Fungal biomineralization

Advances in microbial self-healing concrete: A critical review of mechanisms, developments, and future directions

The self-healing bioconcrete, or bioconcrete as concrete containing microorganisms with self-healing capacities, presents a transformative strategy to extend the service life of concrete structures. This technology harnesses the biological capabilities of specific microorganisms, such as bacteria and fungi, which are integral to the material's capacity to autonomously mend cracks, thereby maintaining structural integrity. This review highlights the complex biochemical pathways these organisms utilize to produce healing compounds like calcium carbonate, and how environmental parameters, such as pH, temperature, oxygen, and moisture critically affect the repair efficacy. A comprehensive analysis of recently published peer-reviewed literature, and contemporary experimental research forms the backbone of this review with a focus on microbiological aspects of the self-healing process. The review assesses the challenges facing self-healing bioconcrete, including the longevity of microbial spores and the cost implications for large-scale implementation. Further, attention is given to potential research directions, such as investigating alternative biological agents and optimizing the concrete environment to support microbial activity. The culmination of this investigation is a call to action for integrating self-healing bioconcrete in construction on a broader scale, thereby realizing its potential to fortify infrastructure resilience and sustainability.

Toward Practical Applications of Engineered Living Materials with Advanced Fabrication Techniques

Engineered Living Materials (ELMs) are materials composed of or incorporating living cells as essential functional units. These materials can be created using bottom-up approaches, where engineered cells spontaneously form well-defined aggregates. Alternatively, top-down methods employ advanced materials science techniques to integrate cells with various kinds of materials, creating hybrids where cells and materials are intricately combined. ELMs blend synthetic biology with materials science, allowing for dynamic responses to environmental stimuli such as stress, pH, humidity, temperature, and light. These materials exhibit unique "living" properties, including self-healing, self-replication, and environmental adaptability, making them highly suitable for a wide range of applications in medicine, environmental conservation, and manufacturing. Their inherent biocompatibility and ability to undergo genetic modifications allow for customized functionalities and prolonged sustainability. This review highlights the transformative impact of ELMs over recent decades, particularly in healthcare and environmental protection. We discuss current preparation methods, including the use of endogenous and exogenous scaffolds, living assembly, 3D bioprinting, and electrospinning. Emphasis is placed on ongoing research and technological advancements necessary to enhance the safety, functionality, and practical applicability of ELMs in real-world contexts.

MICP mediated by indigenous bacteria isolated from tailings for biocementation for reduction of wind erosion

In this study, native ureolytic bacteria were isolated from copper tailings soils to perform microbial-induced carbonate precipitation (MICP) tests and evaluate their potential for biocement formation and their contribution to reduce the dispersion of particulate matter into the environment from tailings containing potentially toxic elements. It was possible to isolate a total of 46 bacteria; among them only three showed ureolytic activity: Priestia megaterium T130-1, Paenibacillus sp. T130-13 and Staphylococcus sp. T130-14. Biocement cores were made by mixing tailings with the isolated bacteria in presence of urea, resulting similar to those obtained with Sporosarcina pasteurii and Bacillus subtilis used as positive control. Indeed, XRD analysis conducted on biocement showed the presence of microcline (B. subtilis 17%; P. megaterium 11. 9%), clinochlore (S. pasteurii, 6.9%) and magnesiumhornblende (Paenibacillus sp. 17.8%; P. megaterium 14.6%); all these compounds were not initially present in the tailings soils. Moreover the presence of calcite (control 0.828%; Paenibacillus sp. 5.4%) and hematite (control 0.989%; B. subtilis 6.4%) was also significant unlike the untreated control. The development of biofilms containing abundant amount of Ca, C, and O on microscopic soil particles was evidenced by means of FE-SEM-EDX and XRD. Wind tunnel tests were carried out to investigate the resistance of biocement samples, accounted for a mass loss five holds lower than the control, i.e., the rate of wind erosion in the control corresponded to 82 g/m2h while for the biocement treated with Paenibacillus sp. it corresponded to only 16.371 g/m2h. Finally, in compression tests, the biocement samples prepared with P. megaterium (28.578 psi) and Paenibacillus sp. (28.404 psi) showed values similar to those obtained with S. pasteurii (27.102 psi), but significantly higher if compared to the control (15.427 psi), thus improving the compression resistance capacity of the samples by 85.2% and 84.1% with respect to the control. According to the results obtained, the biocement samples generated with the native strains showed improvements in the mechanical properties of the soil supporting them as potential candidates in applications for the stabilization of mining liabilities in open environments using bioaugmentation strategies with native strains isolated from the same mine tailing.

Fungal biomineralization of toxic metals accelerates organic pollutant removal

Fungal biomineralization plays an important role in the biogeochemical cycling of metals in the environment and has been extensively explored for bioremediation and element biorecovery. However, the cellular and metabolic responses of fungi in the presence of toxic metals during biomineralization and their impact on organic matter transformations are unclear. This is an important question because co-contamination by toxic metals and organic pollutants is a common phenomenon in the natural environment. In this research, the biomineralization process and oxidative stress response of the geoactive soil fungus Aspergillus niger were investigated in the presence of toxic metals (Co, Cu, Mn, and Fe) and the azo dye orange II (AO II). We have found that the co-existence of toxic metals and AO II not only enhanced the fungal biomineralization of toxic metals but also accelerated the removal of AO II. We hypothesize that the fungus and in situ mycogenic biominerals (toxic metal oxalates) constituted a quasi-bioreactor, where the biominerals removed organic pollutants by catalyzing reactive oxygen species (ROS) generation resulting from oxidative stress. We have therefore demonstrated that a fungal/biomineral system can successfully achieve the goal of toxic metal immobilization and organic pollutant decomposition. Such findings inform the potential development of fungal-biomineral hybrid systems for mixed pollutant bioremediation as well as provide further understanding of fungal organic-inorganic pollutant transformations in the environment and their importance in biogeochemical cycles.

Suillusgrevillei and Suillus luteus promote lead tolerance of Pinus tabulaeformis and biomineralize lead to pyromorphite

Lead (Pb) is a hazardous heavy metal that accumulates in many environments. Phytoremediation of Pb polluted soil is an environmentally friendly method, and a better understanding of mycorrhizal symbiosis under Pb stress can promote its efficiency and application. This study aims to evaluate the impact of two ectomycorrhizal fungi (Suillus grevillei and Suillus luteus) on the performance of Pinus tabulaeformis under Pb stress, and the biomineralization of metallic Pb in vitro. A pot experiment using substrate with 0 and 1,000 mg/kg Pb2+ was conducted to evaluate the growth, photosynthetic pigments, oxidative damage, and Pb accumulation of P. tabulaeformis with or without ectomycorrhizal fungi. In vitro co-cultivation of ectomycorrhizal fungi and Pb shots was used to evaluate Pb biomineralization. The results showed that colonization by the two ectomycorrhizal fungi promoted plant growth, increased the content of photosynthetic pigments, reduced oxidative damage, and caused massive accumulation of Pb in plant roots. The structural characteristics of the Pb secondary minerals formed in the presence of fungi demonstrated significant differences from the minerals formed in the control plates and these minerals were identified as pyromorphite (Pb5(PO4)3Cl). Ectomycorrhizal fungi promoted the performance of P. tabulaeformis under Pb stress and suggested a potential role of mycorrhizal symbiosis in Pb phytoremediation. This observation also represents the first discovery of such Pb biomineralization induced by ectomycorrhizal fungi. Ectomycorrhizal fungi induced Pb biomineralization is also relevant to the phytostabilization and new approaches in the bioremediation of polluted environments.

Heavy Metal Remediation by Dry Mycelium Membranes: Approaches to Sustainable Lead Remediation in Water

Lead contamination poses significant and lasting health risks, particularly in children. This study explores the efficacy of dried mycelium membranes, distinct from live fungal biomass, for the remediation of lead (Pb(II)) in water. Dried mycelium offers unique advantages, including environmental resilience, ease of handling, biodegradability, and mechanical reliability. The study explores Pb(II) removal mechanisms through sorption and mineralization by dried mycelium hyphae in aqueous solutions. The sorption isotherm studies reveal a high Pb(II) removal efficiency, exceeding 95% for concentrations below 1000 ppm and ∼63% above 1500 ppm, primarily driven by electrostatic interactions. The measured infrared peak shifts and the pseudo-second-order kinetics for sorption suggests a correlation between sorption capacity and the density of interacting functional groups. The study also explores novel surface functionalization of the mycelium network with phosphate to enhance Pb(II) removal, which enables remediation efficiencies >95% for concentrations above 1500 ppm. Scanning electron microscopy images show a pH-dependent formation of Pb-based crystals uniformly deposited throughout the entire mycelium network. Continuous cross-flow filtration tests employing a dried mycelium membrane demonstrate its efficacy as a microporous membrane for Pb(II) removal, reaching remediation efficiency of 85-90% at the highest Pb(II) concentrations. These findings suggest that dried mycelium membranes can be a viable alternative to synthetic membranes in heavy metal remediation, with potential environmental and water treatment applications.

Oxygen-dependent biofilm dynamics in leaf decay: an in vitro analysis

Biofilms are important in the natural process of plant tissue degradation. However, fundamental knowledge of biofilm community structure and succession on decaying leaves under different oxygen conditions is limited. Here, we used 16S rRNA and ITS gene amplicon sequencing to investigate the composition, temporal dynamics, and community assembly processes of bacterial and fungal biofilms on decaying leaves in vitro. Leaves harvested from three plant species were immersed in lake water under aerobic and anaerobic conditions in vitro for three weeks. Biofilm-covered leaf samples were collected weekly and investigated by scanning electron microscopy. The results showed that community composition differed significantly between biofilm samples under aerobic and anaerobic conditions, though not among plant species. Over three weeks, a clear compositional shift of the bacterial and fungal biofilm communities was observed. The alpha diversity of prokaryotes increased over time in aerobic assays and decreased under anaerobic conditions. Oxygen availability and incubation time were found to be primary factors influencing the microbial diversity of biofilms on different decaying plant species in vitro. Null models suggest that stochastic processes governed the assembly of biofilm communities of decaying leaves in vitro in the early stages of biofilm formation and were further shaped by niche-associated factors.

Fungal community dynamics on limestone at the Chichén Itzá archaeological site in Mexico driven by protective treatments

Microorganisms naturally colonize rock-based materials in outdoor environments, thereby contributing to their degradation. Fungi, especially in tropical environments with abundant water and favorable temperatures, play a significant role in biodegradation. However, many aspects of the microorganism-stone interaction, including fungal colonization dynamics and the impact of treatment applications, remain unclear. This study conducted a four-year in-situ evaluation of fungal community dynamics on limestone surfaces in the Temple of the Warriors at the Chichén Itzá archaeological site in Mexico, focusing on cleaning and treatment using nanoparticles (NPs). These NPs included zinc oxide (ZnO) and CaZn2(OH)6·2H2O (CZ)-based NPs synthesized via sol-gel (CZ-SG) and mechanochemical methods (CZ-MC), as well as CZ/Ca(OH)2-based products (CZ:Ca-SG). The microbial colonization cover was assessed using colorimetric measurements, and the surface was sampled for fungal community isolation and identification. The results demonstrated significant impacts of cleaning and nanomaterial applications on cultivable fungal communities (melanized filamentous, hyaline, and microcolonial fungi), altering composition, dynamics, and stone surface coloration. In particular, ZnO NPs caused 50 % decline in fungal species and individuals, whereas CZ:Ca-SG NPs displaced most species, indicating effective inhibition of the cultivable fungal community. Microcolonial fungi (MCF), known for their tolerance to withstand harsh environmental conditions, were the only fungal group found in the CZ:Ca-SG treatment. In contrast, CZ-SG and CZ-MC increased the abundance of melanized species, resulting in darkening and reduced color intensity. This study highlights the importance of microcolonial fungi that are tolerant to cleaning and coating procedures in the preservation of stone cultural heritage. These findings enhance our understanding of fungal colonization dynamics following treatment and provide valuable insights into the challenges associated with preserving stone materials in tropical environments.

Formation of Biogenic Manganese Oxide Nodules on Hyphae of a New Fungal Isolate of Periconia That Immobilizes Aqueous Copper

Mn(II)-oxidizing microorganisms are considered to play significant roles in the natural geochemical cycles of Mn and other heavy metals because the insoluble biogenic Mn oxides (BMOs) that are produced by these microorganisms adsorb other dissolved heavy metals and immobilize them as precipitates. In the present study, a new Mn(II)-oxidizing fungal strain belonging to the ascomycete genus Periconia, a well-studied plant-associating fungal genus with Mn(II)-oxidizing activity that has not yet been exami-ned in detail, was isolated from natural groundwater outflow sediment. This isolate, named strain TS-2, was confirmed to oxidize dissolved Mn(II) and produce insoluble BMOs that formed characteristic, separately-located nodules on their hyphae while leaving major areas of the hyphae free from encrustation. These BMO nodules also adsorbed and immobilized dissolved Cu(II), a model analyte of heavy metals, as evidenced by elemental mapping ana-lyses of fungal hyphae-BMO assemblages using a scanning electron microscope with energy-dispersive X-ray spectroscopy (SEM-EDX). Analyses of functional genes within the whole genome of strain TS-2 further revealed the presence of multiple genes predicted to encode laccases/multicopper oxidases that were potentially responsible for Mn(II) oxidation by this strain. The formation of BMO nodules may have functioned to prevent the complete encrustation of fungal hyphae, thereby enabling the control of heavy metal concentrations in their local microenvironments while maintaining hyphal functionality. The present results will expand our knowledge of the physiological and morphological traits of Mn(II)-oxidizing Periconia, which may affect the natural cycle of heavy metals through their immobilization.

Self-decorating cells via surface-initiated enzymatic controlled radical polymerization

Through the innovative use of surface-displayed horseradish peroxidase, this work explores the enzymatic catalysis of both bioRAFT polymerization and bioATRP to prompt polymer synthesis on the surface of Saccharomyces cerevisiae cells, with bioATRP outperforming bioRAFT polymerization. The resulting surface modification of living yeast cells with synthetic polymers allows for a significant change in yeast phenotype, including growth profile, aggregation characteristics, and conjugation of non-native enzymes to the clickable polymers on the cell surface, opening new avenues in bioorthogonal cell-surface engineering.

Exploring the Application and Prospects of Synthetic Biology in Engineered Living Materials

At the intersection of synthetic biology and materials science, engineered living materials (ELMs) exhibit unprecedented potential. Possessing unique "living" attributes, ELMs represent a significant paradigm shift in material design, showcasing self-organization, self-repair, adaptability, and evolvability, surpassing conventional synthetic materials. This review focuses on reviewing the applications of ELMs derived from bacteria, fungi, and plants in environmental remediation, eco-friendly architecture, and sustainable energy. The review provides a comprehensive overview of the latest research progress and emerging design strategies for ELMs in various application fields from the perspectives of synthetic biology and materials science. In addition, the review provides valuable references for the design of novel ELMs, extending the potential applications of future ELMs. The investigation into the synergistic application possibilities amongst different species of ELMs offers beneficial reference information for researchers and practitioners in this field. Finally, future trends and development challenges of synthetic biology for ELMs in the coming years are discussed in detail.

Fungal biorecovery of cerium as oxalate and carbonate biominerals

Cerium is the most sought-after rare earth element (REE) for application in high-tech electronic devices and versatile nanomaterials. In this research, biomass-free spent culture media of Aspergillus niger and Neurospora crassa containing precipitant ligands (oxalate, carbonate) were investigated for their potential application in biorecovery of Ce from solution. Precipitation occurred after Ce3+ was mixed with biomass-free spent culture media and >99% Ce was recovered from media of both organisms. SEM showed that biogenic crystals with distinctive morphologies were formed in the biomass-free spent medium of A. niger. Irregularly-shaped nanoparticles with varying sizes ranging from 0.5 to 2 μm and amorphous biominerals were formed after mixing the carbonate-laden N. crassa supernatant, resulting from ureolysis of supplied urea, with Ce3+. Both biominerals contained Ce as the sole metal, and X-ray diffraction (XRD) and thermogravimetric analyses identified the biominerals resulting from the biomass-free A. niger and N. crassa spent media as cerium oxalate decahydrate [Ce2(C2O4)3·10H2O] and cerium carbonate [Ce2(CO3)3·8H2O], respectively. Thermal decomposition experiments showed that the biogenic Ce oxalates and carbonates could be subsequently transformed into ceria (CeO2). FTIR confirmed that both amorphous and nanoscale Ce carbonates contained carbonate (CO32-) groups. FTIR-multivariate analysis could classify the biominerals into three groups according to different Ce concentrations and showed that Ce carbonate biominerals of higher purity were produced when precipitated at higher Ce3+ concentrations. This work provides new understanding of fungal biotransformations of soluble REE species and their biorecovery using biomass-free fungal culture systems and indicates the potential of using recovered REE as precursors for the biosynthesis of novel nanomaterials.

Fungal-induced fossil biomineralization

Exceptional preservation of fossils has often been attributed to the actions of bacteria that aid in the preservation of soft tissues that normally decay rapidly. However, it is well known that fungi play a major role in organic matter decomposition, biogeochemical cycling of elements, and metal-mineral transformations in modern ecosystems. Although the fungal fossil record can be traced back over a billion years, there are only a few recorded examples of fungal roles in fossilization. In this research, we have carried out a detailed geobiological investigation on early Pleistocene hyena coprolites (fossilized dung) in an attempt to ascertain possible fungal involvement in their formation. Using an advanced microscopic and mineralogical approach, we found that numerous hydroxyapatite nanofibers (25-34 nm on average), interwoven to form spheroidal structures, constituted the matrix of the coprolites in addition to food remains. These structures were found to be extremely similar in texture and mineral composition to biominerals produced during laboratory culture of a common saprophytic and geoactive fungus, Aspergillus niger, in the presence of a solid source of calcium (Ca) and phosphorus (P). This observation, and our other data obtained, strongly suggests that fungal metabolism can provide a mechanism that can result in fossil biomineralization, and we hypothesize, therefore, that this may have contributed to the formation of well-preserved fossils (Lagerstätten) in the geological record. The characteristic polycrystalline nanofibers may also have served as a potential biosignature for fungal life in early Earth and extraterrestrial environments.

Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis

At particular stages during their life cycles, fungi use multiple strategies to form specialized structures to survive unfavorable environmental conditions. These strategies encompass sporulation, as well as cell-wall melanization, multicellular tissue formation or even dimorphism. The resulting structures are not only used to disperse to other environments, but also to survive long periods of time awaiting favorable growth conditions. As a result, these specialized fungal structures are part of the microbial seed bank, which is known to influence the microbial community composition and contribute to the maintenance of diversity. Despite the importance of the microbial seed bank in the environment, methods to study the diversity of fungal structures with improved resistance only target spores dispersing in the air, omitting the high diversity of these structures in terms of morphology and environmental distribution. In this study, we applied a separation method based on cell lysis to enrich lysis-resistant fungal structures (for instance, spores, sclerotia, melanized yeast) to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in-vitro in selected species. The results obtained showed that DNA from fungal spores and from yeast was only obtained after the application of the enrichment method, while mycelium was always lysed. After validation, we compared the diversity of the total and lysis-resistant fractions in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from the salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed at lower taxonomic ranks. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.

Study on the Potential for Stimulating Mulberry Growth and Drought Tolerance of Plant Growth-Promoting Fungi

Drought stress often leads to heavy losses in mulberry planting, especially for fruits and leaves. Application of plant growth-promoting fungi (PGPF) endows various plant beneficial traits to overcome adverse environmental conditions, but little is known about the effects on mulberry under drought stress. In the present study, we isolated 64 fungi from well-growing mulberry trees surviving periodical drought stress, and Talaromyces sp. GS1, Pseudeurotium sp. GRs12, Penicillium sp. GR19, and Trichoderma sp. GR21 were screened out due to their strong potential in plant growth promotion. Co-cultivation assay revealed that PGPF stimulated mulberry growth, exhibiting increased biomass and length of stems and roots. Exogenous application of PGPF could alter fungal community structures in the rhizosphere soils, wherein Talaromyces was obviously enhanced after inoculation of Talaromyces sp. GS1, and Peziza was increased in the other treatments. Moreover, PGPF could promote iron and phosphorus absorption of mulberry as well. Additionally, the mixed suspensions of PGPF induced the production of catalase, soluble sugar, and chlorophyll, which in turn enhanced the drought tolerance of mulberry and accelerated their growth recovery after drought. Collectively, these findings might provide new insights into improving mulberry drought tolerance and further boosting mulberry fruit yields by exploiting interactions between hosts and PGPF.

Diversity and Composition of Culturable Microorganisms and Their Biodeterioration Potentials in the Sandstone of Beishiku Temple, China

Microbial colonization on stone monuments leads to subsequent biodeterioration; determining the microbe diversity, compositions, and metabolic capacities is essential for understanding biodeterioration mechanisms and undertaking heritage management. Here, samples of epilithic biofilm and naturally weathered and exfoliated sandstone particles from different locations at the Beishiku Temple were collected to investigate bacterial and fungal community diversity and structure using a culture-based method. The biodeterioration potential of isolated fungal strains was analyzed in terms of pigmentation, calcite dissolution, organic acids, biomineralization ability, and biocide susceptibility. The results showed that the diversities and communities of bacteria and fungi differed for the different sample types from different locations. The population of culturable microorganisms in biofilm samples was more abundant than that present in the samples exposed to natural weathering. The environmental temperature, relative humidity, and pH were closely related to the variation in and distribution of microbial communities. Fungal biodeterioration tests showed that isolated strains four and five were pigment producers and capable of dissolving carbonates, respectively. Their biomineralization through the precipitation of calcium oxalate and calcite carbonate could be potentially applied as a biotechnology for stone heritage consolidation and the mitigation of weathering for monuments. This study adds to our understanding of culturable microbial communities and the bioprotection potential of fungal biomineralization.

Brackish and Hypersaline Lakes as Potential Reservoir for Enzymes Involved in Decomposition of Organic Materials on Frescoes

This study highlights the decomposing role through the hydrolytic activities of fungi isolated from natural environments represented by brackish and hypersaline lakes in Romania. Novel strains belonging to the Penicillium, Aspergillus, and Emericellopsis genera were isolated and screened for the ability to produce extracellular hydrolytic enzymes, i.e., proteases, lipases, amylases, cellulases, xylanases, and pectinases. According to salt requirements, they were classified as moderate halophilic and halotolerant strains. Agar plate-based assays with Tween 80, slide cultures with organic deposits, and quantitative evaluation allowed the selection of Aspergillus sp. BSL 2-2, Penicillium sp. BSL 3-2, and Emericellopsis sp. MM2 as potentially good decomposers of organic matter not only in lakes but also on deposits covering the mural paintings. Experiments performed on painted experimental models revealed that only Penicillium sp. BSL 3-2 decomposed Paraloid B72, transparent dispersion of casein, beeswax, sunflower oil, and soot. Moreover, using microscopic, spectroscopic, and imaging methods, it was proved the efficiency of Penicillium sp. BSL 3-2 for decomposition of organic deposits artificially applied on frescoes fragments.

Fungi are key players in extreme ecosystems

Extreme environments on Earth are typically devoid of macro life forms and are inhabited predominantly by highly adapted and specialized microorganisms. The discovery and persistence of these extremophiles provides tools to model how life arose on Earth and inform us on the limits of life. Fungi, in particular, are among the most extreme-tolerant organisms with highly versatile lifestyles and stunning ecological and morphological plasticity. Here, we overview the most notable examples of extremophilic and stress-tolerant fungi, highlighting their key roles in the functionality and balance of extreme ecosystems. The remarkable ability of fungi to tolerate and even thrive in the most extreme environments, which preclude most organisms, have reshaped current concepts regarding the limits of life on Earth.