Geomicrobiology of the built environment

Fungal colonization and penetration of mortar as a suitable simulant for concrete: Implications for fungal biodeterioration in the built environment

A range of fungal species showed variable abilities to colonize and penetrate a mortar substrate. Calcium biomineralization was a common feature with calcium-containing crystals deposited in the microenvironment or encrusting hyphae, regardless of the specific mortar composition. Several species caused significant damage to the mortar surface, exhibiting burrowing and penetration, surface etching, and biomineralization. In some cases, extensive biomineralization of hyphae, probably by carbonatization, resulted in the formation of crystalline tubes after hyphal degradation on mortar blocks, including those amended with Co or Sr carbonate. Ca was the only metal detected in the biomineralized formations with Co or Sr undetectable. Aspergillus niger, Stemphylium sp. and Paecilomyces sp. could penetrate mortar with differential responses depending on the porosity. Fluorescent staining of thin sections recorded penetration depths of ∼530 um for A. niger and ∼620 um for Stemphylium sp. Penetration depth varied inversely with porosity and greater penetration depths were achieved in mortar with a lower porosity (lower water/cement ratio). These results have provided further understanding of biodeteriorative fungal interactions with cementitious substrates that can clearly affect structural integrity. The potential significance of fungal colonization and such biodeteriorative phenomena should not be overlooked in built environment contexts, including radionuclide storage and surface decontamination.

The impact of microbial community structure changes on the migration and release of typical heavy metal (loid)s during the revegetation process of mercury-thallium mining waste slag

The effect of changes in microbial community structure on the migration and release of toxic heavy metal (loid)s is often ignored in ecological restoration. Here, we investigated a multi-metal (mercury and thallium, Tl) mine waste slag. With particular focus on its strong acidity, poor nutrition, and high toxicity pollution characteristics, we added fish manure and carbonate to the slag as environmental-friendly amendments. On this basis, ryegrass, which is suitable for the remediation of metal waste dumps, was then planted for ecological restoration. We finally explored the influence of changes in microbial community structure on the release of Tl and As in the waste slag during vegetation reconstruction. The results show that the combination of fish manure and carbonate temporarily halted the release of Tl, but subsequently promoted the release of Tl and arsenic (As), which was closely related to changes in the microbial community structure in the waste slag after fish manure and carbonate addition. The main reason for these patterns was that in the early stage of the experiment, Bacillaceae inhibited the release of Tl by secreting extracellular polymeric substances; with increasing time, Actinobacteriota became the dominant bacterium, which promoted the migration and release of Tl by mycelial disintegration of minerals. In addition, the exogenously added organic matter acted as an electron transport medium for reducing microorganisms and thus helped to reduce nitrate or As (Ⅴ) in the substrate, which reduced the redox potential of the waste slag and promoted As release. At the same time, the phylum Firmicutes, including specific dissimilatory As-reducing bacteria that are capable of converting As into a more soluble form, further promoted the release of As. Our findings provide a theoretical basis for guiding the ecological restoration of relevant heavy-metal (loid) mine waste dumps.

Growth of electroautotrophic microorganisms using hydrovoltaic energy through natural water evaporation

It has been previously shown that devices based on microbial biofilms can generate hydrovoltaic energy from water evaporation. However, the potential of hydrovoltaic energy as an energy source for microbial growth has remained unexplored. Here, we show that the electroautotrophic bacterium Rhodopseudomonas palustris can directly utilize evaporation-induced hydrovoltaic electrons for growth within biofilms through extracellular electron uptake, with a strong reliance on carbon fixation coupled with nitrate reduction. We obtained similar results with two other electroautotrophic bacterial species. Although the energy conversion efficiency for microbial growth based on hydrovoltaic energy is low compared to other processes such as photosynthesis, we hypothesize that hydrovoltaic energy may potentially contribute to microbial survival and growth in energy-limited environments, given the ubiquity of microbial biofilms and water evaporation conditions.

Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation

SUMMARYFungi are ubiquitous and important biosphere inhabitants, and their abilities to decompose, degrade, and otherwise transform a massive range of organic and inorganic substances, including plant organic matter, rocks, and minerals, underpin their major significance as biodeteriogens in the built environment and of cultural heritage. Fungi are often the most obvious agents of cultural heritage biodeterioration with effects ranging from discoloration, staining, and biofouling to destruction of building components, historical artifacts, and artwork. Sporulation, morphological adaptations, and the explorative penetrative lifestyle of filamentous fungi enable efficient dispersal and colonization of solid substrates, while many species are able to withstand environmental stress factors such as desiccation, ultra-violet radiation, salinity, and potentially toxic organic and inorganic substances. Many can grow under nutrient-limited conditions, and many produce resistant cell forms that can survive through long periods of adverse conditions. The fungal lifestyle and chemoorganotrophic metabolism therefore enable adaptation and success in the frequently encountered extremophilic conditions that are associated with indoor and outdoor cultural heritage. Apart from free-living fungi, lichens are a fungal growth form and ubiquitous pioneer colonizers and biodeteriogens of outdoor materials, especially stone- and mineral-based building components. This article surveys the roles and significance of fungi in the biodeterioration of cultural heritage, with reference to the mechanisms involved and in relation to the range of substances encountered, as well as the methods by which fungal biodeterioration can be assessed and combated, and how certain fungal processes may be utilized in bioprotection.

Biomineral deposits and coatings on stone monuments as biodeterioration fingerprints

Biominerals deposition processes, also called biomineralisation, are intimately related to biodeterioration on stone surfaces. They include complex processes not always completely well understood. The study of biominerals implies the identification of organisms, their molecular mechanisms, and organism/rock/atmosphere interactions. Sampling restrictions of monument stones difficult the biominerals study and the in situ demonstrating of biodeterioration processes. Multidisciplinary works are required to understand the whole process. Thus, studies in heritage buildings have taken advantage of previous knowledge acquired thanks to laboratory experiments, investigations carried out on rock outcrops and within caves from some years ago. With the extrapolation of such knowledge to heritage buildings and the advances in laboratory techniques, there has been a huge increase of knowledge regarding biomineralisation and biodeterioration processes in stone monuments during the last 20 years. These advances have opened new debates about the implications on conservation interventions, and the organism's role in stone conservation and decay. This is a review of the existing studies of biominerals formation, biodeterioration on laboratory experiments, rocks, caves, and their application to building stones of monuments.

Microplastic pollution on historic facades: Hidden 'sink' or urban threat?

Despite the increasing concerns surrounding the health and environmental risks of microplastics (MPs), the research focus has primarily been on their prevalence in air and the oceans, consequently neglecting their presence on urban facades, which are integral to our everyday environments. Therefore, there is a crucial knowledge gap in comprehending urban MP pollution. Our pioneering interdisciplinary study not only quantifies but also identifies MPs on historic facades, revealing their pervasive presence in a medium-sized urban area in the UK. In this case study, we estimated a mean density of 975,000 fibres/m^2 (0.10 fibres/mm^2) for fibre lengths between 30 and 1000 μm with a ratio of 1:5 for natural to artificial fibres. Our research identifies three groups of fibre length frequencies across varied exposure scenarios on the investigated urban facade. Sheltered areas (4m height) show a high prevalence of 60-120 μm and 180-240 μm fibres. In contrast, less sheltered areas at 3m exhibit lower fibre frequencies but similar lengths. Notably, the lowest area (2-1.5m) features longer fibres (300-1000 μm), while adjacent area S, near a faulty gutter, shows no fibres, highlighting the impact of exposure, altitude, and environmental variables on fibre distribution on urban facades. Our findings pave one of many necessary paths forward to determine the long-term fate of these fibres and provoke a pertinent question: do historic facades serve as an urban 'sink' that mitigates potentially adverse health impacts or amplifies the effects of mobile microplastics? Addressing MP pollution in urban areas is crucial for public health and sustainable cities. More research is required to understand the multi-scale factors behind MP pollution in large cities and to find mitigation strategies, paving the way for effective interventions and policies against this growing threat.

Uncovering the Fungal Diversity and Biodeterioration Phenomenon on Archaeological Carvings of the Badami Cave Temples: A Microcosm Study

The Badami Caves are a significant example of ancient Indian rock-cut architecture, dating back to the 6th century. These caves are situated in the Malaprabha River valley and are part of the candidate UNESCO World Heritage Site known as the "Evolution of Temple Architecture-Aihole-Badami-Pattadakal", which is considered to be the cradle of temple architecture in India. Our study aimed to investigate the diversity, distribution, and biodeterioration phenomena of the fungal communities present on the cave surfaces. The study also conducted a comprehensive analysis of fungal biodeterioration on the cave carvings. Utilizing specialized techniques, the dissolution of calcite, alterations in pH levels, and biomineralization capabilities of isolated fungal strains were monitored. Additionally, this study analyzed fungal acid production using high-performance liquid chromatography (HPLC). Our findings revealed that the major genera of fungi found on the cave surfaces included Acremonium, Curvularia, Cladosporium, Penicillium, and Aspergillus. These isolated fungi were observed to produce acids, leading to the dissolution of calcium carbonate and subsequent decrease in pH values. Notably, the dominant genus responsible for acid production and the promotion of biomineralization was Aspergillus. These discoveries provide valuable insight into the ecology and functions of fungi inhabiting stone surfaces, contributing to our understanding of how to preserve and protect sculptures from biodeterioration.

Expanding the Microcolonial Black Fungi Aeminiaceae Family: Saxispiralis lemnorum gen. et sp. nov. (Mycosphaerellales), Isolated from Deteriorated Limestone in the Lemos Pantheon, Portugal

With an impressive ability to survive in harsh environments, black fungi are an ecological group of melanized fungi that are widely recognized as a major contributor to the biodeterioration of stone cultural heritage materials. As part of the ongoing efforts to study the fungal diversity thriving in a deteriorated limestone funerary art piece at the Lemos Pantheon, a national monument located in Águeda, Portugal, two isolates of an unknown microcolonial black fungus were retrieved. These isolates were thoroughly studied through a comprehensive analysis based on a multi-locus phylogeny of a combined dataset of ITS rDNA, LSU, and rpb2, along with morphological, physiological, and ecological characteristics. Based on the data obtained from this integrative analysis, we propose a new genus, Saxispiralis gen. nov., and a new species, Saxispiralis lemnorum sp. nov., in the recently described Aeminiaceae family (order Mycosphaerellales). Prior to this discovery, this family only had one known genus and species, Aeminium ludgeri, also isolated from deteriorated limestone. Additionally, considering the isolation source of the fungus and to better understand its potential contribution to the overall stone monument biodeterioration, its in vitro biodeteriorative potential was also evaluated. This work represents a significant contribution to the understanding of the fungal diversity involved in the biodeterioration of limestone heritage.

Biosynthesized gold nanoparticles that activate Toll-like receptors and elicit localized light-converting hyperthermia for pleiotropic tumor immunoregulation

Manipulating the tumor immune contexture towards a more active state can result in better therapeutic outcomes. Here we describe an easily accessible bacterial biomineralization-generated immunomodulator, which we name Ausome (Au + [exo]some). Ausome comprises a gold nanoparticle core covered by bacterial components; the former affords an inducible hyperthermia effect, while the latter mobilizes diverse immune responses. Multiple pattern recognition receptors actively participate in Ausome-initiated immune responses, which lead to the release of a broad spectrum of pro-inflammatory cytokines and the activation of effector immune cells. Upon laser irradiation, tumor-accumulated Ausome elicits a hyperthermic response, which improves tissue blood perfusion and contributes to enhanced infiltration of immunostimulatory modules, including cytokines and effector lymphocytes. This immune-modulating strategy mediated by Ausome ultimately brings about a comprehensive immune reaction and selectively amplifies the effects of local antitumor immunity, enhancing the efficacy of well-established chemo- or immuno-therapies in preclinical cancer models in female mice.

Community structures and biodeterioration processes of epilithic biofilms imply the significance of micro-environments

Epilithic biofilms colonising outdoor stone monuments can intensify the deterioration processes of the stone materials and pose great challenges to their protection. In this study, biodiversity and community structures of the epilithic biofilms colonising the surfaces of five outdoor stone dog sculptures were characterised by high-throughput sequencing. Although they are exposed to the same envrionment in a small yard, the analysis of their biofilm populations revealed high biodiversity and species richness as well as great differences in community compostions. Interestingly, populations responsible for pigment production (e.g., Pseudomonas, Deinococcus, Sphingomonas and Leptolyngbya) and for nitrogen (e.g., Pseudomonas, Bacillus, and Beijerinckia) and sulfur cycling (e.g., Acidiphilium) were the core common taxa in the epilithic biofilms, suggesting the potential biodeterioration processes. Furthermore, significant positive corrolections of metal elements rich in stone with biofilm communities showed that epilithic biofilms could take in minerals of stone. Importantly, geochemical properties of soluble ions (higher concentration of SO₄^2- than NO₃^-) and slightly acidic micro-environments on the surfaces suggest corrosion of biogenic sulfuric acids as a main mechanism of biodeterioration of the sculptures. Interestingly, relative abundacne of Acidiphilium showed a positive correlation with acidic micro-environments and SO₄^2- concentrations, implying they could be an indicator of sulfuric acid corrosion. Together, our findings support that micro-environments are inportant to community assembly of epilithic biofilms and the biodeterioration processes involved.

Nutrient availability and acid erosion determine the early colonization of limestone by lithobiontic microorganisms

Introduction

Microorganisms, including the pioneer microorganisms that play a role in the early colonization of rock, are extremely important biological factors in rock deterioration. The interaction of microorganisms with limestone leads to biodeterioration, accelerates soil formation, and plays an important role in the restoration of degraded ecosystems that cannot be ignored. However, the process of microbial colonization of sterile limestone in the early stages of ecological succession is unclear, as are the factors that affect the colonization. Acid erosion (both organic and inorganic), nutrient availability, and water availability are thought to be key factors affecting the colonization of lithobiontic microorganisms.

Methods

In this study, organic acid (Oa), inorganic acid (Ia), inorganic acid + nutrient solution (Ia + Nut), nutrient solution (Nut), and rain shade (RS) treatments were applied to sterilized limestone, and the interaction between microorganisms and limestone was investigated using high-throughput sequencing techniques to assess the microorganisms on the limestone after 60 days of natural placement.

Results

The results were as follows: (1) The abundance of fungi was higher than that of bacteria in the early colonization of limestone, and the dominant bacterial phyla were Proteobacteria, Bacteroidota, and Actinobacteriota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Chytridiomycota. (2) Acid erosion and nutrient availability shaped different microbial communities in different ways, with bacteria being more sensitive to the environmental stresses than fungi, and the higher the acidity (Ia and Oa)/nutrient concentration, the greater the differences in microbial communities compared to the control (based on principal coordinate analysis). (3) Fungal communities were highly resistant to environmental stress and competitive, while bacterial communities were highly resilient to environmental stress and stable.

Discussion

In conclusion, our results indicate that limestone exhibits high bioreceptivity and can be rapidly colonized by microorganisms within 60 days in its natural environment, and both nutrient availability and acid erosion of limestone are important determinants of early microbial colonization.

The Microbiome of Things: Appliances, Machines, and Devices Hosting Artificial Niche-Adapted Microbial Communities

As it is the case with natural substrates, artificial surfaces of man-made devices are home to a myriad of microbial species. Artificial products are not necessarily characterized by human-associated microbiomes; instead, they can present original microbial populations shaped by specific environmental-often extreme-selection pressures. This review provides a detailed insight into the microbial ecology of a range of artificial devices, machines, and appliances, which we argue are specific microbial niches that do not necessarily fit in the "build environment" microbiome definition. Instead, we propose here the Microbiome of Things (MoT) concept analogous to the Internet of Things (IoT) because we believe it may be useful to shed light on human-made, but not necessarily human-related, unexplored microbial niches.

Culturable and unculturable potential heterotrophic microbiological threats to the oldest pyramids of the Memphis necropolis, Egypt

A large percentage of the world's tangible cultural heritage is made from stone; thus, it deteriorates due to physical, chemical, and/or biological factors. The current study explored the microbial community inhabiting two prehistoric sites with high cultural value in the Memphis necropolis of Egypt (Djoser and Lahun Pyramids) using amplicon-based metabarcoding and culture-dependent isolation methods. Samples were examined by epifluorescent microscopy for biological signs before environmental DNA extraction and in vitro cultivation. The metabarcoding analysis identified 644 bacterial species (452 genera) using the 16S rRNA and 204 fungal species (146 genera) using ITS. In comparison with the isolation approach, an additional 28 bacterial species (13 genera) and 34 fungal species (20 genera) were identified. A total of 19 bacterial and 16 fungal species were exclusively culture-dependent, while 92 bacterial and 122 fungal species were culture-independent. The most abundant stone-inhabiting bacteria in the current study were Blastococcus aggregatus, Blastococcus saxobsidens, and Blastococcus sp., among others. The most abundant rock-inhabiting fungi were Knufia karalitana and Pseudotaeniolina globosa, besides abundant unknown Sporormiaceae species. Based on previous reports, microorganisms associated with biodeterioration were detected on color-altered sites at both pyramids. These microorganisms are potentially dangerous as physical and chemical deterioration factors and require proper conservation plans from a microbiological perspective.

N/S element transformation modulating lithospheric microbial communities by single-species manipulation

BACKGROUND

The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that provide desirable resources for understanding microbial roles in element cycling. However, the strategy and mechanism of modulating indigenous microbial communities for the optimization of community structures and functions are underexplored, despite its significance in energy recovery and environmental remediation.

RESULTS

Here we proposed a novel selective stimulation of indigenous functional microbes by driving nitrogen and sulfur cycling in petroleum reservoirs using injections of an exogenous heterocycle-degrading strain of Pseudomonas. We defined such bacteria capable of removing and releasing organically bound sulfur and nitrogen from heterocycles as "bioredox triggers". High-throughput 16S rRNA amplicon sequencing, metagenomic, and gene transcription-level analyses of extensive production water and sandstone core samples spanning the whole oil production process clarified the microbiome dynamics following the intervention. These efforts demonstrated the feasibility of in situ N/S element release and electron acceptor generation during heterocycle degradation, shifting microbiome structures and functions and increasing phylogenetic diversity and genera engaged in sulfur and nitrogen cycling, such as Desulfovibrio, Shewanella, and Sulfurospirillum. The metabolic potentials of sulfur- and nitrogen-cycling processes, particularly dissimilatory sulfate reduction and dissimilatory nitrate reduction, were elevated in reservoir microbiomes. The relative expression of genes involved in sulfate reduction (dsrA, dsrB) and nitrate reduction (napA) was upregulated by 85, 28, and 22 folds, respectively. Field trials showed significant improvements in oil properties, with a decline in asphaltenes and aromatics, hetero-element contents, and viscosity, hence facilitating the effective exploitation of heavy oil.

CONCLUSIONS

The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. The presented findings demonstrated the immense potential of our microbial modulation strategy for green and enhanced heavy oil recovery. Video Abstract.

Exploring Differences in Culturable Fungal Diversity Using Standard Freezing Incubation-A Case Study in the Limestones of Lemos Pantheon (Portugal)

In this study, we explored the biodiversity and abundance of culturable fungi in four samples associated with different biodeterioration outlines collected from the Lemos Pantheon, a limestone-built artwork in Portugal. We compared the results from prolonged standard freezing with those previously obtained from fresh samples to analyze differences in the obtained community and assess the effectiveness of the standard freezing incubation protocol in uncovering a different segment of culturable fungal diversity. Our results showed a slight decrease in culturable diversity, but over 70% of the obtained isolates were not present in the previously studied fresh samples. We also identified a high number of potential new species with this procedure. Moreover, the use of a wide variety of selective culture media positively influenced the diversity of the cultivable fungi obtained in this study. These findings highlight the importance of developing new protocols under varying conditions to accurately characterize the culturable fraction in a given sample. The identification and study of these communities and their possible contribution to the biodeterioration process is crucial knowledge for formulating effective conservation and restoration plans to prevent further damage to valuable cultural heritage assets.

Efficient bio-cementation between silicate tailings and biogenic calcium carbonate: Nano-scale structure and mechanism of the interface

Biogenic calcium carbonate (bio-CaCO₃) cementing tailings is an efficient technology to immobilize heavy metals in waste tailings. However, the underlying mechanism of interface cementation has not yet been clearly established, which limits the technological development. In this study, we used advanced techniques, including atomic force microscopy-based Lorentz contact resonance (AFM-LCR) spectroscopy, AFM-based nanoscale infrared (AFM-IR) spectroscopy, and solid-state nuclear magnetic resonance (ssNMR) spectroscopy, to reveal the structural, mechanical, and chemical properties of the interface on the nanoscale. Ureolytic bacteria produced bio-CaCO₃ to fill in pore space and to bind cement tailings particles, which prevented the formation of leachate containing heavy metals. After cementation, a strong 40-300 nm thin interface was formed between the taillings and bio-CaCO₃ particles. Unlike chemically synthesized CaCO₃, bio-CaCO₃ is strongly negatively charged, which gives it better adhesion ability. Fourier transform infrared (FTIR), AFM-IR, and ²⁹Si ssNMR spectra indicated that the Si-OH and Si-O-Si groups on the silicate surface were converted to deprotonated silanol groups (≡Si-O^-) at a high pH and they formed strong chemical bonds of Si-O-Ca on the interface through a Ca ion bridge. In addition, hydrogen bonding with Si-OH also played a role at the cementation interface. These findings provide the nano-scale interfacial structure and mechanism of bio-CaCO₃ cementing silicate tailings and accelerate the development of tailings disposal technology.

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.

Metabolite Profile of the Micromycete Lecanicillium gracile Isolated from Plaster and Limestone

Lecanicillium gracile is a recently described micromycete species isolated from mineral-based building materials (plaster and limestone) in interiors of cultural heritage sites in Russia. In this work, the composition of L. gracile metabolites, as well as of the culture liquid, have been characterized. The results suggest that L. gracile is a promising candidate for the search for novel biologically active compounds. During the exponential growth phase, the diversity of metabolites in the mycelium was low; the metabolome profile demonstrated predominant accumulation of monosaccharides and polyols. In the stationary phase, the metabolite diversity in the L. gracile mycelium was high; apparently, at this stage biosynthesis dominated over energy-producing processes. L. gracile synthesized extracellular polymer compounds and shifted medium рН to the alkaline range. When fungi are developing on rock substrates, their extracellular polymer matrix not only serves to facilitate the formation of biofilms with other microorganisms of lithobiont communities, but also, at alkaline pH values, it promotes the formation of secondary calcite on calcium-containing substrates, such as limestone and marble. That is, L. gracile possesses certain biochemical traits that facilitate its long-term growth on rock substrates and reflect the specific character of interactions between the fungus and the substrate materials.

Change in composition and potential functional genes of microbial communities on carbonatite rinds with different weathering times

Organisms and time are important factors for rock weathering to form soils. However, weathering time is usually difficult to quantitatively study, and the potential microorganisms involved in rock weathering are difficult to identify qualitatively. Currently, there is no clear conclusion on how ecological strategies of carbonatite weathering rind microorganisms change with weathering time, and how the microbial composition and functional genes involved in element cycling change over two century-scale weathering time. In this study, we selected abandoned carbonate tombstones as the subject and used the date when the tombstones were erected by humans as the onset of weathering. Using metagenome sequencing methods, we investigated the trends in the composition of fungal, bacterial and archaeal communities of carbonate weathering rind and related elemental cycle functional genes during a weathering time of 19 to 213 years. The results showed that: (1) with the increase in weathering time, at the phylum level, microbial taxa gradually shifted from r-strategists (faster turnover rates, higher mortality rates, higher reproduction, lower competition rate) to K-strategists (slower turnover rates, lower mortality rates, lower reproduction, higher competition rate), which correspondingly increased the abundance of functional genes related to C and N cycles. (2) The properties of the parent rock layer determines the colonization and distribution of weathering rind microorganisms (especially prokaryotic microorganisms) and the corresponding functional gene abundance. Our study provides new insights into the weathering process of carbonate rocks.

Community assembly, potential functions and interactions between fungi and microalgae associated with biodeterioration of sandstone at the Beishiku Temple in Northwest China

Fungi, cyanobacteria and algae are specific microbial groups associated with the deterioration and safety of stone monuments. In this study, high-throughput sequencing analysis was used to investigate the diversity, distributions, ecological functions, and interaction patterns of both the fungal and microalgal (including cyanobacteria and algae) communities on sandstone in the Beishiku Temple, located on the ancient Silk Road. The results showed that the core phyla of fungi were affiliated with unclassified Lecanoromycetes, Engyodontium, Knufia, Epicoccum, Endocarpon, and Cladosporium of Ascomycota whereas the phyla of microalgae were dominated by prokaryotic Cyanobacteria and eukaryotic Chlorophyta. The environmental factors of temperature, relative humidity, and light intensity were monitored simultaneously. The structure of the microbial communities was much more strongly shaped by soluble Cl^-, Na⁺, NO₃^- ions than by the light intensity, moisture content or temperature, especially for the weathered sandstone located outside the caves. The co-occurrence network analysis suggested that a more stable community structure was evident outside the caves than inside. The stronger positive connections and coexistence patterns that were detected indicate a strong adaptability of fungi and microalgae to the distinct oligotrophic microhabitats on sandstone. The metacommunity co-occurrence network exhibited the ecological predominance of fungi, and most of the functional fungi in the biofilms outside the caves belonged to the Lichenized group, based on the FUNGuild prediction. These findings highlight the ecology and functions of stone-inhabiting microorganisms to further advance the current understanding and knowledge of sandstone biodeterioration for protection and management.

Circumfusicillium cavernae gen. et sp. nov. (Bionectriaceae, Hypocreales) Isolated from a Hypogean Roman Cryptoporticus

Stone monuments and relics are prone to biodeterioration processes prompted by microbial proliferation and activity. Among the distinct microbes capable of stone colonization, fungi are known to strongly contribute to stone biodeterioration. During the ongoing efforts aiming to study fungi thriving in dolomitic limestone walls of the Coimbra’s hypogean Roman cryptoporticus (Portugal), two unknown Bionectriaceae isolates were retrieved. The aim of this work was to depict the molecular and phenotypic characteristics of these microorganisms. The phylogenetic analyses revealed that the studied strains could not be assigned to any of the currently known Bionectriaceae genera. Moreover, the isolates exhibited distinctive and peculiar characteristics, such as the packing of conidia by surrounding hyphal segments and the formation of rope-like microsclerotia with a textura globose. Taking into account all the data obtained, a novel genus and species, Circumfusicillium cavernae gen. et sp. nov. in Bionectriaceae (Hypocreales), is proposed here.

Biodeterioration of stone and metal - Fundamental microbial cycling processes with spatial and temporal scale differences

Fundamental processes for the biodeterioration of stone and metal involve many of the same microbially mediated reactions - oxidation, reduction, acid dissolution and elemental cycling - resulting from the activities of many of the same groups of environmental microorganisms. Differences depend on the nature of the substratum - stone vs. metal - and the composition of the surroundings, whether terrestrial (stone) or aquatic (stone and metal). Reactions within surface-related biofilms dominate the biodeterioration of metals and contribute greatly to the biodeterioration of stone. In the latter, phototrophic organisms, and especially cyanobacteria, are important first participants, while metal biodeterioration is almost entirely associated with bacteria, archaea and fungi. Biofilms on metal surfaces can produce chemical and electrochemical responses. While electrochemical responses are absent in stone, extracellular electron transfer can be a biodeterioration mechanism in some iron-rich rocks. Microorganisms in biofilms can penetrate and create fissures or cracks in stone and metals. However, the most obvious differences in the reactions of built stone and metal structures are related to the definition of failure, length of time required for a defined failure of the substratum, the area over which the failure occurs and the consequences of failure. Time and space are, similarly, quite distinct for biological breakdown and mineral cycling of metal and stone, with stone/rock cycling potentially occurring over thousands of years and kilometers.

Long-amplicon MinION-based sequencing study in a salt-contaminated twelfth century granite-built chapel

Abstract

The irregular damp dark staining on the stonework of a salt-contaminated twelfth century granite-built chapel is thought to be related to a non-homogeneous distribution of salts and microbial communities. To enhance understanding of the role of microorganisms in the presence of salt and damp stains, we determined the salt content and identified the microbial ecosystem in several paving slabs and inner wall slabs (untreated and previously bio-desalinated) and in the exterior surrounding soil. Soluble salt analysis and culture-dependent approaches combined with archaeal and bacterial 16S rRNA and fungal ITS fragment as well as with the functional genes nirK, dsr, and soxB long-amplicon MinION-based sequencing were performed. State-of-the-art technology was used for microbial identification, providing information about the microbial diversity and phylogenetic groups present and enabling us to gain some insight into the biological cycles occurring in the community key genes involved in the different geomicrobiological cycles. A well-defined relationship between microbial data and soluble salts was identified, suggesting that poorly soluble salts (CaSO₄) could fill the pores in the stone and lead to condensation and dissolution of highly soluble salts (Ca(NO₃)₂ and Mg(NO₃)₂) in the thin layer of water formed on the stonework. By contrast, no direct relationship between the damp staining and the salt content or related microbiota was established. Further analysis regarding organic matter and recalcitrant elements in the stonework should be carried out.

Key points

• Poorly (CaSO₄) and highly (Ca(NO₃)₂, Mg(NO₃)₂) soluble salts were detected

• Halophilic and mineral weathering microorganisms reveal ecological impacts of salts

• Microbial communities involved in nitrate and sulfate cycles were detected

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-11961-8.

Biocontamination and diversity of epilithic bacteria and fungi colonising outdoor stone and mortar sculptures

Microbial communities colonising outdoor sculptures form intricate and dynamic ecosystems, which can accelerate the deterioration processes of the artworks and pose challenges to their conservation. In this study, the bacterial and fungal communities colonising the surfaces of five contemporary outdoor sculptures were characterised by high-throughput sequencing. The sculptures, made of marble, granite, Ançã limestone and mortar, are in urban parks and squares in the district of Porto, Portugal. The analysis of the microbial populations revealed great taxonomic diversity and species richness, including in well-preserved sculptures showing few visible traces of contamination. Proteobacteria, namely the genera Pseudomonas and Sphingomonas, were the core taxa common to all the sculptures, while Massilia and Aureobasidium were dominant only in granite. An abundance of pigment-producing microorganisms, such as Deinococcus, Methylobacterium, Rhodotorula and Sporobolomyces, was also found in granite. These are relevant taxonomic groups that can negatively impact stone and mortar artworks. The study was complemented with colourimetric analyses and bioluminescence assays to measure the adenosine triphosphate (ATP) content of samples collected from specific contaminated areas of the sculptures. The characterisation of the microbiomes of sculptures can provide further knowledge on the deterioration risks of this type of artwork in the region and help outline future targeted conservation strategies. KEY POINTS: • Rich and abundant microbiomes expose sculptures' vulnerability to deterioration. • Well-preserved sculptures are at risk of deterioration by pigment-producing taxa. • ATP and colourimetry quickly identified the most relevant contaminated areas.

Black Fungi on Stone-Built Heritage: Current Knowledge and Future Outlook

Black fungi are considered as one of the main group of microorganisms responsible for the biodeterioration of stone cultural heritage artifacts. In this paper, we provide a critical analysis and review of more than 30 years of studies on black fungi isolated from stone-built heritage from 1990 to date. More than 109 papers concerning the fungal biodeterioration activity of stone were analysed. The main findings were a check list of the black fungal taxa involved in the biodeterioration of stone-built heritage, with a particular reference to meristematic black fungi, the main biodeterioration pattern attributed to them, and the methods of study including the new molecular advances. A particular focus was to discuss the current approaches to control black fungi from stone-built heritage and future perspectives. Black fungi are notoriously hard to remove or mitigate, so new methods of study and of control are needed, but it is also important to combine classical methods with new approaches to improve current knowledge to implement future conservation strategies.

Fungal-induced CaCO3 and SrCO3 precipitation: a potential strategy for bioprotection of concrete

Biomineralization of CaCO₃ by microorganisms is a well-documented process considered applicable to concrete self-healing and metal bioremediation. Urea hydrolysis is the most widely explored and efficient pathway regarding concrete bioprotection. However, the potential of fungi has received relatively little attention compared to bacteria. In this work, we show that Fusarium cerealis, Phoma herbarum and Mucor hiemalis, isolated from concrete, could produce 828.6-941.3 mg L^-1 ammonium‑nitrogen in liquid media through urea hydrolysis indicating significant urease activity, and could grow in moderate (pH 8.3) or even extremely alkaline (pH 10.6) conditions. After culture in media containing 50 mM CaCl₂, at least 48.8% Ca²⁺ was removed from solution by the selected fungi as calcite. The accumulation of Ca by the biomass was around 83.64-114.21 mg g^-1. In addition, all fungi could mediate strontium carbonate formation with F. cerealis processing the highest ability for Sr removal, with ~61% added Sr being removed from solution. Scanning electron microscopy showed carbonate biominerals were encrusted on hyphae or aggregated in fungal pellets. When equivalent concentrations of Ca²⁺ and Sr²⁺ were supplemented to the media, CaCO₃ with incorporated Sr formed with F. cerealis and M. hiemalis, and Sr(Sr, Ca)(CO₃)₂ with P. herbarum. Our results demonstrate the potential of fungi in providing carbonate coatings for concrete surfaces and simultaneous immobilization of Sr. We anticipate our work will promote further practical field research on porous cementitious materials protection by fungi and immobilization of potentially toxic metals from metal-laden ingredients, such as fly ash and granulated ground blast furnace slag.

Understanding the Complexities and Changes of the Astronaut Microbiome for Successful Long-Duration Space Missions

During space missions, astronauts are faced with a variety of challenges that are unique to spaceflight and that have been known to cause physiological changes in humans over a period of time. Several of these changes occur at the microbiome level, a complex ensemble of microbial communities residing in various anatomic sites of the human body, with a pivotal role in regulating the health and behavior of the host. The microbiome is essential for day-to-day physiological activities, and alterations in microbiome composition and function have been linked to various human diseases. For these reasons, understanding the impact of spaceflight and space conditions on the microbiome of astronauts is important to assess significant health risks that can emerge during long-term missions and to develop countermeasures. Here, we review various conditions that are caused by long-term space exploration and discuss the role of the microbiome in promoting or ameliorating these conditions, as well as space-related factors that impact microbiome composition. The topics explored pertain to microgravity, radiation, immunity, bone health, cognitive function, gender differences and pharmacomicrobiomics. Connections are made between the trifecta of spaceflight, the host and the microbiome, and the significance of these interactions for successful long-term space missions.

Rocks support a distinctive and consistent mycobiome across contrasting dry regions of Earth

Rock-dwelling fungi play critical ecological roles in drylands, including soil formation and nutrient cycling; however, we know very little about the identity, function and environmental preferences of these important organisms, and the mere existence of a consistent rock mycobiome across diverse arid regions of the planet remains undetermined. To address this knowledge gap, we conducted a meta-analysis of rock fungi and spatially associated soil communities, surveyed across 28 unique sites spanning four major biogeographic regions (North America, Arctic, Maritime and Continental Antarctica) including contrasting climates, from cold and hot deserts to semi-arid drylands. We show that rocks support a consistent and unique mycobiome that was different to that found in surrounding soils. Lichenized fungi from class Lecanoromycetes were consistently indicative of rocks across contrasting regions, together with ascomycetous representatives of black fungi in Arthoniomycetes, Dothideomycetes, and Eurotiomycetes. In addition, comparing to soil, rocks had a lower proportion of saprobes and plant symbiotic fungi. The main drivers structuring rock fungi distribution were spatial distance and, to a larger extent, climatic factors regulating moisture and temperature (i.e. mean annual temperature and mean annual precipitation), suggesting that these paramount and unique communities might be particularly sensitive to increases in temperature and desertification.

Examining the Potential of Enzyme-Based Detergents to Remove Biofouling from Limestone Heritage

Commonwealth war cemeteries commemorate the fallen of both world wars. Every casualty is remembered with a memorial or on a headstone. However, the headstones need to be maintained extensively, as microorganisms easily colonise them, affecting legibility and the stone substrate in the longer term. In the past, pesticides and other chemicals were popular to clean headstones, but due to raised environmental concerns, new treatment strategies are necessary. Within conservation science, enzymes have emerged as a popular tool for restoration. However, studies related to the use of enzymes for stone conservation are limited. Within this preliminary study, we applied commercially available enzyme-based treatments on biofouled natural building stones in the laboratory and in situ. Photography and spectrophotometry were used to monitor the effect of the treatment. The application of enzymes resulted in rapid disintegration of biological pigments, whereas visual improvement occurred more gradually. The successful application of enzymes suggests their potential to replace pesticides as the principal cleaning agent for headstones and natural building stones in a more general fashion.

Biofilm control by interfering with c-di-GMP metabolism and signaling

Biofilm formation and biofilm-induced biodeterioration of surfaces have deeply affected the life of our community. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a small nucleic acid signal molecule in bacteria, which functions as a second messenger mediating a wide range of bacterial processes, such as cell motility, biofilm formation, virulence expression, and cell cycle progression. C-di-GMP regulated phenotypes are triggered by a variety of determinants, such as metabolic cues and stress factors that affect c-di-GMP synthesis, the transduction and conduction of signals by specific effectors, and their actions on terminal targets. Therefore, understanding of the regulatory mechanisms of c-di-GMP would greatly benefit the control of the relevant bacterial processes, particularly for the development of anti-biofilm technologies. Here, we discuss the regulatory determinants of c-di-GMP signaling, identify the corresponding chemical inhibitors as anti-biofilm agents, and shed light on further perspectives in the metabolic regulation of c-di-GMP through chemical and biological approaches. This Review will advance the development of anti-biofilm policies applied in the industries of medicine, environment and engineering.

Microbiome characteristics and the key biochemical reactions identified on stone world cultural heritage under different climate conditions

The surfaces of historical stone monuments are visibly covered with a layer of colonizing microorganisms and their degradation products. In this study, a metadata analysis was conducted using the microbial sequencing data available from NCBI database to determine the diversity, biodeterioration potential and functionality of the stone microbiome on important world cultural heritage sites under four different climatic conditions. The retrieved stone microbial community composition in these metagenomes shows a clear association between climate types of the historical monuments and the diversity and taxonomic composition of the stone microbiomes. Shannon diversity values showed that microbial communities on stone monuments exposed to dry climate were more diverse than those under humid ones. In particular, functions associated with photosynthesis and UV resistance were identified from geographical locations under different climate types. The distribution of key microbial determinants responsible for stone deterioration was linked to survival under extreme environmental conditions and biochemical capabilities and reactions. Among them, biochemical reactions of the microbial nitrogen and sulfur cycles were most predominant. These stone-dwelling microbiomes on historical stone monuments were highly diverse and self-sustaining driven by energy metabolism and biomass accumulation. And metabolic products of the internal geomicrobiological nitrogen cycling on these ancient monuments play a unique role in the biodeterioration of stone monuments. These results highlight the significance of identifying the essential microbial biochemical reactions to advance the understanding of stone biodeterioration for protection management.

Fungal biomineralization

Fungi are key organisms of the biosphere with major roles in organic-matter decomposition, element cycling, plant pathogenicity, and symbioses in aquatic and terrestrial habitats. The vast majority exhibit a filamentous, branching growth form and are aerobic chemoorganotrophs that derive carbon and energy from organic substances, and are particularly associated with soil, the plant-root zone, and rock surfaces. It is now known that some fungi are lithotrophs, deriving energy from the oxidation of inorganic materials, whereas others are photoheterotrophs, deriving additional energy from light for organic matter utilization when oxygen is limited. This means that fungi are of much wider environmental significance than previously thought and explains their ubiquity in locations previously thought to be inimical to fungal existence, such as the deep subsurface and other anaerobic locations. In addition to such free-living species, fungi associated with photosynthetic partners are also of profound biosphere importance. For example, lichens, which are composed of a symbiotic association between a fungus and a phototrophic alga and/or cyanobacterium, are pioneer colonizers and bioweathering agents of rocks and minerals. Mycorrhizas are symbiotic, plant-root-associated fungi found to colonize the majority of plant genera, where they improve plant nutrition through solubilization of essential metals and phosphate from soil minerals. Biomineralization in the soil can also immobilize toxic metals in the vicinity of plant roots, thereby benefiting plant colonization and facilitating revegetation of contaminated habitats. Wherever fungi are found, transformation of metals and minerals is a key aspect of their activity, with biomineralization an important feature. Fungal biomineralization is an important facet of geomycology - namely the roles of fungi in geochemical and geophysical processes. This article seeks to highlight the concept of biomineralization as applied to fungi, the occurrence and significance of important fungal biominerals in natural and synthetic environments, and the applied potential of fungal biomineralization in nanobiotechnology.

Current Knowledge on the Fungal Degradation Abilities Profiled through Biodeteriorative Plate Essays

Fungi are known to contribute to the development of drastic biodeterioration of historical and valuable cultural heritage materials. Understandably, studies in this area are increasingly reliant on modern molecular biology techniques due to the enormous benefits they offer. However, classical culture dependent methodologies still offer the advantage of allowing fungal species biodeteriorative profiles to be studied in great detail. Both the essays available and the results concerning distinct fungal species biodeteriorative profiles obtained by amended plate essays, remain scattered and in need of a deep summarization. As such, the present work attempts to provide an overview of available options for this profiling, while also providing a summary of currently known fungal species putative biodeteriorative abilities solely obtained by the application of these methodologies. Consequently, this work also provides a series of checklists that can be helpful to microbiologists, restorers and conservation workers when attempting to safeguard cultural heritage materials worldwide from biodeterioration.

Role of Exposure on the Microbial Consortiums on Historical Rural Granite Buildings

Local granite has been used throughout history in Galicia (NW Spain), forming the basis of much of the region’s architecture. Like any other rock, granite provides an ecological niche for a multitude of organisms that form biofilms that can affect the physical integrity of the stone. In this study, for the first time, characterization of the microbial consortium forming biofilms that developed on historical rural granite buildings is carried out using a combination of culture-dependent and next generation sequencing (NGS) techniques. Results pointed to differences in biofilm composition on the studied rural granite buildings and that of previously analyzed urban granite buildings, especially in terms of abundance of cyanobacteria and lichenized fungi. Exposure was corroborated as an important factor, controlling both the diversity and abundance of microorganisms on walls, with environmental factors associated with a northern orientation favoring a higher diversity of fungi and green algae, and environmental factors associated with the west orientation determining the abundance of lichenized fungi. The orientation also affected the distribution of green algae, with one of the two most abundant species, Trentepohlia cf. umbrina, colonizing north-facing walls, while the other, Desmococcus olivaceus, predominated on west-facing walls.

Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation

Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.

Mineralosphere Microbiome Leading to Changed Geochemical Properties of Sedimentary Rocks from Aiqigou Mud Volcano, Northwest China

The properties of rocks can be greatly affected by seepage hydrocarbons in petroleum-related mud volcanoes. Among them, the color of sedimentary rocks can reflect the changes of sedimentary environment and weathering history. However, little is known about the microbial communities and their biogeochemical significance in these environments. In this study, contrasting rock samples were collected from the Aiqigou mud volcano on the southern margin of the Junggar Basin in Northwest China as guided by rock colors indicative of redox conditions. The physicochemical properties and mineral composition are similar under the same redox conditions. For example, the content of chlorite, muscovite, quartz, and total carbon were higher, and the total iron was lower under reduced conditions compared with oxidized environments. High-throughput sequencing of 16S rRNA gene amplicons revealed that different functional microorganisms may exist under different redox conditions; microbes in oxidized conditions have higher diversity. Statistical analysis and incubation experiments indicated that the microbial community structure is closely related to the content of iron which may be an important factor for color stratification of continental sedimentary rocks in the Aiqigou mud volcano. The interactions between organics and iron-bearing minerals mediated by microorganisms have also been hypothesized.

Effect of pulp density on the bioleaching of metals from petroleum refinery spent catalyst

Bioleaching is one of the well-known methods of metal recovery with Environmental benefits. This process has been extensively used for combating improper waste management issues along with metal reclamation. The aim of this study is to bioleach spent petroleum refinery catalyst at variant pulp densities (PD) (5, 10 and 15%) using microorganisms in acidic pH (1.5-1.6) and mesophilic temperature (30-35 °C). The study includes leaching yields of metals like nickel, molybdenum, copper and aluminum. The three bioleaching experiments with different pulp densities yielded a maximum of more than 90% nickel, 73% copper, 87% molybdenum and 24% aluminum. The results are validated 5, 10, and 15% pulp density and the result is validated with pH, Redox potential, microbial population, sulphate concentration and ferrous iron, concentration. The time saving due to faster nickel dissolution using iron and sulphur oxidizing microorganisms would be economical for the bioleaching process.

Fungal Metabolites with Antagonistic Activity against Fungi of Lithic Substrata

Fungi are among the biotic agents that can cause deterioration of building stones and cultural heritage. The most common methods used to control fungal spread and growth are based on chemical pesticides. However, the massive use of these synthetic chemicals produces heavy environmental pollution and risk to human and animal health. Furthermore, their use is time dependent and relies on the repetition of treatments, which increases the possibility of altering building stones and culture heritage through environmental contamination. One alternative is the use of natural products with high antifungal activity, which can result in reduced toxicity and deterioration of archeological remains. Recently, three fungal strains, namely Aspergillus niger, Alternaria alternata and Fusarium oxysporum, were isolated as damaging agents from the external tuff wall of the Roman remains "Villa of Poppea" in Oplontis, Naples, Italy. In this manuscript, three selected fungal metabolites, namely cyclopaldic acid, cavoxin and epi-epoformin, produced by fungi pathogenic for forest plants, were evaluated as potential antifungal compounds against the above fungi. Cavoxin and epi-epoformin showed antifungal activity against Asperigillus niger and Fusarium oxysporum, while cyclopaldic acid showed no activity when tested on the three fungi. The same antifungal activity was observed in vitro experiments on infected stones of the Neapolitan yellow tuff (NYT), a volcanic lithotype widely diffused in the archeological sites of Campania, Italy. This study represents a first step in the use of these two fungal metabolites to allow better preservation of artworks and to guarantee the conditions suitable for their conservation.

Metagenome Across a Geochemical Gradient of Indian Stone Ruins Found at Historic Sites in Tamil Nadu, India

Although stone surfaces seem unlikely to be habitable, they support microbial life. Life on these surfaces are subjected to many varying harsh conditions and require the inhabitants to exhibit resistance to environmental factors including UV irradiation, toxic metal exposure, and fluctuating temperatures and humidity. Here we report the effect of hosting stone geochemistry on the microbiome of stone ruins found in Tamil Nadu, India. The microbial communities found on the two lithologies, granite and granodiorite, hosted distinct populations of bacteria. Geochemical composition analysis of sampled stones revealed quartz mineral content as a major driver of microbial community structure, particularly promoting community richness and proportions of Cyanobacteria and Deinococcus-Thermus. Other geochemical parameters including ilmenite, albite, anorthite, and orthoclase components or elemental concentrations (Ti, Fe, Mn, Na, and K) also influenced community structure to a lesser degree than quartz. Core members of the stone microbiome community found on both lithologies were also identified and included Cyanobacteria (Chroococcidiopsaceae and Dapisostemonum CCIBt 3536), Rubrobacter, and Deinococcus. A cluster of taxa including Sphingomonas, Geodermatophilus, and Truepera were mostly found in the granodiorite samples. Community diversity correlated with quartz mineral content in these samples may indicate that the microbial communities that attach to quartz surfaces may be transient and regularly changing. This work has expanded our understanding of built-stone microbial community structure based on lithology and geochemistry.

Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland

The aim of the presented investigation was to describe seasonal changes of microbial community composition in situ in different biocenoses on historical sandstone of the Northern Pergola in the Museum of King John III’s Palace at Wilanow (Poland). The microbial biodiversity was analyzed by the application of Illumina-based next-generation sequencing methods. The metabarcoding analysis allowed for detecting lichenized fungi taxa with the clear domination of two genera: Lecania and Rhinocladiella. It was also observed that, during winter, the richness of fungal communities increased in the biocenoses dominated by lichens and mosses. The metabarcoding analysis showed 34 bacterial genera, with a clear domination of Sphingomonas spp. across almost all biocenoses. Acidophilic bacteria from Acidobacteriaceae and Acetobacteraceae families were also identified, and the results showed that a significant number of bacterial strains isolated during the summer displayed the ability to acidification in contrast to strains isolated in winter, when a large number of isolates displayed alkalizing activity. Other bacteria capable of nitrogen fixation and hydrocarbon utilization (including aromatic hydrocarbons) as well as halophilic microorganisms were also found. The diversity of organisms in the biofilm ensures its stability throughout the year despite the differences recorded between winter and summer.

A Review of Asbestos Bioweathering by Siderophore-Producing Pseudomonas: A Potential Strategy of Bioremediation

Asbestos, silicate minerals present in soil and used for building constructions for many years, are highly toxic due primarily to the presence of high concentrations of the transition metal iron. Microbial weathering of asbestos occurs through various alteration mechanisms. Siderophores, complex agents specialized in metal chelation, are common mechanisms described in mineral alteration. Solubilized metals from the fiber can serve as micronutrients for telluric microorganisms. The review focuses on the bioweathering of asbestos fibers, found in soil or manufactured by humans with gypsum (asbestos flocking) or cement, by siderophore-producing Pseudomonas. A better understanding of the interactions between asbestos and bacteria will give a perspective of a detoxification process inhibiting asbestos toxicity.

Microbial Interaction with Clay Minerals and Its Environmental and Biotechnological Implications

Clay minerals are very common in nature and highly reactive minerals which are typical products of the weathering of the most abundant silicate minerals on the planet. Over recent decades there has been growing appreciation that the prime involvement of clay minerals in the geochemical cycling of elements and pedosphere genesis should take into account the biogeochemical activity of microorganisms. Microbial intimate interaction with clay minerals, that has taken place on Earth’s surface in a geological time-scale, represents a complex co-evolving system which is challenging to comprehend because of fragmented information and requires coordinated efforts from both clay scientists and microbiologists. This review covers some important aspects of the interactions of clay minerals with microorganisms at the different levels of complexity, starting from organic molecules, individual and aggregated microbial cells, fungal and bacterial symbioses with photosynthetic organisms, pedosphere, up to environmental and biotechnological implications. The review attempts to systematize our current general understanding of the processes of biogeochemical transformation of clay minerals by microorganisms. This paper also highlights some microbiological and biotechnological perspectives of the practical application of clay minerals–microbes interactions not only in microbial bioremediation and biodegradation of pollutants but also in areas related to agronomy and human and animal health.

Fungal bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals

Abstract

Much research has been carried out on the bacterial bioremediation of soil contaminated with petroleum hydrocarbons and toxic metals but much less is known about the potential of fungi in sites that are co-contaminated with both classes of pollutants. This article documents the roles of fungi in soil polluted with both petroleum hydrocarbons and toxic metals as well as the mechanisms involved in the biotransformation of such substances. Soil characteristics (e.g., structural components, pH, and temperature) and intracellular or excreted extracellular enzymes and metabolites are crucial factors which affect the efficiency of combined pollutant transformations. At present, bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals is mostly focused on the removal, detoxification, or degradation efficiency of single or composite pollutants of each type. Little research has been carried out on the metabolism of fungi in response to complex pollutant stress. To overcome current bottlenecks in understanding fungal bioremediation, the potential of new approaches, e.g., gradient diffusion film technology (DGT) and metabolomics, is also discussed.

Key points

• Fungi play important roles in soil co-contaminated with TPH and toxic metals.

• Soil characteristics, enzymes, and metabolites are major factors in bioremediation.

• DGT and metabolomics can be applied to overcome current bottlenecks.

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.

In situ monitoring of exopolymer-dependent Mn mineralization on bacterial surfaces

Bacterial biomineralization is a widespread process that affects cycling of metals in the environment. Functionalized bacterial cell surfaces and exopolymers are thought to initiate mineral formation, however, direct evidences are hampered by technical challenges. Here, we present a breakthrough in the use of liquid-cell scanning transmission electron microscopy to observe mineral growth on bacteria and the exopolymers they secrete. Two Escherichia coli mutants producing distinct exopolymers are investigated. We use the incident electron beam to provoke and observe the precipitation of Mn-bearing minerals. Differences in the morphology and distribution of Mn precipitates on the two strains reflect differences in nucleation site density and accessibility. Direct observation under liquid conditions highlights the critical role of bacterial cell surface charges and exopolymer types in metal mineralization. This has strong environmental implications because biofilms structured by exopolymers are widespread in nature and constitute the main form of microbial life on Earth.