Biodeterioration of stone: a review

The alteration and weathering of stone is basically determined by natural and anthropogenic impacts influencing various physical, chemical and biological damage factors at the object site. Whether as direct or catalytically enhancing factor, the biodeterioration of stone is coupled with nearly all environmentally induced degradation processes: the presence of the one makes deterioration by the other all the more effective. The bioreceptivity of stone is described by its structure and chemical composition, while the intensity of the microbial contamination is determined by the referring climatic conditions and the anthropogenic euthrophication of the atmosphere. The microflora improves the nutrient and moisture-restricted growth conditions on building stones by the formation of surface-covering biofilms. Besides the aesthetical impairment caused by the coloured biopatina, the biofouling effect promotes even “abiotic” deterioration processes due to the alteration of the material structure as well as their thermo-hygric properties; in addition, mechanical pressure due to the shrinking and swelling of the colloidal biofilms might cause a further weakening of the mineral lattice. Acidolytic and oxido-reductive biocorrosion processes complete the biodeteriorating attack of stone acting as a preliminary precursor for the latter formation of detrimental crusts. Suitable and reliable methods for the detection of biodeterioration processes are available, but only the interdisciplinary diagnosis and evaluation of the entire decay process of stone allows the formulation of adaequate countermeasure strategies. In case the significance of biodeterioration impacts is proven, the possible effects of the microbial contamination on cleaning procedures, protective treatments as well as biocidal applications has to be considered. This paper will give a comprehensive overview to the biodeterioration of stone and stresses the practical relevance for the conservation.     

石质文物的生物风化及其防治研究进展

石质文物的生物风化问题普遍存在,随着全球气候与环境变化加剧,其面临的生物风化挑战日趋严峻,防风化任务愈趋紧迫.本文综述了地衣类微生物介导的石材风化机理及其与气候环境因子间的关系,讨论了地衣的生物保护作用和地衣防治中生物杀灭剂的效力评价,并展望了该领域未来的研究方向.对地衣-岩石界面的大量研究表明,生物风化可主要归因于以菌丝穿透和草酸钙形成为代表的生物物理风化和生物化学风化;露天石质文物的生物风化与包括石材基质、周边环境及气候因素等在内的整个生态系统多种非生物条件息息相关;地衣对石材兼具生物风化作用和生物保护效应.在石质文物风化修复方面,应逐步改善文物赋存的环境条件,建立用于生物风化和杀灭效率评估的行业规范和国家标准等“通用语言”,推进石质文物的科学保护.     

Evidence For In Vitro and In Situ Pyrite Weathering By Microbial Communities Inhabiting Weathered Shale

Microbial pyrite oxidation is an important driver of biological weathering within shale, making a significant contribution toward biogeochemical cycling, bedrock expansion, and soil formation. These processes are of global importance, both within natural systems and in anthropogenic environments. Despite its significance, there is a lack of research that directly investigates microbe– pyrite interactions within shale. In this study, we use both field and laboratory approaches to inspect microbial pyrite oxidation in weathered shale environments within North Yorkshire, UK. Incubation of polished pyrite samples within iron-oxidizing enrichment cultures in vitro resulted in extensive colonization and surface pitting, demonstrating the weathering potential of shale microbial communities. Mineral samples were buried for 1 year within the floor of a shale rock mine, to explore pyrite bioweathering in situ. Image analysis revealed the formation of dissolution channels by microbial filaments, a novel mechanism of pyrite oxidation that broadens the taxonomic range of known microbe-pyrite interactions in weathered shale.     

Investigations of decayed sandstone colonised by a species ofTrentepohlia

The occurrence of a sub-aerial microbial community dominated by a species ofTrentepohlia, a red-orange pigmented filamentous green alga, growing on a 13th century sandstone building in the Scottish borders appears to be associated with unusual stone decay. Decay, in the form of extensive surface spalling and grain dissagregation over large areas of external stonework, are coincident with the distribution of the algal community on the north facade of the building. Comparison of S.E.M. images taken of fresh intact stone and spalled stone from decayed zones suggests that the mechanisms of decay may, in part, be a physical process which results in quartz crystals becoming separated. The investigations carried out revealed little evidence of chemical processes which may be involved in the decay. Large filaments ofTrentepohlia are clearly visible growing vertically between separate grains of stone and the amount of highly absorbent mucilage present makes the friable dry spall become soft and gelatinous on wetting. It is possible that the observed decay may have been created through the mechanical action of wet-dry cycling of mucilage and expansive stress from the growth of algal filaments.     

Effect of physical weathering on the carbon sequestration potential of biochars and hydrochars in soil

Physical weathering can modify the stability of biochar after field exposure. The aim of our study was to determine the potential carbon sequestration of the two chars at different timescales. We investigated the modification in composition and stability resulting from physical weathering of two different chars produced (i) at low temperature (250 °C) by hydrothermal carbonization (HTC); and (ii) at high temperature (1200 °C) by gasification (GS) using contrasting feedstocks. Physical weathering of HTC and GS placed on a water permeable canvas was performed through successive wetting/drying and freezing/thawing cycles. Carbon loss was assessed by mass balance. Chemical stability of the remaining material was evaluated as resistance to acid dichromate oxidation, and biological stability was assessed during laboratory incubation. Moreover, we assessed modification in potential priming effects due to physical weathering. Physical weathering induced a carbon loss ranging between 10 and 40% of the total C mass depending on the feedstock. This C loss is most probably related to leaching of small particulate and dissolved compounds. GS produced from maize silage showed the highest C loss. The chemical stability of HTC and GS was unaffected by physical weathering. In contrast, physical weathering strongly increased the biological stability of HTC and GS char produced from maize silage. After physical weathering, the half‐life (t_1/2) of GS was doubled but only slight increase was noted for those of HTC. During the first weeks of incubation, HTC addition to soil stimulated native soil organic matter (SOM) mineralization (positive priming effect), while the GS addition led to protection of the native SOM against biologic degradation (negative priming effect). Physical weathering led to reduction in these priming effects. Model extrapolations based on our data showed that decadal C sequestration potential of GS and HTC is globally equivalent when all losses including those due to priming and physical weathering were taken into account. However, at century scale only GS may have the potential to increase soil C storage.     

Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments

Fecal coliforms and enterococci are indicator organisms used worldwide to monitor water quality. These bacteria are used in microbial source tracking (MST) studies, which attempt to assess the contribution of various host species to fecal pollution in water. Ideally, all strains of a given indicator organism (IO) would experience equal persistence (maintenance of culturable populations) in water; however, some strains may have comparatively extended persistence outside the host, while others may persist very poorly in environmental waters. Assessment of the relative contribution of host species to fecal pollution would be confounded by differential persistence of strains. Here, freshwater and saltwater mesocosms, including sediments, were inoculated with dog feces, sewage, or contaminated soil and were incubated under conditions that included natural stressors such as microbial predators, radiation, and temperature fluctuations. Persistence of IOs was measured by decay rates (change in culturable counts over time). Decay rates were influenced by IO, inoculum, water type, sediment versus water column location, and Escherichia coli strain. Fecal coliform decay rates were significantly lower than those of enterococci in freshwater but were not significantly different in saltwater. IO persistence according to mesocosm treatment followed the trend: contaminated soil > wastewater > dog feces. E. coli ribotyping demonstrated that certain strains were more persistent than others in freshwater mesocosms, and the distribution of ribotypes sampled from mesocosm waters was dissimilar from the distribution in fecal material. These results have implications for the accuracy of MST methods, modeling of microbial populations in water, and efficacy of regulatory standards for protection of water quality.     

Bacterial bio-mediated calcite precipitation for monumental stones conservation: methods of evaluation.

The weathering of monumental stones is a complex process inserted in the more general 'matter transformation cycle' operated by physical, chemical and biological factors. The consequence of these combined actions is a loss of cohesion with dwindling and scaling of stone material and the induction of a progressive mineral matrix dissolution. In the case of calcareous stones, calcite leaching increases the material porosity and decreases its mechanical features with a general weakening of the superficial structural strength. Attempts to stop, or at least to slow down, deterioration of monumental stones has been made by conservative treatments with both inorganic or organic products. More recent studies show a new approach to hinder these phenomena by inducing a bio-mediated precipitation of calcite directly inside the stone porosity. This can be achieved either through the application of organic matrix macromolecules extracted from sea shells or of living bacteria. The effectiveness of the treatment using calcinogenic bacteria has been evaluated with laboratory tests specifically developed to evaluate the parameters such as : porosity, superficial strength and chromatic changes, influenced by the treatment itself. The results obtained seem to indicate that this type of treatment might not be suitable for monumental stone conservation.     

Biological weathering of silicate minerals

Summary The abilities of biological systems to mobilize potassium from crystal lattices of primary silicate minerals were investigated. Root systems of pine seedlings grown in laboratory cultures and cultures of Aspergillus niger and mixed populations of soil micro-organisms were able to alter biotite mineral particles and cause release of potassium and other ions from mineral lattices. Mineral alterations by the microbial systems used are similar to alterations caused by oxalic, citric and other organic acids. The significance of the weathering processes observed is considered in relation to forest tree nutrition and soil formation     

Investigations of the localisation of bacterial activity on sandstone from ancient monuments

Methods were investigated for the determination of activity levels of bacteria on sandstone using the reduction of 2-(4-iodophenyl)-3-(4 nitrophenyl)-5-phenyl tetrazolium chloride (INT) to INT-formazan as a measure of dehydrogenase activity. A microscopy technique, based on use of acridine orange with bright-field illumination, was developed which gave a good visual image of bacterial cells, including those containing INT-formazan. Surveys at two monuments, Portchester Castle and Tintern Abbey, were carried out using this method which showed that between 20.7 and 51.9% of bacterial cells present in situ were active. Extraction of INT-formazan directly from the stone using methanol indicated that bacteria were tightly bound to stone particles and that microscopic methods would underestimate counts of bacteria. Surveys of five monuments using the extraction method showed that microbial populations on sandstone in situ were active but activity could not be related to decay state of the stone.     

Soft‐Bodied Fossils Are Not Simply Rotten Carcasses – Toward a Holistic Understanding of Exceptional Fossil Preservation

Exceptionally preserved fossils are the product of complex interplays of biological and geological processes including burial, autolysis and microbial decay, authigenic mineralization, diagenesis, metamorphism, and finally weathering and exhumation. Determining which tissues are preserved and how biases affect their preservation pathways is important for interpreting fossils in phylogenetic, ecological, and evolutionary frameworks. Although laboratory decay experiments reveal important aspects of fossilization, applying the results directly to the interpretation of exceptionally preserved fossils may overlook the impact of other key processes that remove or preserve morphological information. Investigations of fossils preserving non‐biomineralized tissues suggest that certain structures that are decay resistant (e.g., the notochord) are rarely preserved (even where carbonaceous components survive), and decay‐prone structures (e.g., nervous systems) can fossilize, albeit rarely. As we review here, decay resistance is an imperfect indicator of fossilization potential, and a suite of biological and geological processes account for the features preserved in exceptional fossils.     

Persistence and Differential Survival of Fecal Indicator Bacteria in Subtropical Waters and Sediments

Fecal coliforms and enterococci are indicator organisms used worldwide to monitor water quality. These bacteria are used in microbial source tracking (MST) studies, which attempt to assess the contribution of various host species to fecal pollution in water. Ideally, all strains of a given indicator organism (IO) would experience equal persistence (maintenance of culturable populations) in water; however, some strains may have comparatively extended persistence outside the host, while others may persist very poorly in environmental waters. Assessment of the relative contribution of host species to fecal pollution would be confounded by differential persistence of strains. Here, freshwater and saltwater mesocosms, including sediments, were inoculated with dog feces, sewage, or contaminated soil and were incubated under conditions that included natural stressors such as microbial predators, radiation, and temperature fluctuations. Persistence of IOs was measured by decay rates (change in culturable counts over time). Decay rates were influenced by IO, inoculum, water type, sediment versus water column location, and Escherichia coli strain. Fecal coliform decay rates were significantly lower than those of enterococci in freshwater but were not significantly different in saltwater. IO persistence according to mesocosm treatment followed the trend: contaminated soil > wastewater > dog feces. E. coli ribotyping demonstrated that certain strains were more persistent than others in freshwater mesocosms, and the distribution of ribotypes sampled from mesocosm waters was dissimilar from the distribution in fecal material. These results have implications for the accuracy of MST methods, modeling of microbial populations in water, and efficacy of regulatory standards for protection of water quality.     

Effect of atrazine in combination with captan or thiram upon fungal and bacterial populations in the soil

Pesticides were added to soil at a rate of 10 mg/kg and then planted with corn, wheat, or bean seeds. Captan and thiram caused an initial decrease in the fungal populations but by 108 days the populations returned to levels found in untreated soils. The bacterial populations fluctuated inversely with the fungal populations. In soil planted with corn, atrazine had no effect on the microbial populations, however, in soil containing wheat and beans, populations of fungi and bacteria increased. Stimulation of the microbial populations in the atrazine-treated soils was attributed to the decay of the dead wheat and bean plants. Atrazine in combination with captan or thiram had neither synergistic nor antagonistic effects on the microbial populations. This study was supported by Public Health Service Research Grant No. CC 00284, from the National Communicable Disease Center, Atlanta, Georgia. This study was supported by Public Health Service Research Grant No. CC 00284, from the National Communicable Disease Center, Atlanta, Georgia.     

Molecular evidence for an active endogenous microbiome beneath glacial ice

Geologic, chemical and isotopic evidence indicate that Earth has experienced numerous intervals of widespread glaciation throughout its history, with roughly 11% of present day Earth''s land surface covered in ice. Despite the pervasive nature of glacial ice both today and in Earth''s past and the potential contribution of these systems to global biogeochemical cycles, the composition and phylogenetic structure of an active microbial community in subglacial systems has yet to be described. Here, using RNA-based approaches, we demonstrate the presence of active and endogenous archaeal, bacterial and eukaryal assemblages in cold (0–1 °C) subglacial sediments sampled from Robertson Glacier, Alberta, Canada. Patterns in the phylogenetic structure and composition of subglacial sediment small subunit (SSU) ribosomal RNA (rRNA) assemblages indicate greater diversity and evenness than in glacial surface environments, possibly due to facilitative or competitive interactions among populations in the subglacial environment. The combination of phylogenetically more even and more diverse assemblages in the subglacial environment suggests minimal niche overlap and optimization to capture a wider spectrum of the limited nutrients and chemical energy made available from weathering of bedrock minerals. The prevalence of SSU rRNA affiliated with lithoautotrophic bacteria, autotrophic methane producing archaea and heterotrophic eukarya in the subglacial environment is consistent with this hypothesis and suggests an active contribution to the global carbon cycle. Collectively, our findings demonstrate that subglacial environments harbor endogenous active ecosystems that have the potential to impact global biogeochemical cycles over extended periods of time.     

Biological protection of hardwood logs destined for panel manufacturing using <Emphasis Type="Italic">Gliocladium roseum</Emphasis> against biodegradation

The objective of the present study was to develop a biological technology that would protect logs destined for oriented strand board (OSB) manufacturing from biodegradation. Aspen, red maple, and yellow birch trees were felled in one summer and the logs either debarked or not debarked, and either treated or not treated with a biological product of Gliocladium roseum. The logs were piled in different treatment groups and stored in a yard for 5 months and 1 year before evaluation. The results showed that all untreated logs, with or without bark, were seriously degraded by moulds, stain and decay fungi after a summer storage period of 5 months. The logs with bark were more degraded than the debarked logs, and the log ends were more degraded than the middle sections. After 5 months, 55–83% of the surface area of the wood discs was degraded in untreated logs. The biological treatment was effective, and only 4–16% of the surface area of the wood discs in treated logs was infected by various fungi. Strands cut from untreated logs consisted of 50–75% grey- or blue-stained strands, whereas those cut from biologically treated logs consisted of 10–25% such strands. Panels made using biologically treated logs had a lower thickness swelling and water absorption values compared to panels made using freshly cut logs and untreated stored logs. The other physical and mechanical properties of the various panels made in this test were comparable. In terms of mould resistance, all panels made from fungal-treated logs had a better mould resistance than those made from freshly cut and untreated logs.     

Effaced preservation in the Ediacara biota and its implications for the early macrofossil record

Abstract: Ediacaran structures known as ‘pizza discs’ or Ivesheadia have long been considered enigmatic. They are amongst the oldest known members of the Ediacara biota, apparently restricted to the Avalonian successions of Newfoundland and the UK, c. 579–560 Ma. Here, we suggest that these impressions are taphomorphs, resulting from the post‐mortem decay of the frondose Ediacaran biota. Ediacaran fossils range from well‐preserved, high‐fidelity variants to almost completely effaced specimens. The effaced specimens are inferred to have undergone modification of their original morphology by post‐mortem microbial decay on the sea floor, combined with sediment trapping and binding. In this style of preservation, morphological details within the organism became variously subdued as a function of the extent of organic decay prior to casting by overlying sediments. Decay and effacement were progressive in nature, producing a continuum of grades of preservation on Ediacaran bedding planes. Fossils preserved by such ‘effaced preservation’ are those that have suffered these processes to the extent that only their gross form can be determined. We suggest that the lack of detailed morphology in effaced specimens renders such fossils unsuitable for use as type material, as it is possible that several taxa may, upon degradation and burial, generate similar morphological taphomorphs. We here reinterpret the genus Ivesheadia as a taphomorph resulting from extensive post‐mortem decay of frondose organisms. Blackbrookia, Pseudovendia and Shepshedia from beds of comparable age in England are likewise regarded as taphomorphs broadly related to Charnia or Charniodiscus spp. To reflect the suggestion that such impressions are likely to be taphomorphs, and not taxonomically discrete, we propose the term ivesheadiomorphs to incorporate all such effaced taphonomic expressions of Ediacaran macrofossil taxa in Avalonian assemblages. Our recognition of effaced preservation has significant implications for Ediacaran taxonomy, and consequently for measures of Ediacaran diversity and disparity. It is implied that Avalonian assemblages preserve both organisms that were alive and organisms that were already dead at the time of burial. As such, the fossil assemblages cannot be taken to represent census populations of living organisms, as in prior interpretations.     

Human disc degeneration is associated with increased MMP 7 expression

During intervertebral disc (IVD) degeneration, normal matrix synthesis decreases and degradation of disc matrix increases. A number of proteases that are increased during disc degeneration are thought to be involved in its pathogenesis. Matrix metalloproteinase 7 (MMP 7) (Matrilysin, PUMP-1) is known to cleave the major matrix molecules found within the IVD, i.e., the proteoglycan aggrecan and collagen type II. To date, however, it is not known how its expression changes with degeneration or its exact location. We investigated the localization of MMP 7 in human, histologically graded, nondegenerate, degenerated and prolapsed discs to ascertain whether MMP 7 is up-regulated during disc degeneration. Samples of human IVD tissue were fixed in neutral buffered formalin, embedded in paraffin, and sections stained with hematoxylin and eosin to score the degree of morphological degeneration. Immunohistochemistry was performed to localize MMP 7 in 41 human IVDs with varying degrees of degeneration. We found that the chondrocyte-like cells of the nucleus pulposus and inner annulus fibrosus were MMP 7 immunopositive; little immunopositivity was observed in the outer annulus. Nondegenerate discs showed few immunopositive cells. A significant increase in the proportion of MMP 7 immunopositive cells was seen in the nucleus pulposus of discs classified as showing intermediate levels of degeneration and a further increase was seen in discs with severe degeneration. Prolapsed discs showed more MMP 7 immunopositive cells compared to nondegenerated discs, but fewer than those seen in cases of severe degeneration.     

Human disc degeneration is associated with increased MMP 7 expression

During intervertebral disc (IVD) degeneration, normal matrix synthesis decreases and degradation of disc matrix increases. A number of proteases that are increased during disc degeneration are thought to be involved in its pathogenesis. Matrix metalloproteinase 7 (MMP 7) (Matrilysin, PUMP-1) is known to cleave the major matrix molecules found within the IVD, i.e., the proteoglycan aggrecan and collagen type II. To date, however, it is not known how its expression changes with degeneration or its exact location. We investigated the localization of MMP 7 in human, histologically graded, nondegenerate, degenerated and prolapsed discs to ascertain whether MMP 7 is up-regulated during disc degeneration. Samples of human IVD tissue were fixed in neutral buffered formalin, embedded in paraffin, and sections stained with hematoxylin and eosin to score the degree of morphological degeneration. Immunohistochemistry was performed to localize MMP 7 in 41 human IVDs with varying degrees of degeneration. We found that the chondrocyte-like cells of the nucleus pulposus and inner annulus fibrosus were MMP 7 immunopositive; little immunopositivity was observed in the outer annulus. Nondegenerate discs showed few immunopositive cells. A significant increase in the proportion of MMP 7 immunopositive cells was seen in the nucleus pulposus of discs classified as showing intermediate levels of degeneration and a further increase was seen in discs with severe degeneration. Prolapsed discs showed more MMP 7 immunopositive cells compared to nondegenerated discs, but fewer than those seen in cases of severe degeneration.     

Human disc degeneration is associated with increased MMP 7 expression.

During intervertebral disc (IVD) degeneration, normal matrix synthesis decreases and degradation of disc matrix increases. A number of proteases that are increased during disc degeneration are thought to be involved in its pathogenesis. Matrix metalloproteinase 7 (MMP 7) (Matrilysin, PUMP-1) is known to cleave the major matrix molecules found within the IVD, i.e., the proteoglycan aggrecan and collagen type II. To date, however, it is not known how its expression changes with degeneration or its exact location. We investigated the localization of MMP 7 in human, histologically graded, nondegenerate, degenerated and prolapsed discs to ascertain whether MMP 7 is up-regulated during disc degeneration. Samples of human IVD tissue were fixed in neutral buffered formalin, embedded in paraffin, and sections stained with hematoxylin and eosin to score the degree of morphological degeneration. Immunohistochemistry was performed to localize MMP 7 in 41 human IVDs with varying degrees of degeneration. We found that the chondrocyte-like cells of the nucleus pulposus and inner annulus fibrosus were MMP 7 immunopositive; little immunopositivity was observed in the outer annulus. Nondegenerate discs showed few immunopositive cells. A significant increase in the proportion of MMP 7 immunopositive cells was seen in the nucleus pulposus of discs classified as showing intermediate levels of degeneration and a further increase was seen in discs with severe degeneration. Prolapsed discs showed more MMP 7 immunopositive cells compared to nondegenerated discs, but fewer than those seen in cases of severe degeneration.     

Algae and bacteria on historic monuments at Alcala de Henares, Spain

Bacteria belonging to the genera Bacillus, Micrococcus and Thiobacillus, yeast and microalgae of the Apatococcus genus colonize the building of two monuments at Alcalá de Henares (Spain). In highly altered zones, polymicrobial communities were observed, mainly beneath the surface of the crusts, which demonstrated that rock surfaces are good substrates and offer possibilities for interaction among several types of populations. Microbial activity in surface layers of the stone was revealed by means of the TTC (triphenyltetrazolium chloride) test. With SEM (scanning electron microscopy), the weathering of the substrate was observed, as well as the presence of pollution particles and microbial structures.