Enhanced calcium carbonate-biofilm complex formation by alkali-generating Lysinibacillus boronitolerans YS11 and alkaliphilic Bacillus sp. AK13

Direct sequencing of insect symbionts via nanopore adaptive sampling

Insect symbionts can alter their host phenotype and their effects can range from beneficial to pathogenic. Moreover, many insects exhibit co-infections, making their study more challenging. Less than 1% of insect species have high-quality referenced genomes available and fewer still also have their symbionts sequenced. Two methods are commonly used to sequence symbionts: whole-genome sequencing to concomitantly capture the host and bacterial genomes, or isolation of the symbiont's genome before sequencing. These methods are limited when dealing with rare or poorly characterized symbionts. Long-read technology is an important tool to generate high-quality genomes as they can overcome high levels of heterozygosity, repeat content, and transposable elements that confound short-read methods. Oxford Nanopore (ONT) adaptive sampling allows a sequencing instrument to select or reject sequences in real time. We describe a method based on ONT adaptive sampling (subtractive) approach that readily permitted the sequencing of the complete genomes of mitochondria, Buchnera and its plasmids (pLeu, pTrp), and Wolbachia genomes in two aphid species, Aphis glycines and Pentalonia nigronervosa. Adaptive sampling is able to retrieve organelles such as mitochondria and symbionts that have high representation in their hosts such as Buchnera and Wolbachia, but is less successful at retrieving symbionts in low concentrations.

Habitat-related variability in the morphological and taxonomic diversity of microbial communities in two Hungarian epigenic karst caves

The physical and chemical characteristics of the bedrock, along with the geological and hydrological conditions of karst caves may influence the taxonomic and functional diversity of prokaryotes. Most studies so far have focused on microbial communities of caves including only a few samples and have ignored the chemical heterogeneity of different habitat types such as sampling sites, dripping water, carbonate precipitates, cave walls, cave sediment and surface soils connected to the caves. The aim of the present study was to compare the morphology, the composition and physiology of the microbiota in caves with similar environmental parameters (temperature, host rock, elemental and mineral composition of speleothems) but located in different epigenic karst systems. Csodabogyós Cave and Baradla Cave (Hungary) were selected for the analysis of bacterial and archaeal communities using electron microscopy, amplicon sequencing, X-ray diffraction, and mass spectroscopic techniques. The microbial communities belonged to the phyla Pseudomonadota, Acidobacteriota, Nitrospirota and Nitrososphaerota, and they showed site-specific variation in composition and diversity. The results indicate that morphological and physiological adaptations provide survival for microorganisms according to the environment. In epigenic karst caves, prokaryotes are prone to increase their adsorption surface, cooperate in biofilms, and implement chemolithoautotrophic growth with different electron-donors and acceptors available in the microhabitats.

Preliminary indication of the role of AHL-dependent quorum sensing systems in calcium carbonate precipitation in Gram-negative bacteria

Numerous microbial species participate in precipitation of carbonates in various natural environments, including soils, geological formations, freshwater biofilms and oceans. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and adaptive aspects remain poorly known. Many Gram-negative bacteria use cell-to-cell communication systems relying on N-acylhomoserine lactone (AHLs) signal molecules to express certain phenotypic traits in a density-dependent manner, a phenomenon referred as to quorum-sensing (QS). In this work, bacterial isolates collected from cave and rhizosphere soil were analyzed to study the occurrence of the AHL-mediated QS in bacterial calcium carbonate (CaCO3) precipitation. To test the production of AHLs signal molecules, we cross-streaked Gram-negative calcifying strains, selected among the environmental strains studied, with the AHL-negative mutant Chromobacterium subtsugae strain CV026. Only Burkholderia ambifaria LMG 11351 was able to restore violacein production in CV026 among the tested strains. The constructed AHL-negative mutant of B. ambifaria LMG 11351 could not precipitate CaCO3 on B-4 agar. Scanning Electron Microscopy (SEM) analysis on CaCO3 crystals obtained in vitro shows crystals of different morphologies, calcified biofilms and bacteria in close contact with the precipitated crystals. In the inner layers of the bioliths deposited by B. ambifaria LMG 11351, a stream-like organization of the Burkholderia imprints was not detected by SEM. Our data provide preliminary evidence that the activation of AHL-regulated genes may be a prerequisite for in vitro bacterial carbonatogenesis, in some cases, confirming the specific role of bacteria as CaCO3 precipitating agents. We enhance the understanding of bacterial CaCO3 biomineralization and its potential biotechnology implications for QS-based strategies to enhance or decrease CaCO3 precipitation through specific bacterial processes. The AHL-negative mutant of B. ambifaria LMG 11351 (a well-known plant growth-promoting bacterium) could also be used to study plant-bacteria interactions. The adaptive role of bacterial CaCO3 biomineralization was also discussed.

Formation mechanism of disc-shaped calcite-a case study on Arthrobacter sp. MF-2

Research on the biogenic-specific morphology of carbonate minerals has made progress in the fields of biomineralization and industrial engineering. In this study, mineralization experiments were performed using Arthrobacter sp. MF-2, including its biofilms. The results showed that a particular morphology of minerals (i.e., disc-shaped) was observed in the mineralization experiments with strain MF-2. The disc-shaped minerals were formed near the air/solution interface. We also observed that disc-shaped minerals formed in experiments with the biofilms of strain MF-2. Therefore, the nucleation of carbonate particles on the biofilm templates produced a novel disc-shaped morphology which was assembled from calcite nanocrystals radiating out from the periphery of the template biofilms. Further, we propose a possible formation mechanism of the disc-shaped morphology. This study may provide new perspectives on the formation mechanism of carbonate morphogenesis in the process of biomineralization.

A Study on the Healing Performance of Mortar with Microcapsules Using Silicate-Based Inorganic Materials

Advancements in material science have led to the development of various self-healing concrete technologies. Among these is the use of microcapsule-based self-healing materials. This study evaluated the effects of self-healing microcapsules on the quality and healing properties of mortar. A silicate-based inorganic material mixture was used as the healing material tested with ordinary Portland cement. Accordingly, the effects of microcapsules (MCs) on the rheological, mechanical, and healing properties of mortar were determined. The mixing of MCs reduced the plastic viscosity and yield stress of the cement composite material owing to the particle properties of the MCs. The reduction was in proportion to the mixing ratio. The evaluation results show that the unit water permeability decreased owing to the healing reaction immediately after crack initiation. The healing rate was more than 95% at 7 days of healing age when more than 3% of MCs was mixed. This study provides a reference for the optimal mixing rate of MCs to achieve an ideal concrete healing rate.

Simultaneous removal of nitrate and heavy metals in a biofilm reactor filled with modified biochar

A biofilm reactor filled with chia seeds gum modified biochar was set up for the simultaneous removal of nitrate, cadmium and zinc from calcium-containing wastewater via denitrification and microbially-induced (calcium) carbonate precipitation. The reactor performance was studied under different conditions of pH, Cd concentration, and hydraulic retention time. The optimal removal efficiency of the reactor for NO₃^--N, Ca²⁺, Cd²⁺, and Zn²⁺ were 99.98, 79.89, 100, and 99.84 %, respectively. 3D-EEM indicated the aromatic compounds confirming the stability of the reactor. FTIR illustrated the presence of -OH, CaCO₃, C-O-C, and C-O-H indicating the precipitation and role of gum in MICP. SEM confirmed that the seed crystal induced the repeated crystallization of free metal ions. XRD showed that heavy metals were removed in the form of CaCO₃, CdCO₃, ZnCO₃, Ca₃(PO₃)₂, Cd₃(PO₃)₂, and Zn₃(PO₃)₂ co-crystallization. SEM-EDS showed the composition and distribution of elements. High-throughput sequencing showed that Curpriavidus sp. GMF1 and Ochrobactrum sp. GMC12 were the dominant bacterial species, with powerful denitrification and MICP mineralization capabilities.

Calcium carbonate precipitation by cave bacteria isolated from Kashmir Cave, Khyber Pakhtunkhwa, Pakistan

The participation of numerous physicochemical and biological functions maintains the evolution and expansion of the remarkable nature. Due to its vast applicability in several engineering disciplines, naturally occurring bio-mineralization or microbially induced calcium carbonate (MICP) precipitation is attracting more interest. Cave bacteria contribute to the precipitation of calcium carbonate (CaCO₃ ). In the present study, soil sediments were collected from Kashmir cave, KPK, Pakistan, and plated on B4 specific nutrients limited medium for bacterial isolation and the viable bacterial count was calculated. Three bacterial strains named GSN-11, TFSN-14, and TFSN-15 were capable of precipitating CaCO₃ . These bacterial isolates were identified through 16S rRNA gene sequencing and strain GSN-11 was identified as Bacillus toyonensis, TFSN-14 as Paracoccus limosus and TFSN-15 as Brevundimonas diminuta. Enhanced CaCO₃ precipitation potential of these bacteria strains was observed at 25°C and pH 5. The precipitated CaCO₃ was confirmed by scanning electron microscopy, X-ray powder diffraction, and Fourier transform infra-red spectroscopy. The findings showed that the precipitates were dominated by calcite, aragonite, and nanosize vaterite. Current research suggests that precipitation of CaCO₃ by proteolytic cave bacteria is widespread in Kashmir cave and these bacterial communities can actively contribute to the formation of CaCO₃ by enhancing the pH of the microenvironment.

Integrating transcriptomics and metabolomics analysis on kojic acid combating Acinetobacter baumannii biofilm and its potential roles

As a major secondary metabolite derived from a dominant marine filamentous fungus A7, kojic acid might confer the strain a competitive advantage in natural colonization. The bioactivities of kojic acid against bacterial growth and biofilm formation were investigated against Acinetobacter baumannii (A. baumannii) ATCC 19606. Then, transcriptomics and metabolomics were integrated to characterize the underlying mechanisms. It turned out that kojic acid exhibited a significantly suppressive impact against biofilm but a weak bacteriostatic activity. Meanwhile, a variety of transcriptional and metabolomic profiles were altered within biofilm formation as a result of kojic acid exposure. The alterations highlighted the mechanisms underlying biofilm formation, comprising of quorum sensing, fimbria assembly, bacterial virulence and metabolic plasticity, which could somewhat be hampered by kojic acid. The present study comprehensively elucidated multifactorial schemes for kojic acid combating biofilm formation of A. baumannii, which might provide mechanistic insights into the development of therapeutic strategies against this notorious pathogen. Meanwhile, our observations might shed new light on the ecological roles of kojic acid, e.g., serving as chemical deterrents for host adaptation to marine niches, which, however, awaits further validation.

Kinetic model of a newly-isolated Lysinibacillus sp. strain YL and elastic properties of its biogenic CaCO3 towards biocement application

BACKGROUND

Biocement, calcifying bacteria-incorporated cement, offers an environmentally-friendly way to increase the cement lifespan. This work aimed to investigate the potential use of Lysinibacillus sp. strain YL towards biocement application in both theoretical and experimental ways.

METHODS AND RESULTS

Strain YL was grown using calcium acetate (Ca(C₂ H₃ O₂ )₂ ), calcium chloride (CaCl₂ ) and calcium nitrate (Ca(NO₃ )₂ ). Maximum bacterial growth of ~0.09 hr-1 and the highest amount of CaCO₃ precipitation of ~8.0 g/L were obtained when using Ca(C₂ H₃ O₂ )₂ . The SEM and XRD results confirmed that biogenic CaCO₃ were calcites. The bulk, Young's and shear moduli of biogenic CaCO₃ calculated via the VRH approximation were ~1.5-2.3 times larger than those of ordinary Portland cement. The Poisson's ratio was 0.382 and negative in some directions, suggesting its ductility and auxetic behaviors. The new model was developed to explain the growth kinetic of strain YL in the presence of Ca(C₂ H₃ O₂ )₂ , whose concentration was optimized for biocement experiments. Strain YL could increase the compressive strength of cement up to ~50% higher than that of the uninoculated cement.

CONCLUSION

Strain YL is a promising candidate for biocement applications. This work represents the trials of experiments and models allowing quantitatively comparison with large-scale production in the future.

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.

Conserved bacterial genomes from two geographically isolated peritidal stromatolite formations shed light on potential functional guilds

Stromatolites are complex microbial mats that form lithified layers. Fossilized stromatolites are the oldest evidence of cellular life on Earth, dating back over 3.4 billion years. Modern stromatolites are relatively rare but may provide clues about the function and evolution of their ancient counterparts. In this study, we focus on peritidal stromatolites occurring at Cape Recife and Schoenmakerskop on the southeastern South African coastline, the former being morphologically and structurally similar to fossilized phosphatic stromatolites formations. Using assembled shotgun metagenomic analysis, we obtained 183 genomic bins, of which the most dominant taxa were from the Cyanobacteria phylum. We identified functional gene sets in genomic bins conserved across two geographically isolated stromatolite formations, which included relatively high copy numbers of genes involved in the reduction of nitrates and phosphatic compounds. Additionally, we found little evidence of Archaeal species in these stromatolites, suggesting that they may not play an important role in peritidal stromatolite formations, as proposed for hypersaline formations.

Agricultural by-products and oyster shell as alternative nutrient sources for microbial sealing of early age cracks in mortar

Bio-concrete using bacterially produced calcium carbonate can repair microcracks but is still relatively expensive due to the addition of bacteria, nutrients, and calcium sources. Agricultural by-products and oyster shells were used to produce economical bio-concrete. Sesame meal was the optimal agricultural by-product for low-cost spore production of the alkaliphilic Bacillus miscanthi strain AK13. Transcriptomic dataset was utilized to compare the gene expressions of AK13 strain under neutral and alkaline conditions, which suggested that NaCl and riboflavin could be chosen as growth-promoting factors at alkaline pH. The optimal levels of sesame meal, NaCl, and riboflavin were induced with the central composite design to create an economical medium, in which AK13 strain formed more spores with less price than in commercial sporulation medium. Calcium nitrate obtained from nitric acid treatment of oyster shell powder increased the initial compressive strength of cement mortar. Non-ureolytic calcium carbonate precipitation by AK13 using oyster shell-derived calcium ions was verified by energy-dispersive X-ray spectroscopy and X-ray diffraction analysis. Stereomicroscope and field emission scanning electron microscopy confirmed that oyster shell-derived calcium ions, along with soybean meal-solution, increased the bacterial survival and calcium carbonate precipitation inside mortar cracks. These data suggest the possibility of commercializing bacterial self-healing concrete with economical substitutes for culture medium, growth nutrient, and calcium sources.

Bacterial Calcium Carbonate Mineralization in situ Strategies for Conservation of Stone Artworks: From Cell Components to Microbial Community

Calcareous stones have been widely used in artworks and buildings by almost all human cultures. Now, more than ever, the increased environmental pollution and global warming are threatening the stone cultural heritage. Weathering due to physical, chemical and biological factors results in monumental calcareous stone deterioration. These agents induce a progressive dissolution of the mineral matrix, increase porosity, and lead to structural weakening. Bacterial Calcium Carbonate Mineralization is a widespread naturally occurring process which in the last decades was proposed as an environmentally friendly tool to protect monumental and ornamental calcareous stones. The advantage of this treatment is that it mimics the natural process responsible for stone formation, producing a mineral product similar to the stone substrate. This mini review highlights the milestones of the biomineralization approaches with focus on in situ stone artworks protection. The strategies explored to date are based on three main approaches: (i) the use of allochthonous and (ii) autochthonous alive cells that, due to the bacterial metabolism, foster biomineralization; (iii) the cell-free approach which uses fractionated cellular components inducing biomineralization. We discuss the challenging aspects of all these techniques, focusing on in situ applications and suggesting perspectives based on recent advances.

Bacillus miscanthi sp. nov., a alkaliphilic bacterium from the rhizosphere of Miscanthus sacchariflorus

A novel bacterial strain, designated AK13^T (=KACC 21401^T=DSM 109981^T), was isolated from the rhizosphere of Miscanthus sacchariflorus. Strain AK13^T was found to be an aerobic, Gram-stain-positive, endospore-forming and rod-shaped bacterium. It formed yellow circular colonies with smooth convex surfaces. The genomic DNA G+C content of strain AK13^T was estimated to be 40 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that this strain was most closely related to Bacillus lehensis MLB2^T (99.4 %), Bacillus oshimensis K11^T (98.8 %) and Bacillus patagoniensis PAT 05^T (96.6 %). The average nucleotide identity values between strain AK13^T and B. lehensis MLB2^T, B. oshimensis K11^T and B. patagoniensis PAT 05^T were 90.93, 91.05 and 71.87 %, respectively, with the digital DNA-DNA hybridization values of 42.7, 42.6 and 18.8 %, respectively. Cells grew at 5-40 °C (optimum, 28-35 °C), pH 6.5-13 (optimum, pH 8-9) and in the presence of 0-13.0 % (w/v) NaCl (optimum, 1 %). The cell wall of strain AK13^T contained meso-diaminopimelic acid, and the major isoprenoid quinone was MK-7. Results of fatty acid methyl ester analysis revealed that iso-C_{15 : 0} was the predominant cellular fatty acid. Two-dimensional thin-layer chromatography analysis indicated that the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and glycolipid. The genotypic and phenotypic characteristics suggested that strain AK13^T represented a novel species of the genus Bacillus, and thus the name Bacillus miscanthi sp. nov. is proposed.

Complete Genome and Calcium Carbonate Precipitation of Alkaliphilic Bacillus sp. AK13 for Self-Healing Concrete

Bacteria that are resistant to high temperatures and alkaline environments are essential for the biological repair of damaged concrete. Alkaliphilic and halotolerant Bacillus sp. AK13 was isolated from the rhizosphere of Miscanthus sacchariflorus. Unlike other tested Bacillus species, the AK13 strain grows at pH 13 and withstands 11% (w/v) NaCl. Growth of the AK13 strain at elevated pH without urea promoted calcium carbonate (CaCO3) formation. Irregular vateritelike CaCO3 minerals that were tightly attached to cells were observed using field-emission scanning electron microscopy. Energy-dispersive X-ray spectrometry, confocal laser scanning microscopy, and X-ray diffraction analyses confirmed the presence of CaCO3 around the cell. Isotope ration mass spectrometry analysis confirmed that the majority of CO32- ions in the CaCO3 were produced by cellular respiration rather than being derived from atmospheric carbon dioxide. The minerals produced from calcium acetate-added growth medium formed smaller crystals than those formed in calcium lactate-added medium. Strain AK13 appears to heal cracks on mortar specimens when applied as a pelletized spore powder. Alkaliphilic Bacillus sp. AK13 is a promising candidate for self-healing agents in concrete.

Optimization of bacterial sporulation using economic nutrient for self-healing concrete

The use of heat- and alkali-resistant bacteria is essential for the biological repair of damaged concrete. Lysinibacillus boronitolerans YS11 was isolated from the rhizosphere of Miscanthus sacchariflorus. The increased pH in the urea-minus condition during the growth of the YS11 strain promoted calcium carbonate (CaCO₃) formation. To identify the optimum medium that promoted the growth of the YS11 strain, a Plackett-Burman design was conducted for the screening process. Consequently, malt powder, rice bran, (NH₄)₂SO₄, and corn syrup were chosen to enhance YS11 growth. The optimization of these four useful factors was carried out using a central composite design. To obtain higher survivability in mortar, the sporulation process is essential, and additional factors such as Mn²⁺, Fe²⁺, and Ca²⁺ were found to contribute to sporulation. A mixture of L. boronitolerans YS11 spore powder, cement, paste, sand, yeast extract, calcium lactate, and water showed a healing effect on a 0.3 mm mortar crack in 7 days. Furthermore, calcium carbonate precipitation was observed over the crack surface. Thus, we confirmed that mortar treated with YS11 spore powder was effective in healing micro-cracks in concrete.