The effect of bacteria on the solubilization of silica in diatom frustules

P atrick , S heila & H olding , A.J. 1985. The effect of bacteria on the solubilization of silica in diatom frustules. Journal of Applied Bacteriology 59 , 7–16.
Natural bacterial populations in samples of water from Loch Leven and Lough Neagh increased the rate of solubilization of frustule silica from an axenic Cyclotella meneghiniana culture, compared with sterile autolysis, at 25C. In the inoculated cultures 50–60% of the silica was solubilized over a period of 30 d. Bacterial populations in Loch Leven water also enhanced the solubilization of silica from non-axenic cultures of Asterionella formosa, Tabellaria flocculosa, Navicula pellicu-losa and C. meneghiniana , compared with control cultures sterilized with mercuric chloride. Similar results were obtained with Lough Neagh populations incubated with A. formosa . In comparison with untreated cells, the treatment of diatom cells with ultra-sonication did not increase the release of silica. Pure cultures of bacteria from Loch Leven water enhanced the release of silica from non-axenic A. formosa and axenic C. meneghiniana compared with sterile control treatments. The variation in the ability of cultures to solubilize the frustule silica appeared to be related to their potential to produce hydrolytic enzymes. Natural populations of Loch Leven and Lough Neagh water bacteria and certain bacterial cultures caused the diatoms to aggregate, which did not enhance the release of silica.     

The Preservation of Bacteria and Fungi on anhydrous Silica Gel: an Assessment of Survival over Four years

The preservation method of Perkins (1962) using suspensions in skim-milk was used to preserve 33 bacteria and 22 fungi on anhydrous silica gel. During storage at room temperature, 64% of the bacteria and 77% of the fungi survived 1 year or more. Storage at 4° often increased the survival period c. 2- to 3-fold: 73% of the bacteria and all 12 of the fungi tested at 4° survived > 1 year. At the last testing, 60% of the bacteria and 36% of the fungi were still viable after storage at 4° for periods between 3 and 4 years. The Gram positive bacilli tended to survive the silica gel preservation process better than most Gram negative bacilli. Some factors influencing survival after preservation on silica gel are discussed; the results support the use of a closed storage tube.     

Effect of various parameters on viability and growth of bacteria immobilized in sol–gel-derived silica matrices

Immobilized bacteria are being extensively used for metabolite production, biocatalysts, and biosensor construction. However, long-term viability and metabolic activity of entrapped bacteria is affected by several conditions such as their physiological state, the presence of high-osmolarity environments, porous structure and shrinkage of the matrix. The aim of this work was to evaluate the effect of various parameters on bacteria immobilized in sol–gel-derived silica matrices. With this purpose, we evaluated the stress of immobilization over bacteria cultures obtained from different growing states, the effect of cell density and bacteria capability to proliferate inside matrices. Best results to attain longer preservation times were obtained when we immobilized suspensions with an optimized bacterial number of 1 × 10⁷ cfu/gel in the presence of LB medium using aqueous silica precursors. Furthermore, the impact of osmotic stress with the subsequent intracellular trehalose accumulation and the addition of osmolites were investigated. Shorter preservation times were found for bacteria immobilized in the presence of osmolites while trehalose accumulation in stressed cells did not produce changes on entrapped bacteria viability. Finally, nutrient addition in silica matrices was studied indicating that the presence of a carbon source without the simultaneous addition of nitrogen was detrimental for immobilized E. coli. However, when both carbon and nitrogen sources were present, bacteria were able to survive longer periods of time.     

Microbial silica deposition in geothermal hot waters

A combined use of molecular ecological techniques and geochemical surveys revealed that thermophilic or hyperthermophilic microorganisms living in geothermal environments are likely to be implicated in the formation of biogenic siliceous deposits. Electron microscopic observations indicated that numerous microorganism-like fabrics were preserved in naturally occurring siliceous deposits such as siliceous sinter, geyserite, and silica scale, which suggests microbial contribution to silica precipitation. Molecular phylogenetic analyses suggested that extreme thermophilic bacteria within the genera Thermus and Hydrogenobacter are predominant components among the indigenous microbial community in siliceous deposits formed in pipes and equipment of Japanese geothermal power plants. These bacteria seem to actively contribute to the rapid formation of huge siliceous deposits. Additionally, in vitro examination suggested that Thermus cells induced the precipitation of supersaturated amorphous silica during the exponential growth phase, concomitant with the production of a specific cell envelope protein. Dissolved silica in geothermal hot water may be a significant component in the maintenance of position and survival of microorganisms in limited niches.     

Kinetics of adherence of Actinomyces viscosus to saliva-coated silica and hydroxyapatite beads

Adherence of 14C-labelled strains of Actinomyces viscosus to uncoated and saliva-coated silica and hydroxyapatite beads had both loose and firm components, probably reflecting different subpopulations of bacteria within a single culture. Adherence was characterized by the proportion of bacteria available for each type of adherence and a constant (Kb) for each combination of bacterial strain and bead surface. Loose adherence, which was greater with silica than with hydroxyapatite beads, always involved many more bacteria than firm adherence. Firm adherence was greater with A. viscosus WVU627 than A. viscosus TF11. The association rate constants (Ka) for loose and firm adherence were similar, indicating simultaneous processes, but the dissociation rate constant (Kd) was lower for loose adherence than for firm adherence. Removal of loosely adhering bacteria by washing may only reflect their distance from the bead surface. Silica beads were convenient for studying bacterial adherence and formed an acceptable coating of salivary glycoprotein.     

Refinement of an adherence assay for the measurement of bacterial attachment to silica beads

An in vitro adherence assay [4] which utilised radiolabelled bacteria and silica beads was used to investigate firm and loose attachment of bacteria. A systematic evaluation of the effects of the assay conditions, including incubation vessel, bacteria to bead interaction, bead washing and bead weight, was carried out in an attempt to improve the reproducibility of adherence measurements. Four oral streptococcal strains (S. mutans NCTC 10449, S. sanguis NCTC 7863 and 10904, S. salivarius NCTC 8618) were studied with saliva coated and uncoated silica beads.Using the improved system, total bacterial adherence to uncoated beads was high (45–60% of bacteria present). While saliva coating of beads reduced total and firm adherence of all strains, these reductions were less marked (P > 0.005) for S. sanguis NCTC 10904.     

Silica Gel Plates for Culture of Marine and Nonmarine Organisms

Marine and nonmarine species of bacteria grew well when a simplified silica gel plate preparation was used.     

High-throughput method for isolating plasmid DNA with reduced lipopolysaccharide content

Isolating plasmid DNA from bacteria is a fundamental step in molecular biology. It is often accomplished by an alkaline lysis of bacteria and the subsequent adsorption of nucleic acids to silica oxide in the presence of chaotropic substances. Here we show that the addition of such chaotropic reagents is not required for the efficient DNA isolation with silica oxide. This surprising finding allowed us to purify plasmid DNA with significantly less lipopolysaccharides (LPS), which is otherwise a common bacterial contaminant of silica oxide-isolated DNA and inhibits subsequent applications. In addition, we have implemented a precipitation step that altogether leads to a reduction of the LPS content by a factor of 900 relative to published methods. Our novel protocol facilitates an inexpensive high-throughput analysis of pure plasmids in a 96-well format without the addition of hazardous reagents.     

Scanning electron micrograph study of Bacillus licheniformis during bioleaching of silica from magnesite ore

We report a scanning electron micrographical study of morphological characteristics of Bacillus licheniformis during bioleaching of silica from magnesite ore and its effect on the ore surface. When grown in the presence of magnesite ore the bacteria were pleomorphic and developed protrusions on the cell surface by which they adhered to the ore surface. A significant amount of soluble silica was released into the leaching solution during incubation for 96 h and was followed by a heavy corrosion of the ore surface. This observation was supported by a petrographic thin-section analysis which showed the absence of silica veins in magnesite ore exposed to the organism.     

Isolation of RNA from mycobacteria grown under in vitro and in vivo conditions

Isolation of RNA from mycobacteria is very difficult to perform, and the yields are generally very low. We describe an approach to isolate RNA from mycobacterial species which combines the disruption of mycobacterial cells by a silica/ceramic matrix in a reciprocal shaker with the ease and efficiency of subsequent RNA purification on spin columns with silica gel-based membranes. This method is rapid, easy to perform and yields high amounts of pure, intact total RNA. Due to its safety, this method is applicable even to group 3 biological hazard organisms like Mycobacterium tuberculosis. By combining a method for the isolation of phagosomal bacteria from infected primary macrophages with the novel RNA isolation technique, we are able to monitor gene expression during infection even in bacteria which are rather resistant to genetic manipulation, like Mycobacterium bovis.     

Bio-deposition of Amorphous Silica by an Extremely Thermophilic Bacterium,Thermus spp.

The bio-deposition of amorphous silica, which occurred in vitro by exposure to the extremely thermophilic bacterium Thermus spp. began from the latter part of the exponential phase of growth of the bacteria. The concentration with which the deposition occurred exceeded the solubility of amorphous silica of neutral pH at the temperature 60~85°C. Our observations suggest that Thermus spp. promotes the formation of siliceous minerals in a geothermal environment.     

Spicules of hexactinellid sponges (Hexactinellida: Porifera) as natural composite materials

This paper reviews studies on the hexactinellid glass sponges (Hexactinellida: Porifera) that have organic silica spicules. According to its physical properties (microdensity, Young’s modulus, and light transmission), the material of the spicules is similar to amorphous silica; however, sponge spicules are birefringent, which suggests that they have a highly ordered crystal-like nature. Mineralized remnants of siliceous spicules composed of chemically inert materials are preserved in sedimentary rocks and provide evidence of the ecological state of the ancient biosphere. Sponges occur in waters with low temperatures; therefore, they grow very slowly and live for hundreds of years. The organic silica spicules exhibit the capacity for triboluminescence. The generated light emission may be used by symbiotic bacteria on the spicule surface.     

Bacterial motion in porous media

The motion of chemotactically different Escherichia coli C600, cheB287, and AW405 cells was studied using a column packed with silica gel. The model chemotaxis of bacteria in porous media seems to be adequate to natural bacterial chemotaxis in soils. The porous structure of silica gel prevents interfering convective flows. Silica gel columns make it possible to separate bacterial cells differing in motility and chemotaxis. Relevant physical phenomena are discussed. The concept of fast and slow chemotaxis is considered.     

Silica Gel Medium for Enumeration of Petroleumlytic Microorganisms in the Marine Environment

A silica gel medium was developed for the enumeration of petroleumlytic microorganisms in the marine environment. The medium was satisfactorily used for the investigation of the vertical distribution of bacteria in seawater from the surface to 1,000 m depth of western north Pacific central water as well as the neritic region of Japan.     

Bacterial Motion in Porous Media

The motion of chemotactically different Escherichia coli C600, cheB287, and AW405 cells was studied using a column packed with silica gel. The model chemotaxis of bacteria in porous media seems to be adequate for natural bacterial chemotaxis in soils. The porous structure of silica gel prevents interfering convective flows. Silica gel columns make it possible to separate bacterial cells differing in motility and chemotaxis. Relevant physical phenomena are discussed. The concept of fast and slow chemotaxis is considered.     

A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species

A silica sands-based method has been developed to isolate high quality genomic DNAs from cells of animals, plants and microorganisms, such as Hemisalanx prognathus, Spinacia oleracea, Pichia pastoris, Bacillus licheniformis and Escherichia coli. To the best of our knowledge, no DNA isolation method has so wide application until now. In addition, this method and a commercially available kit were compared in analysis of microbial communities using high-throughput 16s rDNA sequencing. As a result, the silica sands-based method was found to be even more efficient in isolating genomic DNA from gram-positive bacteria than the kit, indicating that it would become a very valuable choice to faithfully reflect the composition of microbial communities.     

Experimental fossilization of the Thermophilic Gram-positive Bacterium Geobacillus SP7A: A Long Duration Preservation Study

Recent experiments to fossilize microorganisms using silica have shown that the fossilization process is far more complex than originally thought; microorganisms not only play an active role in silica precipitation but may also remain alive while silica is precipitating on their cell wall. To better understand the mechanisms that lead to the preservation of fossilized microbes in recent and ancient rocks, we experimentally silicified a Gram-positive bacterium, Geobacillus SP7A, over a period of five years. The microbial response to experimental fossilization was monitored with the use of LIVE/DEAD staining to assess the structural integrity of the cells during fossilization. It documented the crucial role of silicification on the preservation of the cells and of their structural integrity after several years. Electron microscopy observations showed that initial fossilization of Gram-positive bacteria was extremely rapid, thus allowing very good preservation of Geobacillus SP7A cells. A thick layer of silica was deposited on the outer surface of cell walls in the earliest phase of silicification before invading the cytoplasmic space. Eventually, the cell wall was the only recognizable feature. Heavily mineralized cells thus showed morphological similarities with natural microfossils found in the rock record.     

石油降解菌X-1所产表面活性剂的研究

对石油污染土壤中筛选到的能产生生物表面活性剂的石油降解菌X-1(芽孢杆菌),进行表面活性剂的提取和鉴定,并对其产剂条件进行了优化。结果表明:菌株X-1产生的生物表面活性剂为浅黄色粉末状物质。通过硅胶板薄层层析和红外光谱分析,判定表面活性剂为脂肽、脂蛋白类物质。菌株X-1产生表面活性剂的最佳条件为:温度32℃,pH 7.0,盐度2 g/L NaCl,最佳碳源为淀粉,最佳氮源为蛋白胨。     

The experimental silicification of Aquificales and their role in hot spring sinter formation

Archean microfossils provide some of the earliest physical evidence for life on Earth, yet there remains a great deal of uncertainty regarding which micro‐organisms were actually preserved. Because of the limited cellular detail remaining, interpretation of those microfossils has been based solely on size and morphology. This has led to significant controversy surrounding the presence or absence of cyanobacteria as early as 3.5 billion years. Accordingly, there has been an experimental bias towards studying their silicification. Here we report the very first findings on thermophilic bacteria–silica interactions, and investigate how Sulfurihydrogenibium azorense, a representative of the Aquificales often found as prominent members of modern hot spring vent communities, interacts with highly siliceous hydrothermal fluids. We show that adsorption of silica is limited to silica polymers and colloids, and that the magnitude of silica adsorption is dependent on its chemolithoautotrophic pathway. Intriguingly, when S. azorense is grown as a H₂‐oxidizer, it responds to increasing silica concentrations by producing a protein‐rich biofilm that may afford the cells protection against cell wall silicification. Although the biofilms of Aquificales could potentially contribute to or accelerate siliceous sinter formation under certain growth conditions, the cells themselves show a low preservation potential and are unlikely to have been preserved in the ancient rock record, despite phylogenetic analyses suggesting that they represent one of the most primordial life forms.     

福寿螺不同生长发育阶段的抗菌活性物质及化学成分分析

福寿螺(Pomacea canaliculata)不同生长发育阶段(螺苗、仔螺、中螺、成螺)的软体匀浆物用乙酸乙酯进行提取.提取物分别用硅胶柱进行柱层析,并分别用不同极性的有机溶剂进行洗脱,分离出不同极性组分:非极性组分(石油醚洗脱组分)、弱极性组分(苯洗脱组分)、强极性组分(乙醇洗脱组分).然后用11种细菌对不同极性组分进行抗菌活性检测.结果表明,不同生长发育阶段组分抗菌作用的共同点是:强极性组分的抗菌活性最强,弱极性组分次之,非极性组分无抑菌作用.将不同生长发育阶段抗菌活性最强的乙醇洗脱组分分别进行薄层层析(TLC)分析并进行抗菌实验.薄层层析所用的展层剂不同,分离出条带数不同,各条带抗菌活性也存在差异.将抗菌活性最强的条带用气相色谱.质谱法进行化学成分鉴定,结果表明,各不同生长发育阶段抗菌物质的化学成分大部分是酸类物质,相同的化学成分在不同生长发育阶段的含量及相似度都不一样.