Impact of soil density on biomineralization using EICP and MICP techniques for earthen sites consolidation.

Enzyme-induced calcium carbonate precipitation (EICP) and microbially-induced calcium carbonate precipitation (MICP) techniques represent emerging trends in soil stabilization. However, the impact of soil density on biomineralization, particularly in historical earthen sites, remains unclear. This study compares the consolidation effects of EICP and MICP on cylindrical samples (10 cm × 5 cm) with three densities (1.5 g/cm3, 1.6 g/cm3, and 1.7 g/cm3) derived from the soil near the UNESCO World Cultural Heritage Site of Suoyang Ancient City, Gansu Province, China. Results showed that calcium carbonate production increased across all densities through bio-cementation, with higher densities producing more calcium carbonate. MICP-treated specimens exhibited larger increases in calcium carbonate production compared to those treated with EICP. Specimens with a density of 1.7 g/cm³ showed a wave velocity increase of 3.26% (EICP) and 7.13% (MICP), and an unconfined compressive strength increase of 8% (EICP) and 26% (MICP). These strength increases correlated with the generation of calcium carbonate. The findings suggest that biomineralization can be effectively utilized for in situ consolidation of earthen sites, emphasizing the importance of considering soil density in biologically-based conservation technologies. Furthermore, MICP shows potential advantages over EICP in providing stronger, compatible and more sustainable soil reinforcement.

Research progress on ecological adaptation and prevention of Parengyodontium album on the surface of cultural relics.

Cultural relics as the crystallization of human history are non-renewable and irreplaceable resources. Microorganisms are widely colonized on ancient wall paintings, stone cultural relics, and other types of cultural heritages to cause harm. The dominant disease fungus, Parengyodontium album, is extensively distributed and can seriously threaten the long-term preservation of precious cultural heritage due to surviving in various cultural relics and extreme environments. The classification and nomenclature of P. album have undergone several changes, so its impact on cultural relic received little attention. Here, we summarized the brief histories of its classification and development, distribution range, and cultural heritage preference of P. album. We further analyzed the physiological, biochemical, and ecological characteristics and potential biological degradation mechanism. We proposed that P. album could be used as an indicative species of microbial hazardous effects on cultural heritage. We discussed the prevention and control countermeasures of such typical mural microorganisms and pointed out key research directions in this field.

Dominance by cyanobacteria in the newly formed biofilms on stone monuments under a protective shade at the Beishiku Temple in China.

Following the installation of a protective shade, rapid propagation of microorganisms showing in black and grey colors occurred at Beishiku Temple in Gansu Province of China. This study employed a combination of high-throughput sequencing technology, morphological examinations, and an assessment of the surrounding environmental condition to analyze newly formed microbial disease spots. The investigation unveiled the responsible microorganisms and the instigating factors of the microbial outbreak that subsequently to the erection of the shade. Through comparison of bioinformatics, the ASV method surpasses the OTU method in characterizing community compositional changes by the dominant microbial groups, the phylum Cyanobacteria emerged as the most dominant ones in the microbial community accountable for the post-shade microbial deterioration. The black spot and grey spot are predominantly composed of Mastigocladopsis and Scytonema, respectively. Validation analysis, based on the active RNA-level community results, supported and validated these conclusions. Comparative scrutiny of the microbial community before shade installation and the background environmental data disclosed that the erection of the shade prompted a decrease in temperatures and an increase in humidity within the protected area. Consequently, this spurred the exponential proliferation of indigenous cyanobacteria in the spots observed. The outcomes of this study carry considerable significance in devising preventive conservation strategies for cultural heritage and in managing the process of biodeterioration.

Differences of airborne and mural microorganisms in a 1,500-year-old Xu Xianxiu's Tomb, Taiyuan, China.

Background: Microbial colonization represents one of the main threats to the conservation of subterranean cultural heritage sites. Recently, the microbial colonization on murals in tombs has gradually attracted attention. Methods: In this study, a total of 33 samples, including 27 aerosol samples and 6 mural painting samples, were collected from different sites of Xu Xianxiu's Tomb and analyzed using culture-dependent methods. We compared the diversities of culturable bacteria and fungi isolated from the air and murals and explored the potential impacts of microorganisms on the biodeterioration of the murals. Results: Phylogenetic analyses revealed that the culturable bacteria belonged to Bacillus, Microbacterium, Lysobacter and Arthrobacter. And the most of fungal belonged to the Penicillium, Cladosporium and Aspergillus genera. The composition and structure of airborne bacteria and fungi outside the tomb were both significantly different from that inside the tomb. The variation trends of airborne bacterial and fungal concentrations at different sampling sites were remarkably similar. Bacillus frigoritolerans, Bacillus halotolerans, Bacillus safensis, Exiguobacterium mexicanum, Microbacterium trichothecenolyticum, and Micrococcus yunnanensis were bacterial species commonly isolated from both the mural and air environments. Fungal species commonly isolated from aerosol samples and mural painting samples were Alternaria alternata, Cladosporium cladosporioides, Penicillium brevicompactum, and Peyronellaea glomerata. The prediction of the ecological functions of the bacteria revealed that chemoheterotrophy or aerobic_chemoheterotrophy accounted for substantial relative proportions in all sample types. Conclusion: These results suggest that the aerosol circulation between the inside and outside environments of the tomb was weak and that the outside environment had yet to have an impact on the air microbial community inside the tomb. Selective colonization of microorganisms, which is mediated by interaction between microorganisms and special microenvironmental factors, is an important reason for the biodeterioration of murals.

New insights into Saccharomyces cerevisiae induced calcium carbonate precipitation.

Our previous study reported that Saccharomyces cerevisiae could induce calcium carbonate (CaCO3) precipitation, but the associated mechanism was unclear. In the present study, Saccharomyces cerevisiae was cultured under various conditions, including the presence of different organic acids and initial pH, and the yields of CaCO3 formation induced by the different organic acids were compared. The metabolism of organic acid by the metabolites of S. cerevisiae was also assessed in vitro. The SEM-EDS and XRD results showed that only acetate acid, pyruvic acid, and α-ketoglutaric acid could induce CaCO3 formation, and the weight order of the produced CaCO3 was pyruvic acid, acetate acid, α-ketoglutaric acid. In addition, the presence of only yeast metabolites and the initial neutral or alkaline environment also limited the CaCO3 formation. These results illustrated that organic acid oxidation intracellularly, especially the tricarboxylic acid cycle, was the major mechanism, and the CaCO3 yield was related to the amount of CO2 produced by the metabolism of organic acids. These findings will deepen the knowledge of the mineralization capacity of S. cerevisiae and provide a theoretical basis for the future application of yeast as an alternative microorganism in MICP.

Metagenomic and metaproteomic insights into the microbiome and the key geobiochemical potentials on the sandstone of rock-hewn Beishiku Temple in Northwest China.

Metagenomics and metaproteomics analyses were used to determine the microbial diversity and taxon composition, as well as the biochemical potentials of the microbiome on the sandstone of Beishiku Temple located in Northwest China. Taxonomic annotation of the metagenomic dataset revealed the predominant taxa of the stone microbiome on this cave temple with characteristics of resistance to harsh environmental conditions. Meanwhile, there were also taxa in the microbiome that showed sensitivity to environmental factors. The taxa distribution and the metabolic functional distribution patterns by the metagenome and metaproteome, respectively, showed clear differences. The high abundance of energy metabolism represented in the metaproteome suggested that there were active geomicrobiological cycles of elements within the microbiome. The taxa responsible for reactions in the nitrogen cycle from both metagenome and metaproteome supported a metabolically active nitrogen cycle, and the high activity of Comammox bacteria indicated the strong metabolic activity of ammonia oxidation to nitrate in the outdoor site. The SOX-related taxa involved in the sulfur cycle showed higher activity outdoors than indoors, and on the outdoor ground than at the outdoor cliff, as detected through metaproteomic analysis. The development of petrochemical industry in the vicinity resulting in the deposition of sulfur/oxidized sulfur via atmosphere may stimulate the physiological activity of SOX. Our findings provide metagenomic and metaproteomic evidence for microbially driven geobiochemical cycles that result in the biodeterioration of stone monuments.

The Distribution and Influencing Factors of Hypolithic Microbial Communities in the Hexi Corridor.

The Hexi Corridor is an arid region in northwestern China, where hypoliths are widely distributed, resulting from large amounts of translucent stone pavements. In this region, the water and heat distributions are uneven, with a descent gradient from east to west, which can affect the area's biological composition. The impact of environmental heterogeneity on the distribution of hypolithic microbial communities in this area is poorly understood, and this is an ideal location to investigate the factors that may influence the composition and structure of hypolithic microbial communities. An investigation of different sites with differences in precipitation between east and west revealed that the colonization rate decreased from 91.8% to 17.5% in the hypolithic community. Environmental heterogeneity influenced both the structure and function of the hypolithic community, especially total nitrogen (TN) and soil organic carbon (SOC). However, the effect on taxonomic composition was greater than that on ecological function. The dominant bacterial phyla in all sample sites were Cyanobacteria, Actinobacteria, Proteobacteria, and Deinococcus-Thermus, but the abundances varied significantly between the sampling sites. The eastern site had the highest relative abundance of Proteobacteria (18.43%) and Bacteroidetes (6.32%), while the western site had a higher relative abundance in the phyla Cyanobacteria (62%) and Firmicutes (1.45%); the middle site had a higher relative abundance of Chloroflexi (8.02%) and Gemmatimonadetes (1.87%). The dominant phylum in the fungal community is Ascomycota. Pearson correlation analysis showed that the soil's physicochemical properties were also associated with changes in community diversity at the sample sites. These results have important implications for better understanding the community assembly and ecological adaptations of hypolithic microorganisms.

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 SO42- 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 SO42- 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.

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.

Seasonal Variation of Hypolithic Microbiomes in the Gobi Desert : Seasonal Variation of Hypolithic Microbiomes in the Gobi Desert.

Understanding how microbial communities adapt to environmental stresses is critical for interpreting ecological patterns and microbial diversity. In the case of the Gobi Desert, little is known on the environmental factors that explain hypolithic colonization under quartz stones. By analyzing nine hypolithic communities across an arid gradient and the effects of the season of the year in the Hexi Corridor of this desert, we found a significant decrease in hypolithic colonization rates (from 47.24 to 15.73%) with the increasing drought gradient and found two distinct communities in Hot and Cold samples, which survived or proliferated after a hot or a cold period. While Cold communities showed a greater species diversity and a predominance of Cyanobacteria, Hot communities showed a predominance of members of the Proteobacteria and the Firmicutes. In comparison, Cold communities also possessed stronger functions in the photosynthesis and carbon metabolism. Based on the findings of this study, we proposed that the hypolithic communities of the Hexi Corridor of the Gobi Desert might follow a seasonal developmental cycle in which temperature play an important role. Thus after a critical thermal threshold is crossed, heterotrophic microorganisms predominate in the hot period, while Cyanobacteria predominate in the cold period.

Influence of biosynthesized nanoparticles exposure on mortality, residual deposition, and intestinal bacterial dysbiosis in Cyprinus carpio.

Nanotechnology has revealed profound possibilities for the applications in applied sciences. The nanotechnology works based on nanoparticles. Among nanoparticles, silver nanoparticles largely introduced into aquatic environments during fabrication. Which cause severe contamination in the environment specially in freshwater fish. Therefore, the current study was a pioneer attempt to use the animal blood to fabricate AgNPs and investigate their toxicity in Cyprinus carpio (C. carpio) by recording mortality, tissue bioaccumulation, and influence on intestinal bacterial diversity. For this purpose, fish groups were exposed to different concentrations of B-AgNPs including 0.03, 0.06, and 0.09 mg/L beside the control group for 1, 10, and 20 days. Initially, the highest concentration caused mortality. The results revealed that B-AgNPs were significantly (p < 0.005) accumulated in the liver followed by intestines, gills, and muscles. In addition, the accumulation of B-AgNPs in the intestine led to bacterial dysbiosis in Cyprinus carpio. At the phylum level, Tenericutes, Bacteroidetes, and Planctomycetes were gradually decreased at the highest concentration of B-AgNPs (0.09 mg/L) on days 1, 10, and 20 days. The genera Cetobacterium and Luteolibactor were increased at the highest concentration on day 20. Moreover, the principal coordinate analysis (PCoA) based on Bray-Curtis showed that the B-AgNPs had led to a variation in the intestinal bacterial community. Based on findings, the B-AgNPs induced mortality, and residual deposition in different tissues, and had a stress influence on intestinal homeostasis by affecting the intestinal bacterial community in C. carpio which could have a significant effect on fish growth.

Biofilms on stone monuments: biodeterioration or bioprotection?

Debate on whether biofilms on stone monuments are biodeteriorative or bioprotective is long-standing. We propose a criterion of 'relative bioprotective ratio' for assessing the ambivalent role of the biofilms by comparing biodeterioration with weathering. A boundary between biodeterioration and bioprotection exists and fluctuates with dynamic microflora influenced by environmental conditions.

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.

Innovative approaches for the processes involved in microbial biodeterioration of cultural heritage materials.

Microbial colonization and development into biofilms on cultural heritage have significant implications for the deterioration of materials, particularly in the tropic and humid environments. To advance the fundamental knowledge on the biofilm-mediated (bio)deterioration processes, future investigations must focus more on the metabolically active microorganisms and biochemical reactions by a combination of methods available. Newly accessible culture-independent techniques of high-throughput sequencing and multi-omics can be coupled with culture-dependent ones and specific biochemical assays, including stable isotopes and DNA probing. Here, we describe the recent advances on this subject matter, highlight a systematic analytical approach for an integrative diagnosis of 'microbial diseases' of cultural heritage, and provide future prospects for a new paradigm of research on microbial biodeterioration of heritage materials.

Variation in Soil Microbial Communities Along an Elevational Gradient in Alpine Meadows of the Qilian Mountains, China.

Bacterial, archaeal, and eukaryota diversity in mountainous areas varies along elevational gradients, but details remain unclear. Here, we use a next-generation sequencing method based on 16S/18S rRNA to reveal the soil microbial diversity and community compositions of alpine meadow ecosystems along an elevation span of nearly 2,000 m (1,936-3,896 m) in China's Qilian Mountains. Both bacterial and eukaryota diversity increased linearly with increasing elevation, whereas archaeal diversity increased, but not significantly. The diversity patterns of several phyla in the bacterial, archaeal, and eukaryota communities were consistent with the overall elevational trend, but some phyla did not follow this pattern. The soil microbial community compositions were shaped by the coupled effects of regional climate and local soil properties. Intradomain links were more important than interdomain links in the microbial network of the alpine meadows, and these links were mostly positive. The bacteria formed more connections than either archaea or eukaryota, but archaea may be more important than bacteria in building the soil microbial co-occurrence network in this region. Our results provide new visions on the formation and maintenance of soil microbial diversity along an elevational gradient and have implications for microbial responses to climate change in alpine ecosystems.

The presence of Toxoplasma gondii in soil, their transmission, and their influence on the small ruminants and human population: A review.

The ecosystem approach has been developed since the 1940s. An ecosystem is a community of living organism and their interaction and conjugation with abiotic factors of the environment. The ecosystem is not endemic to the aquatic environment only but, the terrestrial environment is also considered to be a part of an ecosystem. Soil act as mother role for the survival of different microorganism. The Toxoplasma gondii oocysts stay survive for a long time in the soil. This presence of these oocysts might critically enhance the success of this parasite in two ways. First, this parasite can widespread; second, it can create a lot of consequences regarding animals and their economic value. Soil contamination caused by Toxoplasma gondii Y is a significant and profound issue for animals and public health. Therefore, the current study was aimed to summarize and correlate the soil and parasite, their transmission, infection, and some aspects related to T. gondii. The small animals are pose at a high risk therefore, it was concluded that some preventive measures should be taken to keep secure itself from zoonotic diseases.

Biological synthesis of silver nanoparticles using animal blood, their preventive efficiency of bacterial species, and ecotoxicity in common carp fish.

Possible high biodeterioration of the microorganisms due to their metabolic pathway and activities on stone materials causes solemn problems in cultural heritage. Different kinds of laboratory-scale methods have been used for the reduction of microbial growth, that is, chemical, mechanical, and physical, which are cost-effective and not ecofriendly. In the current study, an ecofriendly approach utilizing silver nanoparticles were synthesized using sheep blood serum. Transmission electron microscopy results have confirmed the spherical and well dispersed silver nanoparticles with an average size of 32.49 nm, while energy dispersive X-ray has shown the abundance of silver nanoparticles. The efficiency against bacterial species was verified through laboratory-scale testing. The strong antibacterial activity was confirmed when B-AgNPs was tested against different bacterial species isolated from the Beishiku Cave Temple. The largest zone of inhibition was measured 26.48 ± 0.14 mm against Sphingomonas sp. while the smallest zone of inhibition measured was 9.70 ± 0.27 mm against Massilia sp. Moreover, these ecofriendly B-AgNPs were tested for daily based dose in different concentrations (0.03, 0.06, and 0.09 mg/L) against common carp fish for a long exposure (20 days) and 6.5% fatality was found. The highest lethal concentration (LC50 ) for fish (0.61 ± 0.09 mg/L). No doubt, the laboratory scale applications have revealed the best results with minute toxicity in fish. Therefore, sheep serum should be continued to synthesize silver nanoparticles on a large scale. A strict monitoring system should be developed for the synthesis and application of AgNPs.

[Research progress on the bioweathering and controlling of stone cultural relics]. / çŸ³è´¨æ–‡ç‰©çš„ç”Ÿç‰©é£ŽåŒ–åŠå ¶é˜²æ²»ç ”ç©¶è¿›å±•.

The bioweathering of stone cultural relics is a ubiquitous problem. Weathering prevention is an escalating challenge under the increasing global climate and environmental changes. Here, the mechanisms of lichen-microorganism mediated weathering of stone materials and their relationships with climatic and environmental factors were reviewed. The biological protection of lichens and the evaluation of the efficacy of biocides in lichen-control were discussed. The potential research directions in this field were proposed. Research on lichen-rock interfaces suggested that biological weathe-ring could be mainly attributed to physical and chemical weathering which represented by mycelium penetration and calcium oxalate formation. Bioweathering of outdoor stone cultural relics is closely related with the whole ecosystem encompassing factors, such as stone matrix, surrounding environment, and climate factors. Lichens have both biological weathering and protection effects on stone heritage. For the restoration of bioweathered stone cultural relics, environmental conditions for pre-servation of stone cultural relics should be improved step by step. The related industry regulations and national standards for evaluating biological weathering and control efficiency should be established to promote the efficient development of scientific protection.

Description of Naumannella cuiyingiana sp. nov., isolated from a ca. 1500-year-old mural painting, and emended description of the genus Naumannella.

Strain AFT2T was isolated from a mural painting sample from a ca. 1500-year-old tomb located in Shanxi Province, China. The isolate was a Gram-stain-positive, non-motile, non-spore-forming, aerobic and oval to short-rod-shaped bacterium that formed white-pigmented colonies. Phylogenetic analyses based on 16S rRNA gene sequence revealed that strain AFT2T was most closely (97.01 %) correlated and formed a monophyletic clade with Naumannella halotolerans WS4616T (=DSM 24323T). The G+C content of the genomic DNA was 71.97 mol%, and the strain showed 37.27 % DNA-DNA relatedness to N. halotolerans DSM 24323T. The major cellular fatty acid was anteiso-C15 : 0 (55.32 %), and MK-9(H4) was the only respiratory quinone. The polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, two unknown phospholipids and five unknown glycolipids. ll-Diaminopimelic acid was detected in the cell-wall peptidoglycan (type A3γ), and the whole-cell sugars consisted of ribose, mannose, arabinose and galactose. On the basis of its phenotypic and phylogenetic characteristics, it is proposed that strain AFT2T should be classified as a representative of a novel species of the genus Naumannella, for which the name Naumannella cuiyingiana sp. nov. is proposed. The type strain is AFT2T (=CCTCC AB 2015428T=DSM 103164T).

Correction: The microbial community characteristics of ancient painted sculptures in Maijishan Grottoes, China.

[This corrects the article DOI: 10.1371/journal.pone.0179718.].