scholarly journals Effect of Biostimulation and Bioaugmentation on Degradation of Polyurethane Buried in Soil

2009 ◽  
Vol 76 (3) ◽  
pp. 810-819 ◽  
Author(s):  
L. Cosgrove ◽  
P. L. McGeechan ◽  
P. S. Handley ◽  
G. D. Robson
Keyword(s):  
Yeast Extract ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Fungal Communities ◽  
Soil Microcosms ◽  
Polyurethane Waste ◽  
Solid Media ◽  
Dependent Change ◽  
Dispersion Agent ◽  
Gradient Gel Electrophoresis ◽  
Fungal Populations

ABSTRACT This work investigated biostimulation and bioaugmentation as strategies for removing polyurethane (PU) waste in soil. Soil microcosms were biostimulated with the PU dispersion agent “Impranil” and/or yeast extract or were bioaugmented with PU-degrading fungi, and the degradation of subsequently buried PU was determined. Fungal communities in the soil and colonizing buried PU were enumerated on solid media and were analyzed using denaturing gradient gel electrophoresis (DGGE). Biostimulation with yeast extract alone or in conjunction with Impranil increased PU degradation 62% compared to the degradation in untreated control soil and was associated with a 45% increase in putative PU degraders colonizing PU. Specific fungi were enriched in soil following biostimulation; however, few of these fungi colonized the surface of buried PU. Fungi used for soil bioaugmentation were cultivated on the surface of sterile wheat to form a mycelium-rich inoculum. Wheat, when added alone to soil, increased PU degradation by 28%, suggesting that wheat biomass had a biostimulating effect. Addition of wheat colonized with Nectria haematococca, Penicillium viridicatum, Penicillium ochrochloron, or an unidentified Mucormycotina sp. increased PU degradation a further 30 to 70%, suggesting that biostimulation and bioaugmentation were operating in concert to enhance PU degradation. Interestingly, few of the inoculated fungi could be detected by DGGE in the soil or on the surface of the PU 4 weeks after inoculation. Bioaugmentation did, however, increase the numbers of indigenous PU-degrading fungi and caused an inoculum-dependent change in the composition of the native fungal populations, which may explain the increased degradation observed. These results demonstrate that both biostimulation and bioaugmentation may be viable tools for the remediation of environments contaminated with polyurethane waste.

Survival of enterococci and Tn916-like conjugative transposons in soil

2004 ◽  
Vol 50 (11) ◽  
pp. 957-966 ◽  
Author(s):  
Robert E Andrews Jr. ◽  
Wesley S Johnson ◽  
Abby R Guard ◽  
Jonathan D Marvin
Keyword(s):  
Enterococcus Faecalis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Soil Microflora ◽  
Swine Waste ◽  
Soil System ◽  
Soil Microcosms ◽  
Conjugative Transposons ◽  
Native Soil ◽  
Gradient Gel Electrophoresis ◽  
Normal Soil

The persistence of Enterococcus faecalis, fecal enterococci from swine waste, and Tn916-like elements was determined following inoculation into autoclaved and native soil microcosms. When cells of E. faecalis CG110 (Tn916) were inoculated into native microcosms, enterococcal viability in the soil decreased approximately 5 orders of magnitude (4.8 × 105CFU/g soil to < 10 CFU/g) after 5 weeks. In autoclaved microcosms, the viability of E. faecalis decreased by only 20% in 5 weeks. In contrast, the content of Tn916, based on PCR of DNA extracts from soil microcosms, decreased by about 20% in both native and autoclaved microcosms. Similar results were obtained when the source of fecal enterococci and Tn916-like elements was swine waste. Because the concentration of Tn916-independent E. faecalis DNA (the D-alanine D-alanine ligase gene), based on PCR, decreased to nearly undetectable levels (at least 3 orders of magnitude) after 5 weeks in the native microcosms, the evidence suggests Tn916 stability in the soil results from en masse transfer of the transposon to the normal soil microflora and not survival of E. faecalis DNA in the soil system. Results from denaturing gradient gel electrophoresis suggest that multiple forms of Tn916 occur in swine waste, but only forms most like Tn916 exhibit stability in the soil.Key words: Tn916, Enterococcus faecalis, soil, antibiotic resistance, conjugation, transposon.

Relationship between wood-inhabiting fungi determined by molecular analysis (denaturing gradient gel electrophoresis) and quality of decaying logs

2010 ◽  
Vol 40 (12) ◽  
pp. 2384-2397 ◽  
Author(s):  
Tiina Rajala ◽  
Mikko Peltoniemi ◽  
Taina Pennanen ◽  
Raisa Mäkipää
Keyword(s):  
Tree Species ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Lignin Content ◽  
Fruit Body ◽  
Fungal Communities ◽  
Important Species ◽  
European Aspen ◽  
Gradient Gel Electrophoresis ◽  
Decaying Wood

We investigated the fungal communities inhabiting decaying logs in a seminatural boreal forest stand in relation to host tree species, stage of decay, density, diameter, moisture, C to N ratio, Klason lignin content, and water- and ethanol-soluble extractives. Communities were profiled using denaturing gradient gel electrophoresis fingerprinting of the rDNA ITS1 region coupled with sequencing of fungal DNA extracted directly from the wood. In addition, polypore fruit bodies were inventoried. Logs from different tree species had different fungal communities and different physicochemical properties (e.g., C to N ratio, density, ethanol extractives, and diameter). Ascomycetes comprised a larger portion of communities inhabiting deciduous birch ( Betula spp.) and European aspen ( Populus tremula L.) logs compared with those living on coniferous Norway spruce ( Picea abies (L.) Karst.) and Scots pine ( Pinus sylvestris L.). A relationship between mycelial community structure and density of decaying spruce logs suggested a succession of fungi with mass loss of wood. The fruit body inventory underestimated fungal diversity in comparison with the culture-free denaturing gradient gel electrophoresis analysis that also detected inconspicuous but important species inhabiting decaying wood.

Characterization of bacterial and fungal communities in composted biosolids over a 2 year period using denaturing gradient gel electrophoresis

2009 ◽  
Vol 55 (4) ◽  
pp. 375-387 ◽  
Author(s):  
Amy Novinscak ◽  
Nadine J. DeCoste ◽  
Céline Surette ◽  
Martin Filion
Keyword(s):  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Fungal Species ◽  
Fungal Communities ◽  
Whole Process ◽  
Agricultural Applications ◽  
Gradient Gel Electrophoresis ◽  
Microbial Groups ◽  
Key Microorganisms

Composting is a microbial process that converts organic waste into a nutrient-rich end product used in horticultural and agricultural applications. The diversity and long-term succession of microorganisms found in composted biosolids has been less characterized than other composts. In this study, bacterial and fungal communities found in composted biosolids aging from 1 to 24 months were studied using denaturing gradient gel electrophoresis (DGGE) and sequencing. The results revealed high levels of diversity, where 53 bacterial species belonging to 10 phyla and 21 fungal species belonging to 4 phyla were identified. Significant differences were observed when comparing the bacterial DGGE patterns of young compost samples, whereas no differences were observed in samples over 8 months. For fungal patterns, no significant differences were observed during the first 4 months of composting, but the diversity then significantly shifted until 24 months. The results indicate that patterns of bacterial species vary during the first few months of composting, whereas fungal patterns generally vary throughout the whole process, except during early stages. The description of the main microbial groups found in composted biosolids could find various applications, including the discovery of biotechnologically relevant microorganisms and the development of novel markers allowing quantitative monitoring of key microorganisms.

scholarly journals Exposure of Sink Drain Microcosms to Triclosan: Population Dynamics and Antimicrobial Susceptibility

2003 ◽  
Vol 69 (9) ◽  
pp. 5433-5442 ◽  
Author(s):  
Andrew J. McBain ◽  
Robert G. Bartolo ◽  
Carl E. Catrenich ◽  
Duane Charbonneau ◽  
Ruth G. Ledder ◽  
...  
Keyword(s):  
Antimicrobial Susceptibility ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Viable Cell ◽  
Consumer Products ◽  
Achromobacter Xylosoxidans ◽  
Culturable Bacteria ◽  
16S Rdna Sequence Analysis ◽  
Cell Counts ◽  
Solid Media ◽  
Gradient Gel Electrophoresis

ABSTRACT Recent concern that the increased use of triclosan (TCS) in consumer products may contribute to the emergence of antibiotic resistance has led us to examine the effects of TCS dosing on domestic-drain biofilm microcosms. TCS-containing domestic detergent (TCSD) markedly lowered biofouling at 50% (wt/vol) but was poorly effective at use levels. Long-term microcosms were established and stabilized for 6 months before one was subjected to successive 3-month exposures to TCSD at sublethal concentrations (0.2 and 0.4% [wt/vol]). Culturable bacteria were identified by 16S rDNA sequence analysis, and their susceptibilities to four biocides and six antibiotics were determined. Microcosms harbored ca. 10 log10 CFU/g of biofilm, representing at least 27 species, mainly gamma proteobacteria, and maintained dynamic stability. Viable cell counts were largely unaffected by TCSD exposure, but species diversity was decreased, as corroborated by denaturing gradient gel electrophoresis analysis. TCS susceptibilities ranged widely within bacterial groups, and TCS-tolerant strains (including aeromonads, pseudomonads, stenotrophomonads, and Alcaligenes spp.) were isolated before and after TCSD exposure. Several TCS-tolerant bacteria related to Achromobacter xylosoxidans became clonally expanded during dosing. TCSD addition did not significantly affect the community profiles of susceptibility to the test biocides or antibiotics. Several microcosm isolates, as well as reference bacteria, caused clearing of particulate TCS in solid media. Incubations of consortia and isolates with particulate TCS in liquid led to putative TCS degradation by the consortia and TCS solubilization by the reference strains. Our results support the view that low-level exposure of environmental microcosms to TCS does not affect antimicrobial susceptibility and that TCS is degradable by common domestic biofilms.

scholarly journals Combining Culture-Dependent and -Independent Methodologies for Estimation of Richness of Estuarine Bacterioplankton Consuming Riverine Dissolved Organic Matter

2003 ◽  
Vol 69 (6) ◽  
pp. 3607-3616 ◽  
Author(s):  
Veljo Kisand ◽  
Johan Wikner
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Experimental System ◽  
Community Diversity ◽  
Rrna Gene ◽  
Solid Media ◽  
Gradient Gel Electrophoresis ◽  
Culture Dependent

ABSTRACT Three different methods for analyzing natural microbial community diversity were combined to maximize an estimate of the richness of bacterioplankton catabolizing riverine dissolved organic matter (RDOM). We also evaluated the ability of culture-dependent quantitative DNA-DNA hybridization, a 16S rRNA gene clone library, and denaturing gradient gel electrophoresis (DGGE) to detect bacterial taxa in the same sample. Forty-two different cultivatable strains were isolated from rich and poor solid media. In addition, 50 unique clones were obtained by cloning of the bacterial 16S rDNA gene amplified by PCR from the community DNA into an Escherichia coli vector. Twenty-three unique bands were sequenced from 12 DGGE profiles, excluding a composite fuzzy band of the Cytophaga-Flavobacterium group. The different methods gave similar distributions of taxa at the genus level and higher. However, the match at the species level among the methods was poor, and only one species was identified by all three methods. Consequently, all three methods identified unique subsets of bacterial species, amounting to a total richness of 97 operational taxonomic units in the experimental system. The confidence in the results was, however, dependent on the current precision of the phylogenetic determination and definition of the species. Bacterial consumers of RDOM in the studied estuary were primarily both cultivatable and uncultivable taxa of the Cytophaga-Flavobacterium group, a concordant result among the methods applied. Culture-independent methods also suggested several not-yet-cultivated β-proteobacteria to be RDOM consumers.

scholarly journals Fungal Communities in the Native New Zealand Medicinal Plant Pseudowintera colorata (Horopito) Are Determined by Plant Organ Type and Host Maturity with Key Members Promoting Plant Growth

2021 ◽  
Vol 9 (12) ◽  
pp. 2576
Author(s):  
Neeraj Purushotham ◽  
Eirian Jones ◽  
Jana Monk ◽  
Hayley Ridgway
Keyword(s):  
New Zealand ◽  
Endophytic Fungi ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phytopathogenic Fungi ◽  
Fungal Communities ◽  
Dual Culture ◽  
Fungal Community Composition ◽  
Factors Influencing ◽  
Gradient Gel Electrophoresis ◽  
Set Up

The plant Pseudowintera colorata is well known for its antimicrobial and medicinal properties and is endemic to New Zealand. Using PCR-Denaturing gradient gel electrophoresis (DGGE), we investigated the factors influencing the composition of endophytic fungal communities in P. colorata from ten distinct sites across New Zealand. Our results showed that plant organs of P. colorata influenced the diversity and richness of endophytic fungi (PERMANOVA, p < 0.05). In addition, plant maturity and its interactions revealed that endophytic fungal communities formed discrete clusters in leaves, stems, and roots of mature and immature P. colorata plants (PERMANOVA; p = 0.002, p = 0.001 and p = 0.039, respectively). For identifying isolates with biocontrol potential, dual culture tests were set up against four different phytopathogenic fungi. Isolates with high activity (zone of inhibition >10 mm) were sequenced and identified as Trichoderma harzianum, Pezicula neosporulosa, Fusarium tricinctum, Metarhizium sp., and Chaetomium sp. Applying selected endophytic fungi (n = 7) as soil drenchers significantly increased the growth of P. colorata seedlings and produced more internodes. Seedling shoots treated with Trichoderma sp. PRY2BA21 were 2.2 × longer (8.36 cm) than the untreated controls (3.72 cm). Our results elucidate the main plant factors influencing fungal community composition and demonstrate a role for endophytic fungi in P. colorata growth and further demonstrate that medicinal plants are a rich source of endophytes with potential as biocontrol agents.

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