Loring Nies

Detection and Enumeration of Aromatic Oxygenase Genes by Multiplex and Real-Time PCR

ABSTRACT Our abilities to detect and enumerate pollutant-biodegrading microorganisms in the environment are rapidly advancing with the development of molecular genetic techniques. Techniques based on multiplex and real-time PCR amplification of aromatic oxygenase genes were developed to detect and quantify aromatic catabolic pathways, respectively. PCR primer sets were identified for the large subunits of aromatic oxygenases from alignments of known gene sequences and tested with genetically well-characterized strains. In all, primer sets which allowed amplification of naphthalene dioxygenase, biphenyl dioxygenase, toluene dioxygenase, xylene monooxygenase, phenol monooxygenase, and ring-hydroxylating toluene monooxygenase genes were identified. For each primer set, the length of the observed amplification product matched the length predicted from published sequences, and specificity was confirmed by hybridization. Primer sets were grouped according to the annealing temperature for multiplex PCR permitting simultaneous detection of various genotypes responsible for aromatic hydrocarbon biodegradation. Real-time PCR using SYBR green I was employed with the individual primer sets to determine the gene copy number. Optimum polymerization temperatures for real-time PCR were determined on the basis of the observed melting temperatures of the desired products. When a polymerization temperature of 4 to 5°C below the melting temperature was used, background fluorescence signals were greatly reduced, allowing detection limits of 2 × 102 copies per reaction mixture. Improved in situ microbial characterization will provide more accurate assessment of pollutant biodegradation, enhance studies of the ecology of contaminated sites, and facilitate assessment of the impact of remediation technologies on indigenous microbial populations.

Development of Catechol 2,3-Dioxygenase-Specific Primers for Monitoring Bioremediation by Competitive Quantitative PCR

ABSTRACT Benzene, toluene, xylenes, phenol, naphthalene, and biphenyl are among a group of compounds that have at least one reported pathway for biodegradation involving catechol 2,3-dioxygenase enzymes. Thus, detection of the corresponding catechol 2,3-dioxygenase genes can serve as a basis for identifying and quantifying bacteria that have these catabolic abilities. Primers that can successfully amplify a 238-bp catechol 2,3-dioxygenase gene fragment from eight different bacteria are described. The identities of the amplicons were confirmed by hybridization with a 238-bp catechol 2,3-dioxygenase probe. The detection limit was 102 to 103 gene copies, which was lowered to 100 to 101 gene copies by hybridization. Using the dioxygenase-specific primers, an increase in catechol 2,3-dioxygenase genes was detected in petroleum-amended soils. The dioxygenase genes were enumerated by competitive quantitative PCR with a 163-bp competitor that was amplified using the same primers. Target and competitor sequences had identical amplification kinetics. Potential PCR inhibitors that could coextract with DNA, nonamplifying DNA, soil factors (humics), and soil pollutants (toluene) did not impact enumeration. Therefore, this technique can be used to accurately and reproducibly quantify catechol 2,3-dioxygenase genes in complex environments such as petroleum-contaminated soil. Direct, non-cultivation-based molecular techniques for detecting and enumerating microbial pollutant-biodegrading genes in environmental samples are powerful tools for monitoring bioremediation and developing field evidence in support of natural attenuation.

Information and Communication Technology for Industrial Symbiosis

Industrial symbiosis describes the mutualistic interaction of different industries for beneficial reuse of waste flows or energy cascading that results in a more resource-efficient production system and fewer adverse environmental impacts. Research shows that many information and communication technology (ICT) tools for industrial symbiosis development have been created, but the results of those efforts are unclear. Drawing from advancements in knowledge-based economics and management, this article applies a knowledge-based framework to evaluate opportunities for ICT within industrial symbiosis development. ICT systems designed to enable industrial symbiosis are surveyed and evaluated within the proposed framework to identify strengths, trends, and opportunities for continued development. An appendix provides a capsule summary of the 17 ICT tools that are assessed in the article.

Response of Soil Microorganisms to As-Produced and Functionalized Single-Wall Carbon Nanotubes (SWNTs)

The use of single-wall carbon nanotubes (SWNTs) in manufacturing and biomedical applications is increasing at a rapid rate; however data on the effects of a potential environmental release of the materials remain sparse. In this study, soils with either low or high organic matter contents as well as pure cultures of E. coli are challenged with either raw as-produced SWNTs (AP-SWNTs) or SWNTs functionalized with either polyethyleneglycol (PEG-SWNTs) or m-polyaminobenzene sulfonic acid (PABS-SWNTs). To mimic chronic exposure, the soil systems were challenged weekly for six weeks; microbial activities and community structures for both the prokaryote and eukaryote community were evaluated. Results show that repeated applications of AP-SWNTs can affect microbial community structures and induce minor changes in soil metabolic activity in the low organic matter systems. Toxicity of the three types of SWNTs was also assessed in liquid cultures using a bioluminescent E. coli-O157:H7 strain. Although decreases in light were detected in all treated samples, low light recovery following glucose addition in AP-SWNTs treatment and light absorption property of SWNTs particles suggest that AP-SWNTs suppressed metabolic activity of the E. coli, whereas the two functionalized SWNTs are less toxic. The metals released from the raw forms of SWNTs would not play a role in the effects seen in soil or the pure culture. We suggest that sorption to soil organic matter plays a controlling role in the soil microbiological responses to these nanomaterials.

Environmental implications of nanomaterials: are we studying the right thing?

A fundamental lack of data on the potential impacts of carbon based nanomaterials on natural ecosystems currently exists. The gap between what we know about environmental impacts and new products that may contain nanomaterials continues to get wider especially related to knowledge about nanocomposites. In this paper we present ideas and concerns about the current state of knowledge on nanomaterials in the environment and present a number of points about what recent work has provided us about the novel materials.

Transformation of 17α-Estradiol, 17β-Estradiol, and Estrone in Sediments Under Nitrate- and Sulfate-Reducing Conditions

The natural manure-borne hormones, 17α-estradiol (17α-E2), 17β-estradiol (17β-E2), and estrone (E1), are routinely detected in surface water near agricultural land and wastewater treatment facilities. Once in the stream network, hormones may enter the sediment bed where they are subject to anaerobic conditions. This study focuses on the difference in anaerobic transformation rates and formation of metabolites from 17α-E2, 17β-E2, and E1 (applied at ∼3.66 μmol kg(-1) of sediment on a dry weight basis) under nitrate- and sulfate-reducing conditions. Sediment extracts were analyzed using negative electrospray ionization tandem mass spectrometry. Under both redox conditions, degradation was stereospecific and followed similar trends in half-lives, 17β-E2 < 17α-E2 < E1, with degradation considerably slower under sulfate-reducing conditions. Both E2 isomers were predominantly converted to E1; however, isomeric conversion also occurred with peak concentrations of ∼1.7 mol % of 17β-E2 formed in 17α-E2 amended sediments and peak concentrations of ∼2.4 mol % of 17α-E2 formed from 17β-E2. In E1-amended systems, E1 transformed to E2 with preferential formation of the more potent 17β isomer up to ∼30 mol % suggesting that isomer interconversion is through E1. Sediments, therefore, may serve as both a sink and a source of the more estrogenic compound E2. Transformation of amended hormones in autoclaved sediments was markedly slower than in nonautoclaved sediments. Results support the inclusion of isomer-specific behavior and the potential for reversible transformation and interconversion in anaerobic sediments in modeling fate in stream networks and developing risk management strategies.

Enumeration of aromatic oxygenase genes to evaluate biodegradation during multi-phase extraction at a gasoline-contaminated site

Multi-phase extraction (MPE) is commonly used at petroleum-contaminated sites to volatilize and recover hydrocarbons from the vadose and saturated zones in contaminant source areas. Although primarily a physical treatment technology, the induced subsurface air flow can potentially increase oxygen supply and promote aerobic biodegradation of benzene, toluene, ethylbenzene, and xylenes (BTEX), the contaminants of concern at gasoline-contaminated sites. In this study, real-time PCR enumeration of aromatic oxygenase genes and PCR-DGGE profiles were used to elucidate the impact of MPE operation on the aquifer microbial community structure and function at a gasoline-contaminated site. Prior to system activation, ring-hydroxylating toluene monooxygenase (RMO) and naphthalene dioxygenase (NAH) gene copies were on the order of 10(6) to 10(10)copies L(-1) in groundwater samples obtained from BTEX-impacted wells. Aromatic oxygenase genes were not detected in groundwater samples obtained during continuous MPE indicating decreased populations of BTEX-utilizing bacteria. During periods of pulsed MPE, total aromatic oxygenase gene copies were not significantly different than prior to system activation, however, shifts in aromatic catabolic genotypes were noted. The consistent detection of RMO, NAH, and phenol hydroxylase (PHE), which catabolizes further oxidation of hydroxylated BTEX metabolites indicated the potential for aerobic biodegradation of dissolved BTEX during pulsed MPE.

Aerobic biodegradation of 8:2 fluorotelomer stearate monoester and 8:2 fluorotelomer citrate triester in forest soil

Aerobic biodegradation of 8:2 fluorotelomer stearate (FTS) and 8:2 fluorotelomer citrate triester (TBC) was evaluated in a forest soil in closed bottle microcosms. Loss of parent, production of 8:2 fluorotelomer alcohol (8:2 FTOH), which is released along with stearic acid (SA) by microbial ester linkage, and subsequent metabolites from FTOH degradation were monitored for up to 7months. Soil microcosms were extracted with ethyl acetate followed by two heated 90/10 v/v acetonitrile/200mM NaOH extractions. Cleavage of the ester linkage in the 8:2 FTS occurred (t1/2∼28d), producing 8:2 FTOH and various levels of subsequent metabolites. Quantifying the generation of SA from ester cleavage in FTS was complicated by the natural production and degradation of SA in soil, which was probed in an additional FTS and SA study with the same soil that had been stored at 4°C for 12months. In the latter study, FTS degraded faster (t1/2∼5d) such that SA production well above soil background levels was clearly observed along with rapid subsequent SA degradation. Cold storage was hypothesized to enrich fungal enzymes, which are known to be effective at hydrolytic cleavage. 8:2 TBC biotransformation was slow, but evident with the production of PFOA well above levels expected from known FTOH residuals. Slower degradation of TBC compared to FTS is likely due to steric hindrances arising from the close proximity of three 8:2 FT chains on the citrate backbone limiting the enzyme access.

Broad substrate specificity of naphthalene-and biphenyl-utilizing bacteria

Abstract Although aromatic compounds are most often present in the environment as components of complex mixtures, biodegradation studies commonly focus on the degradation of individual compounds. The present study was performed to investigate the range of aromatic substrates utilized by biphenyl- and naphthalene-degrading environmental isolates and to ascertain the effects of co-occurring substrates during the degradation of mono-aromatic compounds. Bacterial strains were isolated on the basis of their ability to utilize either biphenyl or naphthalene as a sole source of carbon. Growth and transformation assays were conducted on each isolate to determine the range of substrates degraded. One isolate, Pseudomonas putida BP18, was tested for the ability to biodegrade benzene, toluene, ethylbenzene and xylene isomers (BTEX) individually and as components of mixtures. Overall, the results indicate that organisms capable of growth on multi-ring aromatic compounds may be particularly versatile in terms of aromatic hydrocarbon biodegradation. Furthermore, growth and transformation assays performed with strain BP18 suggest that the biodegradation of BTEX and biphenyl by this strain is linked to a catabolic pathway with overlapping specificities. The broad substrate specificity of these environmental isolates has important implications for bioremediation efforts in the field.

Microbial transformation of 8:2 fluorotelomer acrylate and methacrylate in aerobic soils

Biotransformation of fluorotelomer (FT) compounds, such as 8:2 FT alcohol (FTOH) is now recognized to be a source of perfluorooctanoic acid (PFOA) as well as other perfluoroalkyl acids. In this study, microbially mediated hydrolysis of FT industrial intermediates 8:2 FT acrylate (8:2 FTAC) and 8:2 FT methacrylate (8:2 FTMAC) was evaluated in aerobic soils for up to 105d. At designated times, triplicate microcosms were sacrificed by sampling the headspace for volatile FTOHs followed by sequential extraction of soil for the parent monomers as well as transient and terminal degradation products. Both FTAC and FTMAC were hydrolyzed at the ester linkage as evidenced by 8:2 FTOH production. 8:2 FTAC and FTMAC degraded rapidly with half-lives ⩽5d and 15d, respectively. Maximum 8:2 FTOH levels were 6-13mol% within 3-6d. Consistent with the known biotransformation pathway of 8:2 FTOH, FT carboxylic acids and perfluoroalkyl carboxylic acids were subsequently generated including up to 10.3mol% of PFOA (105d). A total mass balance (parent plus metabolites) of 50-75mol% was observed on the last sampling day. 7:2 sFTOH, a direct precursor to PFOA, unexpectedly increased throughout the incubation period. The likely, but unconfirmed, concomitant production of acrylic acids was proposed as altering expected degradation patterns. Biotransformation of 8:2 FTAC, 8:2 FTMAC, and previously reported 8:2 FT-stearate for the same soils revealed the effect of the non-fluorinated terminus group linked to the FT chain on the electronic differences that affect microbially-mediated ester cleavage rates.