Silicates,Silicate Weathering,and Microbial Ecology

Mineralogy, microbial ecology, and mineral weathering in the subsurface are an intimately linked biogeochemical system. Although bacteria have been implicated indirectly in the accelerated weathering of minerals, it is not clear if this interaction is simply the coincidental result of microbial metabolism, or if it represents a specific strategy offering the colonizing bacteria a competitive ecological advantage. Our studies provide evidence that silicate weathering by bacteria is sometimes driven by the nutrient requirements of the microbial consortium, and therefore depends on the trace nutrient content of each aquifer mineral. This occurrence was observed in reducing groundwaters where carbon is abundant but phosphate is scarce; here, even resistant feldspars are weathered rapidly. This suggests that the progression of mineral weathering may be influenced by a mineral's nutritional potential, with microorganisms destroying only beneficial minerals. The rock record, therefore, may contain a remnant mineralogy that reflects early microbial destruction of biologically valuable minerals, leaving a residuum of "useless" minerals, where "value" depends on the organism, its metabolic needs, and the diagenetic environment. Conversely, the subsurface distribution of microorganisms may, in part, be controlled by the mineralogy and by the ability of an organism to take advantage of mineral-bound nutrients.     

Almond Harvesting, Processing, and Microbial Flora

This survey was set up on a statistical sampling plan to determine the microbial quality of almonds as they are received at the processing plant. The total aerobic bacterial count and yeast and mold count distribution were skewed by a few high counts compared with the majority of relatively low counts. Hard shell varieties of almonds had lower counts than did soft shell, and almonds with complete shells had lower counts than shelled almonds. Almonds harvested onto canvas had lower counts than those harvested by knocking onto the ground. Nuts with the least amounts of foreign material mixed into the sample had the lowest counts, as did nuts with the least amount of insect damage. Coliforms, Escherichia coli, and Streptococcus were isolated from the nuts, and their presence was correlated with soil contamination. When almonds are stored, the total plate count, the Streptococcus count, and the E. coli count after an initial drop remain nearly constant for more than 3 months. In addition to the indicator organisms, several genera of bacteria were isolated including Bacillus, Xanthomonas, Achromobacter, Pseudomonas, Micrococcus or Staphylococcus, and Brevibacterium.     

Microbial Biomass, N Mineralization and Nitrification, Enzyme Activities, and Microbial Community Diversity in Tea Orchard Soils

Understanding the chronological changes in soil microbial and biochemical properties of tea orchard ecosystems after wasteland has been reclaimed is important from ecological, environmental, and management perspectives. In this study, we determined microbial biomass, net N mineralization, and nitrification, enzyme (invertase, urease, proteinase, and acid phosphatase) activities, microbial community diversity assessed by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA polymerase chain reaction (PCR) products, and related ecological factors in three tea orchard systems (8-, 50-, and 90-year-old tea orchards), adjacent wasteland and 90-year-old forest. Soil microbial biomass C (C_mic) and activity, i.e., soil basal respiration (R_mic), microbial biomass C as a percent of soil organic C (C_mic/C_org), N mineralization, invertase, urease, proteinase, and acid phosphatase, significantly increased after wasteland was reclaimed; however, with the succeeding development of tea orchard ecosystems, a decreasing trend from the 50- to 90-year-old tea orchard became apparent. Soil net nitrification showed an increasing trend from the 8- to 50-year-old tea orchard and then a decreasing trend from the 50- to 90-year-old tea orchard, and was significantly higher in the tea orchards compared to the wasteland and forest. Urea application significantly stimulated soil net nitrification, indicating nitrogen fertilizer application may be an important factor leading to high-nitrification rates in tea orchard soils. The Shannon’s diversity index (H) and richness (S) based on DGGE profiles of 16S rRNA genes were obviously lower in all three tea orchards than those in the wasteland; nevertheless, they were significantly higher in all three tea orchards than those in the forest. As for the three tea orchard soils, comparatively higher community diversity was found in the 50-year-old tea orchard.     

Substrate Degradation Kinetics, Microbial Diversity, and Current Efficiency of Microbial Fuel Cells Supplied with Marine Plankton

The decomposition of marine plankton in two-chamber, seawater-filled microbial fuel cells (MFCs) has been investigated and related to resulting chemical changes, electrode potentials, current efficiencies, and microbial diversity. Six experiments were run at various discharge potentials, and a seventh served as an open-circuit control. The plankton consisted of a mixture of freshly captured phytoplankton and zooplankton (0.21 to 1 mm) added at an initial batch concentration of 27.5 mmol liter⁻¹ particulate organic carbon (OC). After 56.7 days, between 19.6 and 22.2% of the initial OC remained, sulfate reduction coupled to OC oxidation accounted for the majority of the OC that was degraded, and current efficiencies (of the active MFCs) were between 11.3 and 15.5%. In the open-circuit control cell, anaerobic plankton decomposition (as quantified by the decrease in total OC) could be modeled by three terms: two first-order reaction rate expressions (0.79 day⁻¹ and 0.037 day⁻¹, at 15°C) and one constant, no-reaction term (representing 10.6% of the initial OC). However, in each active MFC, decomposition rates increased during the third week, lagging just behind periods of peak electricity generation. We interpret these decomposition rate changes to have been due primarily to the metabolic activity of sulfur-reducing microorganisms at the anode, a finding consistent with the electrochemical oxidization of sulfide to elemental sulfur and the elimination of inhibitory effects of dissolved sulfide. Representative phylotypes, found to be associated with anodes, were allied with Delta-, Epsilon-, and Gammaproteobacteria as well as the Flavobacterium-Cytophaga-Bacteroides and Fusobacteria. Based upon these results, we posit that higher current efficiencies can be achieved by optimizing plankton-fed MFCs for direct electron transfer from organic matter to electrodes, including microbial precolonization of high-surface-area electrodes and pulsed flowthrough additions of biomass.     

Microbial Conversion of alpha-Ionone, alpha-Methylionone, and alpha-Isomethylionone

alpha-Ionone, alpha-methylionone, and alpha-isomethylionone were converted by Aspergillus niger JTS 191. The individual bioconversion products from alpha-ionone were isolated and identified by spectrometry and organic synthesis. The major products were cis-3-hydroxy-alpha-ionone, trans-3-hydroxy-alpha-ionone, and 3-oxo-alpha-ionone. 2,3-Dehydro-alpha-ionone, 3,4-dehydro-beta-ionone, and 1-(6,6-dimethyl-2-methylene-3-cyclohexenyl)-buten-3-one were also identified. Analogous bioconversion products from alpha-methylionone and alpha-isomethylionone were also identified. From results of gas-liquid chromatographic analysis during the fermentation, we propose a metabolic pathway for alpha-ionones and elucidation of stereochemical features of the bioconversion.     

Microbial Enzymes: Production,Purification, and Isolation

Abstract

The cytoplasmic membranes of many aerobic and facultative bacteria contain enzymes that catalyze the reduction of dissolved oxygen to water. Preparations of small particles derived from such membranes can be filter sterilized without loss of the oxygen-reducing enzymes. These particle preparations can be used to produce anaerobic conditions in a variety of biological environments. They have been shown to stimulate the growth of many anaerobic bacteria and can also be used to stabilize oxygen-sensitive chemical reagents. The particle preparations are stable for long periods of time. They are functional over a pH range and temperature range frequently encountered in biological systems. Various techniques for using the particles are presented. The advantages and limitations of this new approach to achieving oxygen-free conditions are discussed.     

Microbial beta-glucosidases: cloning,properties, and applications

Beta-glucosidases constitute a major group among glycosylhydrolase enzymes. Out of the 82 families classified under glycosylhydrolase category, these belong to family 1 and family 3 and catalyze the selective cleavage of glucosidic bonds. This function is pivotal in many crucial biological pathways, such as degradation of structural and storage polysaccharides, cellular signaling, oncogenesis, host-pathogen interactions, as well as in a number of biotechnological applications. In recent years, interest in these enzymes has gained momentum owing to their biosynthetic abilities. The enzymes exhibit utility in syntheses of diverse oligosaccharides, glycoconjugates, alkyl- and aminoglucosides. Attempts are being made to understand the structure-function relationship of these versatile biocatalysts. Earlier reviews described the sources and properties of microbial beta-glucosidases, yeast beta-glucosidases, thermostable fungal beta-glucosidase, and the physiological functions, characteristics, and catalytic action of native beta-glucosidases from various plant, animal, and microbial sources. Recent efforts have been directed towards molecular cloning, sequencing, mutagenesis, and crystallography of the enzymes. The aim of the present article is to describe the sources and properties of recombinant beta-glucosidases, their classification schemes based on similarity at the structural and molecular levels, elucidation of structure-function relationships, directed evolution of existing enzymes toward enhanced thermostability, substrate range, biosynthetic properties, and applications.     

Interrelationships between Rates of Microbial Production,Exopolymer Production,Microbial Biomass,and Sediment Stability in Biofilms of Intertidal Sediments

Abstract The upper few millimeters of intertidal sediment supports a varied biomass of microbial consortia and microphytobenthos. Many of these organisms release extracellular polymers into the surrounding sediment matrix that can result in sediment cohesion and the increased stability of the sediment. The relationship between the heterotrophic and autotrophic components of these biofilms is not well understood. A combination of mesocosm and field investigations were used to investigate the relationship between microbial production rate (algae and bacteria), the extracellular carbohydrates, biomass, and stability in conjunction with a variety of environmental factors. An inverse relationship was found between rates of algal production and sediment stability both in the field and in laboratory mesocosms, though the relationship was significant only in the field (P < 0.001). Stability of sediments increased with increasing bacterial production rate (P < 0.001). Positive correlations were found between sediment stability and a range of other variables, including algal biomass (P < 0.001), colloidal-S EPS (P < 0.001), colloidal-S carbohydrate (P < 0.01), colloidal-S EDTA (P < 0.01), and sediment water content (P < 0.001). Using the data acquired, a preliminary model was developed to predict changes in sediment stability. Chlorophyll a, water content, and colloidal-S EPS were found to be the most important predictors of stability in intact cores incubated under laboratory conditions. Differences observed in patterns of the surface (0–2 mm) distribution of colloidal-S carbohydrate and chlorophyll a when expressed on a dry weight or areal basis were attributed to effects of dewatering and concomitant changes in wet bulk density. The polymeric carbohydrate (colloidal-S EPS) component of the biofilms was not found to be a constant fraction of the colloidal-S carbohydrate extract, varying from 16 to 58%, and the percentage of polymer decreased logarithmically as chlorophyll a concentrations increased and the biofilms matured (P < 0.001). Changes in the relationships between these variables over the period of biofilm development and maturation highlight the difficulties in their use to predict sediment stability. Exopolymer concentrations were more closely correlated with algal biomass than with bacterial numbers. Rates of algal carbon fixation were considerably greater than those for bacteria, suggesting that the algae have a much greater potential for exopolymer production. It is suggested that the microphytobenthos secretions make a more important contribution to sediment stability. Received: 12 May 1999; Accepted: 13 October 1999; Online Publication: 24 March 2000     

Quantifying Microbial Diversity: Morphotypes, 16S rRNA Genes, and Carotenoids of Oxygenic Phototrophs in Microbial Mats

We quantified the diversity of oxygenic phototrophic microorganisms present in eight hypersaline microbial mats on the basis of three cultivation-independent approaches. Morphological diversity was studied by microscopy. The diversity of carotenoids was examined by extraction from mat samples and high-pressure liquid chromatography analysis. The diversity of 16S rRNA genes from oxygenic phototrophic microorganisms was investigated by extraction of total DNA from mat samples, amplification of 16S rRNA gene segments from cyanobacteria and plastids of eukaryotic algae by phylum-specific PCR, and sequence-dependent separation of amplification products by denaturing-gradient gel electrophoresis. A numerical approach was introduced to correct for crowding the results of chromatographic and electrophoretic analyses. Diversity estimates typically varied up to twofold among mats. The congruence of richness estimates and Shannon-Weaver indices based on numbers and proportional abundances of unique morphotypes, 16S rRNA genes, and carotenoids unveiled the underlying diversity of oxygenic phototrophic microorganisms in the eight mat communities studied.     

Microbial β-Glucosidases: Cloning,Properties, and Applications

ABSTRACT:?

β-Glucosidases constitute a major group among glycosylhydrolase enzymes. Out of the 82 families classified under glycosylhydrolase category, these belong to family 1 and family 3 and catalyze the selective cleavage of glucosidic bonds. This function is pivotal in many crucial biological pathways, such as degradation of structural and storage polysaccharides, cellular signaling, oncogenesis, host-pathogen interactions, as well as in a number of biotechnological applications. In recent years, interest in these enzymes has gained momentum owing to their biosynthetic abilities. The enzymes exhibit utility in syntheses of diverse oligosaccharides, glycoconjugates, alkyl- and amino-glucosides. Attempts are being made to understand the structure-function relationship of these versatile biocatalysts. Earlier reviews described the sources and properties of microbial β-glucosidases, yeast β-glucosidases, thermostable fungal β-glucosidase, and the physiological functions, characteristics, and catalytic action of native β-glucosidases from various plant, animal, and microbial sources. Recent efforts have been directed towards molecular cloning, sequencing, mutagenesis, and crystallography of the enzymes. The aim of the present article is to describe the sources and properties of recombinant β-glucosidases, their classification schemes based on similarity at the structural and molecular levels, elucidation of structure-function relationships, directed evolution of existing enzymes toward enhanced thermostability, substrate range, biosynthetic properties, and applications.     

Microbial activity under alpine snowpacks, Niwot Ridge, Colorado

Experiments were conducted during 1993 at Niwot Ridge in the Colorado Front Range to determine if the insulating effect of winter snow cover allows soil microbial activity to significantly affect nitrogen inputs and outputs in alpine systems. Soil surface temperatures under seasonal snowpacks warmed from –14 °C in January to 0 °C by May 4th. Snowmelt began in mid-May and the sites were snow free by mid June. Heterotrophic microbial activity in snow-covered soils, measured as C0₂ production, was first identified on March 4, 1993. Net C0₂ flux increased from 55 mg CO₂-C m^–2 day^–1 in early March to greater than 824 mg CO₂-C m-2 day^–1 by the middle of May. Carbon dioxide production decreased in late May as soils became saturated during snowmelt. Soil inorganic N concentrations increased before snowmelt, peaking between 101 and 276 mg kg^–1 soil in May, and then decreasing as soils became saturated with melt water. Net N mineralization for the period of March 3 to May 4 ranged from 2.23 to 6.63 g N m^–2, and were approximately two orders of magnitude greater than snowmelt inputs of 50.4 mg N m^–2 for NH₄ ⁺ and 97.2 mg N m^–2 for NO₃ ^–. Both NO₃ ^– and NH₄ ⁺ concentrations remained at or below detection limits in surface water during snowmelt, indicating the only export of inorganic N from the system was through gaseous losses. Nitrous oxide production under snow was first observed in early April. Production increased as soils warned, peaking at 75 g N₂O-N m^–2 day^–1 in soils saturated with melt water one week before the sites were snow free. These data suggest that microbial activity in snow-covered soils may play a key role in alpine N cycling before plants become active.     

Risk Assessment,Microbial Communities,and Pollution-Induced Community Tolerance

Until recently, parameters from microorganisms were generally not included in risk assessment at a comparable level to animals and plants. However, the major part of global biomass, biodiversity, and ecosystem processes is present in the microbial world and microbiological techniques applicable to risk assessment are becoming available. Two microbial indicators are described based on the usage of multiwell plates with different substrates and a redox indicator for monitoring mineralisation. With both techniques autochthonous microbial communities are analysed. Producing functional fingerprints of the microbial community gives insights into the composition of different functions. This is equivalent to observations of ecological abundance and species composition. When lack of reference sites or reference data renders risk assessment difficult, measurement of the pollution-induced community tolerance (PICT) can provide useful information.     

Microbial nitrilases: versatile, spiral forming, industrial enzymes

The nitrilases are enzymes that convert nitriles to the corresponding acid and ammonia. They are members of a superfamily, which includes amidases and occur in both prokaryotes and eukaryotes. The superfamily is characterized by having a homodimeric building block with a αββα–αββα sandwich fold and an active site containing four positionally conserved residues: cys, glu, glu and lys. Their high chemical specificity and frequent enantioselectivity makes them attractive biocatalysts for the production of fine chemicals and pharmaceutical intermediates. Nitrilases are also used in the treatment of toxic industrial effluent and cyanide remediation. The superfamily enzymes have been visualized as dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers and variable length helices, but all nitrilase oligomers have the same basic dimer interface. Moreover, in the case of the octamers, tetradecamers, octadecamers and the helices, common principles of subunit association apply. While the range of industrially interesting reactions catalysed by this enzyme class continues to increase, research efforts are still hampered by the lack of a high resolution microbial nitrilase structure which can provide insights into their specificity, enantioselectivity and the mechanism of catalysis. This review provides an overview of the current progress in elucidation of structure and function in this enzyme class and emphasizes insights that may lead to further biotechnological applications.