Microbial studies of a selenium-contaminated mine site and potential for on-site remediation.

Surface water Selenium (Se) concentrations are above regulatory standards at several active and inactive phosphate mine sites in the US Western Phosphate Resource Area. The focus of the present study was to examine the impacts of the microbial communities on the oxidation state of Se in overburden waste from the Smoky Canyon phosphate mine in Idaho, USA. Microbial populations were found that reduce soluble selenate (SeO (4) (2-) ) to insoluble elemental Se. Microcosm experiments were conducted for molecular genetic analysis of this microbial community by rRNA gene profiling. An acetone pretreatment step was developed to remove interfering pre-petroleum hydrocarbons from the samples prior to extraction. PCR was used to amplify 16S and 18S rRNA genes present in the microbial community DNA. The amplified products were subjected to denaturing gradient gel electrophoresis (DGGE). Isolates and excised DGGE bands were amplified and sequenced for identification to determine the relative importance of culturable isolates to the total microbial population. Analysis of samples from different sites at the mine showed how Se contamination and previous remediation treatments changed the microbial populations across the site. Members of the family Enterobacteriaceae were dominant among the selenate reducing isolates from the site containing high Se levels. In particular, Serratia fonticola was isolated repeatedly from contaminated Smoky Canyon Mine site samples. Packed column studies were performed with seleniferous waste rock fractions from Smoky Canyon Mine. Column amendments consisted of combinations of iron, compost, and whey. Eh, pH, and extractable Se measurements were taken. Tests with infiltrated water showed columns containing an organic amendment combined with iron metal were the most resistant to Se leaching. Iron-based compounds from the corroding metal are thought to strongly bind the Se reduced by microbial activity, thereby stabilizing the Se in an insoluble form. We conclude that long-term stabilization of selenium at contaminated mine sites may require reductive microbial processes combined with abiotic immobilization by iron, either natural or engineered, to stabilize the Se and retard re-oxidation and release. Iron-selenide or iron-selenite compounds are more stable and resistant to leaching, especially when removed from active weathering.

Studies on the microbial populations of the rhizosphere of big sagebrush ( Artemisia tridentata).

Prolonged use of broad-spectrum antibiotics has led to the emergence of drug-resistant pathogens, both in medicine and in agriculture. New threats such as biological warfare have increased the need for novel and efficacious antimicrobial agents. Natural habitats not previously examined as sources of novel antibiotic-producing microorganisms still exist. One such habitat is the rhizosphere of desert shrubs. Here, we show that one desert shrub habitat, the rhizosphere of desert big sagebrush ( Artemisia tridentata) is a source of actinomycetes capable of producing an extensive array of antifungal metabolites. Culturable microbial populations from both the sagebrush rhizosphere and nearby bulk soils from three different sites were enumerated and compared, using traditional plate-count techniques and antibiotic activity bioassays. There were no statistical differences between the relative numbers of culturable non-actinomycete eubacteria, actinomycetes and fungi in the rhizosphere versus bulk soils, but PCR amplification of the 16S rRNA gene sequences of the total soil DNA and denaturing gradient gel electrophoresis showed that the community structure was different between the rhizosphere and the bulk soils. A high percentage of actinomycetes produced antimicrobials; and the percentage of active producers was significantly higher among the rhizosphere isolates, as compared with the bulk soil isolates. Also, the rhizosphere strains were more active in the production of antifungal compounds than antibacterial compounds. 16S rRNA gene sequence analysis showed that sagebrush rhizospheres contained a variety of Streptomyces species possessing broad spectrum antifungal activity. Scanning electron microscopy studies of sagebrush root colonization by one of the novel sagebrush rhizosphere isolates, Streptomyces sp. strain RG, showed that it aggressively colonized young sagebrush roots, whereas another plant rhizosphere-colonizing strain, S. lydicus WYEC108, not originally isolated from sagebrush, was a poor colonizer of the roots of this plant, as were two other Streptomyces isolates from forest soil. These results support the hypothesis that the rhizosphere of desert big sagebrush is a promising source of habitat-adapted actinomycetes, producing antifungal antibiotics.

Detection and decontamination of residual energetics from ordnance and explosives scrap.

Extensive manufacturing of explosives in the last century has resulted in widespread contamination of soils and waters. Decommissioning and cleanup of these materials has also led to concerns about the explosive hazards associated with residual energetics still present on the surfaces of ordnance and explosives scrap. Typically, open burning or detonation is used to decontaminate ordinance and explosive scrap. Here the use of an anaerobic microbiological system applied as a bioslurry to decontaminate energetics from the surfaces of metal scrap is described. Decontamination of model metal scrap artificially contaminated with 2,4,6-trinitrotoluene and of decommissioned mortar rounds still containing explosives residue was examined. A portable ion mobility spectrometer was employed for the detection of residual explosives residues on the surfaces of the scrap. The mixed microbial populations of the bioslurries effectively decontaminated both the scrap and the mortar rounds. Use of the ion mobility spectrometer was an extremely sensitive field screening method for assessing decontamination and is a method by which minimally trained personnel can declare scrap clean with a high level of certainty.

Mechanisms of cadmium resistance in anaerobic bacterial enrichments degrading pentachlorophenol.

The mechanisms of heavy-metal resistance used by adapted sulfidogenic and methanogenic enrichments degrading pentachlorophenol in the presence of cadmium (Cd) were studied. The enrichment cultures adapted to and readily tolerated bioavailable Cd concentrations up to 50 ppm while degrading an equal concentration of pentachlorophenol. Both cultures removed >95% of the Cd from solution. Transmission electron micrographs revealed (i). the presence of electron-dense particles surrounding the cells in the sulfidogenic enrichments and (ii). the unusual clumping of cells and the presence of an exopolymer in the methanogenic enrichments. Energy dispersive X-ray analysis showed that the sulfidogenic enrichments removed Cd by extracellular precipitation of cadmium sulfide, while the methanogenic enrichment culture removed Cd by extracellular sequestration of Cd into the exopolymer.

Cadmium stress studies: media development, enrichment, consortia analysis, and environmental relevance.

The effects of Cadmium (Cd) toxicity on bacterial consortia originating from an-aerobic sewage sludge and cultivated under differing enrichment conditions were studied. Cultures were enriched in minimal media developed specifically for Cd stress studies. At inoculation all Cd was soluble in free ion or chelated form. Electron donors and acceptors were varied to obtain each physiological enrichment type. Adaptation leading to higher levels of Cd resistance of the consortia over time was observed under all physiological conditions. Initial and increased Cd tolerances were consistently greatest in multiphysiological enrichments (MPH). Sulfate reducing (SRB), methanogenic (MET), and fermentative (FRM) enrichments had less tolerance however, the level of tolerance to the Cd varied from one inoculation to the next. The Cd remained soluble as free Cd in MPH and FRM conditions and was precipitated significantly in SRB and moderately in MET conditions. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplified 16S rRNA of the SRB, MPH, and FRM enrichments were followed over time. The consortia underwent succession under all physiological conditions when compared with the profile of the inoculum. Microbial population diversity decreased as the consortia were subcultured. The effects of chelators in the MPH medium were also evaluated. The addition of chelators transiently decreased toxicity. Effects of MPH medium on the Cd sorption capacity of soil were evaluated. Microbial growth decreased the amount of Cd left in solution.

Actinobacterial chitinase-like enzymes: profiles of rhizosphere versus non-rhizosphere isolates.

The objective of this study was to determine if antifungal actinomycetes isolated from rhizosphere and non-rhizosphere soils exhibit different chitinase-like production and (or) induction patterns. Selected isolates from both habitats were compared. Chitinase-like levels and isoform characteristic patterns were evaluated over time in culture fluids of isolates grown on media containing different combinations of colloidal chitin and fungal cell wall (FCW) preparation. Supernatants were also subjected to native and non-native polyacrylamide gel electrophoresis (PAGE), using glycol chitin amended gels. For non-native PAGE, protein samples were denatured by two different approaches. Multiple active bands, ranging from 20 to 53 kDa and present in varying amounts, were detected in gels for most strains. Different substrate preferences were observed among strains, and different chitinase-like enzymes were produced, depending upon the substrate combinations used. The presence of FCW in the medium induced specific chitinase-like enzymes not observed otherwise. Enzymatic activities and profiles of the isolates, however, were strain and substrate specific rather than habitat specific. However, a sagebrush rhizosphere soil had a larger actinomycete community with higher chitinolytic activities than the nearby bulk soil. The use of PAGE to compare chitinase-like proteins induced in media with and without FCW was useful for identifying chitinase-like enzymes potentially involved in antifungal activity.

Effect of amino acids on thaxtomin A biosynthesis by Streptomyces scabies.

The regulatory effect of amino acids on the production of thaxtomin A, a phytotoxin produced by Streptomyces scabies, was investigated. Tryptophan had an important inhibitory effect on the toxin biosynthesis in all five strains of S. scabies tested. Two other aromatic amino acids (tyrosine and phenylalanine) also inhibited thaxtomin A biosynthesis, while aliphatic amino acids did not cause an important decline in thaxtomin A production. Methylation of tryptophan prevented or reduced the inhibitory effect on thaxtomin A biosynthesis. In spite of the inhibitory action of tryptophan and phenylalanine on thaxtomin A production, incorporation of these radiolabeled molecules into thaxtomin A confirmed that they are metabolic precursors for the biosynthesis of the phytotoxin.

Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC108 and the pea plant (Pisum sativum).

A previously undescribed plant-microbe interaction between a root-colonizing Streptomyces species, S. lydicus WYEC108, and the legume Pisum sativum is described. The interaction is potentially of great importance to the health and growth in nature of this nodulating legume. The root-colonizing soil actinomycete S. lydicus WYEC108 influences pea root nodulation by increasing root nodulation frequency, possibly at the level of infection by Rhizobium spp. S. lydicus also colonizes and then sporulates within the surface cell layers of the nodules. Colonization leads to an increase in the average size of the nodules that form and improves the vigor of bacteroids within the nodules by enhancing nodular assimilation of iron and possibly other soil nutrients. Bacteroid accumulation of the carbon storage polymer, poly-beta-hydroxybutyrate, is reduced in colonized nodules. Root nodules of peas taken from agricultural fields in the Palouse hills of northern Idaho were also found to be colonized by actinomycete hyphae. We hypothesize that root and nodule colonization is one of several mechanisms by which Streptomyces acts as a naturally occurring plant growth-promoting bacterium in pea and possibly other leguminous plants.