Towards environmental toxicogenomics -- development of a flow-through, high-density DNA hybridization array and its application to ecotoxicity assessment.

Assessment of the environmental hazard posed by soils/sediments containing low to moderate levels of contaminants using standard analytical chemical methods is uncertain due (in part) to a lack of information on contaminant bioavailability, the unknown interactive effects of contaminant mixtures, our inability to determine the species of a metal in an environmental matrix, and the relative sensitivity of bioassay species. Regulatory agencies compensate for this uncertainty by lowering cleanup goals, but in this process they effectively exclude otherwise attractive cleanup options (i.e. bioremediation). Direct evaluations of soil and sediment toxicity preclude uncertainty from most of these sources. However, the time and cost of chronic toxicity tests limits their general application to higher levels of tiered toxicity assessments. Transcriptional level (mRNA) toxicity assessments offer great advantages in terms of speed, cost and sample throughput. These advantages are currently offset by questions about the environmental relevance of molecular level responses. To this end a flow-through, high-density DNA hybridization array (genosensor) system specifically designed for environmental risk assessment was developed. The genosensor is based on highly regular microchannel glass wafers to which gene probes are covalently bound at discrete (200-microm diameter spot) and addressable (250-microm spot pitch) locations. The flow-through design enables hybridization and washing times to be reduced from approximately 18 h to 20 min. The genosensor was configured so that DNA from 28 environmental samples can be simultaneously hybridized with up to 64 different gene probes. The standard microscopic slide format facilitates data capture with most automated array readers and, thus high sample throughput (> 350 sample/h). In conclusion, hardware development for molecular analysis is enabling very tractable means for analyzing RNA and DNA. These developments have underscored the need for further developmental work in probe design software, and the need to relate transcriptional level data to whole-organism toxicity indicators.

Succession of phenotypic, genotypic, and metabolic community characteristics during in vitro bioslurry treatment of polycyclic aromatic hydrocarbon-contaminated sediments.

Dredged harbor sediment contaminated with polycyclic aromatic hydrocarbons (PAHs) was removed from the Milwaukee Confined Disposal Facility and examined for in situ biodegradative capacity. Molecular techniques were used to determine the successional characteristics of the indigenous microbiota during a 4-month bioslurry evaluation. Ester-linked phospholipid fatty acids (PLFA), multiplex PCR of targeted genes, and radiorespirometry techniques were used to define in situ microbial phenotypic, genotypic, and metabolic responses, respectively. Soxhlet extractions revealed a loss in total PAH concentrations of 52%. Individual PAHs showed reductions as great as 75% (i.e., acenapthene and fluorene). Rates of (14)C-PAH mineralization (percent/day) were greatest for phenanthrene, followed by pyrene and then chrysene. There was no mineralization capacity for benzo[a]pyrene. Ester-linked phospholipid fatty acid analysis revealed a threefold increase in total microbial biomass and a dynamic microbial community composition that showed a strong correlation with observed changes in the PAH chemistry (canonical r(2) of 0.999). Nucleic acid analyses showed copies of genes encoding PAH-degrading enzymes (extradiol dioxygenases, hydroxylases, and meta-cleavage enzymes) to increase by as much as 4 orders of magnitude. Shifts in gene copy numbers showed strong correlations with shifts in specific subsets of the extant microbial community. Specifically, declines in the concentrations of three-ring PAH moieties (i.e., phenanthrene) correlated with PLFA indicative of certain gram-negative bacteria (i.e., Rhodococcus spp. and/or actinomycetes) and genes encoding for naphthalene-, biphenyl-, and catechol-2,3-dioxygenase degradative enzymes. The results of this study suggest that the intrinsic biodegradative potential of an environmental site can be derived from the polyphasic characterization of the in situ microbial community.

Environmental behavior of explosives in groundwater from the Milan Army Ammunition Plant in aquatic and wetland plant treatments. Uptake and fate of TNT and RDX in plants.

Uptake and fate of TNT and RDX by three aquatic and four wetland plants were studied using hydroponic, batch, incubations in explosives-contaminated groundwater amended with [U-14C]-TNT or [U-14C]-RDX in the laboratory. Substrates in which the plants were rooted were also tested. Plants and substrates were collected from a small-scale wetland constructed for explosives removal, and groundwater originated from a local aquifer at the Milan Army Ammunition Plant. This study demonstrated rapid uptake of [U-14C]-TNT derived 14C, concentration at the uptake sites and limited transport in all plants. Per unit of mass, uptake was higher in submersed than in emergent species. Biotransformation of TNT had occurred in all plant treatments after 7-day incubation in 1.6 to 3.4 mg TNT L-i, with labeled amino-dinitrotoluenes (ADNTs), three unidentified compounds unique for plants, and mostly polar products as results. Biotransformation occurred also in the substrates, yielding labeled ADNT, one unidentified compound unique for substrates, and polar products. TNT was not recovered by HPLC in plants and substrates after incubation. Uptake of [U-14C]-RDX derived 14C in plants was slower than that of TNT, transport was substantial, and concentration occurred at sites where new plant material was synthesized. As for TNT, uptake per unit of mass was higher in submersed than in emergent species. Biotransformation of RDX had occurred in all plant treatments after 13-day incubation in 1.5 mg RDX L-1, with one unidentified compound unique for plants, and mostly polar products as results. Biotransformation had occurred also in the substrates, but to a far lower extent than in plants. Substrates and plants had one unidentified 14C-RDX metabolite in common. HPLC analysis confirmed the presence of RDX in most plants and in three out of four substrates at the end of the incubation period.

Effect of novel biosurfactants on biodegradation of polychlorinated biphenyls by pure and mixed bacterial cultures.

A study was conducted to determine the potential positive effect of novel biosurfactants on the enhancement of Aroclor 1248 metabolization in both in vitro and in situ experiments. Among two lipopeptides tested the highest activity was found in experiments with a hydrolytically opened form of lichenysin A. Lichenysin A itself did not enhance the degradation activity of chosen microorganism-degraders and in most cases inhibited their PCB mineralization rates. Glucolipid surfactant from marine bacterium Alcanivorax borkumensis showed in several tests a strong enhancing effect on microbial metabolization of Aroclor 1248 congeners. Biosurfactants appeared to act very specifically, i.e. depending on strain and concentration used. Experiments set up with soil samples did not give a clear answer whether bioemulsifiers applied at low concentration could sufficiently increase the rates of biodegradation in situ. Only A. borkumiensis glucose lipid caused the most marked enhancement of Aroclor 1248 metabolization in soil microcosm. We suggest that taking into account the specificity of surface- and biological activities of various biosurfactants they may promote the mineralization of sorbed PCBs in polluted soils, when the optimized biosurfactant-degrader combination is used.

Environmental behavior of explosives in groundwater from the Milan Army Ammunition Plant in aquatic and wetland plant treatments. Removal, mass balances and fate in groundwater of TNT and RDX.

Phytoremediation of 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in groundwater using constructed wetlands is a potentially economical remediation alternative. To evaluate Explosives removal and fate was evaluated using hydroponic batch incubations of plant and substrate treatments with explosives-contaminated groundwater amended with [U-14C]-TNT or [U-14C]-RDX. Plants and substrates were collected from a small-scale wetland constructed for explosives removal, and groundwater originated from a local aquifer at the Milan Army Ammunition Plant. The study surveyed three aquatic, four wetland plant species and two substrates in independent incubations of 7 days with TNT and 13 days with RDX. Parent compounds and transformation products were followed using 14C and chemical (HPLC) analyses. Mass balance of water, plants, substrates and air was determined. It was demonstrated that TNT disappeared completely from groundwater incubated with plants, although growth of most plants except parrot-feather was low in groundwater amended to contain 1.6 to 3.4 mg TNT L-1. Highest specific removal rates were found in submersed plants in water star-grass and in all emergent plants except wool-grass. TNT declined less with substrates, and least in controls without plants. Radiolabel was present in all plants after incubation. Mineralization to 14CO2 was very low, and evolution into 14C-volatile organics negligible. RDX disappeared less rapidly than TNT from groundwater. Growth of submersed plants was normal, but that of emergent plants reduced in groundwater amended to contain 1.5 mg RDX L-1. Highest specific RDX removal rates were found in submersed plants in elodea, and in emergent plants in reed canary grass. RDX failed to disappear with substrates. Mineralization to 14CO2 was low, but relatively higher than in the TNT experiment. Evolution into 14C-volatile organics was negligible. Important considerations for using certain aquatic and wetland plants in constructed wetlands aimed at removing explosives from water are: (1) plant persistence at the explosives level to which it is exposed, (2) specific plant-mass based explosives removal rates, (3) plant productivity, and (4) fate of parent compounds and transformation products in water, plants, and sediments.

Screening of aquatic and wetland plant species for phytoremediation of explosives-contaminated groundwater from the Iowa Army Ammunition Plant.

The results of this study indicate that the presence of plants did enhance TNT and TNB removal from IAAP groundwater. Most effective at 25 degrees C were reed canary grass, coontail and pondweed. Groundwater and plant tissue analyses indicate that in presence of the plants tested TNT is degraded to reduced by-products and to other metabolites that were not analyzed. TNT removal was best modeled using first order kinetics, with rate constants at 25 degrees C incubations ranging from 0.038 microgram L-1 h-1 for reed canary grass to 0.012 microgram L-1 h-1 for parrot-feather. These kinetics predict hydraulic retention times (HRTs) ranging from 4.9 days to 19.8 days to reach a TNT concentration of 2 micrograms L-1. Decreasing incubation temperature to 10 degrees C affected reed canary grass more than parrot-feather, increasing estimated HRTs by factors of four and two, respectively. The plant species tested showed a far lower potential for RDX removal from the IAAP groundwater. Most effective at 25 degrees C were reed canary grass and fox sedge. Analyses of plant material indicated the presence of RDX in under-water plant portions and in aerial plant portions, and RDX accumulation in the latter. RDX removal was best modeled using zero order kinetics, with rate constants for the 25 degrees C incubation ranging from 13.45 micrograms L-1 h-1 for reed canary grass to no removal in four species. Based on these kinetics, estimated HRTs to reach 2 micrograms L-1 RDX increased from 39 days. Decreasing the temperature to 10 degrees C increased HRT 24-fold for reed canary grass. By using the biomass-normalized K value, submersed plants are identified as having the highest explosives-removing activity (microgram explosive L-1 h-1 g DW-1). However, biomass production of submersed plants is normally five to ten times less than that of emergent plants per unit area, and, thus, in plant selection for wetland construction, both, explosives removal potential and biomass production are important determinants.

Effect of heterogeneity of hydrophobic moieties on surface activity of lichenysin A, a lipopeptide biosurfactant from Bacillus licheniformis BAS50.

Lichenysin A, a surface-active lipopeptide produced by Bacillus licheniformis, strain BAS50, contains longchain beta-hydroxy fatty acids. Regulation of the synthesis of fatty acids and beta-hydroxy fatty acids was studied by modifying the culture medium. Addition of branched-chain alpha-amino acids to the medium caused similar changes to both cellular fatty acid and to beta-hydroxy fatty acid composition in the lipophilic part of lichenysin A. Production of lichenysin A was enhanced about two- and four-fold by addition of L-glutamic acid and L-asparagine respectively. It is suggested that these amino acids may be involved in the control of lipopeptide formation. Elucidation of the structure-function relationship of surface-active lipopeptides by analysis of the activities of structurally characterized compounds is discussed. Fractions of lichenysin A with branched beta-hydroxy acids in the lipid tail demonstrated lower surface-tension activity than the fractions of lichenysin A having straight beta-hydroxy acids. The presence of a lichenysin A fraction with beta-hydroxymyristic [(C14)n] acid residues appears to have an important influence on the surface activity of a mixture of lichenysins A.

Characterization of a new lipopeptide surfactant produced by thermotolerant and halotolerant subsurface Bacillus licheniformis BAS50.

Strain BAS50, isolated from a petroleum reservoir at a depth of 1,500 m and identified as Bacillus licheniformis, grew and produced a lipopeptide surfactant when cultured on a variety of substrates at salinities of up to 13% NaCl. Surfactant production occurred both aerobically and anaerobically and was optimal at 5% NaCl and temperatures between 35 and 45 degrees C. The biosurfactant, termed lichenysin A, was purified and chemically characterized. A tentative structure and composition for the surfactant are described. Lichenysin A is a mixture of lipopeptides, with the major components ranging in size from 1,006 to 1,034 Da. The lipid moiety contains a mixture of 14 linear and branched beta-hydroxy fatty acids ranging in size from C12 to C17. There are seven amino acids per molecule. The peptide moiety is composed of the following amino acids: glutamic acid as the N-terminal amino acid, asparagine, valine, leucine, and isoleucine as the C-terminal amino acid, at a ratio of 1.1:1.1:1.0:2.8:1.0, respectively. Purified lichenysin A decreases the surface tension of water from 72 mN/m to 28 mN/m and achieves the critical micelle concentration with as little as 12 mg/liter, characterizing the product as a powerful surface-active agent that compares favorably to others surfactants. The antibacterial activity of lichenysin A has been demonstrated.

Fast atom bombardment mass spectrometry as a rapid means of screening mixtures of ether-linked polar lipids from extremely halophilic archaebacteria for the presence of novel chemical structures.

Fast atom bombardment mass spectrometry was used to analyse intact polar ether lipids present at microgram levels in crude lipid mixtures extracted from Halobacterium halobium, Natronococcus occultus and Halobacterium marismortui. Negative-ion spectra showed the intact deprotonated lipid molecules and in some instances their sodium salts. The simplicity of the mass spectra permits the rapid screening of polar lipid mixtures for the presence of novel lipids. Additional structural information of ions with selected masses was obtained after collisionally induced decomposition.

Sensitive assay, based on hydroxy fatty acids from lipopolysaccharide lipid A, for Gram-negative bacteria in sediments.

Biochemical measures have provided insight into the biomass and community structure of sedimentary microbiota without the requirement of selection by growth or quantitative removal from the sediment grains. This study used the assay of the hydroxy fatty acids released from the lipid A of the lipopolysaccharide in sediments to provide an estimate of the gram-negative bacteria. The method was sensitive to picomolar amounts of hydroxy fatty acids. The recovery of lipopolysaccharide hydroxy fatty acids from organisms added to sediments was quantitative. The lipids were extracted from the sediments with single-phase chloroform-methanol extraction. The lipid-extraction residue was hydrolyzed in 1 N HCl, and the hydroxy fatty acids of the lipopolysaccharide were recovered in chloroform for analysis by gas-liquid chromatography. This method proved to be about fivefold more sensitive than the classical phenol-water or trichloroacetic acid methods when applied to marine sediments. By examination of the patterns of hydroxy fatty acids, it was also possible to help define the community structure of the sedimentary gram-negative bacteria.