A Sphingomonas species that mineralizes high concentrations of pentachlorophenol (PCP) was isolated from a PCP-contaminated EPA Superfund site. This bacterium, identified as Sphingomonas sp. strain RA2, is able to degrade PCP at concentrations of up to 300 micrograms/mL in liquid culture. This organism was tested for its ability to degrade high concentrations of PCP in a soil that did not contain organisms capable of degrading high concentrations of PCP. When inoculated into contaminated soil, Sphingomonas sp. RA2 mineralized PCP at concentrations of 300, 600, 900, and 1200 micrograms PCP/g of soil, but was unable to mineralize 1500 micrograms PCP/g of soil. Only very minimal loss of PCP was seen in uninoculated soils. The results of this study demonstrate that Sphingomonas sp. RA2 may be a useful organism for remediation of sites contaminated with high concentrations of PCP.

A pentachlorophenol (PCP)-mineralizing bacterium was isolated from polluted soil and identified as Pseudomonas sp. strain RA2. In batch cultures, Pseudomonas sp. strain RA2 used PCP as its sole source of carbon and energy and was capable of completely degrading this compound as indicated by radiotracer studies, stoichiometric release of chloride, and biomass formation. Pseudomonas sp. strain RA2 was able to mineralize a higher concentration of PCP (160 mg liter-') than any previously reported PCP-degrading pseudomonad. At a PCP concentration of 200 mg liter-1, cell growth was completely inhibited and PCP was not degraded, although an active population of Pseudononas sp. RA2 was still present in these cultures after 2 weeks. The inhibitory effect of PCP was partially attributable to its effect on the growth rate of Pseudomonas sp. strain RA2. The highest specific growth rate (FL = 0.09 h-1) was reached at a PCP concentration of 40 mg liter-' but decreased at higher or lower PCP concentrations, with the lowest , (0.05 h-1) occurring at 150 mg liter-'. Despite this reduction in growth rate, total biomass production was proportional to PCP concentration at all PCP concentrations degraded by Pseudomonas sp. RA2. In contrast, final cell density was reduced to below expected values at PCP concentrations greater than 100 mg liter-'. These results indicate that, in addition to its effect as an uncoupler of oxidative phosphorylation, PCP may also inhibit cell division in Pseudomonas sp. strain RA2. PCP and glucose were simultaneously mineralized by Pseudomonas sp. strain RA2, but glucose had no effect on the rate of PCP mineralization. PCP, on the other hand, significantly enhanced the metabolism of glucose by Pseudomonas sp. strain RA2.

Community level interactions were studied in non-axenic sequencing batch reactors (SBRs) being used to treat 2,4-dinitrophenol (DNP). Increasing the influent DNP concentrations from 1 to 10 µg ml(-1) eliminated large predatory organisms such as rotifers and ciliated protozoa from the SBRs. Under steady-state conditions at a DNP concentration of 10 µg ml(-1), supplemental additions of glucose enhanced DNP degradation and led to the establishment of a microbial community consisting of five species of bacteria and a variety of microflagellates. The bacteria and flagellates exhibited oscillating population dynamics in this system, possibly indicating predator-prey interactions between these two groups. Only two of the five bacteria isolated from this system could utilize glucose as a growth substrate, and one of these two species was the only organism that could mineralize DNP in the system. The other three bacteria could grow using metabolic by-products of one of the glucose-utilizing strains (Bacillus cereus) found in the reactors. Supplemental glucose additions increased the average size of bacterial floc particles to 172 µm, compared with 41 µm in SBRs not receiving glucose. It is theorized that the enhanced mineralization of DNP in this non-axenic system was attributable to increased community interactions resulting in increased bacterial flocculation in SBRs receiving supplemental glucose additions.

We have developed a substrate-induced growth response (SIGR) method for quantifying activity and population dynamics of microorganisms involved in bioremediation processes in soil and bioreactors. The biomass of organisms that can mineralize a given chemical can be estimated based on the concentration of that chemical needed to induce the growth of the standing population. Estimates of population size are obtained by using nonlinear regression techniques to fit a simple model of microbial population dynamics to biodegradation curves. Using this approach we obtain estimates of values for parameters such as initial population size and growth rate of organisms carrying out biodegradative processes. Our approach was validated by comparing model parameter estimates with independent estimates of the same parameters from the same bioremediation systems. Examples studied include pentachlorophenol degraders introduced into soil and 2,4-dinitrophenol degrading organisms in a bioreactor.

We previously reported the establishment of a rare xenograft derived from a recurrent oligodendroglioma with 1p/19q codeletion. Here, we analyzed in detail the exome sequencing datasets from the recurrent oligodendroglioma (WHO grade III, recurrent O 2010 ) and the first-generation xenograft (xenograft 1 ). Somatic SNVs and small InDels ( n = 80) with potential effects at the protein level in recurrent O 2010 included variants in IDH1 (NM_005896:c.395G>A; p. Arg132His), FUBP1 (NM_003902:c.1307_1310delTAGA; p.Ile436fs), and CIC (NM_015125:c.4421T>G; p.Val1474Gly). All but 2 of these 80 variants were also present in xenograft 1 , along with 7 new variants. Deep sequencing of the 87 SNVs and InDels in the original tumor (WHO grade III, primary O 2005 ) and in a second-generation xenograft (xenograft 2 ) revealed that only 11 variants, including IDH1 (NM_005896:c.395G>A; p. Arg132His), PSKH1 (NM_006742.2:c.650G>A; p.Arg217Gln), and SNX12 (NM_001256188:c.470G>A; p.Arg157His), along with a variant in the TERT promoter (C250T, NM_198253.2: c.-146G>A), were already present in primary O 2005 . Allele frequencies of the 11 variants were calculated to assess their potential as putative driver genes. A missense change in NDST4 (NM_022569:c.2392C>G; p.Leu798Val) on 4q exhibited an increasing allele frequency (~ 20%, primary O 2005 , 80%, recurrent O 2010 and 100%, xenograft 1 ), consistent with a selection event. Sequencing of NDST4 in a cohort of 15 oligodendrogliomas, however, revealed no additional cases with potential protein disrupting variants. Our analysis illuminated a tumor evolutionary series of events, which included 1p/19q codeletion, IDH1 R132H, and TERT C250T as early events, followed by loss of function of NDST4 and mutations in FUBP1 and CIC as late events.