Biomedical subjects

T L Kieft

Publications and source records attributed to T L Kieft.

11 recordsLinked to original sources

PubMed2003

Identification of iron-reducing Thermus strains as Thermus scotoductus.

Thermus strain SA-01, previously isolated from a deep (3.2 km) South African gold mine, is closely related to Thermus strains NMX2 A.1 and VI-7 (previously isolated from thermal springs in New Mexico, USA, and Portugal, respectively). Thermus strains SA-01 and NMX2 A.1 have also been shown previously to grow using nitrate, Fe(III), Mn(IV) or S(O) as terminal electron acceptors and to be capable of reducing Cr(VI), U(VI), Co(III), and the quinone-containing compound anthraquinone-2,6-disulfonate. The objectives of this study were to determine the phylogenetic positions of the three known metal-reducing Thermus strains and to determine the phylogenetic significance of metal reduction within the genus Thermus. Phylogenetic analyses of 16S rDNA sequences, BOX PCR genomic fingerprinting, and DNA-DNA reassociation analyses indicated that these strains belong to the previously described genospecies T. scotoductus. The morphologies and lipid fatty acid profiles of these metal-reducing strains are consistent with their identification as T. scotoductus; however, the T. scotoductus strains tested in this study evinced a wide intraspecies variability in some other phenotypic traits, e.g., carbon substrate utilization and pigmentation. Iron reduction occurred in all strains of T. scotoductus tested except the mixotrophic, sulfur-oxidizing strain IT-7254. Thermus strains belonging to other species did not reduce Fe(III) to Fe(II) or reduced it only poorly.

Base Composition↗

PubMed2003

Indigenous and contaminant microbes in ultradeep mines.

Rock, air and service water samples were collected for microbial analyses from 3.2 kilometres depth in a working Au mine in the Witwatersrand basin, South Africa. The approximately metre-wide mined zone was comprised of a carbonaceous, quartz, sulphide, uraninite and Au bearing layer, called the Carbon Leader, sandwiched by quartzite and conglomerate. The microbial community in the service water was dominated by mesophilic aerobic and anaerobic, alpha-, beta- and gamma-Proteobacteria with a total biomass concentration approximately 10(4) cells ml(-1), whereas, that of the mine air was dominated by members of the Chlorobi and Bacteroidetes groups and a fungal component. The microorganisms in the Carbon Leader were predominantly mesophilic, aerobic heterotrophic, nitrate reducing and methylotrophic, beta- and gamma-Proteobacteria that were more closely related to service water microorganisms than to air microbes. Rhodamine WT dye and fluorescent microspheres employed as contaminant tracers, however, indicated that service water contamination of most of the rock samples was < 0.01% during acquisition. The microbial contaminants most likely originated from the service water, infiltrated the low permeability rock through and accumulated within mining-induced fractures where they survived for several days before being mined. Combined PLFA and terminal restriction fragment length profile (T-RFLP) analyses suggest that the maximum concentration of indigenous microorganisms in the Carbon Leader was < 10(2) cells g(-1). PLFA, 35S autoradiography and enrichments suggest that the adjacent quartzite was less contaminated and contained approximately 10(3) cells gram(-1) of thermophilic, sulphate reducing bacteria, SRB, some of which are delta-Proteobacteria. Pore water and rock geochemical analyses suggest that these SRB's may have been sustained by sulphate diffusing from the adjacent U-rich, Carbon Leader where it was formed by radiolysis of sulphide.

Air Microbiology↗

PubMed2000

Microscopic physical biomarkers in carbonate hot springs: implications in the search for life on Mars.

Physical evidence of life (physical biomarkers) from the deposits of carbonate hot springs were documented at the scale of microorganisms--submillimeter to submicrometer. The four moderate-temperature (57 to 72 degrees C), neutral pH springs reported on in this study, support diverse communities of bacteria adapted to specific physical and chemical conditions. Some of the microbes coexist with travertine deposits in endolithic communities. In other cases, the microbes are rapidly coated and destroyed by precipitates but leave distinctive mineral fabrics. Some microbes adapted to carbonate hot springs produce an extracellular polymeric substance which forms a three-dimensional matrix with living cells and cell remains, known as a biofilm. Silicon and iron oxides often coat the biofilm, leading to long-term preservation. Submicrometer mineralized spheres composed of calcium fluoride or silica are common in carbonate hot spring deposits. Sphere formation is biologically mediated, but the spheres themselves are apparently not fossils or microbes. Additionally, some microbes selectively weather mineral surfaces in distinctive patterns. Hot spring deposits have been cited as prime locations for exobiological exploration of Mars. The presence of preserved microscopic physical biomarkers at all four sites supports a strategy of searching for evidence of life in hot spring deposits on Mars.

Arkansas↗

PubMed1999

Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate.

A thermophilic bacterium that can use O2, NO3-, Fe(III), and S0 as terminal electron acceptors for growth was isolated from groundwater sampled at a 3.2-km depth in a South African gold mine. This organism, designated SA-01, clustered most closely with members of the genus Thermus, as determined by 16S rRNA gene (rDNA) sequence analysis. The 16S rDNA sequence of SA-01 was >98% similar to that of Thermus strain NMX2 A.1, which was previously isolated by other investigators from a thermal spring in New Mexico. Strain NMX2 A.1 was also able to reduce Fe(III) and other electron acceptors. Neither SA-01 nor NMX2 A.1 grew fermentatively, i.e., addition of an external electron acceptor was required for anaerobic growth. Thermus strain SA-01 reduced soluble Fe(III) complexed with citrate or nitrilotriacetic acid (NTA); however, it could reduce only relatively small quantities (0.5 mM) of hydrous ferric oxide except when the humic acid analog 2,6-anthraquinone disulfonate was added as an electron shuttle, in which case 10 mM Fe(III) was reduced. Fe(III)-NTA was reduced quantitatively to Fe(II); reduction of Fe(III)-NTA was coupled to the oxidation of lactate and supported growth through three consecutive transfers. Suspensions of Thermus strain SA-01 cells also reduced Mn(IV), Co(III)-EDTA, Cr(VI), and U(VI). Mn(IV)-oxide was reduced in the presence of either lactate or H2. Both strains were also able to mineralize NTA to CO2 and to couple its oxidation to Fe(III) reduction and growth. The optimum temperature for growth and Fe(III) reduction by Thermus strains SA-01 and NMX2 A.1 is approximately 65 degrees C; their optimum pH is 6.5 to 7.0. This is the first report of a Thermus sp. being able to couple the oxidation of organic compounds to the reduction of Fe, Mn, or S.

Biodegradation, Environmental↗

PubMed1997

Survival and phospholipid Fatty Acid profiles of surface and subsurface bacteria in natural sediment microcosms.

Although starvation survival has been characterized for many bacteria, few subsurface bacteria have been tested, and few if any have been tested in natural subsurface porous media. We hypothesized that subsurface bacteria may be uniquely adapted for long-term survival in situ. We further hypothesized that subsurface conditions (sediment type and moisture content) would influence microbial survival. We compared starvation survival capabilities of surface and subsurface strains of Pseudomonas fluorescens and a novel Arthrobacter sp. in microcosms composed of natural sediments. Bacteria were incubated for up to 64 weeks under saturated and unsaturated conditions in sterilized microcosms containing either a silty sand paleosol (buried soil) or a sandy silt nonpaleosol sediment. Direct counts, plate counts, and cell sizes were measured. Membrane phospholipid fatty acid (PLFA) profiles were quantified to determine temporal patterns of PLFA stress signatures and differences in PLFAs among strains and treatments. The Arthrobacter strains survived better than the P. fluorescens strains; however, differences in survival between surface and subsurface strains of each genus were not significant. Bacteria survived better in the paleosol than in the nonpaleosol and survived better under saturated conditions than under unsaturated conditions. Cell volumes of all strains decreased; however, sediment type and moisture did not influence rates of miniaturization. Both P. fluorescens strains showed PLFA stress signatures typical for gram-negative bacteria: increased ratios of saturated to unsaturated fatty acids, increased ratios of trans- to cis-monoenoic fatty acids, and increased ratios of cyclopropyl to monoenoic precursor fatty acids. The Arthrobacter strains showed few changes in PLFAs. Environmental conditions strongly influenced PLFA profiles.

Journal Article↗

PubMed1997

Factors limiting microbial growth and activity at a proposed high-level nuclear repository, yucca mountain, nevada.

As part of the characterization of Yucca Mountain, Nev., as a potential repository for high-level nuclear waste, volcanic tuff was analyzed for microbial abundance and activity. Tuff was collected aseptically from nine sites along a tunnel in Yucca Mountain. Microbial abundance was generally low: direct microscopic cell counts were near detection limits at all sites (3.2 x 10(sup4) to 2.0 x 10(sup5) cells g(sup-1) [dry weight]); plate counts of aerobic heterotrophs ranged from 1.0 x 10(sup1) to 3.2 x 10(sup3) CFU g(sup-1) (dry weight). Phospholipid fatty acid concentrations (0.1 to 3.7 pmol g(sup-1)) also indicated low microbial biomasses; diglyceride fatty acid concentrations, indicative of dead cells, were in a similar range (0.2 to 2.3 pmol g(sup-1)). Potential microbial activity was quantified as (sup14)CO(inf2) production in microcosms containing radiolabeled substrates (glucose, acetate, and glutamic acid); amendments with water and nutrient solutions (N and P) were used to test factors potentially limiting this activity. Similarly, the potential for microbial growth and the factors limiting growth were determined by performing plate counts before and after incubating volcanic tuff samples for 24 h under various conditions: ambient moisture, water-amended, and amended with various nutrient solutions (N, P, and organic C). A high potential for microbial activity was demonstrated by high rates of substrate mineralization (as much as 70% of added organic C in 3 weeks). Water was the major limiting factor to growth and microbial activity, while amendments with N and P resulted in little further stimulation. Organic C amendments stimulated growth more than water alone.

Journal Article↗

PubMed1995

Microbiological Comparisons within and across Contiguous Lacustrine, Paleosol, and Fluvial Subsurface Sediments.

Twenty-six subsurface samples were collected from a borehole at depths of 173.3 to 196.8 m in the saturated zone at the Hanford Site in south-central Washington State. The sampling was performed throughout strata that included fine-grained lacustrine (lake) sediments, a paleosol (buried soil) sequence, and coarse-grained fluvial (river) sediments. A subcoring method and tracers were used to minimize and quantify contamination to obtain samples that were representative of subsurface strata. Sediment samples were tested for total organic carbon, inorganic carbon, total microorganisms by direct microscopic counts, culturable aerobic heterotrophs by plate counts, culturable anaerobes by most-probable-number enumeration, basal respiration rates, and mineralization of (sup14)C-labeled glucose and acetate. Total direct microscopic counts of microorganisms were low, ranging from below detection to 1.9 x 10(sup5) cells g (dry weight)(sup-1). Culturable aerobes and anaerobes were below minimum levels of detection in most samples. Direct microscopic counts, basal respiration rates, and (sup14)C-glucose mineralization were all positively correlated with total organic carbon and were highest in the lacustrine sediments. In contrast to previous subsurface studies, these saturated-zone samples did not have higher microbial abundance and activities than unsaturated sediments sampled from the same borehole, the fine-textured lacustrine sediment had higher microbial numbers and activities than the coarse-textured fluvial sands, and the paleosol samples did not have higher biomass and activities relative to the other sediments. The results of this study expand the subsurface microbiology database to include information from an environment very different from those previously studied.

Journal Article↗

PubMed1994

Influence of the Gas-Water Interface on Transport of Microorganisms through Unsaturated Porous Media.

In this article, a new mechanism influencing the transport of microorganisms through unsaturated porous media is examined, and a new method for directly visualizing bacterial behavior within a porous medium under controlled chemical and flow conditions is introduced. Resting cells of hydrophilic and relatively hydrophobic bacterial strains isolated from groundwater were used as model microorganisms. The degree of hydrophobicity was determined by contact-angle measurements. Glass micromodels allowed the direct observation of bacterial behavior on a pore scale, and three types of sand columns with different gas saturations provided quantitative measurements of the observed phenomena on a porous medium scale. The reproducibility of each break-through curve was established in three to five repeated experiments. The data collected from the column experiments can be explained by phenomena directly observed in the micromodel experiments. The retention rate of bacteria is proportional to the gas saturation in porous media because of the preferential sorption of bacteria onto the gas-water interface over the solid-water interface. The degree of sorption is controlled mainly by cell surface hydrophobicity under the simulated groundwater conditions because of hydrophobic forces between the organisms and the interfaces. The sorption onto the gas-water interface is essentially irreversible because of capillary forces. This preferential and irreversible sorption at the gas-water interface strongly influences the movement and spatial distribution of microorganisms.

Journal Article↗

PubMed1994

Changes in Ester-Linked Phospholipid Fatty Acid Profiles of Subsurface Bacteria during Starvation and Desiccation in a Porous Medium.

Ester-linked phospholipid fatty acid (PLFA) profiles of a Pseudomonas aureofaciens strain and an Arthrobacter protophormiae strain, each isolated from a subsurface sediment, were quantified in a starvation experiment in a silica sand porous medium under moist and dry conditions. Washed cells were added to sand microcosms and maintained under saturated conditions or subjected to desiccation by slow drying over a period of 16 days to final water potentials of approximately - 7.5 MPa for the P. aureofaciens and - 15 MPa for the A. protophormiae. In a third treatment, cells were added to saturated microcosms along with organic nutrients and maintained under saturated conditions. The numbers of culturable cells of both bacterial strains declined to below detection level within 16 days in both the moist and dried nutrient-deprived conditions, while direct counts and total PLFAs remained relatively constant. Both strains of bacteria maintained culturability in the nutrient-amended microcosms. The dried P. aureofaciens cells showed changes in PLFA profiles that are typically associated with stressed gram-negative cells, i.e., increased ratios of saturated to unsaturated fatty acids, increased ratios of trans- to cis-monoenoic fatty acids, and increased ratios of cyclopropyl fatty acids to their monoenoic precursors. P. aureofaciens starved under moist conditions showed few changes in PLFA profiles during the 16-day incubation, whereas cells incubated in the presence of nutrients showed decreases in the ratios of both saturated fatty acids to unsaturated fatty acids and cyclopropyl fatty acids to their monoenoic precursors. The PLFA profiles of A. protophormiae changed very little in response to either nutrient deprivation or desiccation. Diglyceride fatty acids, which have been proposed to be indicators of dead or lysed cells, remained relatively constant throughout the experiment. Only the A. protophormiae desiccated for 16 days showed an increase in the ratio of diglyceride fatty acids to PLFAs. The results of this laboratory experiment can be useful for interpreting PLFA profiles of subsurface communities of microorganisms for the purpose of determining their physiological status.

Journal Article↗

PubMed1990

Characterization of biological ice nuclei from a lichen.

Biological ice nuclei (active at approximately -4 degrees C) were extracted from cells of the lichen Rhizoplaca chrysoleuca by sonication. Sensitivity to proteases, guanidine hydrochloride, and urea showed these nuclei to be proteinaceous. The nuclei were relatively heat stable, active from pH 1.5 to 12, and active without lipids, thereby demonstrating significant differences from bacterial ice nuclei.

Bacteria↗

PubMed1988

Ice nucleation activity in lichens.

A newly discovered form of biological ice nucleus associated with lichens is described. Ice nucleation spectra of a variety of lichens from the southwestern United States were measured by the drop-freezing method. Several epilithic lichen samples of the genera Rhizoplaca, Xanthoparmelia, and Xanthoria had nuclei active at temperatures as warm as -2.3 degrees C and had densities of 2.3 x 10 to more than 1 x 10 nuclei g at -5 degrees C (2 to 4 orders of magnitude higher than any plants infected with ice nucleation-active bacteria). Most lichens tested had nucleation activity above -8 degrees C. Lichen substrates (rocks, plants, and soil) showed negligible activity above -8 degrees C. Ice nucleation-active bacteria were not isolated from the lichens, and activity was not destroyed by heat (70 degrees C) or sonication, indicating that lichen-associated ice nuclei are nonbacterial in origin and differ chemically from previously described biological ice nuclei. An axenic culture of the lichen fungus Rhizoplaca chrysoleuca showed detectable ice nucleation activity at -1.9 degrees C and an ice nucleation density of 4.5 x 10 nuclei g at -5 degrees C. It is hypothesized that these lichens, which are both frost tolerant and dependent on atmospheric moisture, derive benefit in the form of increased moisture deposition as a result of ice nucleation.

Journal Article↗