Biodeteriorative processes on glass: experimental proof of the role of fungi and cyanobacteria

Biodeterioration of glass under the influence of fungi and cyanobacteria was simulated on model glasses produced according to the old recipes. Strains of fungi and cyanobacteria chosen for the investigation were isolated from biodeteriorated glass windows or similar indoor environment and are reported to be frequently involved in glass alteration. Growth of fungi and cyanobacteria resulted in the dense colonisation of the material with an expressed biofilm formation on the glass surface. The following deterioration phenomena were observed: micropitting and crack formation by all studied fungi and cyanobacteria; delineatingtraces of cells, hyphae and filaments on the glass surface; colour change of the surface due to fungal or cyanobacterial growth; biogenic minerals deposition as a consequence of the microbial metabolism on the glass surface. The pattern of glass biopitting produced in the experiment was very similar to the biopits observed on antique and medieval glasses (Krumbein et al., 1991). Crack formation pattern was strain-specific, but appeared to be independent of the chemical composition of the glass itself. The degree of deterioration was changing according to the sensitivity of the glass in question to corrosion.     

Study of the bacterial flora of a non-carbonated natural mineral water.

Natural mineral water from a UK spring was monitored at various stages after it was pumped from the ground, through to bottling and during shelf life before consumption. Samples were collected in commercial PVC bottles, in PVC bottles previously sterilized and hand-filled and in glass bottles. The bacterial flora was counted on plate count agar (PCA) and on PCA diluted 10 times (PCA/10). The predominant bacteria were identified to genus level. Growth rates and nutrient types of isolates were determined by the nutrient-tolerance test (NT). The plate counts at the pre-bottling stage were low. During storage larger numbers of bacteria grew in glass than PVC bottles; the largest number grew in PVC bottles filled by hand. Most of the pigmented bacteria isolated were oligocarbotolerant.     

Study of the bacterial flora of a non-carbonated natural mineral water

Natural mineral water from a UK spring was monitored at various stages after it was pumped from the ground, through to bottling and during shelf life before consumption. Samples were collected in commercial PVC bottles, in PVC bottles previously sterilized and hand-filled and in glass bottles. The bacterial flora was counted on plate count agar (PCA) and on PCA diluted 10 times (PCA/10). The predominant bacteria were identified to genus level. Growth rates and nutrient types of isolates were determined by the nutrient-tolerance test (NT). The plate counts at the prebottling stage were low. During storage larger numbers of bacteria grew in glass than PVC bottles; the largest number grew in PVC bottles filled by hand. Most of the pigmented bacteria isolated were oligocarbotolerant.     

小麦内生细菌的分离及其对小麦纹枯菌的拮抗作用

利用涂布平板法从小麦根系中分离出8株内生细菌,从中筛选出1株对小麦纹枯菌(Rhizoctonia cerealis)具有拮抗作用的内生菌。室内测定该菌株培养液对小麦纹枯病菌的抑制作用,结果发现,小麦纹枯病菌在培养液中生长缓慢,培养6d后菌丝量与对照相比下降了89％,同时发现病菌菌丝生长畸形,出现断裂和细胞壁瓦解。双抗标记法测定该拮抗菌在小麦根系中的定殖情况,发现该菌能够在根系中长期定殖。初步的鉴定结果表明该菌为蜡样芽孢杆菌。     

The microbe–mineral environment and gypsum neogenesis in a weathered polar evaporite

Evaporitic deposits are a globally widespread habitat for micro‐organisms. The microbe–mineral environment in weathered and remobilized gypsum from exposed mid‐Ordovician marine evaporite beds in the polar desert of Devon Island, Nunavut, Canadian High Arctic was examined. The gypsum is characterized by internal green zones of cyanobacterial colonization (dominated by Gloeocapsa/Aphanothece and Chroococcidiopsis spp. morphotypes) and abundant black zones, visible from the surface, that contain pigmented cyanobacteria and fungi. Bioessential elements in the gypsum are primarily provided by allochthonous material from the present‐day polar desert. The disruption, uplift and rotation of the evaporite beds by the Haughton meteorite impact 39 Ma have facilitated gypsum weathering and its accessibility as a habitat. No cultured cyanobacteria, bacteria and fungi were halophilic consistent with the expectation that halophily is not required to persist in gypsum habitats. Heterotrophic bacteria from the evaporite were slightly or moderately halotolerant, as were heterotrophs isolated from soil near the gypsum outcrop showing that halotolerance is common in arctic bacteria in this location. Psychrotolerant Arthrobacter species were isolated. No psychrophilic organisms were isolated. Two Arthrobacter isolates from the evaporite were used to mediate gypsum neogenesis in the laboratory, demonstrating a potential role for microbial biomineralization processes in polar environments.     

Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site

The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.     

Biogenic Forsterite and Opal as a Product of Biodeterioration and Lichen Stromatolite Formation in Table Mountain Systems (Tepuis) of Venezuela

Biogenic physical weathering and leaching of the quartzite dominated table mountain systems of South America is a slow but strongly biologically influenced process. Observations and analyses on the basis of sample materials collected during an expedition to the protected areas of the most conspicuous tepuis of Venezuela are reported. The rock material consists of more than 98% silica, and the waters collected reflect rainwater quality further deprived of some essential elements. Wear-down of these rocks is recognized as a biogeomorphogenetic process ruled by the microbiota surviving under harsh and nutrient-poor conditions. Poikilotrophic subaerial biofilms of cyanobacteria, fungi, and some lichens perforate quartz grains and idiomorphic quartz crystals, as well as the subcrystalline cement. The typical pattern of biopitting is regarded as proof of biogenic quartz destruction. Within the subaerial biofilms, which form a massive cover of the slowly biocorroded rock surface, lichens were found that mineralize to microstromatolitic structures in situ. The mineralization occurs exclusively in the lichen thalli and not in the associated massive biofilms of free-living cyanobacteria and fungi. The minerals deposited were identified as opal and considerable amounts of forsterite, the pure Mg end-member of the olivine mixing series (fayalite being the pure iron silicate). Forsterite, thus far, has been regarded as an igneous mineral phase typical for mantle-derived rocks, highly metamorphic dolomitic marbles, and as a planetary mineral found in meteorites. The biogenic dissolution/mineralization paragenesis is explained by the slow weathering and bioleaching processes dominant on these table mountains and by the exclusion of all other potential biomineralization products due to the peculiar geochemistry of the interstitial and run-off water on these plateaus, thus leading to the exceptional biogenesis of forsterite under surface conditions.     

Biological treatments for the control of decay in tree wounds.: Laboratory tests

Non-decay fungi and bacteria which had been isolated from pruning wounds of beech (Fagus sylvatica) were examined for their ability to check the growth of decay fungi in a number of laboratory tests. Several fungi and bacteria inhibited growth although the degree of inhibition varied to some extent with the test. The most consistently antagonistic fungi were Trichoderma spp., especially an isolate of T. viride. The most antagonistic bacteria were Bacillus spp.     

Fungal biodeterioration of stained-glass windows

Biodeterioration of stained-glass windows by fungi was studied using historically accurate glass production methods. Glass reproductions were made according to the chemical composition determined by micro energy dispersive X-Ray Fluorescence of two historical glass windows belonging to King Ferdinand II's collection dating from the 15th and 17th centuries. Three distinct glasses compositions with different colours were selected and reproduced: i) a mixed-alkali colourless glass: ii) a purple potash-glass with manganese as chromophore, and iii) a brown potash-glass coloured by iron ions. The reproduced glass samples, with two initial surface morphologies (corroded and non-corroded), were inoculated with fungi previously isolated and identified on the original stained-glass windows as species of the genera Penicillium and Cladosporium. Physical and chemical glass surface alterations were analysed by means of optical microscopy, Raman microscopy, micro Infrared spectroscopy, and scanning electron microscopy with energy dispersive spectroscopy analysis. Results showed that fungi produced clear damage on all glass surfaces, present as spots and stains, fingerprints, biopiting, leaching and deposition of elements, and formation of biogenic crystals. Therefore, the inoculated fungi were able to biodeteriorate glasses with distinct compositions. Regarding the biodeterioration degree, there were no differences between the initial non-corroded and corroded glass surfaces.     

Degradation of biogenic amines by vineyard ecosystem fungi. Potential use in winemaking

Aims: To evaluate the ability of grapevine ecosystem fungi to degrade histamine, tyramine and putrescine in synthetic medium and in wines. Methods and Results: Grapevine and vineyard soil fungi were isolated from four locations of Spain and were subsequently identified by PCR. A total of 44 fungi were evaluated for in vitro amine degradation in a microfermentation system. Amine degradation by fungi was assayed by reversed‐phase (RP)‐HPLC. All fungi were able to degrade at least two different primary amines. Species of Pencillium citrinum, Alternaria sp., Phoma sp., Ulocladium chartarum and Epicoccum nigrum were found to exhibit the highest capacity for amine degradation. In a second experiment, cell‐free supernatants of P. citrinum CIAL‐274,760 (CECT 20782) grown in yeast carbon base with histamine, tyramine or putrescine, were tested for their ability to degrade amines in three different wines (red, white and synthetic). The highest levels of biogenic amine degradation were obtained with histamine‐induced enzymatic extract. Conclusion: The study highlighted the ability of grapevine ecosystem fungi to degrade biogenic amines and their potential application for biogenic amines removal in wine. Significance and Impact of Study: The fungi extracts described in this study may be useful in winemaking to reduce the biogenic amines content of wines, thereby preventing the possible adverse effects on health in sensitive individuals and the trade and export of wine.     

Biodeterioration of mineral materials by microorganisms—biogenic sulfuric and nitric acid corrosion of concrete and natural stone

In general, microorganisms such as chemolithotrophic and chemo‐organotrophic bacteria, cyanohacteria, algae, fungi, and lichens living on and in stone material may be of importance in biodeterioration. These groups contribute substantially to the deterioration of mineral materials such as natural stone, concrete, ceramics, and glass. The attack on mineral materials may be either strongly or mildly aggressive or both. A strongly aggressive attack is caused by biogenic mineral or organic acids. A mildly aggressive attack results from hydrophilic slimes such as heteropolysaccharides and/or proteins (biofilm) and their ability to accumulate water and salts. Attack by exoenzymes seems to be unimportant.

In recent years it has become possible to test the resistance of mineral materials to microbial attack by means of a biotest. Three simulation apparatuses were constructed; each allowed the incubation of test materials under microbiologically optimized conditions. Biodeterioration involving biogenic sulfuric acid corrosion, which under natural conditions needs eight times as long, was detectable within a few months. The results differed from those of purely chemical and/or physical tests of materials. Physical/chemical test methods are not sufficient to determine the resistance of materials to biological attack, because they do not include the interactions between microorganisms and their substrate, the mineral material. In the case of biogenic sulfuric acid corrosion, simulation experiments demonstrated differences in resistance of various concrete types, which ranged from I to 20% weight loss of test blocks within I year. With chemical testing only negligible differences in weight loss were noted. This was also the case with biogenic nitric acid corrosion. Thus, biotests assist in the selection of appropriate materials from many different ones.     

Alterations in the major heterotrophic bacterial populations isolated from a still bottled mineral water

M orais , P.V. & D a C osta , M.S. 1990. Alterations in the major heterotrophic bacterial populations isolated from a. still bottled mineral water. Journal of Applied Bacteriology 69 , 750–757.
The heterotrophic bacterial population of a bottled mineral water stored in returnable glass bottles and in polyvinyl chloride (PVC) bottles at room temperature was studied over 9–12 months. The plate counts in R₂A medium incubated at 22 and 37C were low initially, increasing to 10⁴-10⁵ cfu/ml within a few days of bottling. The number of bacteria recovered at 22C from PVC bottles was fairly constant during the storage period, but the population isolated at 37C decreased markedly after storage for 1 year. The major components of the population were Pseudomonas strains, one of which was identified as Pseudomonas vesicularis . Major changes took place during storage; two groups of bacteria (B and C) were dominant initially, but during the latter period of storage other groups (F, G and H) increased in number.     

Experimental Evidence that Fungi are Dominant Microbes in Carbon Content and Growth Response to Added Soluble Organic Carbon in Moss‐rich Tundra Soil

Global warming significantly affects Arctic tundra, including permafrost thaw and soluble C release that may differentially affect tundra microbial growth. Using laboratory experiments, we report some of the first evidence for the effects of soluble glucose‐C enrichment on tundra soil prokaryotes (bacteria and archaea) and fungi, with comparisons to microbial eukaryotes. Fungal increase in C‐biomass was equivalent to 10% (w/w) of the added glucose‐C, and for prokaryote biomass 2% (w/w), the latter comparable to prior published results. The C‐gain after 14 d was 1.3 mg/g soil for fungi, and ~200 μg/g for prokaryotes.     

MALDI‐TOF‐MS‐based species identification and typing approaches in medical mycology

MALDI‐TOF MS‐based species identification has found its place in many clinical routine diagnostic laboratories over the past years. Several well‐established commercial systems exist and these allow precise analyses not only among bacteria, but also among clinically important yeasts. This methodology shows higher precision than biochemical and microscopic methods at significantly reduced turnaround times. Furthermore, the differentiation of different filamentous fungi including most dermatophytes and zygomycetes has been established. The direct identification of yeasts from blood culture bottles will be possible in a routine fashion with new standardized procedures. In addition to species identification, the MALDI‐TOF MS technology offers several further possibilities, like assays to detect or predict resistance phenotypes in fungi as well as subtyping approaches to detect clinically relevant subgroups. The differences between the commercial systems are discussed with respect to fungi and an overview of their performances provided. Factors influencing outcome of MALDI‐TOF‐based species identification are discussed.     

The microbial degradation of silk: a laboratory investigation

A few bacterial species, mostly gram-negatives, were found to attach themselves and grow on silk buried in soil. On the contrary, no fungi were isolated in such experiments. Growth was more abundant on raw silk (composed of sericin and fibroin) than on degummed silk (fibroin only) indicating that the majority of these bacteria use sericin rather than fibroin for growth. Electron microscopy demonstrated that bacteria formed a biofilm on the fabric and caused extensive damage to the fibers resulting in considerable reduction in the mechanical properties. Of the three main bacterial species isolated from silk exposed to soil or by enrichment cultures of silk cocoons, only Pseudomonas (Burkholderia) cepacia appeared to be able to use fibroin as a sole source of carbon and nitrogen for growth. Indeed, in laboratory experiments, pure cultures of P. cepacia were found to form a well-developed biofilm on fibroin, to hydrolyze fibroin, and to produce an extracellular enzyme attacking this protein. The reported data indicate that bacteria but not fungi may attack and degrade silk proteins and thus cause irreversible damage to silk artifacts of artistic or historical interest.     

Biodeterioration of Mayan buildings at uxmal and tulum,Mexico

Uxmal and Tulum are two important Mayan sites in the Yucatan peninsula. The buildings are mainly composed of limestone and grey/black discoloration is seen on exposed walls and copious greenish biofilms on inner walls. The principal microorganisms detected on interior walls at both Uxmal and Tulum were cyanobacteria; heterotrophic bacteria and filamentous fungi were also present. A dark‐pigmented mitosporic fungus and Bacillus cereus, both isolated from Uxmal, were shown to be acidogenic in laboratory cultures. Cyanobacteria belonging to rock‐degrading genera Synechocystis and Gloeocapsa were identified at both sites. Surface analysis previously showed that calcium ions were present in the biofilms on buildings at Uxmal and Tulum, suggesting the deposition of biosolubilized stone. Apart from their potential to degrade the substrate, the coccoid cyanobacteria supply organic nutrients for bacteria and fungi, which can produce organic acids, further increasing stone degradation.     

Alterations in the major heterotrophic bacterial populations isolated from a still bottled mineral water

The heterotrophic bacterial population of a bottled mineral water stored in returnable glass bottles and in polyvinyl chloride (PVC) bottles at room temperature was studied over 9-12 months. The plate counts in R2A medium incubated at 22 degrees and 37 degrees C were low initially, increasing to 10(4)-10(5) cfu/ml within a few days of bottling. The number of bacteria recovered at 22 degrees C from PVC bottles was fairly constant during the storage period, but the population isolated at 37 degrees C decreased markedly after storage for 1 year. The major components of the population were Pseudomonas strains, one of which was identified as Pseudomonas vesicularis. Major changes took place during storage; two groups of bacteria (B and C) were dominant initially, but during the latter period of storage other groups (F, G and H) increased in number.     

A functional screen identifies lateral transfer of beta-glucuronidase (gus) from bacteria to fungi

Lateral gene transfer (LGT) from prokaryotes to microbial eukaryotes is usually detected by chance through genome-sequencing projects. Here, we explore a different, hypothesis-driven approach. We show that the fitness advantage associated with the transferred gene, typically invoked only in retrospect, can be used to design a functional screen capable of identifying postulated LGT cases. We hypothesized that beta-glucuronidase (gus) genes may be prone to LGT from bacteria to fungi (thought to lack gus) because this would enable fungi to utilize glucuronides in vertebrate urine as a carbon source. Using an enrichment procedure based on a glucose-releasing glucuronide analog (cellobiouronic acid), we isolated two gus(+) ascomycete fungi from soils (Penicillium canescens and Scopulariopsis sp.). A phylogenetic analysis suggested that their gus genes, as well as the gus genes identified in genomic sequences of the ascomycetes Aspergillus nidulans and Gibberella zeae, had been introgressed laterally from high-GC gram(+) bacteria. Two such bacteria (Arthrobacter spp.), isolated together with the gus(+) fungi, appeared to be the descendants of a bacterial donor organism from which gus had been transferred to fungi. This scenario was independently supported by similar substrate affinities of the encoded beta-glucuronidases, the absence of introns from fungal gus genes, and the similarity between the signal peptide-encoding 5' extensions of some fungal gus genes and the Arthrobacter sequences upstream of gus. Differences in the sequences of the fungal 5' extensions suggested at least two separate introgression events after the divergence of the two main Euascomycete classes. We suggest that deposition of glucuronides on soils as a result of the colonization of land by vertebrates may have favored LGT of gus from bacteria to fungi in soils.     

Consequences of the colonisation of leaves by fungi and oomycetes for leaf consumption by a gammarid shredder

1. Leaf litter breakdown by shredders in the field is affected by leaf toughness, nutritional value and the presence of secondary compounds such as polyphenols. However, experiments involving the use of single fungal strains have not supported the assumption that leaf parameters determine food selection by shredders perhaps because of a failure to test for high consumption prior to isolation of fungal strains, overrepresentation of hyphomycetes or the potential effects of accompanying bacteria. In this study, we used bacteria‐free, actively growing fungi and oomycetes isolated from conditioned leaf litter for which a shredder had already shown high consumption rates. 2. Black alder (Alnus glutinosa) leaf litter was exposed to the littoral zone of Lake Constance in autumn, and subsamples were analysed for leaf parameters and consumption by Gammarus roeselii under standard conditions at regular intervals. On dates with a high consumption rate of the exposed leaves, 14 single strains of fungi and oomycetes were isolated, freed of bacteria and grown on autoclaved leaves. 3. Six of eight measured leaf parameters of exposed leaves were significantly correlated with Gammarus consumption rates, with high colinearity among leaf parameters hampering the identification of causal relations between leaf parameters and feeding activity. 4. When single strains of fungi and oomycetes were grown on autoclaved leaf litter, toughness of colonised leaves was always lower than in the control and the content of protein, N and P were increased. There were pronounced strain‐specific effects on leaf parameters. Consumption rates also differed significantly, with nine of fourteen isolates consumed at higher rates than controls and none proving to be a deterrent. Protein and polyphenol content were significantly correlated with consumption rates. Oomycete‐colonised leaves were consumed at similar rates but were of lower food quality than fungi‐colonised leaves. 5. We argue that direct strain‐specific attractant or repellent effects of fungi and oomycetes on consumption by G. roeselii are not important. However, we found indirect strain‐specific role operating via effects on leaf parameters.     

The importance of bacterivorous protists in the decomposition of stream leaf litter

1. Allochthonous organic matter, in the form of senesced leaves, is a major source of carbon supporting detrital food webs. While studies have documented the role of bacteria and fungi in the decomposition of leaf litter, little information is available regarding the role of protists in the decomposition process. 2. We tested the hypothesis that the presence of stream‐dwelling bacterivorous protists leads to an increased rate of leaf decomposition through grazing pressure on bacteria. We isolated live protists from decomposing leaves collected in a stream in Northern Virginia, U.S.A. (Goose Creek) and established laboratory cultures of common bacterivorous protists. 3. Recently senesced leaves from the field were used in laboratory microcosm experiments to determine if the rate of litter decomposition differed between four treatments: bacteria only, bacteria + flagellates, bacteria + flagellates + ciliates, autoclaved stream water (control). We determined the dry weight of leaf remaining, bacterial abundance, flagellate abundance and ciliate abundance for each replicate on days 0, 7, 14, 30, 60 and 120. 4. The rate of leaf decomposition was significantly higher in treatments with protists than without and bacterial abundance declined in protist treatments compared with bacteria only treatment. Weight loss in the presence of flagellates was three to four times higher when protists were present compared with treatments with bacteria alone. These results provide experimental evidence that protists could play a significant role in the detrital processes of streams.