Molecular biomarker-based biokinetic modeling of a PCE-dechlorinating and methanogenic mixed culture.

Bioremediation of chlorinated ethenes via anaerobic reductive dechlorination relies upon the activity of specific microbial populations--most notably Dehalococcoides (DHC) strains. In the lab and field Dehalococcoides grow most robustly in mixed communities which usually contain both fermenters and methanogens. Recently, researchers have been developing quantitative molecular biomarkers to aid in field site diagnostics and it is hoped that these biomarkers could aid in the modeling of anaerobic reductive dechlorination.

Cytochrome P450 initiates degradation of cis-dichloroethene by Polaromonas sp. strain JS666.

Polaromonas sp. strain JS666 grows on cis-1,2-dichoroethene (cDCE) as the sole carbon and energy source under aerobic conditions, but the degradation mechanism and the enzymes involved are unknown. In this study, we established the complete pathway for cDCE degradation through heterologous gene expression, inhibition studies, enzyme assays, and analysis of intermediates.

Using FTIR spectroscopy to model alkaline pretreatment and enzymatic saccharification of six lignocellulosic biomasses.

Fourier transform infrared, attenuated total reflectance (FTIR-ATR) spectroscopy, combined with partial least squares (PLS) regression, accurately predicted solubilization of plant cell wall constituents and NaOH consumption through pretreatment, and overall sugar productions from combined pretreatment and enzymatic hydrolysis. PLS regression models were constructed by correlating FTIR spectra of six raw biomasses (two switchgrass cultivars, big bluestem grass, a low-impact, high-diversity mixture of prairie biomasses, mixed hardwood, and corn stover), plus alkali loading in pretreatment, to nine dependent variables: glucose, xylose, lignin, and total solids solubilized in pretreatment; NaOH consumed in pretreatment; and overall glucose and xylose conversions and yields from combined pretreatment and enzymatic hydrolysis. PLS models predicted the dependent variables with the following values of coefficient of determination for cross-validation (Q²): 0.

Using FTIR to predict saccharification from enzymatic hydrolysis of alkali-pretreated biomasses.

Fourier transform infrared, attenuated total reflectance (FTIR-ATR) spectroscopy combined with partial least squares (PLS) regression accurately predicted 72-h glucose and xylose conversions (g sugars/100 g potential sugars) and yields (g sugars/100 g dry solids) from cellulase-mediated hydrolysis of alkali-pretreated lignocellulose. Six plant biomasses that represent a variety of potential biofuel feedstocks--two switchgrass cultivars, big bluestem grass, a low-impact, high-diversity mixture of 32 species of prairie biomasses, mixed hardwood, and corn stover--were subjected to four levels of low-temperature NaOH pretreatment to produce 24 samples with a wide range of potential digestibility. PLS models were constructed by correlating FTIR spectra of pretreated samples to measured values of gluose and xylose conversions and yields.

Assessment of commercial hemicellulases for saccharification of alkaline pretreated perennial biomass.

The objective of this research was to measure the effects of different cellulase and hemicellulase mixtures on fermentable sugar production from two different perennial biomasses--switchgrass and a low-impact, high-diversity prairie biomass mixture (LIHD). Each was subjected to NaOH pretreatment, followed by hydrolysis with a commercial cellulase and β-glucosidase mixture [CB] supplemented with either of two hemicellulases. For both biomasses, there was little gain in sugar yield when using CB alone beyond 20-25 mg/g TS; further gain in yield was possible only through hemicellulase supplementation.

Sustained aerobic oxidation of vinyl chloride at low oxygen concentrations.

One possible explanation for unexplained disappearance of vinyl chloride (VC) from what are thought to be anaerobic subsurface environments is that the environments are, in fact, not anaerobic. Rather, they might be subject to low, steady influx of oxygen, and aerobic oxidation could be occurring at extremely low oxygen concentrations. Studies were conducted with VC-oxidizing transfer cultures derived from two chloroethene-contaminated sites, as well as with microcosms constructed from sediment and groundwater from one of these sites.

Proteomic and transcriptomic analyses reveal genes upregulated by cis-dichloroethene in Polaromonas sp. strain JS666.

Polaromonas sp. strain JS666 is the only bacterial isolate capable of using cis-dichloroethene (cDCE) as a sole carbon and energy source. Studies of cDCE degradation in this novel organism are of interest because of potential bioremediation and biocatalysis applications.

Optimization of spore and antifungal lipopeptide production during the solid-state fermentation of Bacillus subtilis.

Bacillus subtilis strain TrigoCor 1448 was grown on wheat middlings in 0.5-l solid-state fermentation (SSF) bioreactors for the production of an antifungal biological control agent. Total antifungal activity was quantified using a 96-well microplate bioassay against the plant pathogen Fusarium oxysporum f.

Modeling production of antifungal compounds and their role in biocontrol product inhibitory activity.

Partial least squares (PLS) regression modeling was used to relate the antifungal activity of Bacillus subtilis solid-state fermentation extracts to the individual high-performance liquid chromatography (HPLC) peaks from those extracts. A model was developed that predicted bioassay inhibition based on the extract HPLC profile (R(2) = 0.99).

Mechanism controlling the extended lag period associated with vinyl chloride starvation in Nocardioides sp. strain JS614.

The extended lag period associated with vinyl chloride (VC) starvation in VC- and ethene-assimilating Nocardioides sp. strain JS614 was examined. The extended lag periods were variable (3-7 days), only associated with growth on VC or ethene, and were observed in VC- or ethene-grown cultures following 24 h carbon starvation and mid-exponential phase cultures grown on non-alkene carbon sources (e.

Effects of oxygen on aerobic solid-state biodegradation kinetics.

Oxygen is a critical control variable for composting and other solid-state biodegradation processes. In this study we examined the effect of varying oxygen concentrations (1%, 4%, and 21% O2 (v/v)) on biodegradation kinetics under different substrate (sewage sludge and synthetic food waste), temperature (35, 45, 55, and 65 degrees C), and moisture (36-60% H2O) conditions. Three forms of a saturation or Monod-type model and one form of an exponential model were evaluated against data from extensive experiments under carefully controlled environmental conditions.

Comparative study of methanol, butyrate, and hydrogen as electron donors for long-term dechlorination of tetrachloroethene in mixed anerobic cultures.

This study examined the ability of different electron donors (i.e., hydrogen, methanol, butyrate, and yeast extract) to sustain long-term (500 days) reductive dechlorination of tetrachloroethene (PCE) in anerobic fill-and-draw bioreactors operated at 3:1 donor:PCE ratio (defined on a total-oxidation basis for the donor).

Carbon isotopic fractionation during aerobic vinyl chloride degradation.

Vinyl chloride (VC) is a carcinogenic contaminant commonly found in groundwater. Much research has focused on anaerobic reductive dechlorination of VC, and recently on aerobic VC degradation. In this study, the stable carbon isotope enrichment factor associated with aerobic VC assimilation was determined for Mycobacterium sp.

Physiological and molecular genetic analyses of vinyl chloride and ethene biodegradation in Nocardioides sp. strain JS614.

Nocardioides sp. strain JS614 utilizes vinyl chloride and ethene as carbon and energy sources. JS614 could be influential in natural attenuation and biogeochemical ethene cycling, and useful for bioremediation, biocatalysis and metabolic engineering, but a fundamental understanding of the physiological and genetic basis of vinyl chloride and ethene assimilation in strain JS614 is required.

Quantifying bacterial population dynamics in compost using 16S rRNA gene probes.

Composting provides a dynamic setting for studying ecological topics such as succession, competition, and community stability in a relatively short period of time. This study used hierarchical small sub-unit-based rRNA gene probes to quantify the change in the relative abundance of phylogenetic groups common to compost in laboratory scale reactors. Bacterial 16S rRNA gene targets accounted for only 37% of all small subunit (SSU) rRNA genes initially, but increased to a maximum of 83% of the total at 84 h.

Phylogenetic and kinetic diversity of aerobic vinyl chloride-assimilating bacteria from contaminated sites.

Aerobic bacteria that grow on vinyl chloride (VC) have been isolated previously, but their diversity and distribution are largely unknown. It is also unclear whether such bacteria contribute to the natural attenuation of VC at chlorinated-ethene-contaminated sites. We detected aerobic VC biodegradation in 23 of 37 microcosms and enrichments inoculated with samples from various sites.

Biodegradation of cis-dichloroethene as the sole carbon source by a beta-proteobacterium.

An aerobic bacterium capable of growth on cis-dichloroethene (cDCE) as a sole carbon and energy source was isolated by enrichment culture. The 16S ribosomal DNA sequence of the isolate (strain JS666) had 97.9% identity to the sequence from Polaromonas vacuolata, indicating that the isolate was a beta-proteobacterium.