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PubMed1997

Cross-Polarized Magic-Angle Spinning (sup13)C Nuclear Magnetic Resonance Spectroscopic Characterization of Soil Organic Matter Relative to Culturable Bacterial Species Composition and Sustained Biological Control of Pythium Root Rot.

We report the use of a model system that examines the dynamics of biological energy availability in organic matter in a sphagnum peat potting mix critical to sustenance of microorganism-mediated biological control of pythium root rot, a soilborne plant disease caused by Pythium ultimum. The concentration of readily degradable carbohydrate in the peat, mostly present as cellulose, was characterized by cross-polarized magic-angle spinning (sup13)C nuclear magnetic resonance spectroscopy. A decrease in the carbohydrate concentration in the mix was observed during the initial 10 weeks after potting as the rate of hydrolysis of fluorescein diacetate declined below a critical threshold level required for biological control of pythium root rot. Throughout this period, total microbial biomass and activity, based on rates of [(sup14)C]acetate incorporation into phospholipids, did not change but shifts in culturable bacterial species composition occurred. Species capable of inducing biocontrol were succeeded by pleomorphic gram-positive genera and putative oligotrophs not or less effective in control. We conclude that sustained efficacy of naturally occurring biocontrol agents was limited by energy availability to this microflora within the organic matter contained in the potting mix. We propose that this critical role of organic matter may be a key factor explaining the variability in efficacy typically encountered in the control of pythium root rot with biocontrol agents.

Journal Article↗
PubMed1998

Ethylene removal by a biofilter with immobilized bacteria

A biofilter which eliminated ethylene (C2H4) from the high parts-per-million range to levels near the limit for plant hormonal activity (0.01 to 0.1 ppm) was developed. Isolated ethylene-oxidizing bacteria were immobilized on peat-soil in a biofilter (687 cm3) and subjected to an atmospheric gas flow (73.3 ml min-1) with 2 or 117 ppm of C2H4. Ethylene was eliminated to a minimum level of 0.017 ppm after operation with 2.05 ppm of C2H4 for 16 days. Also, the inlet C2H4 concentration of 117 ppm was reduced to <0.04 ppm. During operation with 2 and 117 ppm of C2H4, an increase in the C2H4 removal rate was observed, which was attributed to proliferation of the immobilized bacteria, notably in the first 0- to 5-cm segment of the biofilter. The maximal C2H4 elimination capacity of the biofilter was 21 g of C2H4 m-3 day-1 during operation with 117 ppm of C2H4 in the inlet gas. However, for the first 0- to 5-cm segment of the biofilter, an elimination capacity of 146 g of C2H4 m-3 day-1 was calculated. Transition of the biofilter temperature from 21 to 10 degreesC caused a 1.6-fold reduction in the C2H4 removal rate, which was reversed during operation for 18 days. Batch experiments with inoculated peat-soil demonstrated that C2H4 removal still occurred after storage at 2, 8, and 20 degreesC for 2, 3, and 4 weeks. However, the C2H4 removal rate decreased with increasing storage time and was reduced by ca. 50% after storage for 2 weeks at all three temperatures. The biofilter could be a suitable tool for C2H4 removal in, e.g., horticultural storage facilities, since it (i) removed C2H4 to 0.017 ppm, (ii) had a good operational stability, and (iii) operated efficiently at 10 degreesC.

Journal Article↗
PubMed2000

Measurement of T-cell-derived antigen binding molecules and immunoglobulin G specific to Candida albicans mannan in sera of patients with recurrent vulvovaginal candidiasis.

Immunoglobulin G (IgG) and T-cell-derived antigen binding molecules (TABM) specific to whole Candida extract and to Candida-derived mannans prepared by both the cetryltrimethylammonium bromide (CTAB) and alkaline degradation (PEAT) methods were measured in the sera of women with vulvovaginal candidiasis and controls. In the patients there were significantly higher levels of IgG to both CTAB and PEAT mannans and of TABM to CTAB mannan. TABM specific to CTAB mannan was purified from the serum of a patient with a high titer of this TABM. The purified TABM bound specifically to CTAB mannan and to other yeast and mold extracts. This TABM preparation was associated with transforming growth factor beta2 (TGF-beta2), and on specific binding to mannan there was a marked increase in the level of detectable TGF-beta2. This increase in TGF-beta2 level was critically dependent on the relative concentrations of the purified TABM and mannan, being smallest when either was in excess. The TABM specific to CTAB mannan was also shown to inhibit Candida-stimulated gamma interferon production. The results suggest that CTAB mannan-specific TABM may increase susceptibility to vulvovaginal candidiasis in association with a shift in the immune response to the Th2 type.

Adult↗
PubMed1996

Analysis of the region between amino acids 30 and 42 of intact UmuD by a monocysteine approach.

On the basis of characterizations of a set of UmuD monocysteine derivatives, we had suggested that positions 24, 34, and 44 are closer to the intact UmuD homodimer interface than other positions tested (M. H. Lee, T. Ohta, and G. C. Walker, J. Bacteriol. 176:4825-4837, 1994). Because this region of UmuD also appeared to be important for interactions with RecA, we followed up on our previous study by constructing a second set of monocysteine UmuD derivatives with single cysteine substitutions at positions 30 to 42. We found that like the VC34 mutant, UmuD derivatives with monocysteine substitutions at positions 32 and 35 showed deficiencies in in vivo and in vitro RecA-mediated cleavage as well as in UV mutagenesis, suggesting that the position 32 to 35 region may be important for RecA-mediated cleavage of UmuD. Interestingly, UmuD with monocysteine substitutions at residues 33 and 40 showed a reduction in UV mutagenesis while retaining the ability to be cleaved by RecA in vivo, suggesting a deficiency in the subsequent role of the UmuD' derivatives in mutagenesis. All of the UmuD monocysteine derivatives in the position 30 to 42 series purified indistinguishably from the wild-type protein. The observations that purified proteins of the UmuD derivatives RC37 and IC38 could be disulfide cross-linked quantitatively upon addition of iodine and yet were poorly modified with iodoacetate led us to suggest that the pairs of residues at positions 37 and 38 are extremely close to the UmuD2 homodimer interface. These observations indicate that the structure of the UmuD2 homodimer in solution is very different from the crystal structure of the UmuD'2 homodimer reported by Peat et al. (T. S. Peat, E. G. Frank, J. P. McDonald, A. S. Levine, R. Woodgate, and W. A. Hendrickson, Nature [London] 380:727-730, 1996).

Amino Acid Sequence↗
PubMed1978

Biological nitrogen fixation in the terrestrial environment of a high Arctic ecosystem (Truelove Lowland, Devon Island, N.W.T.).

Arranged in descending order of nitrogen-fixing (acetylene-reducing) potential the sites examined were mesic meadow and peat polygon troughs (equal rank), transition zone between mesic meadow and gravel ridge, gravel ridge, polar dessert, and peat polygon tops. The dominant nitrogen-fixing microorganisms, as in other Arctic areas, were blue-green bacteria, especially those epiphytic on Arctic mosses. The epiphytic association exhibited an optimum temperature for fixation of 20 degrees C. Other bacteria potentially able to fix nitrogen were present in the soils examined but their activity was severely restricted by low soil temperatures and lack of readily utilizable energy sources. These bacteria included members of the genera Klebsiella (the most numerous), Bacillus, Clostridium, and Beijerinckia (scarce). Also present at many of the sites was an unidentified yellow-pigmented fixer which was not Mycobacterium flavum. All fixers were psychotrophic rather than psychrophilic, having an optimum temperature greater than 20 degrees C but capable of slow growth at 5 degrees C or lower. The rate of acetylene reduction by the epiphytic system increased with the number of successive exposures to acetylene, a phenomenon of some significance in any calculations designed to measure the amount of nitrogen fixed in certain ecosystems.

Acetylene↗
PubMed1987

Conversion of viridin to viridiol by viridin-producing fungi.

The fungistatic compound viridin, produced by the fungus Gliocladium virens, was found to be irreversibly reduced to the phytotoxin viridiol in liquid culture. Conversion occurred only in the presence of viridin-producing fungi and was subsequent to viridin production. Radiolabelled viridin was rapidly taken up by the mycelium of G. virens and reduced to radiolabelled viridiol, while labelled viridiol was not taken up to any significant extent by the mycelium. Reduction of viridin to viridiol was independent of culture pH, carbon source, and nitrogen source or quantity. A simple production system consisting of peat moss amended with dextrose and calcium nitrate and inoculated with G. virens supported production of 86 micrograms viridiol/g peat. This production system, when applied to soil, may have value as a herbicide.

Androstenediols↗
PubMed1994

Identification of variability of ribosomal DNA spacer from Pseudomonas soil isolates.

The polymerase chain reaction was used to amplify the spacer region located between the 16S and 23S ribosomal RNA genes of strains of Pseudomonas fluorescens and Pseudomonas putida isolated from peat bog, canola field, or arctic plants. Some of spacer region of four of the P. fluorescens strains examined, strains 64-3, 63-28, QP5, and R17-FP2, was about 515 base pairs (bp) in length, and contained the genes for tRNA(Ile) and tRNA(Ala). The DNA sequences of two strains from canola, 64-3 and 63-28, differed at only two positions. The sequences of the peat bog strains QP5 and R17-FP2 were identical. However, differences were noted between the DNA sequence common to the pair of strains 64-3 and 63-28 and the corresponding common sequence for strains QP5 and R17-FP2. These differences were mainly concentrated in two DNA segments of 10 and 19 bp, respectively. A probe for the 19-bp variable segment that occurs in the ribosomal spacer of strains QP5 and R17-FP2 recognized total DNA from these two strains, but not DNA from other bacteria of different origins. These results suggest the existence of a limited degree of variability within the 16S-23S ribosomal DNA spacer region, and that this variability may be useful to the recognition of particular Pseudomonas strains from environmental samples.

Base Sequence↗
PubMed1993

Hepatocellular carcinoma: CT appearance after percutaneous ethanol ablation therapy. Work in progress.

Nine patients with biopsy-proved hepatocellular carcinoma underwent percutaneous ethanol ablation therapy (PEAT) with computed tomographic (CT) guidance. Twenty-five ablation sessions were performed in nine lesions ranging in size from 1.8 to 6.5 cm. Repeat biopsy was performed in seven of those nine lesions between 1 and 2 months after completion of therapy. CT scans obtained immediately after ablation demonstrated a necrotic area equal in size to the target lesion in five patients; four of those five patients have had negative findings at biopsy and are free of known disease. None of the patients with CT evidence of limited necrosis are currently free of disease. Peripheral nodularity was demonstrated after ablation in three patients at CT; none are free of disease. All four patients in whom there was no peripheral nodularity are free of known disease. Thus, CT evidence of necrosis and lack of nodularity immediately after PEAT are suggestive of absence of disease.

Aged↗
PubMed2025

Molecular signatures of adaptive introgression and selection in contact zones of closely related pine species (Pinus genus).

BACKGROUND: Natural hybridization plays a key role in shaping genetic diversity, local adaptation, and the dynamics of speciation through interspecific gene flow. Hybrid zones serve as valuable natural systems for studying these processes. In this research, we used genotypic data at thousands of nuclear SNPs to investigate genomic outcomes of hybridization and selection across three contact zones of closely related pine species including Scots pine (Pinus sylvestris L.) and dwarf mountain pine (P. mugo T.). Reference allopatric stands of parental species were used to assess introgression dynamics. RESULTS: Individuals from the hybrid zones showed distinct genetic ancestry patterns and were assigned to groups including putative pure species, first-generation hybrids, and advanced backcrosses. Genotypes of the majority of hybrids were shifted towards P. mugo ancestry. Most outlier loci were shared across all sympatric populations, although some were specific to individual contact zones. The identified outliers were mainly associated with regulatory biological processes related to phosphorylation, proteolysis, and transmembrane transport. Signatures of local adaptation varied in different genetic classes in contact zones and they were strongest in pure P. sylvestris and hybrids with a majority of P. sylvestris ancestry. The pattern suggests that it may be driven by adaptation to peat bog habitats situated outside the species&#x2019; core ecological niche. CONCLUSIONS: Our findings indicate strong selective pressure acting on multiple genes in groups of hybrids and pure Pinus sylvestris individuals across all studied hybrid zones. In contrast, the weaker signal of selection observed in individuals with P. mugo ancestry suggests that relict populations of this species, which historically spread across postglacial peat bogs, were pre-adapted to such environments. While several outlier loci were shared across different contact zones, others were unique for one of them, indicating that local environmental pressures and adaptive introgression shape the genomic composition of the populations. These results highlight the role of hybridization in generating adaptive diversity and emphasize the evolutionary significance of hybrid zones in pines.

Hybridization, Genetic↗
PubMed1989

Cerebral evoked potentials in human chronic Chagas' disease.

Seventy five patients with the diagnosis of chronic Chagas' disease were studied by employing EPs techniques. Two of them had delayed arrival of the signal to the Erb's point and one to the spinal cord when looking at SEPs. Two patients had increment of the time interval between waves Ist and IIIrd, when studying PEATs. These findings were interpreted as due to peripheral nerve fibers damage, a feature described in previous papers. The most striking finding was the prolonged time interval between waves N13 and N20 (SEPs) found in two patients and between waves IIIrd and Vth (PEAT) seen in 7 affected subjects. These observations suggested the development of some sort of CNS involvement, perhaps related to myelin damage, in patients who reached the chronic state of the infection.

Adolescent↗
PubMed2005

Quantitative sampling method for fungus gnat (Diptera: Sciaridae) eggs in soilless growing media.

A simple method is described for separating fungus gnat eggs from soilless growing media. The flotation/extraction method primarily involves the use of a MgSO4 solution (density 1.065 g cm(-3)) and a series of sieving procedures. Bradysia sp. nr. coprophila Lintner eggs were collected in an isolation chamber containing adult fungus gnats. Three soilless growing media were used: Metro-Mix 560 with Scott's Coir, Sunshine LC1 Mix, and Universal SB 300 Mix. Each growing medium was inoculated with 100 fungus gnat eggs. Growing medium samples were processed using separatory funnels and a MgSO4 solution. Eggs were washed through a 250-microm sieve and collected on a 53-microm sieve, and then the eggs were rinsed into glass petri dishes. The sieving process separated fungus gnat eggs from the larger growing medium particulates (perlite, bark, and peat), providing a sample consisting of water, eggs, and fine growing medium particulates (peat). Using a vortex for 60 s increased the number of fungus gnat eggs recovered (37.4 +/- 3.7-67.1 +/- 1.9 [mean +/- SEM]) for all three growing media. The mean number of fungus gnat eggs recovered from the three soilless growing media was significantly different, with the growing medium containing coir (Metro-Mix 560) having the highest recovery rate of 61.0 +/- 2.1. For all three growing media, there was > 50% recovery of fungus gnat eggs. In addition to fungus gnat eggs, this method also may prove useful for quantitative recovery of shore fly (Scatella sp.) eggs and the eggs of other arthropods from soilless growing media.

Animals↗
PubMed2004

Enhancing the attenuation of explosives in surface soils at military facilities: combined sorption and biodegradation.

This research evaluated soil amendments designed to enhance the adsorption and biodegradation of explosives at military training facilities, thus minimizing their potential for transport to subsurface environments. Several carbon cosubstrates were tested in soil slurries for their ability to stimulate the biodegradation of 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (royal demolition exposive [RDX]), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (high-melting explosive [HMX]) by indigenous soil microorganisms. Crude soybean oil and molasses stimulated mineralization of RDX (30-40%) and HMX (approximately 10%). The TNT was not significantly mineralized in any of the treatments, but high-performance liquid chromatography (HPLC) analysis indicated extensive transformation of TNT to amino-containing compounds. The biodegradation of explosives was then examined in unsaturated soil microcosms amended with crude soybean oil and molasses combined with sphagnum peat moss and sawdust. Minimal TNT mineralization was observed, and HMX mineralization was only observed with molasses addition. In contrast, RDX mineralization was extensive in microcosms amended with soybean oil or molasses. The presence of peat moss decreased soybean oil-stimulated RDX mineralization by approximately 5%, but resulted in about 5% greater RDX mineralization compared with molasses only. Sawdust markedly decreased mineralization regardless of cosubstrate type. Mass balance results indicated that the formation of bound residues likely was occurring, especially for TNT. These results indicate that the application of inexpensive adsorbents and cosubstrates to soils may significantly improve the protection of groundwater resources underlying live fire ranges.

Adsorption↗
PubMedDate not supplied

Adsorption of arsenate and arsenite on ferrihydrite in the presence and absence of dissolved organic carbon.

The adsorption of As(V) and As(III) on synthetic two-line ferrihydrite in the presence and absence of a peat humic acid (HAp), Suwannee River fulvic acid (FA), or citric acid (CA) was investigated. Previous work with goethite has demonstrated the ability of dissolved organic carbon (DOC) to decrease As(V) and As(III) adsorption. The results obtained demonstrate that As(V) adsorption on ferrihydrite was decreased only in the presence of CA. Arsenate decreased the adsorption of all organic acids except HAp. Both FA and CA reduced As(III) adsorption on ferrihydrite, while HAp had no effect. Fulvic and citric acid adsorption on ferrihydrite was decreased in the presence of As(III); however, FA and CA adsorption increased at lower pH, which was consistent with decreased As(III) adsorption. Peat humic acid did not decrease As(III) adsorption, and we believe that the adsorption process of HAp and As(III) and As(V) on ferrihydrite are independent of each other. Previously, we observed that As(V) adsorption on goethite decreased in the presence of HAp > FA > CA, while As(III) adsorption on goethite was decreased similarly to that on ferrihydrite in the presence of CA > FA approximately HAp, yet As(III) adsorption on ferrihydrite was greater than on goethite. The observed differences between this study and the earlier study on goethite are believed to be an intricate function of ferrihydrite's surface characteristics, which affect the mechanisms of adsorption and hence the affinity of organic acids such as HAp, FA, and CA for the ferrihydrite surface. As such, the adsorption of DOCs to ferrihydrite are assumed to be less favorable and to occur with a fewer number of ligands, resulting in lower surface coverage of weaker bond strength.

Adsorption↗
PubMedDate not supplied

Leaching of nitrogen and phosphorus during production of forest seedlings in containers.

Little information is available concerning the contamination risk caused by forest seedling nurseries to local surface and ground waters compared with agricultural and horticultural production. Leaching of nitrogen (N) and phosphorus (P) through peat growing medium in containers and nutrient uptake of seedlings were monitored in production of silver birch (Betula pendula Roth), Norway spruce [Picea abies (L.) Karst], and Scots pine (Pinus sylvestris L.) seedlings. About half of the applied nutrients (total amount applied = 149 to 260 kg N ha(-1) and 60 to 108 kg P ha(-1)) was premixed into the peat medium, as is usual in Finnish nursery practice, and the other half was applied to seedlings in liquid form with mobile booms. Depending on tree species, 11 to 19% of the applied N was recovered in leachates and 15 to 63% in seedlings. The undiscovered proportion varied from 19 to 71%. The amounts of leached N were 19 to 41 kg ha(-1). Only 5 to 31% of the applied P was recovered in seedlings; 16 to 64% (11 to 56 kg ha(-1)) was found in leachates. Total N and P load to the environment may increase substantially if nutrients applied in liquid fertilization outside container trays are included. Consequently, it is important to determine the sources of nutrient load in container seedling production to mitigate the risk of environment contamination.

Betula↗
PubMed2003

Phylogenetic comparison of methanogen diversity in different wetland soils.

Aspects of archaeal diversity in peat soil samples from climatically and geographically distinct wetlands (subarctic: West Siberia Bog, Russia; temperate: Akaiyachi Mire, Japan; subtropical: Okefenokee Swamp, USA) were studied by molecular phylogenetic techniques. DNA was extracted directly from the soil samples and 16S rRNA genes were amplified by polymerase chain reaction. Partial sequences of the amplified 16S rDNAs (total 426 clones) were compared with known sequences from GenBank and the Ribosome Database Project (RDP). Peat-derived sequences were mostly related to Euryarchaeota, principally methanogens. Sets of sequences (operational taxonomic unit; OTU) were created for each wetland (21 OTUs for West Siberia; 22 OTUs for Akaiyachi; 33 OTUs for Okefenokee). The majority of the OTUs clustered in and showed low similarities to the Methanosarcinales family (West Siberia) or the Methanomicrobiales family (Akaiyachi and Okefenokee). In terms of the Shannon-Weaver diversity index, the archaeal community diversity in Okefenokee Swamp was greater than that of the other wetlands.

Base Sequence↗
PubMed2001

Progress in the research and demonstration of Everglades periphyton-based stormwater treatment areas.

The South Florida Water Management District (District) is conducting research focused on potential advanced treatment technologies to support reduction of phosphorus (P) loads in surface water entering the remaining Everglades. Periphyton-based stormwater treatment areas (PSTA) are one of the advanced treatment technologies being researched by the District. This detailed research and demonstration project is being conducted in two phases. Basic research in field-based mesocosm experiments was conducted during the first phase within the District's Everglades Nutrient Removal Project (ENR). Studies were conducted in 24 portable PSTA mesocosms and three of the south ENR test cells. Phase 1 studies addressed the effects of system substrate (shellrock, organic peat, or sand), water depth, hydraulic loading rate, vegetation presence, depth:width ratio, and inhibition of algal growth on total phosphorus removal performance of the PSTA mesocosms. A second phase of research is currently under way, during which PSTA feasibility will be evaluated further in four field-scale constructed mesocosms totaling about 2 ha, and follow up studies within the ENR test cells and portable mesocosms will be conducted to further investigate the effects of other inorganic substrates, shallow water depth, and velocity on treatment performance. Phase 1 monitoring has determined that periphyton-dominated communities can be established in constructed wetlands within 5 months. The algal component of these periphyton plant communities is characteristic of natural Everglades periphyton. High macrophyte densities resulted from use of peat soils in PSTA mesocosms, while shellrock and sand soils promoted more desirable sparse macrophyte stands. P removal rates under the conditions of this research were relatively high considering the low influent total P concentrations tested (average 23 microg/L). PSTA mesocosms on shellrock soils were able to attain long-term average outflow total P concentrations as low as 11 microg/L. The maximum one-parameter TP first-order removal rate constant (k1) measured was 27 m/y. Minimum attainable outflow total P concentrations and mass removals appear to be the result of a balance between internal P loading from antecedent soils, uptake and burial processes in new sediments, and rainfall inputs. A different soil type (limerock) will be tested for effectiveness during Phase 2. Selected existing treatments will also be continued to look for trends over a second growing season.

Conservation of Natural Resources↗
PubMed2001

Nitrogen and phosphorus budget in rewetted fens.

A former dewatered fen was flooded for a multi-purpose landuse system including cattail production, fen protection, and water purification. These research plants with an area of 6 ha consist of three constructed surface-flow wetlands. The inflowing water is polluted by non-point sources due to intensive agriculture. The focus of this paper is the estimation of the potential of rewetted fens to reduce phosphorus and nitrogen. The dominating forms of nitrogen in the inflow are organic nitrogen and nitrate. The reduction rate is higher for nitrate than for organic nitrogen, although the nitrate reductions occur only during the summer season. If no nitrate is available for denitrification, there is a release of ammonia from the peat into the water. The main form of phosphorus in the in- and outflow is ortho-phosphate. In contrast to the values of nitrate, the concentrations of phosphorus are very regular with no significant seasonal pattern. When nitrate isn't available in the water any more, the release of phosphorus begins and the rewetted fens change from a sink for phosphorus to a source of it. Rewetted fens can be a sink for phosphorus and nitrogen with nitrate as the limiting factor. Only if denitrification can occur, can the release of ammonia and phosphorus from the peat layer be prevented.

Ammonia↗
PubMed2003

Hydroponic chrysanthemum production: cultural and pathological issues.

Hydroponic culture has not replaced soil culture in greenhouse production of chrysanthemum (commonly known as 'mum'). This study examines cultural or pathological conditions that might have affected the conversion from soil to hydroponic production. Cultural factors investigated included hydroponic container size and shape and oxygenation of the nutrient solution. Disorders encountered during the studies included salt wicking during rooting of the cuttings and severe Pythium infection in the third and successive crops in a hydroponic system. Mums did not appear to respond to various shapes and sizes of containers and troughs in which they were grown. Also, increased oxygenation had little effect on pythium root rot and plant growth. Rooting of cuttings in a polyethylene covered hydroponic system reduced wilting, whereas salt wicking was severe without a plastic covering. Pythium disease was severe in the third and successive crops in the same hydroponic system. The disease could be overcome by raising the cuttings in a peat-based growing medium in perforated plastic cells and then transplanting the seedlings along with the peat moss cubes into a hydroponic system.

Chrysanthemum↗