Microbial community structure and trichloroethylene degradation in groundwater.

Trichloroethylene (TCE) is a prevalent contaminant of groundwater that can be cometabolically degraded by indigenous microbes. Groundwater contaminated with TCE from a US Department of Energy site in Ohio was used to characterize the site-specific impact of phenol on the indigenous bacterial community for use as a possible remedial strategy. Incubations of 14C-TCE-spiked groundwater amended with phenol showed increased TCE mineralization compared with unamended groundwater. Community structure was determined using DNA directly extracted from groundwater samples. This DNA was then analyzed by amplified ribosomal DNA restriction analysis. Unique restriction fragment length polymorphisms defined operational taxonomic units that were sequenced to determine phylogeny. DNA sequence data indicated that known TCE-degrading bacteria including relatives of Variovorax and Burkholderia were present in site water. Diversity of the amplified microbial rDNA clone library was lower in phenol-amended communities than in unamended groundwater (i.e., having Shannon-Weaver diversity indices of 2.0 and 2.2, respectively). Microbial activity was higher in phenol-amended ground water as determined by measuring the reduction of 2-(p-iodophenyl)-3(p-nitrophenyl)-5-phenyl tetrazolium chloride. Thus phenol amendments to groundwater correlated with increased TCE mineralization, a decrease in diversity of the amplified microbial rDNA clone library, and increased microbial activity.

Measurement of carbon dioxide levels during use of ELSA and the effect of venting on these levels.

DESIGN: A prospective, objective assessment of ELSA use, in order to determine whether venting of the ELSA influences carbon dioxide (CO2) levels. PRIMARY ENDPOINT: Inspired and expired CO2 levels. SETTING: On board RFA ARGUS during Operation TELIC. METHODS: 10 volunteers had a baseline of inspired and expired CO2 levels taken. These levels were measured at one minute intervals during use of an ELSA in 3 conditions--sitting, jogging and jogging with venting. RESULTS: There was no difference in expired CO2 levels between baseline and use of ELSA whilst sitting. Periodic venting of the ELSA made no difference to inspired and expired CO2 levels. CONCLUSIONS: Venting of the ELSA during use makes no difference to CO2 levels whether inspired or expired. Therefore, venting is unnecessary and potentially wastes vital time during escape from a smoke-filled compartment and adds additional stress to the escapee.

Immunotoxicity of explosives-contaminated soil before and after bioremediation.

Soils from the Yorktown Naval Base contaminated with trinitrotoluene (TNT) and other explosives were used to prepare eluates before and after bioremediation using microbial growth amendments in the presence (P1 eluates) or absence (P2 eluates) of exogenous white rot fungus. Effectiveness of bioremediation was examined by several immunotoxicity assays-viability/growth of lymphocytes, cytokine production, and expression of the interleukin-2 (IL-2) receptor-using human peripheral blood mononuclear cells exposed to the eluates. Although TNT concentrations decreased in both P1 and P2 eluates relative to untreated baseline soil (BL) eluates, a recovery in lymphocyte growth/viability and IL-2 secretion was seen with P2 but not P1 eluates relative to BL eluates. IL-2 receptor levels were higher in cells exposed to BL and P2 eluates than when exposed to P1 eluates. Interferon-gamma, tumor necrosis factor-beta, and IL-10 levels were highest in BL and P2 eluates and lowest in P1 eluates. Taken together, these results suggest that treatment of the soil with microbial growth amendments in the absence but not the presence of exogenous white rot fungi lead to partial bioremediation as assessed by lymphocyte functions.

Idiopathic eosinophilic meningoencephalitis in rottweiler dogs: three cases (1992-1997).

We report three cases of eosinophilic meningitis in young male Rottweiler type dogs in New Zealand. No cause for the disease was identified. There were variable clinical signs referable to central nervous system dysfunction, and a variable response to treatment.

Identification and characterization of ICH-2, a novel member of the interleukin-1 beta-converting enzyme family of cysteine proteases.

Interleukin-1 beta converting enzyme (ICE) is a cytoplasmic cysteine protease required for generating the bioactive form of the interleukin-1 beta cytokine from its inactive precursor. We report the identification of ICH-2, a novel human gene encoding a member of the ICE cysteine protease family, and characterization of its protein product. ICH-2 mRNA is widely expressed in human tissues in a pattern similar to, but distinct from, that of ICE. Overexpression of ICH-2 in insect cells induces apoptosis. Purified ICH-2 is functional as a protease in vitro. A comparison of the inhibitor profiles and substrate cleavage by ICH-2 and ICE shows that the enzymes share catalytic properties but may differ in substrate specificities, suggesting that the two enzymes have different functions in vivo.

Detection of Phanerochaete chrysosporium in soil by PCR and restriction enzyme analysis.

A nonradioactive method to detect Phanerochaete chrysosporium grown in a soil matrix was developed. This method involved DNA extraction, PCR amplification, and restriction enzyme analysis. Amplification of ligninase H8 DNA from pure cultures of P. chrysosporium was not as sensitive as amplification of the internal transcribed spacer (ITS) of the highly repetitive nuclear ribosomal DNA. Amplified ITS DNA was digested with restriction enzymes for analysis. The restriction enzyme pattern of PCR-amplified ITS DNA of P. chrysosporium was unique compared with those of unrelated fungi. Two strains of Phanerochaete chrysosporium and two strains of Phanerochaete sordida were indistinguishable by restriction enzyme analysis, while a third strain of P. chrysosporium had an unique pattern. These results were confirmed by sequence information and indicate that species designations of Phanerochaete spp. should be reexamined. The restriction enzyme pattern of DNA extracted and PCR amplified from P. chrysosporium grown in soil was identical to that from P. chrysosporium grown in pure culture. The ITS sequence was detected in 14 ng of the 100 micrograms of total DNA extracted from 1 g of soil.

Transcription of ligninase H8 by Phanerochaete chrysosporium under nutrient nitrogen sufficient conditions.

Dot blot analyses showed that more ligninase H8 mRNA was present in ammonium sufficient cultures of Phanerochaete chrysosporium than in ammonium limited cultures. Reverse transcription followed by polymerase chain reaction and DNA sequencing verified that H8 mRNA was present under both conditions. Fast protein liquid chromatography profiles indicated that H8 was present but lacked heme in ammonium sufficient cultures. These data indicated that H8 was transcribed and translated by day 5 under ammonium sufficient conditions, but was inactive due to lack of heme.

Biogeochemistry of oxalate in the antarctic cryptoendolithic lichen-dominated community.

Cryptoendolithic (hidden in rock) lichen-dominated microbial communities from the Ross Desert of Antarctica were shown to produce oxalate (oxalic acid). Oxalate increased mineral dissolution, which provides nutrients, creates characteristic weathering patterns, and may ultimately influence the biological residence time of the community. Oxalate was the only organic acid detectable by HPLC, and its presence was verified by GC/MS. Community photosynthetic metabolism was involved in oxalate production since rates of (14)C-oxalate production from (14)C02 were higher in light than in dark incubations. Flaking of the sandstone at the level of the lichen-dominated zone a few millimeters beneath the rock surface can be explained by dissolution of the sandstone cement, which was enhanced by Si, Fe, and Al oxalate complex formation. Added oxalate was observed to increase the solubility of Si, Fe, Al, P, and K. Oxalate's ability to form soluble trivalent metal-oxalate complexes correlated with the observed order of metal oxide depletion from the lichen-dominated zone (Mn > Fe > Al). Thermodynamic calculations predict that Fe oxalate complex formation mobilizes amorphous Fe oxides (ferrihydrite) in the lichen-dominated zone, and where oxalate is depleted, ferrihydrite should precipitate. Hematite, a more crystalline Fe oxide, should remain solid at in situ oxalate concentrations. Oxalate was not a carbon source for the indigenous heterotrophs, but the microbiota were involved in oxalate mineralization to CO2, since oxalate mineralization was reduced in poisoned incubations. Photooxidation of oxalate to C02 coupled with photoreduction of Fe(Ill) may be responsible for oxalate removal in situ, since rates of (14)C-oxalate mineralization in dark incubations were at least 50% lower than those in the light. Removal of oxalate from Si, Fe, and Al complexes should allow free dissolved Si, Fe, and Al to precipitate as amorphous silicates and metal oxides. This may explain increased siliceous crust (rock varnish or desert varnish) formation near the surface of colonized rocks were light intensity is greatest.

The Drosophila ACE3 chorion element autonomously induces amplification.

The Drosophila chorion genes amplify in the follicle cells by repeated rounds of reinitiation of DNA replication. ACE3 (amplification control element from the third chromosome) has been identified by a series of deletion experiments as an important control element for amplification of the third-chromosome chorion cluster. Several elements that quantitatively enhance amplification also have been defined. We show that a single 440-bp ACE3 sequence is sufficient to regulate amplification with proper developmental specificity autonomously from other chorion DNA sequences and regulatory elements. Although ACE3 is sufficient for amplification, the levels of amplification are low even when ACE3 is present in multiple copies. When controlled solely by ACE3, amplification initiates either at ACE3 or within closely linked sequences. Amplification of an ACE3 transposon insertion produces a gradient of amplified DNA that extends into flanking sequences approximately the same distance as does the amplification gradient at the endogenous chorion locus. The profile and extent of the amplified gradient imply that the low levels of amplification observed are the result of limited rounds of initiation of DNA replication. Transposon inserts containing multiple copies of ACE3 in a tandem, head-to-tail array are maintained stably in the chromosome. However, mobilization of the P-element transposons containing ACE3 multimers results in deletions within the array at a high frequency.

Photosynthetic carbon incorporation and turnover in antarctic cryptoendolithic microbial communities: are they the slowest-growing communities on Earth?

The main forms of terrestrial life in the cold, desolate Ross Desert of Antarctica are lichen-dominated or cyanobacterium-dominated cryptoendolithic (hidden in rock) microbial communities. Though microbial community biomass (as measured by extractable lipid phosphate) was well within the range of values determined for other microbial communities, community lipid carbon turnover times (calculated from community lipid biomass, rates of community photosynthetic carbon incorporation into lipids versus temperature, and the in situ temperature record) were among the longest on Earth (ca. 20,000 years). When the temperature is above freezing and moisture is present, moderate rates of photosynthesis can be measured. Lichen communities had a psychrophilic temperature response (maximal rate of 4.5 ng of C h m at 10 degrees C) while cyanobacteria communities had maximal rates at 20 to 30 degrees C (3 ng of C h m). These extraordinarily slowly growing communities were not nutrient limited. No significant changes in photosynthetic metabolism were observed upon additions of 100 nM to 1 mM nitrate, ammonium, phosphate, and manganese. These simple, tenacious microbial communities demonstrate strategies of survival under conditions normally considered too extreme for life.

The role of ACE3 in Drosophila chorion gene amplification.

ACE3, an amplification control element for the third chromosome chorion cluster of Drosophila melanogaster, was identified previously as a cis-regulatory element for amplification of transposons containing the three chorion genes s18, s15 and s19. The deletion defining ACE3, located from -620 to -190 bp upstream of s18, disrupted both amplification and s18 transcription, suggesting that ACE3 might contain a transcription enhancer that regulated replication, as had been observed in a number of eukaryotic viruses. We show here that transcription control can be separated from replication control in delineating ACE3 to a 320 bp region. Addition of heterologous enhancers fails to activate amplification in tissues other than the follicle cells. Therefore ACE3 does not appear to be analogous to a transcription enhancer. However, further deletions within the ACE3 region revealed that it contains multiple functional domains. In addition, ACE3 functions independently of orientation with respect to other chorion sequences, and can be moved 1.5 kb away from other chorion sequences without eliminating amplification.

Distribution of inorganic species in two Antarctic cryptoendolithic microbial communities.

Chemical differences were noted between two Antarctic cryptoendolithic (hidden within rock) microenvironments colonized by different microbial communities. Microenvironments dominated by cyanobacteria (BPC) had a higher pH (pH 7-8) than those dominated by lichen (LTL) (pH 4.5-5.5). In order to understand the interactions between the microbiota and the inorganic environment, the inorganic environment was characterized. Water-soluble, carbonate-bound, metal-oxide, organically bound, and residual inorganic species were sequentially extracted from rock samples by chemical means. Each fraction was then quantified using inductively coupled plasma atomic emission spectrometry. BPC contained much more water-soluble and carbonate-bound Ca and Mg than LTL. Metal-oxide species of Al, Fe, and Mn were more abundant in LTL than BPC. Metal oxides appeared to be mobilized (in the order Mn > Fe > Al) from the LTL lichen zone but remained immobile in BPC sandstone. The distribution of K and P bound to metal oxide reflected the distribution of iron oxide in LTL, an indication of the importance of iron in controlling the availability of nutrients in this ecosystem. Metal oxides in turn were likely controlled or influenced by organic matter associated with the lichen community. Despite overall depletion of Fe, Al, and K in the lichen zone, SEM X-ray analysis showed that they were enriched in fungal hyphae. Water-soluble P was present despite the presence of metal oxides, which sequester phosphate. This has biological relevance since P is an essential nutrient.

Microbially Mediated Mn(II) Oxidation in an Oligotrophic Arctic Lake.

Rates of oxidation of Mn(II) were measured by an in situ incubation technique in the water column of Toolik Lake, Alaska. Measured rates were lower than those observed in other aquatic systems but were sufficient to oxidize all Mn(II) in the lake within a 3-month period. Measured rates compared favorably with rates estimated from a previous study of the geochemical cycling of Mn in Toolik Lake. The Mn(II) oxidation was largely microbially mediated, as indicated by inhibition of oxidation rates by sodium azide. Azide had been previously demonstrated to be a suitable microbial poison for studying Mn(II) oxidation in seawater. This study demonstrates that azide is also a suitable poison for freshwaters and that it inhibits microbial but not abiotic oxidation of Mn(II). Manganese(II) oxidation rates were similar during cold, under-ice conditions in early spring and during warmer summer conditions. This observation suggests that Mn(II) concentration, rather than temperature or oxygen concentration, is the most important factor regulating Mn(II) oxidation rates in Toolik Lake.

Does iron inhibit cryptoendolithic microbial communities?

Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.