Characterization of Microbial Activities and U Reduction in a Shallow Aquifer Contaminated by Uranium Mill Tailings

A characterization of the Shiprock, NM, uranium mill tailing site focused on the geochemical and microbiological factors governing in-situ uranium-redox reactions. Groundwater and aqueous extracts of sediment samples contained a wide concentration range of sulfate, nitrate, and U(VI) with median values of 21.2 mM, 16.1 µM, and 2.7 µM, respectively. Iron(III) was not detected in groundwater, but a median value of 0.3 mM in sediment extracts was measured. Bacterial diversity down gradient from the disposal pile reflected the predominant geochemistry with relatively high numbers of sulfate- and nitrate-reducing microorganisms, and smaller numbers of acetogenic, methanogenic, nitrate-dependent Fe(II)-oxidizing, Fe(III)-reducing, and sulfide-oxidizing bacteria. In aquifer slurry incubations, nitrate reduction was always preferred and had a negative impact on sulfate-, Fe(III)-, and U-reduction rates. We also found that sulfate-reduction rates decreased sharply in the presence of clay, while Fe(III)-reduction increased with no clear impact on U reduction. In the absence of clay, iron and sulfate reduction correlated with concentrations of Fe(III) and sulfate, respectively. Rates of U(VI) loss did not correlate with the concentration of any electron acceptor. With the exception of Fe(III), electron donor amendment was largely unsuccessful in stimulating electron acceptor loss over a 2-week incubation period, suggesting that endogenous forms of organic matter were sufficient to support microbial activity. Our findings suggest that efforts to accelerate biological U reduction should initially focus on stimulating nitrate removal.     

A Shallow BTEX and MTBE Contaminated Aquifer Supports a Diverse Microbial Community

Microbial communities in subsurface environments are poorly characterized and the impacts of anthropogenic contamination on their structure and function have not been adequately addressed. The release of contaminant(s) to a previously unexposed environment is often hypothesized to decrease the diversity of the affected community. We characterized the structure of microbial communities along a gradient of benzene, toluene, ethylbenzene, and xylene (BTEX) and methyl-tert-butyl-ether (MTBE) contamination, resulting from a petroleum spill, within a shallow sandy aquifer at Vandenberg Air Force Base (VAFB) in Lompoc, CA. Differences in microbial community composition along the contaminant plume were assessed via a combinatorial approach utilizing denaturing gradient gel electrophoresis (DGGE), cloning and sequencing, intergenic transcribed spacer analysis (ITS), and comparative phylogenetic analysis of partial 16S rDNA sequences. Substantial bacterial sequence diversity, similar levels of species richness, and similar phylo-groups (including the Cytophaga–Flavobacterium–Bacteroidetes group and numerous members of the -, -, -, -, and -groups of the proteobacteria) were observed in both uncontaminated and contaminated regions of the aquifer. High-resolution measures (ITS fingerprinting and phylogenetic inference) readily separated communities impacted by the original petroleum spill (in source zone) from those in other parts of the aquifer and indicated that communities exposed to MTBE only were similar to communities in uncontaminated regions. Collectively, these data suggest that petroleum contamination alters microbial community structure at the species and subspecies level. Further study is required to determine whether these changes have an impact on the functioning of this subsurface ecosystem.     

A Fatty Acid Messenger Is Responsible for Inducing Dispersion in Microbial Biofilms

It is well established that in nature, bacteria are found primarily as residents of surface-associated communities called biofilms. These structures form in a sequential process initiated by attachment of cells to a surface, followed by the formation of matrix-enmeshed microcolonies, and culminating in dispersion of the bacteria from the mature biofilm. In the present study, we have demonstrated that, during growth, Pseudomonas aeruginosa produces an organic compound we have identified as cis-2-decenoic acid, which is capable of inducing the dispersion of established biofilms and of inhibiting biofilm development. When added exogenously to P. aeruginosa PAO1 biofilms at a native concentration of 2.5 nM, cis-2-decenoic acid was shown to induce the dispersion of biofilm microcolonies. This molecule was also shown to induce dispersion of biofilms, formed by Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Streptococcus pyogenes, Bacillus subtilis, Staphylococcus aureus, and the yeast Candida albicans. Active at nanomolar concentrations, cis-2-decenoic acid appears to be functionally and structurally related to the class of short-chain fatty acid signaling molecules such as diffusible signal factor, which act as cell-to-cell communication molecules in bacteria and fungi.Biofilms are comprised of microorganisms enmeshed in a hydrated polymer matrix attached to a solid surface. Biofilm growth is a leading cause of materials damage, product quality degradation, and risk to public health. Bacterial biofilms are an important cause of chronic inflammatory and infectious diseases in plants and animals. In humans, biofilms have been implicated in chronic otitis media, native valve endocarditis, gastrointestinal ulcers, urinary tract and middle ear infections, and chronic lung infections in patients with cystic fibrosis (8, 11, 13, 15, 16, 29). Unfortunately, the control of biofilm growth and persistence has been problematic due to the enhanced resistance of biofilms to treatment with microbicides and antibiotics when compared to planktonic cells (30).Biofilm formation has been most intensively studied in the bacterium Pseudomonas aeruginosa, which has been shown to progress through multiple developmental stages, beginning with reversible attachment to a surface, followed by irreversible attachment and the development of microcolonies, which continue to grow to the final stage of development when dispersion occurs, releasing cells into the bulk liquid (27, 32). Bacteria have been shown to display unique phenotypes at each stage of biofilm development and possess properties that are markedly different from planktonic cells of the same species (27, 28, 32, 33, 36, 38). As a behavioral characteristic of bacteria, biofilm dispersion is of major significance because of its promise to provide a mechanism for the control of the growth and persistence of biofilms, particularly in household, medical, and industrial settings.The search for an extracellular signal responsible for biofilm dispersion has uncovered a range of factors that have been shown to stimulate biofilm disruption. In 2000, Chen and Stewart (6) reported that reactive chemicals (e.g., NaCl, CaCl₂, hypochlorite, monochloramine, and concentrated urea), chelating agents, surfactants (e.g., sodium dodecyl sulfate, Tween 20, and Triton X-100), and lysozyme, as well as a number of antimicrobial agents, when added to mixed biofilms of P. aeruginosa and Klebsiella pneumoniae, resulted in the removal of more than 25% of protein from the surface, indicating cell release from the biofilms. Sauer et al. (27) have shown that a sudden increase in the concentration of organic carbon causes bacteria to disaggregate from a biofilm. Thormann et al. (33) reported that a rapid reduction in oxygen could induce biofilm dispersion after cessation of flow in an oxygen-limited growth medium. Other studies have shown that starvation may be a trigger for dispersion (14), that a prophage in P. aeruginosa may mediate cell death and provide a vehicle for cell cluster disaggregation (37), and that nitric oxide may play a role in the biofilm dispersion process (3). Finally, the chelator EDTA has been shown to induce killing and dispersion in P. aeruginosa biofilms (1). Although the mechanism of dispersion induction is unknown in these cases, a common thread throughout these studies is that they induce major perturbations of cellular metabolism and likely also activate stress regulons, which may be involved in biofilm dispersion.The identification of a cell-to-cell communication molecule responsible for biofilm dispersion has been the focus of a number of researchers over the past decade. Recently, indole has been shown to act as an intercellular messenger, inhibiting biofilm formation in Escherichia coli but enhancing biofilm formation in P. aeruginosa (19, 20). To date, however, indole has not been shown to activate a dispersion response in existing biofilms. Rice et al. (23) described a limited role for N-butanoyl-l-homoserine lactone in modulating detachment, or sloughing, of Serratia marcescens; however, the role of quorum-sensing molecules in biofilm dispersion remains controversial. Dow et al. (10) have characterized a substituted fatty acid messenger, cis-11-methyl-2-dodecenoic acid, called diffusible signal factor (DSF), recovered from Xanthomonas campestris and shown it to be responsible for virulence, as well as induction of the release of endo-β-1,4-mannanase. Intriguingly, DSF was shown to be able to disaggregate cell flocs formed in broth culture by X. campestris, although no activity against extracellular xanthan was detected (10).In the present study we demonstrate that an unsaturated fatty acid, cis-2-decenoic acid, produced by P. aeruginosa both in batch and biofilm cultures is responsible for inducing a dispersion response in biofilms formed by a range of gram-negative bacteria, including P. aeruginosa, and by gram-positive bacteria. Furthermore, cis-2-decenoic acid was also capable of inducing dispersion in biofilms of Candida albicans, indicating that this molecule has cross-kingdom functional activity.     

Distribution of Microbial Physiologic Types in an Aquifer Contaminated by Crude Oil

Abstract We conducted a plume-scale study of the microbial ecology in the anaerobic portion of an aquifer contaminated by crude-oil compounds. The data provide insight into the patterns of ecological succession, microbial nutrient demands, and the relative importance of free-living versus attached microbial populations. The most probable number (MPN) method was used to characterize the spatial distribution of six physiologic types: aerobes, denitrifiers, iron-reducers, heterotrophic fermenters, sulfate-reducers, and methanogens. Both free-living and attached numbers were determined over a broad cross-section of the aquifer extending horizontally from the source of the plume at a nonaqueous oil body to 66 m downgradient, and vertically from above the water table to the base of the plume below the water table. Point samples from widely spaced locations were combined with three closely spaced vertical profiles to create a map of physiologic zones for a cross-section of the plume. Although some estimates suggest that less than 1% of the subsurface microbial population can be grown in laboratory cultures, the MPN results presented here provide a comprehensive qualitative picture of the microbial ecology at the plume scale. Areas in the plume that are evolving from iron-reducing to methanogenic conditions are clearly delineated and generally occupy 25–50% of the plume thickness. Lower microbial numbers below the water table compared to the unsaturated zone suggest that nutrient limitations may be important in limiting growth in the saturated zone. Finally, the data indicate that an average of 15% of the total population is suspended. Received: 28 October 1998; Accepted: 26 February 1999     

Development of a Microbial Consortium from a Contaminated Soil That Degrades Pentachlorophenol and Wood-Preserving Oil

An indigenous microbial consortium capable of degrading pentachlorophenol (PCP) and petroleum hydrocarbons (C₁₀-C₅₀) was produced from a soil contaminated with wood-preserving oil. Two 10-L stainless steel soil slurry (10% w/v) bioreactors were operated in fed-batch mode. To verify the growth and efficiency of PCP degraders in the presence of other contaminants, one bioreactor was fed with a PCP-based wood-preserving mixture (WPM) and a second reactor was fed with technical-grade NaPCP. During the 90-day period of activation, PCP, C₁₀-C₅₀, Cl^-, pH, and dissolved oxygen levels were monitored. The microbial community was monitored using specific most probably number (MPN) bacterial counts and mineralization tests. PCP degradation rates increased similarly in both reactors, from 19 to 132 mg/L-d in the NaPCP reactor, and from 41 to 112 mg/L-d in the WPM reactor. Contaminant loss calculations showed that 99.5% of PCP and 92.5% of C₁₀-C₅₀ added to the WPM reactor were biodegraded. It also revealed that 83% of polychlorinated dioxins and furans were removed. PCP-degrading bacteria increased from 7×10² to 1.6×10⁶ bacteria/mL in both reactors, and petroleum hydrocarbon degraders increased from 1.7×102 to 3.4×108 bacteria/mL in the WPM reactor, indicating that the activity of PCP degraders was not inhibited by the presence of microorganisms growing on petroleum hydrocarbons.     

Limited Entry of Adenovirus Vectors into Well-Differentiated Airway Epithelium Is Responsible for Inefficient Gene Transfer

Investigations of the efficiency and safety of human adenovirus vector (AdV)-mediated gene transfer in the airways of patients with cystic fibrosis (CF) in vivo have demonstrated little success in correcting the CF bioelectrical functional defect, reflecting the inefficiency of AdV-mediated gene transfer to the epithelial cells that line the airway luminal surface. In this study, we demonstrate that low AdV-mediated gene transfer efficiency to well-differentiated (WD) cultured airway epithelial cells is due to three distinct steps in the apical membrane of the airway epithelial cells: (i) the absence of specific adenovirus fiber-knob protein attachment receptors; (ii) the absence of α_vβ_3/5 integrins, reported to partially mediate the internalization of AdV into the cell cytoplasm; and (iii) the low rate of apical plasma membrane uptake pathways of WD airway epithelial cells. Attempts to increase gene transfer efficiency by increasing nonspecific attachment of AdV were unsuccessful, reflecting the inability of the attached vector to enter (penetrate) WD cells via nonspecific entry paths. Strategies to improve the efficiency of AdV for the treatment of CF lung disease will require methods to increase the attachment of AdV to and promote its internalization into the WD respiratory epithelium.     

A Review of Processes Responsible for Metal Removal in Wetlands Treating Contaminated Mine Drainage

Many reports have documented wetlands removing a wide variety of contaminants in mine drainage, including aluminum, arsenic, cadmium, cobalt, copper, cyanide, iron, lead, manganese, nickel, selenium, uranium, and zinc. This article reviews biogeochemical processes responsible for their ability to transform and retain metals into insoluble forms. Shallow depth and large inputs of organic matter are key characteristics of wetlands that promote chemical and biological processes effecting metal removal. Aquatic macrophytes play an essential role in creating and maintaining this environment, but their uptake of metals usually accounts for a minor proportion of the total mass removed. Sorption onto organic matter is important in metal removal, particularly for copper, nickel, and uranium. Aluminum, iron, and manganese are often removed by hydrolysis, with the resulting acidification of water buffered by alkalinity produced in wetland sediments by anaerobic bacteria. Bacterial sulfate reduction accounts for much of this alkalinity. It can also contribute significantly to metal removal by formation of insoluble sulfides. Other important processes include the formation of insoluble carbonates, reduction to nonmobile forms, and adsorption onto iron oxides and hydroxides. Examples from field studies are presented throughout the review to illustrate these processes.     

Metabolic Commensalism and Competition in a Two-Species Microbial Consortium

We analyzed metabolic interactions and the importance of specific structural relationships in a benzyl alcohol-degrading microbial consortium comprising two species, Pseudomonas putida strain R1 and Acinetobacter strain C6, both of which are able to utilize benzyl alcohol as their sole carbon and energy source. The organisms were grown either as surface-attached organisms (biofilms) in flow chambers or as suspended cultures in chemostats. The numbers of CFU of P. putida R1 and Acinetobacter strain C6 were determined in chemostats and from the effluents of the flow chambers. When the two species were grown together in chemostats with limiting concentrations of benzyl alcohol, Acinetobacter strain C6 outnumbered P. putida R1 (500:1), whereas under similar growth conditions in biofilms, P. putida R1 was present in higher numbers than Acinetobacter strain C6 (5:1). In order to explain this difference, investigations of microbial activities and structural relationships were carried out in the biofilms. Insertion into P. putida R1 of a fusion between the growth rate-regulated rRNA promoter rrnBP1 and a gfp gene encoding an unstable variant of the green fluorescent protein made it possible to monitor the physiological activity of P. putida R1 cells at different positions in the biofilms. Combining this with fluorescent in situ hybridization and scanning confocal laser microscopy showed that the two organisms compete or display commensal interactions depending on their relative physical positioning in the biofilm. In the initial phase of biofilm development, the growth activity of P. putida R1 was shown to be higher near microcolonies of Acinetobacter strain C6. High-pressure liquid chromatography analysis showed that in the effluent of the Acinetobacter strain C6 monoculture biofilm the metabolic intermediate benzoate accumulated, whereas in the biculture biofilms this was not the case, suggesting that in these biofilms the excess benzoate produced by Acinetobacter strain C6 leaks into the surrounding environment, from where it is metabolized by P. putida R1. After a few days, Acinetobacter strain C6 colonies were overgrown by P. putida R1 cells and new structures developed, in which microcolonies of Acinetobacter strain C6 cells were established in the upper layer of the biofilm. In this way the two organisms developed structural relationships allowing Acinetobacter strain C6 to be close to the bulk liquid with high concentrations of benzyl alcohol and allowing P. putida R1 to benefit from the benzoate leaking from Acinetobacter strain C6. We conclude that in chemostats, where the organisms cannot establish in fixed positions, the two strains will compete for the primary carbon source, benzyl alcohol, which apparently gives Acinetobacter strain C6 a growth advantage, probably because it converts benzyl alcohol to benzoate with a higher yield per time unit than P. putida R1. In biofilms, however, the organisms establish structured, surface-attached consortia, in which heterogeneous ecological niches develop, and under these conditions competition for the primary carbon source is not the only determinant of biomass and population structure.     

Kinetics of Sulfate Reduction in a Coastal Aquifer Contaminated with Petroleum Hydrocarbons

An integrated field and laboratory study was conducted to quantify the effect of environmental determinants on the activity of sulfate reducers in a freshwater aquifer contaminated with petroleum hydrocarbons (PHC). Within the contaminated zone, PHC-supported in␣situ sulfate reduction rates varied from 11.58±3.12 to 636±53 nmol cm⁻³ d⁻¹ and a linear increase (R ²=0.98) in reduction rate was observed with increasing in situ sulfate concentrations suggesting sulfate limitation. Half-saturation concentration (K _s) for sulfate reduction coupled to PHC mineralization was determined for the first time. At two different sites within the␣aquifer, maximum sulfate reduction rate under␣non-limiting conditions (R _max) was 5,000 nmol cm⁻³ d⁻¹, whereas the retrieved K _s values were 3.5 and 7.5 mM, respectively. The K _s values are the highest ever reported from a natural environment. Furthermore, the K _s values were significantly higher than in situ sulfate concentrations confirming sulfate limited growth. On addition of lactate and formate, sulfate reduction rate increased indicating that reactivity and bioavailability of organic substrate may also have played a role in rate inhibition in certain parts of the aquifer. Experiments with sulfide amendments show statistically minor decrease in sulfate reduction rates on addition of sulfide and analogous increase in sulfide toxicity with increasing sulfide concentrations (0.5–10 mM) was not apparent.     

Enhanced Biodegradation of Methyl tert-butyl-ether by a Microbial Consortium

The widespread use of Methyl tert-butyl-ether (MTBE) as a gasoline additive has resulted in a higher detection rate of MTBE in groundwater systems. Therefore, the researchers show more concern about the bioremediation of MTBE-impacted aquifers. In this paper, a MTBE-direct-degrading bacterial consortium was enriched (named RS1) and further studied. In order to identify the microbial community of the consortium, 17 and 12 different single strains were isolated from nutrient medium and MSM media (with MTBE as the sole carbon source), respectively. 16S rDNA-based phylogenetic analysis revealed that these diverse bacteria belonged to 14 genera, in which Pseudomonas was dominant. Several strains which can grow with MTBE as the sole carbon and energy source were also identified, such as M1, related to MTBE-degrading Arthrobacter sp. ATCC27778. Furthermore, the appropriate addition of certain single strain in consortium RS1 (M1:RS1 = 1:2) facilitates MTBE degradation by increasing the quantity of efficient MTBE-degrading bacteria. This work will provide microbial source and theoretical fundament for further bioremediation of MTBE-contaminated aquifers, which has applied potential and environmental importance.     

Augmentation of a Microbial Consortium for Enhanced Polylactide (PLA) Degradation

Bioplastics are eco-friendly and derived from renewable biomass sources. Innovation in recycling methods will tackle some of the critical issues facing the acceptance of bioplastics. Polylactic acid (PLA) is the commonly used and well-studied bioplastic that is presumed to be biodegradable. Considering their demand and use in near future, exploration for microbes capable of bioplastic degradation has high potential. Four PLA degrading strains were isolated and identified as Penicillium chrysogenum, Cladosporium sphaerospermum, Serratia marcescens and Rhodotorula mucilaginosa. A consortium of above strains degraded 44 % (w/w) PLA in 30 days time in laboratory conditions. Subsequently, the microbial consortium employed effectively for PLA composting.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-015-0559-z) contains supplementary material, which is available to authorized users.     

Microbial Diversity in a Hydrocarbon- and Chlorinated-Solvent-Contaminated Aquifer Undergoing Intrinsic Bioremediation

A culture-independent molecular phylogenetic approach was used to survey constituents of microbial communities associated with an aquifer contaminated with hydrocarbons (mainly jet fuel) and chlorinated solvents undergoing intrinsic bioremediation. Samples were obtained from three redox zones: methanogenic, methanogenic-sulfate reducing, and iron or sulfate reducing. Small-subunit rRNA genes were amplified directly from aquifer material DNA by PCR with universally conserved or Bacteria- or Archaea-specific primers and were cloned. A total of 812 clones were screened by restriction fragment length polymorphisms (RFLP), approximately 50% of which were unique. All RFLP types that occurred more than once in the libraries, as well as many of the unique types, were sequenced. A total of 104 (94 bacterial and 10 archaeal) sequence types were determined. Of the 94 bacterial sequence types, 10 have no phylogenetic association with known taxonomic divisions and are phylogenetically grouped in six novel division level groups (candidate divisions WS1 to WS6); 21 belong to four recently described candidate divisions with no cultivated representatives (OP5, OP8, OP10, and OP11); and 63 are phylogenetically associated with 10 well-recognized divisions. The physiology of two particularly abundant sequence types obtained from the methanogenic zone could be inferred from their phylogenetic association with groups of microorganisms with a consistent phenotype. One of these sequence types is associated with the genus Syntrophus; Syntrophus spp. produce energy from the anaerobic oxidation of organic acids, with the production of acetate and hydrogen. The organism represented by the other sequence type is closely related to Methanosaeta spp., which are known to be capable of energy generation only through aceticlastic methanogenesis. We hypothesize, therefore, that the terminal step of hydrocarbon degradation in the methanogenic zone of the aquifer is aceticlastic methanogenesis and that the microorganisms represented by these two sequence types occur in syntrophic association.     

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.     

OsNRAMP3 Is a Vascular Bundles-Specific Manganese Transporter That Is Responsible for Manganese Distribution in Rice

Manganese (Mn) is an essential trace element for plants. Recently, the genes responsible for uptake of Mn in plants were identified in Arabidopsis and rice. However, the mechanism of Mn distribution in plants has not been clarified. In the present study we identified a natural resistance-associated macrophage protein (NRAMP) family gene in rice, OsNRAMP3, involved in Mn distribution. OsNRAMP3 encodes a plasma membrane-localized protein and was specifically expressed in vascular bundles, especially in phloem cells. Yeast complementation assay showed that OsNRAMP3 is a functional Mn-influx transporter. When OsNRAMP3 was absent, rice plants showed high sensitivity to Mn deficiency. Serious necrosis appeared on young leaves and root tips of the OsNRAMP3 knockout line cultivated under low Mn conditions, and high Mn supplies could rescue this phenotype. However, the necrotic young leaves of the knockout line possessed similar levels of Mn to the wild type, suggesting that the necrotic appearance was caused by disturbed distribution of Mn but not a general Mn shortage. Additionally, compared with wild type, leaf Mn content in osnramp3 plants was mostly in older leaves. We conclude that OsNRAMP3 is a vascular bundle-localized Mn-influx transporter involved in Mn distribution and contributes to remobilization of Mn from old to young leaves.     

Structure of a Natural Microbial Community in a Nitroaromatic Contaminated Groundwater Is Altered during Biodegradation of Extrinsic,but Not Intrinsic Substrates

A BSTRACTThis study demonstrates microbial community changes over time in a nitroaromatic-contaminated groundwater upon amendment with hydrocarbons previously unknown to the microbial community (extrinsic) and hydrocarbons previously known to the microbial community (intrinsic). Sealed flasks, shaken and incubated at 25 degrees C, containing contaminated groundwater and salts were amended twice with extrinsic hydrocarbons including phenol, benzoic acid, and naphthalene, and intrinsic hydrocarbons including 2,4-dinitrotoluene (2,4-DNT) and para-nitrotoluene ( p-NT). Microbial growth, biodegradation, and community structure changes measured by random amplified polymorphic DNA (RAPD) and quantitative PCR (qPCR) targeting catechol-2,3-dioxygenase (C23O) genes were monitored over time. All amended substrates were biodegraded after both substrate amendments except for 2,4-DNT, which was only partially degraded after the second amendment. Unique microbial communities were developed in flasks amended with phenol, benzoic acid, and naphthalene. However, in the flasks amended with intrinsic hydrocarbons the microbial community remained similar to the unamended control flasks. The relative amount of C23O genes detected by qPCR correlated with the biodegradation of phenol and naphthalene but not with 2,4-DNT. The results showed that a selection for microorganisms capable of catabolizing extrinsic hydrocarbons naturally and initially present in the nitroaromatic-contaminated groundwater occurred. However, growth-linked biodegradation of added intrinsic hydrocarbons was not selective.     

Acetaldehyde Is a Causal Agent Responsible for Ethanol-Induced Ripening Inhibition in Tomato Fruit

Inhibition of tomato (Lycopersicon esculentum Mill.) fruit ripening by exogenously applied ethanol was shown to be caused by elevated endogenous levels of acetaldehyde (AA). Exposure of excised pericarp discs of mature-green tomato fruit to ethanol or AA vapors produced elevated levels of both compounds in the tissue, but only the levels of AA were associated with ripening inhibition. Ripening inhibition was dependent on both the applied concentration and the duration of exposure. Discs treated with inhibitory levels of AA had levels of ethanol that were elevated but below that associated with inhibition of ripening. The in vivo activity of alcohol dehydrogenase was inhibited 40 to 60% by 4-methylpyrazole (4-MP), a competitive inhibitor of this enzyme. The inhibitory effect of ethanol on ripening was reduced by the simultaneous application of 4-MP. Tissue treated with 4-MP plus AA vapors had higher endogenous levels of AA and ripening was inhibited longer than in tissue without 4-MP. The tissue AA level resulting from ethanol or AA application appears to be the critical determinant of ripening inhibition.     

Carbon Source Utilization Profiles for Microbial Communities from Hydrologically Distinct Zones in a Basalt Aquifer

Abstract The Eastern Snake River Plain aquifer has hydrologically distinct zones in basalt flow units and interbedded sediments. The zones that differ markedly in physical features (e.g., porosity and permeability) have similar groundwater chemistries. The primary objective of this study was to determine whether intervals within the aquifer that contrast on the basis of permeability have distinct communities of unattached microorganisms based on functional attributes. Aquifer sampling was conducted using a submersible pump to obtain whole-well (w) samples, and a straddle-packer pump (SPP) to obtain samples from specific aquifer intervals that were vertically distributed in the open borehole. The SPP intervals ranged from 4.6 to 6.1 m in length and were located from 142 to 198 m below land surface. A community-level physiological profile (CLPP) was used to determine functional characteristics of the microbial community in the groundwater samples based on the community response to 95 sole organic carbon sources. Surface soil samples at the site were analyzed in a similar manner for comparison. The total bacterial population in the groundwater samples was determined using acridine orange direct counts. Principal components analysis (PCA) of the CLPP dataset distinguished between surface soil and aquifer microbial communities. Soils scored low in the respiration of polymers, esters, and amines and high in bromosuccinate, when compared to aquifer samples. The W samples were distinct from SPP samples. The 180- to 198-m interval, with the lowest hydraulic conductivity of all intervals, yielded samples that grouped together by PCA and cluster analysis. Direct counts varied between 10⁴ and 10⁵ cells ml⁻¹, and showed no relationship to the depth of the sample or to the hydraulic conductivity of the sample interval. Differences between microbial communities based on respired carbon compounds were discerned in separate, hydrologically distinct intervals within the borehole, although these differences were slight. Differences among aquifer intervals were less apparent than differences between surface soils and groundwater, and may be related to variations in hydrologic properties over the intervals sampled. The results suggest that free-living microbial communities in basalt aquifers, as characterized by CLPP are relatively unaffected by wide ranges in hydraulic conductivity when other abiotic factors are essentially equal. Received: 14 December 1995; Revised: 12 April 1996