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  • 1
    Electronic Resource
    Electronic Resource
    Determination of Microbial Cell Numbers in Subsurface Samples (1985)
    Oxford, UK : Blackwell Publishing Ltd
    Ground water 23 (1985), S. 0 
    Details
    ISSN: 1745-6584
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Geosciences
    Notes: Ground-water pollution by organic compounds has become a major environmental concern. Because the transport and fate of the organic pollutants may be influenced by microorganisms present in subsurface material, reliable measurements of the number of organisms in subsurface samples and their metabolic activity are needed. A special drilling rig and aseptic procedures have been developed by the Robert S. Kerr Environmental Research Laboratory of the United States Environmental Protection Agency to yield uncontaminated subsurface samples. The number of bacteria in subsurface samples has been determined by microscopic counting after acridine orange staining; the proportion of cells capable of respiration was determined by INT reduction. An independent measure of metabolic activity was obtained by measuring ATP extracted from the samples. A procedure and extradant for the extraction of ATP from subsurface material have been developed. The extractant contains reagents to reduce the loss of the extracted ATP. Subsurface samples from Oklahoma and Texas contain 106-107 cells per g of subsurface material (depths of 2–9 m). Both methods show that usually between 1 and 10% of the cells were metabolically active. Thus, significant numbers of metabolically active bacteria exist in subsurface material with the potential to modify pollutants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1745-6584.1985.tb02775.x
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  • 2
    Electronic Resource
    Electronic Resource
    Survey of Microbial Populations in Buried-Valley Aquifer Sediments from Northeastern Kansas (1990)
    Oxford, UK : Blackwell Publishing Ltd
    Ground water 28 (1990), S. 0 
    Details
    ISSN: 1745-6584
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Geosciences
    Notes: Twenty-two aseptically collected sediment core samples were obtained from below the water table (60 to 280 feet deep) at four pristine sites along a major buried-valley aquifer system in northeastern Kansas. Samples were examined for total numbers of bacteria, viable aerobic bacteria, protozoa, and fungi. Contiguous samples were obtained in some transition zones of sediment texture or color in order to detect possible population shifts over small vertical distances related to changes in sediment characteristics. Total counts of bacteria varied between 106 and 108 per gram of dry sediment. Viable bacterial counts varied between 0 and 108 colony forming units per gram, usually being higher in sandy or gravelly sediments than in silty or clayey sediments. The relationship between sediment texture and microbial population density was confirmed statistically. Total numbers of bacteria correlated highly with variations in sediment sand and clay content. The population densities of viable bacteria and protozoa correlated moderately with these indicators of sediment texture. In some samples, populations of viable bacteria approached the total count of bacteria and the diversity of bacterial colony types appraoched that found in surface soil. Protozoa were found at low population densities in the coarser textured samples. The protozoa were similar to types commonly encountered in surface soil. No actinomycetes, fungi, or algae were detected in any samples.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1745-6584.1990.tb02266.x
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  • 3
    Electronic Resource
    Electronic Resource
    Microbial growth and resuscitation alter community structure after perturbation (1995)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 17 (1995), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract: An increase in the number of culturable organisms and a decrease in the diversity of recoverable microbiota have been reported in deep subsurface materials after storage perturbation. The magnitude of the microbial community shift in stored samples was more pronounced at 4°C compared to −20°C. Phospholipid fatty acid analyses and acridine orange direct counts indicated that biomass did not increase significantly throughout storage. Changes in the types of fatty acid methyl esters determined over the time course indicated that some of the microbial community shift was due to bacterial proliferation. However, the recovery of new bacterial types only after the storage process suggested that some of the increase in culturable cell count was due to the resuscitation of dormant microorganisms, possibly activated by some aspect of sampling, sample handling, and/or storage. Comparison of acridine orange direct counts with phospholipid and diglyceride fatty acid content suggested that much of the biomass may have been non-living at early time points; however, after 30 days of storage most of the bacterial biomass was viable.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1995.tb00124.x
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  • 4
    Electronic Resource
    Electronic Resource
    Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA (2001)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 35 (2001), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: High-temperature (≥60°C) synthetic food waste compost was examined by cultivation-dependent and -independent methods to determine predominant microbial populations. Fluorescent direct counts totaled 6.4 (±2.5)×1010 cells gdw−1 in a freeze-dried 74°C compost sample, while plate counts for thermophilic heterotrophic aerobes averaged 2.6 (±1.0)×108 CFU gdw−1. A pre-lysis cell fractionation method was developed to obtain community DNA and a suite of 16S and 18S rDNA-targeted PCR primers was used to examine the presence of Bacteria, Archaea and fungi. Bacterial 16S rDNA, including a domain-specific 1500-bp fragment and a 300-bp fragment specific for Actinobacteria, was amplified by PCR from all compost samples tested. Archaeal rDNA was not amplified in any sample. Fungal 18S rDNA was only amplified from a separate dairy manure compost that reached a peak temperature of 50°C. Amplified rDNA restriction analysis (ARDRA) was used to screen isolated thermophilic bacteria and a clone library of full-length rDNA fragments. ARDRA screening revealed 14 unique patterns among 63 isolates, with one pattern accounting for 31 of the isolates. In the clone library, 52 unique patterns were detected among 70 clones, indicating high diversity of uncultivated bacteria in hot compost. Phylogenetic analysis revealed that the two most abundant isolates belonged in the genera Aneurinibacillus and Brevibacillus, which are not commonly associated with hot compost. With the exception of one Lactobacillus-type sequence, the clone library contained only sequences that clustered within the genus Bacillus. None of the isolates or cloned sequences could be assigned to the group of obligate thermophilic Bacillus spp. represented by B. stearothermophilus, commonly believed to dominate high-temperature compost. Amplified partial fragments from Actinobacteria, spanning the V3 variable region (Neefs et al. (1990) Nucleic Acids Res. 18, 2237–2242), included sequences related to the genera Saccharomonospora, Gordonia, Rhodococcus and Corynebacterium, although none of these organisms were detected among the isolates or full-length cloned rDNA sequences. All of the thermophilic isolates and sequenced rDNA fragments examined in this study were from Gram-positive organisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2001.tb00805.x
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  • 5
    Electronic Resource
    Electronic Resource
    Physiology and ultrastructure of Leptothrix discophora SS-1 (1986)
    Springer
    Archives of microbiology 145 (1986), S. 126-135 
    Details
    ISSN: 1432-072X
    Keywords: Leptothrix discophora ; Mn2+-oxidation ; Enter-Doudoroff pathway ; Plate organelles ; PHB granules ; Outer membrane evaginations ; Blebs ; Extracellular polymers ; Fibrillar matrix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Leptothrix discophora strain SS-1 (ATCC 43182) is a Gram-negative, Mn2+-oxidizing, aerobic heterotroph which lost its sheath-forming ability after 18 months of cultivation on laboratory media. SS-1 possesses high 6-phosphogluconate dehydratase and KDPG aldolase activities, and a very low level of phosphofructokinase, indicating carbohydrate catabolism by the Entner-Doudoroff pathway. The strain is polarly flagellated, accumulates PHB up to 67% of its dry weight when grown in pyruvate-containing medium, and has a G+C content of 69.8 mol%. These properties indicate that L. discophora is essentially a pseudomonad which can form a sheath and oxidize Mn2+. Ultrastructural observations made before SS-1 lost its sheath-forming ability indicated two cell types. Short, flagellated, non-sheathed cells seen under the electron microscope probably corresponded to swarmer cells observed under phase-contrast microscopy. These cells contained plate organelles and PHB granules, and produced extracellular blebs approx. 25–50 nm in diameter. Larger sheathed cells also contained plate organelles, PHB granules, and blebs that were often sandwiched between the outer membrane and the sheath. Cells grown in the presence of added Mn2+ were surrounded by an extensive fibrillar matrix, rendered electron dense by precipitation of manganic oxide. The matrix was connected to various points of the cell by outer membrane evaginations or electron dense threads. We propose that the outer membrane blebs represent vehicles for excretion of unorganized sheath material and/or Mn2+-oxidizing protein produced by L. discophora.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00446769
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  • 6
    Electronic Resource
    Electronic Resource
    The intracellular polyglucose storage granules of Spirochaeta aurantia (1988)
    Springer
    Archives of microbiology 150 (1988), S. 289-295 
    Details
    ISSN: 1432-072X
    Keywords: Spirochaeta aurantia ; Glycogen ; Spirochetes ; Cytochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Extracts of Spirochaeta aurantia contained granules approximately 36 nm in diameter. These granules were purified by isopycnic centrifugation on CsCl gradients and shown on the basis of chemical and spectroscopic evidence to be glycogen. Electron microscopic cytochemical methods revealed glycogen-like granules in S. aurantia cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00407794
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  • 7
    Electronic Resource
    Electronic Resource
    Formation of Metallogenium-like structures by a manganese-oxiding fungus (1989)
    Springer
    Archives of microbiology 151 (1989), S. 223-231 
    Details
    ISSN: 1432-072X
    Keywords: Metallogenium ; Manganese-oxidizing fungus ; Mn oxidation ; Extracellular polymers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Structures resembling Metallogenium spp. were observed in agar and in liquid cultures of a Mn-oxidizing basidiomycetous fungus only when Mn2+ was oxidized. Fungal viability was necessary for formation of the structures; Mn2+ concentration and the presence or absence of agar in the medium were important factors determining their morphology. Slide cultures revealed no identifiable cells in any stage of development. Fluorescent dyes that stained nucleic acids and polysaccharides in the fungal hyphae did not stain the Metallogenium-like structures. Likewise, Rhodamine 123, a fluorescent probe for membrane potential, stained fungal mitochondria, but did not stain the structures. Thin sections through the structures showed no biological membranes or other cellular features. Only the characteristic ultrastructure of biological Mn oxides were observed in serial thin sections. In agar, unfixed structures disappeared permanently during reduction of Mn oxides with hydroxylamine. Glutaraldehyde fixation stabilized these structures. Fixed structures lost most of their original phase density during reduction with hydroxylamine, but continuous microscopic observations showed that their phase density could be restored by staining with Coomassie blue. Structures that formed in liquid medium did not require stabilization with glutaraldehyde during reduction of Mn oxides. They, too, lost their original phase density during reduction with hydroxylamine; phase density could be restored by staining with cationic colloidal iron or Coomassie blue. The results suggest that the Metallogenium-like structures were formed as a result of Mn oxidation associated with exopolymers produced by the fungus.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00413134
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  • 8
    Electronic Resource
    Electronic Resource
    Distribution and activity of microorganisms in subsurface sediments of a pristine study site in Oklahoma (1988)
    Springer
    Microbial ecology 16 (1988), S. 85-97 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Distribution and activity of microorganisms in surface soil and subsurface sediments were studied in depth profiles of six different microbial biomass and activity indicators (total direct counts, number of cells capable of electron transport system activity, viable cell plate counts, most Probable numbers of protozoa, and 4-hydroxybenzoate-degrading microorganisms, and ATP content). The profiles showed the same general trends on two different dates (January and June 1985). Seasonal variations were noted, but they were not extreme. Biomass and activity values declined sharply with depth in the unsaturated zone, reaching minima in a clay confining layer in the interface zone between 3 and 4 m. Contiguous 10-cm samples from the interface zone showed significant textural and microbiological variability. Higher and more stable biomass and activity values were detected in the saturated zone, the highest being a very permeable gravelly loamy sand layer at approximately 7.5 m. In this layer, viable counts were nearly equal to total counts and they approached the viable counts in surface soil. Surface-type protozoa and cyanobacteria also were detected in this layer, suggesting that it was connected hydrologically to a nearby river. Lowest values were detected in an underlying bedrock clay layer at 8 m, which, despite its impermeability and low viable counts, did contain measurable total counts, 4-hydroxybenzoate-degrading microorganisms, and ATP. Correlations were noted between sediment texture and microbial activity (i.e., sandy texture=high activity, clayey texture=low activity), but other hydrogeological and geochemical factors probably also influenced microbial distribution and activity in the profile.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02097407
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  • 9
    Electronic Resource
    Electronic Resource
    Nitrifying populations and the destruction of nitrogen dioxide in soil (1977)
    Springer
    Microbial ecology 4 (1977), S. 233-240 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The nitrite formed from nitrogen dioxide (NO2) was oxidized more readily in soil that had been treated previously with the gas than in soil not so pre-exposed. The reaction was inhibited by 1.0 but not by 0.01 mM chlorate. The population of nitrite-oxidizing autotrophs estimated by the most-probable-number procedure was too small and often grew too late to account for oxidation of the nitrite generated from NO2. The reaction also proceeded in soil heated to 42° to 45°C or treated with 0.16 mM chlorate, although the countable autotrophs did not increase during the transformation or grew only late in the active period of nitrite oxidation. The data suggest that unknown populations are responsible for metabolism of the nitrite produced from NO2 entering soil.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02015079
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  • 10
    Electronic Resource
    Electronic Resource
    Contrasts between subsurface microbial communities and their metabolic adaptation to polycyclic aromatic hydrocarbons at a forested and an urban coal-tar disposal site (1992)
    Springer
    Microbial ecology 24 (1992), S. 199-213 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The abundance and distribution of microorganisms and their potential for mineralizing polycyclic aromatic hydrocarbons (PAHs) were measured in subsurface sediment samples at two geographically separate buried coal-tar sites. At a relatively undisturbed forested site in the northeastern United States, metabolic adaptation to the PAHs was evident: Radiolabeled naphthalene and phenanthrene were converted to 14CO2 in core material from inside but not outside a plume of groundwater contamination. However, at the urban site in the midwestern United States these PAHs were mineralized in sediments from both contaminated and uncontaminated boreholes. Thus, clear qualitative evidence showing an adaptational response by the subsurface microbial community was not obtained at the urban site. Instead, subtler clues suggesting metabolic adaptation by subsurface microorganisms from the urban site were discerned by comparing lag periods and extents of 14CO2 production from radiolabeled PAHs added to samples from contaminated and uncontaminated boreholes. Despite slightly higher PAH mineralization activity in contaminated borehole samples, p-hydroxybenzoate was mineralized equally in all samples from the urban site regardless of location. No striking trends in the abundances of actinomycetes, fungi, and either viable or total bacteria were encountered. However, colonies of the soil bacterium, Bacillus mycoides, were detected on enumeration plates of several samples from unsaturated and saturated zones in both urban boreholes. Furthermore, other common soil bacteria, Myxococcus xanthus and Chromobacterium violaceum, were identified in samples from the uncontaminated urban borehole. The occurrence of bacteria usually restricted to surface soil, combined with the observation of fragments of building materials in many of the core samples, suggested that past excavation and backfilling operations may have caused mixing of surface soil with subsurface materials at the urban site. We speculate that this mixing, as well as non-coal-tar-derived sources of PAHs, contributed to the PAH-mineralizing activity present in the sediment samples from the uncontaminated urban borehole.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00174455
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