Bacterial endophyte communities of two wheatgrass varieties following propagation in different growing media.

Bacterial endophyte communities of two wheatgrass varieties currently being used in the revegetation of military training ranges were studied. Culturable and direct 16S rDNA PCR amplification techniques were used to describe bacterial communities present in Siberian and slender wheatgrass seeds, leaf tissues, and root tissues following propagation in either sand or a peat-based growing mix. Our hypothesis was that the resulting plant endophytic communities would be distinct, showing not only the presence of endophytes originating from the seed but also the characteristics of growth in the two different growing media. Both culture and culture-independent assays showed the likely translocation of Actinobacteria, Firmicutes, and Gammaproteobacteria from seed to mature plant tissues as well as subsequent colonization by exogenous organisms. Statistical analysis of 16S terminal restriction fragment profiles identified growing media as having a greater significant effect on the formation of the endpoint endophytic communities than either plant tissue or wheatgrass variety. In silico digests of the ribosomal database produced putative identifications indicating an increase in overall species diversity and increased relative abundances of Firmicutes and Cyanobacteria following propagation in sand and Betaproteobacteria following propagation in the peat-based growing mix. Results indicated a substantial translocation of endophytes from seed to mature plant tissues for both growing media and that growing medium was a dominant determinant of the final taxonomy of the endpoint plant endophytic communities.

A modified acid digestion procedure for extraction of tungsten from soil.

Interest in tungsten occurrence and geochemistry is increasing due to increased use of tungsten compounds and its unknown biochemical effects. Tungsten has a complex geochemistry, existing in most environmental matrices as the soluble and mobile tungstate anion, as well as poly- and heteropolytungstates. Because the geochemistry of tungsten is substantially different than most trace metals, including the formation of insoluble species under acidic conditions, it is not extracted from soil matrices using standard acid digestion procedures. Therefore, the current work describes a modification to a commonly used acid digestion procedure to facilitate quantification of tungsten in soil matrices. Traditional soil digestion procedures, using nitric and hydrochloric acids with hydrogen peroxide yield <1 up to 50% recovery on soil matrix spike samples, whereas the modified method reported here, which includes the addition of phosphoric acid, yields spike recoveries in the 76-98% range. Comparison of the standard and modified digestion procedures on National Institute of Standards and Technology Standard Reference Materials yielded significantly improved tungsten recoveries for the phosphoric acid modified method. The modified method also produces comparable results for other acid extractable metals as the standard methods, and therefore can be used simultaneously for tungsten and other metals of interest.

Investigations of tungsten mobility in soil using column tests.

The geochemistry of tungsten has recently gained attention in the scientific and regulatory communities. Tungsten has a complex geochemistry, existing in many environmental matrices as the soluble and mobile tungstate anion, as well as a series of ill-defined polymeric species. Previous work has shown that soluble tungsten leached from a metallic tungsten-spiked Grenada Loring soil will reach an equilibrium concentration >150 mgL(-1), and the concentration is greatly influenced by co-occurring analytes in the matrix, such as calcium and phosphate. In the present work, the mobility of tungsten compounds was investigated in a model soil with a range of aqueous leach solutions using column experiments. The relative column leachate concentrations measured followed trends from previously reported tungstate and polytungstate partition coefficients determined in the model soil under identical aqueous matrix conditions. Neutral to alkaline conditions produced maximum effluent tungsten concentrations >40 mgL(-1), whereas acid leach eluents produced concentrations in the <1-3 mgL(-1) range. The change in leached tungsten speciation over time was also measured as monomeric and polymeric tungsten species have different sorptive behaviors.

Tungsten effects on microbial community structure and activity in a soil.

Tungsten, once deposited onto a soil as a result of private, industrial, and military activities, may persist as tungstate anion or, via polymerization, as a variety of poly-tungstate species, each with varying solubility and soil sorption characteristics. In this study, the impact of weathered tungsten on a soil microbial community was measured. Fatty acid analyses indicated that weathered tungsten at < or =2500 mg kg(-1) was associated with a significant increase in microbial biomass and that concentrations up to 6500 mg kg(-1) did not result in a significant decrease in measured biomass, relative to the control. Analysis of cellular fatty acids also identified significant microbial community shifts between 0 and 325, 1300 and 2600, and 3900 and 6500 mg W kg(-1) soil. In general, the positive effect of tungsten on microbial biomass coincided with an increase in Gram-negative bacterial fatty acids, whereas fatty acids indicative of actinomycetes and Gram-positive bacteria were more abundant at the highest soil tungsten concentrations. The weathered tungsten also inhibited N2 fixing activity of a free living diazotroph at > or =1300 mg W kg(-1) soil. These results indicate that tungsten in soil can alter both the structure and the function of an indigenous soil microbial community.

Differentiation of live-viable versus dead bacterial endospores by calibrated hyperspectral reflectance microscopy.

This paper describes the use of hyperspectral imaging microscopy (HIM) for the characterization and differentiation of live viable versus dead/non-viable bacterial endospores for two species of Bacillus. To accomplish this, endospore-forming Bacillus were cultured and differentiated into endospores. Non-viable endospores were produced using sporicidal methods representing standard decontamination procedures incorporating chlorine and peroxide. Finally, endospore samples were lyophilized to prepare them for spectral analysis. Prior to HIM, baseline spectral reflectance characterizing the endospores was measured using an ASD (400-900 nm) reflectance spectrometer. These data were used to calibrate the resulting spectral image data. HIM data comprising 32 images ranging from 400 to 720 nm (visible to near infrared) were recorded using a C-mounted VariSpec hyperspectral camera attached to an epifluorescent microscope. The images produced by the system record the reflectance and absorption features of endospores based on the structure of the outer coat. Analysis of the HIM data was performed using accepted image and spectral processing routines. Where peroxide was the sporicide, changes in the outer endospore coat contributed to structurally significant visible and near infrared signature differences between live-viable versus dead, non-viable endospores. A statistical test for divergence, a method for scoring spectral structural diversity, also showed the difference between viable and non-viable peroxide killed endospores to be statistically significant. These findings may lead to an improved optical procedure to rapidly identify viable and non-viable endospores in situations of decontamination.

Geochemical parameters influencing tungsten mobility in soils.

The biogeochemistry of tungsten and its effects on mobility have recently gained attention due to the existence of human cancer clusters, such as in Fallon, NV. Tungsten exists in many environmental matrices as the soluble and mobile tungstate anion. However, tungsten can polymerize with itself and other anions, creating poly- and heteropoly-tungstates with variable geochemical and toxicological properties. In the present work, geochemical parameters are determined for tungstate species in a model soil that describe the potential for tungsten mobility. Soluble tungsten leached from a metallic tungsten-spiked soil after six to twelve months aging reached an equilibrium concentration >150 mg/L within 4 h of extraction with deionized water. Partition coefficients determined for various tungstate and polytungstate compounds in the model soil suggest a dynamic system in which speciation changes over time affect tungsten geochemical behavior. Partition coefficients for tungstate and some poly-species have been observed to increase by a factor of 3 to 6 over a four month period, indicating decreased mobility with soil aging.

Utility of lipid biomarkers in support of bioremediation efforts at army sites.

Lipid biomarker analysis has proven valuable in testing the hypothesis that attributes of the extant microbiota can directly reflect the occurrence of contaminant biodegradation. Two past research efforts have demonstrated this utility and are described here. A 4.5 m vertical core was obtained from a diesel fuel oil contamination plume. Core material was assayed for total petroleum hydrocarbons (TPH) and bacterial membrane phospholipids (PLFA) via a single solvent extraction. Microbial viable biomass and the relative abundance of Gram-negative bacterial PLFA biomarkers were found to be significantly correlated with TPH concentration. The core TPH profile also revealed two distinct areas where the average TPH level of 3,000 microg g(-1) fell to near detection limits. Both areas were characterized by a three-fold decrease in the hexadecane/pristane ratio, indicating alkane biodegradation, and a distinct PLFA profile that showed a close similarity to the uncontaminated surface soil. Low-order, incomplete detonations can deposit hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) into training range surface soils. Since surface soils are exposed to temporal and diurnal moisture cycles, we investigated the effect two very different soil moisture tensions had on the in situ microbiota and RDX biodegradation. Saturated soils were characterized by rapid RDX biodegradation, 4 day half-life, a decrease in number of species detected and increase in PLFA biomarkers for Gram-negative proteobacteria (n16:1omega7c, n18:1omega9c, and n18:1omega7c) and Gram-positive firmicutes (i15:0 and a15:0). Terminal restriction fragment length polymorphism (T-RFLP) profiles of endpoint microbial communities indicated a shift from 18 to 36% firmicutes, the loss of gamma-proteobacteria and the emergence of alpha-proteobacteria. These two past research efforts demonstrated the utility of the lipid biomarker analysis in identifying microbial community characteristics that were associated with two very different soil contaminants. Lipid biomarkers defined areas of TPH biodegradation and identified community shifts as a result of soil conditions that affected explosives fate. Information like this can be used to enhance the predictive power of ecological models such as the Army Training and Testing Area Carrying Capacity for munitions model [ATTACC].

The determination of tungsten, molybdenum, and phosphorus oxyanions by high performance liquid chromatography inductively coupled plasma mass spectrometery.

The toxic properties of tungsten compounds have recently been brought to the forefront with clusters of human cancer cases, such as in Fallon, NV. Such instances have made the determination of tungsten in natural water supplies vitally important. Tungsten exists in most environmental matrices as the soluble and mobile tungstate anion, although it can polymerize with itself and other anions, such as molybdate and phosphate. Because the geochemical and toxicological properties of these polymer species will vary from the monomeric tungstate parent, determination of tungstate speciation is as critical as determination of total dissolved tungsten concentration. Use of chromatographic separations, followed by element-specific detection is a proven technology for elemental speciation. In the present work, anion exchange chromatography has been coupled to inductively coupled plasma mass spectrometry to determine tungstate, molybdate, and phosphate species at the sub-microg l(-1) and microg l(-1) levels. The method provides quantitative determination of these species in about 10 min with the capability to simultaneously determine other oxyanion species. The method has been applied to groundwater and extracts of soils amended with tungsten powder. The water soluble tungsten in 1-h deionized water extracts after six months of soil aging was >15 mg l(-1), however, only approximately 50% of the tungsten was present as monomeric tungstate.

RDX loss in a surface soil under saturated and well drained conditions.

On military training ranges, low-order, incomplete detonations deposit RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) into surface soils. In this study, we evaluated RDX biodegradation in surface soils obtained from a military training range in Alaska. Two factors were compared: (i) soil water potential during the incubations; and (ii) the use of acetonitrile (ACN) as an RDX carrier to spike samples. Organic solvents have been used in laboratory studies to dissolve slightly water-soluble contaminants before addition to soil. We added ACN to obtain final soil ACN concentrations of 0 mg kg(-1) (0%), 1000 mg kg(-1) (0.1%) and 10 000 mg kg(-1) (1%). We then compared RDX attenuation in the soil under saturated and unsaturated conditions. RDX fell below the limit of detection within 3 wk of study initiation under the saturated condition. A maximum degradation rate of 0.15 mg RDX L(-1) d(-1) was measured. Under the unsaturated condition, 42% of the original RDX was still present at study termination (5 wk). The addition of acetonitrile at 0.1 or 1.0% had no affect on RDX loss in the saturated soil. In the unsaturated soil, however, ACN at 1.0% inhibited RDX loss by as much as 25%. These findings indicate that soil water potential and carrier solvent concentrations can impact the rate and extent to which RDX is attenuated in a surface soil.

Toxicity of sediment-associated nitroaromatic and cyclonitramine compounds to benthic invertebrates.

The toxicity of nitroaromatic (2,4-diaminonitrotoluene [2,4-DANT] and 1,3,5-trinitrobenzene [TNB]) and 14C-labeled cyclonitramine compounds (hexahydro-1,3,5-trinitro-1,3,5-triazine [RDX] and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine [HMX]) to the marine polychaete Neanthes arenaceodentata and the estuarine amphipod Leptocheirus plumulosus following 10- or 28-d exposures to spiked sediments was investigated. Organismal-level effects on survival, growth, and reproduction and cellular-level effects on apoptosis (programmed cell death) were evaluated. Because cyclonitramines have low affinity for sediment, overlying water was not exchanged in the RDX and HMX exposures. Nitroaromatics sorbed strongly to sediment, resulting in near complete resistance to solvent extraction. Cyclonitramines sorbed weakly to sediment, as more 14C-activity was found in the overlying water than in the sediment at exposure termination. No significant decrease in survival or growth was observed with cyclonitramines at initial sediment concentrations as high as 1,000 microg/g. Survival was significantly affected by nitroaromatics at nominal sediment concentrations as low as 200 microg/g, with L. plumulosus being more sensitive than N. arenaceodentata. Growth was significantly decreased at sublethal concentrations of 2,4-DANT for N. arenaceodentata. Reproduction, measured only with L. plumulosus, was significantly decreased only in the highest RDX treatment and also in the lower TNB treatment. However, no decrease was observed in higher concentrations of TNB. Body burden at exposure termination was below detection limit (1 microg/kg) for all compounds. Significant inhibition of apoptosis was not accompanied by significant decreases in growth or reproduction. Because of its critical function in many biological processes. alterations in this endpoint may result in adverse effects on the organism and could be used as an early indicator of toxicity.

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.

Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments.

Forty strains of Gram-positive, aerobic, heterotrophic bacteria isolated from saturated subsurface lacustrine, paleosol and fluvial sediments at the US Department of Energy's Hanford Site in south central Washington State were characterized by phylogenetic analysis of 16S rRNA gene sequences and by determination of selected morphological, physiological and biochemical traits. Phylogenetic analyses of 16S rDNA sequences from subsurface isolates in the context of similar sequences from previously described bacterial species indicated that 38 of the subsurface strains were most closely related to Arthrobacter: The other two strains appeared to be most closely related to Kocuria. The subsurface isolates fell into seven phylogenetically coherent and distinct clusters, indicating that there was a significant degree of diversity among them. Additional diversity was detected by analysis of cellular fatty acids and physiological traits. The general morphological, physiological and biochemical traits of the subsurface strains were consistent with those of Arthrobacter, Micrococcus and genera recently separated from Micrococcus, such as Kocuria. Some of the subsurface strains were phylogenetically closely related to certain species of Arthrobacter. (16S rDNA sequence similarities >99%). However, most of the subsurface isolates did not cluster with previously established species in phylogenetic analyses of 16S rRNA gene sequences or with hierarchical cluster analysis of cellular fatty acid profiles. Moreover, many of the subsurface isolates that were most closely related to Arthrobacter. also differed from all established species of that genus in several of their specific physiological characteristics. Most of the subsurface isolates, then, are likely to be novel strains or species of Arthrobacter.

Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer.

Microbial community composition associated with benzene oxidation under in situ Fe(III)-reducing conditions in a petroleum-contaminated aquifer located in Bemidji, Minn., was investigated. Community structure associated with benzene degradation was compared to sediment communities that did not anaerobically oxidize benzene which were obtained from two adjacent Fe(III)-reducing sites and from methanogenic and uncontaminated zones. Denaturing gradient gel electrophoresis of 16S rDNA sequences amplified with bacterial or Geobacteraceae-specific primers indicated significant differences in the composition of the microbial communities at the different sites. Most notable was a selective enrichment of microorganisms in the Geobacter cluster seen in the benzene-degrading sediments. This finding was in accordance with phospholipid fatty acid analysis and most-probable-number-PCR enumeration, which indicated that members of the family Geobacteraceae were more numerous in these sediments. A benzene-oxidizing Fe(III)-reducing enrichment culture was established from benzene-degrading sediments and contained an organism closely related to the uncultivated Geobacter spp. This genus contains the only known organisms that can oxidize aromatic compounds with the reduction of Fe(III). Sequences closely related to the Fe(III) reducer Geothrix fermentans and the aerobe Variovorax paradoxus were also amplified from the benzene-degrading enrichment and were present in the benzene-degrading sediments. However, neither G. fermentans nor V. paradoxus is known to oxidize aromatic compounds with the reduction of Fe(III), and there was no apparent enrichment of these organisms in the benzene-degrading sediments. These results suggest that Geobacter spp. play an important role in the anaerobic oxidation of benzene in the Bemidji aquifer and that molecular community analysis may be a powerful tool for predicting a site's capacity for anaerobic benzene degradation.

Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.

The genus Shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used to impart an additional layer of information. Molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA-DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specific PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition to the ten described Shewanella species, two new species, Shewanella oneidensis and 'Shewanella pealeana', were recognized; Shewanella oneidensis sp. nov. is described here for the first time.

Factors limiting microbial growth and activity at a proposed high-level nuclear repository, yucca mountain, nevada.

As part of the characterization of Yucca Mountain, Nev., as a potential repository for high-level nuclear waste, volcanic tuff was analyzed for microbial abundance and activity. Tuff was collected aseptically from nine sites along a tunnel in Yucca Mountain. Microbial abundance was generally low: direct microscopic cell counts were near detection limits at all sites (3.2 x 10(sup4) to 2.0 x 10(sup5) cells g(sup-1) [dry weight]); plate counts of aerobic heterotrophs ranged from 1.0 x 10(sup1) to 3.2 x 10(sup3) CFU g(sup-1) (dry weight). Phospholipid fatty acid concentrations (0.1 to 3.7 pmol g(sup-1)) also indicated low microbial biomasses; diglyceride fatty acid concentrations, indicative of dead cells, were in a similar range (0.2 to 2.3 pmol g(sup-1)). Potential microbial activity was quantified as (sup14)CO(inf2) production in microcosms containing radiolabeled substrates (glucose, acetate, and glutamic acid); amendments with water and nutrient solutions (N and P) were used to test factors potentially limiting this activity. Similarly, the potential for microbial growth and the factors limiting growth were determined by performing plate counts before and after incubating volcanic tuff samples for 24 h under various conditions: ambient moisture, water-amended, and amended with various nutrient solutions (N, P, and organic C). A high potential for microbial activity was demonstrated by high rates of substrate mineralization (as much as 70% of added organic C in 3 weeks). Water was the major limiting factor to growth and microbial activity, while amendments with N and P resulted in little further stimulation. Organic C amendments stimulated growth more than water alone.

Survival and phospholipid Fatty Acid profiles of surface and subsurface bacteria in natural sediment microcosms.

Although starvation survival has been characterized for many bacteria, few subsurface bacteria have been tested, and few if any have been tested in natural subsurface porous media. We hypothesized that subsurface bacteria may be uniquely adapted for long-term survival in situ. We further hypothesized that subsurface conditions (sediment type and moisture content) would influence microbial survival. We compared starvation survival capabilities of surface and subsurface strains of Pseudomonas fluorescens and a novel Arthrobacter sp. in microcosms composed of natural sediments. Bacteria were incubated for up to 64 weeks under saturated and unsaturated conditions in sterilized microcosms containing either a silty sand paleosol (buried soil) or a sandy silt nonpaleosol sediment. Direct counts, plate counts, and cell sizes were measured. Membrane phospholipid fatty acid (PLFA) profiles were quantified to determine temporal patterns of PLFA stress signatures and differences in PLFAs among strains and treatments. The Arthrobacter strains survived better than the P. fluorescens strains; however, differences in survival between surface and subsurface strains of each genus were not significant. Bacteria survived better in the paleosol than in the nonpaleosol and survived better under saturated conditions than under unsaturated conditions. Cell volumes of all strains decreased; however, sediment type and moisture did not influence rates of miniaturization. Both P. fluorescens strains showed PLFA stress signatures typical for gram-negative bacteria: increased ratios of saturated to unsaturated fatty acids, increased ratios of trans- to cis-monoenoic fatty acids, and increased ratios of cyclopropyl to monoenoic precursor fatty acids. The Arthrobacter strains showed few changes in PLFAs. Environmental conditions strongly influenced PLFA profiles.

Relating ground water and sediment chemistry to microbial characterization at a BTEX-contaminated site.

The National Center for Manufacturing Science is investigating bioremediation of petroleum hydrocarbon at a site near Belleville, MI. As part of this study, we examined the microbial communities to help elucidate biodegradative processes currently active at the site. We observed high densities of aerobic hydrocarbon degraders and denitrifiers in the less-contaminated sediments. Low densities of iron and sulfate reducers were measured in the same sediments. In contrast, the highly contaminated sediments showed low densities of aerobic hydrocarbon degraders and denitrifiers, and high densities of iron and sulfate reducers. Methanogens were also found in these highly contaminated sediments. These contaminated sediments also showed a higher biomass, by the phospholipid fatty acids, and greater ratios of phospholipid fatty acids, which indicate stress within the microbial community. Aquifer chemistry analyses indicated that the highly contaminated area was more reduced and had lower sulfate than the less-contaminated area. These conditions suggest that the subsurface environment at the highly contaminated area had progressed into sulfate reduction and methanogenesis. The less-contaminated area, although less reduced, also appeared to be progressing into primarily iron- and sulfate-reducing microbial communities. The proposed treatment to stimulate bioremediation includes addition of oxygen and nitrate to the subsurface. Ground water chemistry and microbial analyses revealed significant differences that resulted from the injection of dissolved oxygen and nitrate. These differences included an increase in Eh, small decrease in pH, and large decreases in BTEX, dissolved iron, and sulfate concentrations at the injection well. Injected nitrate was rapidly utilized by the subsurface microbial communities, and significant nitrite amounts were observed in the injection well and in nearby down-gradient observation wells. Microbial and molecular analyses indicated an increase in denitrifying bacteria after nitrate injection. The activity and population of denitrifying bacteria were significantly increased at the injection well relative to a down-gradient well for as long as 2 mo after the nitrate injection ended.

Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.

Phylogenetic analyses of 16S rRNA gene sequences by distance matrix and parsimony methods indicated that six strains of bacteria isolated from deep saturated Atlantic coastal plain sediments were closely related to the genus Sphingomonas. Five of the strains clustered with, but were distinct from, Sphingomonas capsulata, whereas the sixth strain was most closely related to Blastobacter natatorius. The five strains that clustered with S. capsulata, all of which could degrade aromatic compounds, were gram-negative, non-spore-forming, non-motile, rod-shaped organisms that produced small, yellow colonies on complex media. Their G + C contents ranged from 60.0 to 65.4 mol%, and the predominant isoprenoid quinone was ubiquinone Q-10. All of the strains were aerobic and catalase positive. Indole, urease, and arginine dihydrolase were not produced. Gelatin was not liquified, and glucose was not fermented. Sphingolipids were present in all strains; 2OH14:0 was the major hydroxy fatty acid, and 18:1 was a major constituent of cellular lipids. Acid was produced oxidatively from pentoses, hexoses, and disaccharides, but not from polyalcohols and indole. All of these characteristics indicate that the five aromatic-degrading strains should be placed in the genus Sphingomonas as currently defined. Phylogenetic analysis of 16S rRNA gene sequences, DNA-DNA reassociation values, BOX-PCR genomic fingerprinting, differences in cellular lipid composition, and differences in physiological traits all indicated that the five strains represent three previously undescribed Sphingomonas species. Therefore, we propose the following new species: Sphingomonas aromaticivorans (type strain, SMCC F199), Sphingomonas subterranea (type strain, SMCC B0478), and Sphingomonas stygia (type strain, SMCC B0712).

The genus Sphingomonas: physiology and ecology.

Exploitation of the metabolic capabilities of the genus Sphingomonas could provide important commercial benefits to biotechnology. Recent advances have demonstrated that these organisms have unique abilities to degrade refractory contaminants, to serve as bacterial antagonists to phytopathogenic fungi, and to secrete the highly useful gellan exopolysaccharides. Unfortunately, Sphingomonas are also animal pathogens and can readily degrade the copper pipes in drinking water distribution systems. The closely related Zymomonas could be important for commercial ethanol production. These Gram-negative aerobic bacteria are characterized by an outer membrane that contains glycosphingolipids, but lacks lipopolysaccharide. Their distribution in environmental samples has not been systematically examined as yet.

Aromatic-degrading Sphingomonas isolates from the deep subsurface.

An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southeast Coastal Plain subsurface sediments and shown to degrade toluene, naphthalene, and other aromatic compounds (J. K. Fredrickson, F. J. Brockman, D. J. Workman, S. W. Li, and T. O. Stevens, Appl. Environ. Microbiol. 57:796-803, 1991) was characterized by analysis of its 16S rRNA nucleotide base sequence and cellular lipid composition. Strain F199 contained 2-OH14:0 and 18:1 omega 7c as the predominant cellular fatty acids and sphingolipids that are characteristic of the genus Sphingomonas. Phylogenetic analysis of its 16S rRNA sequence indicated that F199 was most closely related to Sphingomonas capsulata among the bacteria currently in the Ribosomal Database. Five additional isolates from deep Southeast Coastal Plain sediments were determined by 16S rRNA sequence analysis to be closely related to F199. These strains also contained characteristic sphingolipids. Four of these five strains could also grow on a broad range of aromatic compounds and could mineralize [14C]toluene and [14C]naphthalene. S. capsulata (ATCC 14666), Sphingomonas paucimobilis (ATCC 29837), and one of the subsurface isolates were unable to grow on any of the aromatic compounds or mineralize toluene or naphthalene. These results indicate that bacteria within the genus Sphingomonas are present in Southeast Coastal Plain subsurface sediments and that the capacity for degrading a broad range of substituted aromatic compounds appears to be common among Sphingomonas species from this environment.