP technology at commercial scale.