Assessment of PCB contamination, the potential for in situ microbial dechlorination and natural attenuation in an urban watershed at the East Coast of the United States

Sediment contamination is a major environmental issue in many urban watersheds and coastal areas due to the potential toxic effects of contaminants on biota and human health. Characterizing and delineating areas of sediment contamination and toxicity are important goals of coastal resource management in terms of ecological and economical perspectives. Core and surficial sediment samples were collected from an industrialized urban watershed at the East Coast of the United Stated and analyzed to evaluate the PCB contamination profile and toxicity resulting from dioxin-like PCBs as well as reductive dechlorination potential of indigenous PCB halorespiring bacteria through dechlorination activity assays. To support the experimental results an anaerobic dechlorination model was applied to identify microbial dechlorination pathways. The total PCB concentration in core samples ranged from 3.9 to 225.6 ng/g·dry weight (dw) decreasing with depth compared to 353.2 to 1213.7 ng/g·dw in surficial samples. The results of this study indicated an increase in PCB contamination over the last century as the industrial activity intensified. The toxicity resulting from dioxin-like PCBs was reduced up to 94% in core samples via 21 pathways resulting from the dechlorination model. Dechlorination rates in surficial sediment were between 1.8 and 13.2 · 10^-3 mol% PCB116/day, while lower rates occurred in the core sediment samples. Dechlorination was achieved mainly through meta followed by para dechlorination. However, the rarer ortho dechlorination was also observed. Detection of indigenous PCB dechlorinating bacteria in the sediments and reduction of toxicity indicated potential for natural attenuation when point and nonpoint source PCBs in the urban watershed are controlled and PCB loading reduced.

Kinetics of PCB Microbial Dechlorination Explained by Freely Dissolved Concentration in Sediment Microcosms

While microbial dechlorination of polychlorinated biphenyls (PCBs) has been observed in sediments over the last 3 decades, translation to the field has been difficult due to a lack of a clear understanding of the kinetic limitations. To address this issue, the present study used passive dosing/sampling to accurately measure the biological rate of dechlorination of 2,3,4,5-tetrachlorobiphenyl (PCB 61) to 2,3,5-trichlorobiphenyl (PCB 23) by an organohalide-respiring bacterium, Dehalobium chlorocoercia (DF-1). The biological rates were measured over an environmentally relevant concentration range of 1-50 ng/L of freely dissolved concentrations with and without the presence of sediment in bench-scale microcosm studies. The rate of dechlorination was found to be linearly dependent on the freely dissolved concentration of PCB 61 both in sediment and in sediment-free microcosms. The observed rate of dechlorination in sediment microcosms could be predicted within a factor of 2 based on the kinetics measured in sediment-free microcosms. A threshold for dechlorination was not observed down to an aqueous concentration of about 1 ng/L PCB 61. We demonstrate that with the combination of an accurate measurement of the aqueous-phase dechlorination kinetics and an understanding of the site-specific partitioning characteristics, it is possible to predict PCB microbial dechlorination in sediments.

A Pilot-Scale Field Study: In Situ Treatment of PCB-Impacted Sediments with Bioamended Activated Carbon

A combined approach involving microbial bioaugmentation and enhanced sorption was demonstrated to be effective for in situ treatment of polychlorinated biphenyls (PCBs). A pilot study was conducted for 409 days on PCB impacted sediments in four 400 m² plots located in a watershed drainage pond in Quantico, VA. Treatments with activated carbon (AC) agglomerate bioamended with PCB dechlorinating and oxidizing bacteria decreased the PCB concentration in the top 7.5 cm by up to 52% and the aqueous concentrations of tri- to nonachlorobiphenyl PCB congeners by as much as 95%. Coplanar congeners decreased by up to 80% in sediment and were undetectable in the porewater. There was no significant decrease in PCB concentrations in non-bioamended plots with or without AC. All homologue groups decreased in bioamended sediment and porewater, indicating that both anaerobic dechlorination and aerobic degradation occurred concurrently. The titer of the bioamendments based on quantitative PCR of functional marker genes decreased but were still detectable after 409 days, whereas indigenous microbial diversity was not significantly different between sites, time points, or depths, indicating that bioaugmentation and the addition of activated carbon did not significantly alter total microbial diversity. In situ treatment of PCBs using an AC agglomerate as a delivery system for bioamendments is particularly well-suited for environmentally sensitive sites where there is a need to reduce exposure of the aquatic food web to sediment-bound PCBs with minimal disruption to the environment.

Colonization and growth of dehalorespiring biofilms on carbonaceous sorptive amendments

Removal of polychlorinated biphenyls (PCBs) from contaminated sediments is a priority due to accumulation in the food chain. Recent success with reduction of PCB bioavailability due to adsorption onto activated carbon led to the recognition of in situ treatment as a remediation approach. In this study, reduced bioavailability and subsequent break-down of PCBs in dehalorespiring biofilms was investigated using Dehalobium chlorocoercia DF1. DF1 formed a patchy biofilm ranging in thickness from 3.9 to 6.7 µm (average 4.6 ± 0.87 µm), while the biofilm coverage varied from 5.5% (sand) to 20.2% (activated carbon), indicating a preference for sorptive materials. Quantification of DF1 biofilm bacteria showed 1.2-15.3 × 10⁹ bacteria per gram of material. After 22 days, coal activated carbon, bone biochar, polyoxymethylene, and sand microcosms had dechlorinated 73%, 93%, 100%, and 83%, respectively. These results show that a biofilm-based inoculum for bioaugmentation of PCBs in sediment can be an efficient approach.

A comparative evaluation of anaerobic dechlorination of PCB-118 and Aroclor 1254 in sediment microcosms from three PCB-impacted environments

Aroclor 1254 (A1254) is the most toxic commercial PCB mixture produced, primarily due to its relatively high concentrations of dioxin-like congeners. This study demonstrates a comparative evaluation of dechlorination of A1254 and PCB-118 by indigenous organohalide respiring bacteria enriched from three PCB impacted sites: Grasse River (GR), NY; Fox River (FR), WI; and Baltimore Harbor (BH), MD. PCB-118 dechlorination rates in GR, BH, and FR was 0.0308, 0.015, and 0.0006 Cl^-/biphenyl/day, respectively. A1254 dechlorination rates in GR, FR, and BH were 0.0153, 0.0144, and 0.0048 Cl^-/biphenyl/day, respectively. A1254 dechlorination was achieved through the removal of doubly-/singly-flanked chlorines in meta and para positions of mostly penta- followed by hexa- and hepta-chlorinated congeners by 88%, 69%, and 51% in GR, and 88%, 87%, and 83% in FR, respectively, while in BH mostly hepta- (70%) followed by hexa-chlorinated congeners (66%) were dechlorinated. A previously developed Anaerobic Dechlorination Model (ADM) quantified a total of 17 toxicity-related dechlorination pathways in all three sediment microcosms. The toxic equivalency of A1254 based on seven dioxin-like congeners decreased by about 53%, 45% and 21%, in GR, FR and BH microcosms, respectively. The dechlorination products were generally tetra- and tri-chlorinated congeners with unflanked chlorines, all of which is susceptible to further degradation by aerobic bacteria. Concerning the toxic congeners, ADM can be useful to initiate further research focusing on the stimulation of the toxicity reducing pathways for risk assessment and effective remediation strategies.

Mesocosm Studies on the Efficacy of Bioamended Activated Carbon for Treating PCB-Impacted Sediment

This report describes results of a bench-scale treatability study to evaluate the efficacy of bioaugmentation with bioamended activated carbon (AC) for in situ treatment of polychlorinated biphenyl (PCB) impacted sediments. To this end, the ability of PCB transforming microorganisms to degrade and reduce the overall concentration of PCBs in sediment was determined in 2 L recirculating mesocosms designed to simulate conditions in Abraham's Creek in Quantico, Virginia. Ten sediment mesocosms were tested for the effects of AC alone, AC with slow release electron donor (cellulose) and different concentrations and combinations of PCB dehalogenating and degrading microorganisms added as bioamendments. A 78% reduction of total PCBs was observed using a cell titer of 5 × 10⁵ Dehalobium chlorocoercia and Paraburkholderia xenovorans cells g^-1 sediment with 1.5% AC as a delivery system. Levels of both higher and lower chlorinated congeners were reduced throughout the sediment column indicating that both anaerobic reductive dechlorination and aerobic degradation occurred concurrently. Porewater concentrations of all PCB homologues were reduced 94-97% for bioaugmented treatments. Toxicity associated with coplanar PCBs was reduced by 90% after treatment based on toxic equivalency of dioxin-like congeners. These results suggest that an in situ treatment employing the simultaneous application of anaerobic and aerobic microorganisms on AC could be an effective, environmentally sustainable strategy to reduce PCB levels in contaminated sediment.

Potential risk reduction of Aroclor 1254 by microbial dechlorination in anaerobic Grasse River sediment microcosms

Aroclor 1254 was the second most produced commercial PCB mixture and is found in soils, sediments and sewage throughout the globe. This commercial PCB mixture is considered particularly toxic because of the relatively high concentrations of congeners with dioxin-like properties. The potential for risk reduction by microbial reductive dechlorination of Aroclor 1254 (A1254) was investigated in sediment microcosms from Grasse River (GR), Massena, NY. The specificity of A1254 dechlorination was doubly- and singly-flanked chlorines in meta positions and to a less extent doubly-flanked para chlorines of 2345-substituted chlorobiphenyl rings. The average dechlorination rate of A1254 was 0.0153 Cl^-/biphenyl/day, and dechlorination rates of single congeners ranged between 0.001 and 0.0074 Cl^-/biphenyl/day. Potential risk associated with A1254 based on the toxic equivalency factors of the dioxin-like congeners was reduced by 83%. Additional potential risk associated with bioaccumulation in fish was reduced by 35% based on biota-sediment accumulation factor estimates for all detected congeners. Finally, the dechlorination end-products were tri- and tetra-chlorobiphenyls with unflanked chlorines, all of which are susceptible to further degradation by aerobic microorganisms. The combined results indicate that microbial reductive dechlorination has the potential for reducing risk associated with toxicity and bioaccumulation in fish in sites contaminated with A1254.

Evaluation of PCB dechlorination pathways in anaerobic sediment microcosms using an anaerobic dechlorination model

A detailed quantitative analysis of anaerobic dechlorination (AD) pathways of polychlorinated biphenyls (PCBs) in sediment microcosms was performed by applying an anaerobic dechlorination model (ADM). The purpose of ADM is to systematically analyze changes in a contaminant profile that result from microbial reductive dechlorination according to empirically determined dechlorination pathways. In contrast to prior studies that utilized modeling tools to predict dechlorination pathways, ADM also provides quantification of individual pathways. As only microbial reductive dechlorination of PCBs occurred in the modeled laboratory microcosms, extensive analysis of AD pathways was possible without the complicating effect of concurrent physico-chemical or other weathering mechanisms. The results from this study showed: (1) ninety three AD pathways are active; (2) tetra- to hepta-chlorobiphenyl (CB) congeners were common intermediates in several AD pathways, penta-CBs being the most frequently observed; (3) the highest rates of dechlorination were for penta-CB homologs during the initial 185 days; (4) the dominant terminal products of AD were PCB 32(26-4), 49(24-25), 51(24-26), 52(25-25), 72(25-35), 73(26-35) and 100(246-24), (5) potential toxicity of the sediment was reduced. ADM serves as a powerful tool not only for a thorough analysis of AD pathways, but also for providing necessary input for numerical fate models (as a degradation term) that investigate dechlorination products or outcome of natural attenuation, or bioremediation/bioaugmentation of PCB-impacted sediments.

Kinetics and threshold level of 2,3,4,5-tetrachlorobiphenyl dechlorination by an organohalide respiring bacterium

The time required for a PCB-contaminated site to recover cannot yet be predicted due in part to lack of quantitative information on rates of PCB dechlorination in the porewater phase. We developed a method to measure rate of dechlorination in the aqueous phase at very low PCB concentrations. This approach utilizes a polymer functioning concurrently as a passive dosing system for maintaining a steady-state PCB substrate concentration in the water phase and as a passive equilibrium sampler to monitor the dechlorination product. Rates of dechlorination of 2,3,4,5-tetrachlorobiphenyl (PCB 61) to 2,3,5-trichlorobiphenyl (PCB 23) by an organohalide respiring bacterium, Dehalobium chlorocoercia DF-1, were measured over an environmentally relevant range of 1 to 500 ng L(-1) in sediment-free medium using a high concentration of cells (>10(6) cells mL(-1)). The results indicate that rate of dechlorination is a linear function of PCB substrate concentration below the maximum aqueous solubility of PCB 61 and occurs at concentrations as low as 1 ng L(-1). Demonstration of PCB 61 dechlorination at environmentally relevant concentrations suggests that low numbers of organohalide respiring bacteria rather than bioavailability accounts for low rates of dechlorination typically observed in sediments. Using passive samplers to measure the concentration of dissolved PCBs in the porewater combined with knowledge of congener-specific rates for organohalide respirer(s), it will be possible to project the in situ rate and final concentration of PCBs for a specific site after treatment by bioaugmentation.

Effects of activated carbon on reductive dechlorination of PCBs by organohalide respiring bacteria indigenous to sediments

Polychlorinated biphenyls (PCBs) have accumulated in aquatic sediments due to their inherent chemical stability and their presence poses a risk due to their potential toxicity in humans and animals. Granular activated carbon (GAC) has been applied to PCB contaminated sediment sites to reduce the aqueous concentration by sequestration thus reducing the PCB exposure and toxicity to both benthic and aquatic organisms. However, it is not known how the reduction of PCB bioavailability by adsorption to GAC affects bacterial transformation of PCBs by indigenous organohalide respiring bacteria. In this study, the impact of GAC on anaerobic dechlorination by putative organohalide respiring bacteria indigenous to sediment from Baltimore Harbor was examined. It was shown that the average Cl/biphenyl after dehalogenation of Aroclor 1260 was similar between treatments with and without GAC amendment. However, GAC caused a substantial shift in the congener distribution whereby a smaller fraction of highly chlorinated congeners was more extensively dechlorinated to mono- through tri-chlorinated congeners compared to the formation of tri- through penta-chlorinated congeners in unamended sediment. The results combined with comparative sequence analysis of 16S rRNA gene sequences suggest that GAC caused a community shift to putative organohalide respiring phylotypes that coincided with more extensive dechlorination of ortho and unflanked chlorines. This shift in activity by GAC shown here for the first time has the potential to promote greater degradation in situ by promoting accumulation of less chlorinated congeners that are generally more susceptible to complete mineralization by aerobic PCB degrading bacteria.

In situ treatment of PCBs by anaerobic microbial dechlorination in aquatic sediment: are we there yet?

The remediation of polychlorinated biphenyls (PCBs) in soils and sediments remains a particularly difficult problem to solve. The possibility of in situ degradation by microorganisms has been pursued for many years since this approach has the potential to provide a cost-effective and environmentally sustainable alternative to dredging for treatment of PCB impacted sites. Being hydrophobic, PCBs partition into organic material and accumulate in anoxic environments well poised to support anaerobic dechlorination of highly chlorinated congeners; products of which are susceptible to complete aerobic degradation. Laboratory research over the past 25 years is now leading to new microbial technologies that could soon be tested for treatment of PCB impacted sediments in the field.

Electrical stimulation of microbial PCB degradation in sediment

Bioremediation of polychlorinated biphenyls (PCBs) has been precluded in part by the lack of a cost-effective method to stimulate microbial degradation in situ. A common limitation is the lack of an effective method of providing electron donors and acceptors to promote in situ PCB biodegradation. Application of an electric potential to soil/sediment could be an effective means of providing electron-donors/-acceptors to PCB dechlorinating and degrading microorganisms. In this study, electrical stimulation of microbial PCB dechlorination/degradation was examined in sediment maintained under simulated in situ conditions. Voltage was applied to open microcosms filled with PCB-impacted (Aroclor 1242) freshwater sediment from a Superfund site (Fox River, WI). The effect of applied low voltages (1.5-3.0 V) on the microbial transformation of PCBs was determined with: 1) spiked PCBs, and 2) indigenous weathered PCBs. The results indicate that both oxidative and reductive microbial transformation of the spiked PCBs was stimulated but oxidation was dominant and most effective with higher voltage. Chlorobenzoates were produced as oxidation metabolites of the spiked PCBs, but increasing voltage enhanced chlorobenzoate consumption, indicating that overall degradation was enhanced. In the case of weathered PCBs, the total concentration decreased 40-60% in microcosms exposed to electric current while no significant decrease of PCB concentration was observed in control reactors (0 V or sterilized). Single congener analysis of the weathered PCBs showed significant loss of di- to penta-chlorinated congeners, indicating that microbial activity was not limited to anaerobic dechlorination of only higher chlorinated congeners. Degradation was most apparent with the application of only 1.5 V where anodic O(2) was not generated, indicating a mechanism of degradation independent of electrolytic O(2). Low voltage stimulation of the microbial degradation of weathered PCBs observed in this study suggests that this approach could be a cost-effective, environmentally sustainable strategy to remediate PCBs in situ.

Linking energy production and protein synthesis in hydrogenotrophic methanogens

Hydrogenotrophic methanogens possessing the hydrogen-dependent dehydrogenase Hmd also encode paralogs of this protein whose function is poorly understood. Here we present biochemical evidence that the two inactive Hmd paralogs of Methanocaldococcus jannaschii, HmdII and HmdIII, form binary and ternary complexes with several components of the protein translation apparatus. HmdII and HmdIII, but not the active dehydrogenase Hmd, bind with micromolar binding affinities to a number of tRNAs and form ternary complexes with tRNA(Pro) and prolyl-tRNA synthetase (ProRS). Fluorescence spectroscopy experiments also suggest that binding of HmdII and ProRS involves distinct binding determinants on the tRNA. These biochemical data suggest the possibility of a regulatory link between energy production and protein translation pathways that may allow a rapid cellular response to altered environmental conditions.

Enhanced reductive dechlorination of polychlorinated biphenyl impacted sediment by bioaugmentation with a dehalorespiring bacterium

Anaerobic reductive dehalogenation of commercial PCBs such as Aroclor 1260 has a critical role of transforming highly chlorinated congeners to less chlorinated congeners that are then susceptible to aerobic degradation. The efficacy of bioaugmentation with the dehalorespiring bacterium Dehalobium chlorocoercia DF1 was tested in 2-L laboratory mesocosms containing sediment contaminated with weathered Aroclor 1260 (1.3 ppm) from Baltimore Harbor, MD. Total penta- and higher chlorinated PCBs decreased by approximately 56% (by mass) in bioaugmented mesocosms after 120 days compared with no activity observed in unamended controls. Bioaugmentation with DF-1 enhanced the dechlorination of doubly flanked chlorines and stimulated the dechlorination of single flanked chlorines as a result of an apparent synergistic effect on the indigenous population. Addition of granulated activated carbon had a slight stimulatory effect indicating that anaerobic reductive dechlorination of PCBs at low concentrations was not inhibited by a high background of inorganic carbon that could affect bioavailability. The total number of dehalorespiring bacteria was reduced by approximately half after 60 days. However, a steady state level was maintained that was greater than the indigenous population of putative dehalorespiring bacteria in untreated sediments and DF1 was maintained within the indigenous population after 120 days. The results of this study demonstrate that bioaugmentation with dehalorespiring bacteria has a stimulatory effect on the dechlorination of weathered PCBs and supports the feasibility of using in situ bioaugmentation as an environmentally less invasive and lower cost alternate to dredging for treatment of PCB impacted sediments.

Effects of bioaugmentation on indigenous PCB dechlorinating activity in sediment microcosms

Bioaugmentation is an attractive mechanism for reducing recalcitrant pollutants in sediments, especially if this technology could be applied in situ. To examine the potential effectiveness of a bioaugmentation strategy for PCB contamination, PCB dehalorespiring populations were inoculated into Baltimore Harbor sediment microcosms. A culture containing the two most predominant indigenous PCB dehalorespiring microorganisms and a culture containing a strain with a rare ortho dechlorination activity and a non-indigenous strain that attacks double-flanked chlorines, were inoculated into sediment microcosms amended with 2,2',3,5,5',6-hexachlorobiphenyl (PCB 151) and Aroclor 1260. Although we observed a similar reduction in the concentration of PCB 151 in all microcosms at day 300, a reduced lag time for dechlorination activity was observed only in the bioaugmented microcosms and the pattern of dechlorination was altered depending on the initial combination of microorganisms added. Dechlorination of Aroclor 1260 was most extensive when dehalorespiring microorganisms were added to sediment. Overall numbers of dehalorespiring microorganisms in both bioaugmented and non-bioaugmented microcosms increased 100- and 1000-fold with PCB 151 and Aroclor 1260, respectively, and they were sustained for the full 300 days of the experiments. The ability of bioaugmentation to redirect dechlorination reactions in the sediment microcosms indicates that the inoculated PCB dehalorespiring microorganisms effectively competed with the indigenous microbial populations and cooperatively enhanced or altered the specific pathways of PCB dechlorination. These observations indicate that bioaugmentation with PCB dehalorespiring microorganisms is a potentially tractable approach for in situ treatment of PCB impacted sites.

Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14

The modified nucleosides N²-methylguanosine and N22-dimethylguanosine in transfer RNA occur at five positions in the D and anticodon arms, and at positions G6 and G7 in the acceptor stem. Trm1 and Trm11 enzymes are known to be responsible for several of the D/anticodon arm modifications, but methylases catalyzing post-transcriptional m²G synthesis in the acceptor stem are uncharacterized. Here, we report that the MJ0438 gene from Methanocaldococcus jannaschii encodes a novel S-adenosylmethionine-dependent methyltransferase, now identified as Trm14, which generates m²G at position 6 in tRNA^Cys. The 381 amino acid Trm14 protein possesses a canonical RNA recognition THUMP domain at the amino terminus, followed by a γ-class Rossmann fold amino-methyltransferase catalytic domain featuring the signature NPPY active site motif. Trm14 is associated with cluster of orthologous groups (COG) 0116, and most closely resembles the m²G10 tRNA methylase Trm11. Phylogenetic analysis reveals a canonical archaeal/bacterial evolutionary separation with 20–30% sequence identities between the two branches, but it is likely that the detailed functions of COG 0116 enzymes differ between the archaeal and bacterial domains. In the archaeal branch, the protein is found exclusively in thermophiles. More distantly related Trm14 homologs were also identified in eukaryotes known to possess the m²G6 tRNA modification.

Disaggregation of Methanosarcina spp. and Growth as Single Cells at Elevated Osmolarity

The effect of medium osmolarity on the morphology and growth of Methanosarcina barkeri, Methanosarcina thermophila, Methanosarcina mazei, Methanosarcina vacuolata, and Methanosarcina acetivorans was examined. Each strain was adapted for growth in NaCl concentrations ranging from 0.05 to 1.0 M. Methanosarcina spp. isolated from both marine and nonmarine sources exhibited similar growth characteristics at all NaCl concentrations tested, demonstrating that these species are capable of adapting to a similar range of medium osmolarities. Concomitant with the adaptation in 0.4 to 1.0 M NaCl, all strains disaggregated and grew as single cells rather than in the characteristic multicellular aggregates. Aggregated cells had a methanochondroitin outer layer, while disaggregated single cells lacked the outer layer but retained the protein S-layer adjacent to the cell membrane. Synthesis of glucuronic acid, a major component of methanochondroitin, was reduced 20-fold in the single-cell form of M. barkeri when compared with synthesis in aggregated cells. Strains with the methanochondroitin outer cell layer exhibited enhanced stability at low (<0.2 M NaCl) osmolarity and grew at higher temperatures. Disaggregated cells could be converted back to aggregated cells by gradually readapting cultures to lower NaCl (<0.2 M) and Mg (<0.005 M) concentrations. Disaggregated Methanosarcina spp. could also be colonized and replica plated with greater than 95% recovery rates on solidified agar basal medium that contained 0.4 to 0.6 M NaCl and either trimethylamine, methanol, or acetate as the substrate. The ability to disaggregate and grow Methanosarcina spp. as viable, detergent-sensitive, single cells on agar medium makes these species amenable to mutant selection and screening for genetic studies and enables cells to be gently lysed for the isolation of intact genetic material.

Anaerobic ortho Dechlorination of Polychlorinated Biphenyls by Estuarine Sediments from Baltimore Harbor

Reductive dechlorination of the ortho moiety of polychlorinated biphenyls (PCBs) as well as of meta and para moieties is shown to occur in anaerobic enrichments of Baltimore Harbor sediments. These estuarine sediments ortho dechlorinated 2,3,5,6-chlorinated biphenyl (CB), 2,3,5-CB, and 2,3,6-CB in freshwater or estuarine media within a relatively short period of 25 to 44 days. ortho dechlorination developed within 77 days in marine medium. High levels of ortho dechlorination (>90%) occurred when harbor sediments were supplied with only 2,3,5-CB. Incubation with 2,3,4,5,6-CB or 2,3,4,5-CB resulted in the formation of the ortho dechlorination product 3,5-CB; however, para dechlorination of these congeners always preceded ortho chlorine removal. ortho dechlorination of PCBs is an exceedingly rare event that has not been reported previously for marine or estuarine conditions. The activity was reproducible and could be sustained through sequential transfers. In contrast, freshwater sediments incubated under the same conditions exhibited only meta and para dechlorinations. The results indicate that unique anaerobic dechlorinating activity is catalyzed by microorganisms in the estuarine sediments from Baltimore Harbor.

Methanosarcina acetivorans sp. nov., an Acetotrophic Methane-Producing Bacterium Isolated from Marine Sediments

A new acetotrophic marine methane-producing bacterium that was isolated from the methane-evolving sediments of a marine canyon is described. Exponential phase cultures grown with sodium acetate contained irregularly shaped cocci that aggregated in the early stationary phase and finally differentiated into communal cysts that released individual cocci when ruptured or transferred to fresh medium. The irregularly shaped cocci (1.9 +/- 0.2 mm in diameter) were gram negative and occurred singly or in pairs. Cells were nonmotile, but possessed a single fimbria-like structure. Micrographs of thin sections showed a monolayered cell wall approximately 10 nm thick that consisted of protein subunits. The cells in aggregates were separated by visible septation. The communal cysts contained several single cocci encased in a common envelope. An amorphous form of the communal cyst that had incomplete septation and internal membrane-like vesicles was also present in late exponential phase cultures. Sodium acetate, methanol, methylamine, dimethylamine, and trimethylamine were substrates for growth and methanogenesis; H(2)-CO(2) (80:20) and sodium formate were not. The optimal growth temperature was 35 to 40 degrees C. The optimal pH range was 6.5 to 7.0. Both NaCl and Mg were required for growth, with maximum growth rates at 0.2 M NaCl and 0.05 M MgSO(4). The DNA base composition was 41 +/- 1% guanine plus cytosine. Methanosarcina acetivorans is the proposed species. C2A is the type strain (DSM 2834, ATCC 35395).

Halotolerance in Methanosarcina spp.: Role of N(sup(epsilon))-Acetyl-(beta)-Lysine, (alpha)-Glutamate, Glycine Betaine, and K(sup+) as Compatible Solutes for Osmotic Adaptation

The methanogenic Archaea, like the Bacteria and Eucarya, possess several osmoregulatory strategies that enable them to adapt to osmotic changes in their environment. The physiological responses of Methanosarcina species to different osmotic pressures were studied in extracellular osmolalities ranging from 0.3 to 2.0 osmol/kg. Regardless of the isolation source, the maximum rate of growth for species from freshwater, sewage, and marine sources occurred in extracellular osmolalities between 0.62 and 1.0 osmol/kg and decreased to minimal detectable growth as the solute concentration approached 2.0 osmol/kg. The steady-state water-accessible volume of Methanosarcina thermophila showed a disproportionate decrease of 30% between 0.3 and 0.6 osmol/kg and then a linear decrease of 22% as the solute concentration in the media increased from 0.6 to 2.0 osmol/kg. The total intracellular K(sup+) ion concentration in M. thermophila increased from 0.12 to 0.5 mol/kg as the medium osmolality was raised from 0.3 to 1.0 osmol/kg and then remained above 0.4 mol/kg as extracellular osmolality was increased to 2.0 osmol/kg. Concurrent with K(sup+) accumulation, M. thermophila synthesized and accumulated (alpha)-glutamate as the predominant intracellular osmoprotectant in media containing up to 1.0 osmol of solute per kg. At medium osmolalities greater than 1.0 osmol/kg, the (alpha)-glutamate concentration leveled off and the zwitterionic (beta)-amino acid N(sup(epsilon))-acetyl-(beta)-lysine was synthesized, accumulating to an intracellular concentration exceeding 1.1 osmol/kg at an osmolality of 2.0 osmol/kg. When glycine betaine was added to culture medium, it caused partial repression of de novo (alpha)-glutamate and N(sup(epsilon))-acetyl-(beta)-lysine synthesis and was accumulated by the cell as the predominant compatible solute. The distribution and concentration of compatible solutes in eight strains representing five Methanosarcina spp. were similar to those found in M. thermophila grown in extracellular osmolalities of 0.3 and 2.0 osmol/kg. Results of this study demonstrate that the mechanism of halotolerance in Methanosarcina spp. involves the regulation of K(sup+), (alpha)-glutamate, N(sup(epsilon))-acetyl-(beta)-lysine, and glycine betaine accumulation in response to the osmotic effects of extracellular solute.

Isolation and Characterization of a Methylotrophic Marine Methanogen, Methanococcoides methylutens gen. nov., sp. nov

A new genus of marine methanogenic bacteria is described that utilizes trimethylamine, diethylamine, monomethylamine, and methanol as substrates for growth and methanogenesis. Methane was not produced from H(2)-CO(2), sodium formate, or sodium acetate. Growth on trimethylamine was stimulated by yeast extract, Trypticase (BBL Microbiology Systems, Cockeysville, Md.), rumen fluid, or B vitamins. The optimal growth temperature was 30 to 35 degrees C. The maximum growth rate was between pH 7.0 and 7.5. Na (0.4 M) and MgSO(4) (0.05 M) were required for maximum growth. Colonies of the type strain, TMA-10, were yellow, circular, and convex with entire edges. Cells were nonmotile, nonsporeforming, irregular cocci 1 mum in diameter which stained gram negative and occurred singly or in pairs. Micrographs of thin sections revealed a monolayered cell wall approximately 10-nm thick which consisted of protein. Cells were lysed in 0.01% sodium dodecyl sulfate or 0.001% Triton X-100. The DNA base composition was 42 mol% guanine plus cytosine. Methanococcoides is the proposed genus and Methanococcoides methylutens is the type species. TMA-10 is the type strain (ATCC 33938).

Biocorrosion and biofilm formation in a nutrient limited heating system subjected to alternating microaerophilic conditions

Severe biofilm formation and biocorrosion have been observed in heating systems even when the water quality complied with existing standards. The coupling between water chemistry, biofilm formation, species composition, and biocorrosion in a heating system was investigated by adding low concentrations of nutrients and oxygen under continuous and alternating dosing regimes. Molecular analysis of 16S rRNA gene fragments demonstrated that the amendments did not cause changes in the overall bacterial community composition. The combined alternating dosing of nutrients and oxygen caused increased rates of pitting (bio-) corrosion. Detection of bacteria involved in sulfide production and oxidation by retrieval of the functional dsrAB and apsA genes revealed the presence of Gram-positive sulfate- and sulfite-reducers and an unknown sulfur-oxidizer. Therefore, to control biocorrosion, sources of oxygen and nutrients must be limited, since the effect of the alternating operational conditions apparently is more important than the presence of potentially corrosive biofilm bacteria.

The archetype gamma-class carbonic anhydrase (Cam) contains iron when synthesized in vivo

A recombinant protein overproduction system was developed in Methanosarcina acetivorans to facilitate biochemical characterization of oxygen-sensitive metalloenzymes from strictly anaerobic species in the Archaea domain. The system was used to overproduce the archetype of the independently evolved gamma-class carbonic anhydrase. The overproduced enzyme was oxygen sensitive and had full incorporation of iron instead of zinc observed when overproduced in Escherichia coli. This, the first report of in vivo iron incorporation for any carbonic anhydrase, supports the need to reevaluate the role of iron in all classes of carbonic anhydrases derived from anaerobic environments.

In situ detection of bacteria involved in cathodic depolarization and stainless steel surface corrosion using microautoradiography

AIMS

To examine the activity of bacteria involved in cathodic depolarization and surface corrosion on stainless steel in an in situ model system.

METHODS AND RESULTS

The microautoradiographic technique (MAR) was used to evaluate the activity of bacterial populations on stainless steel surfaces with a single cell resolution. Anaerobic uptake and fixation of (14)C-labelled bicarbonate occurred within corrosion sites in the absence of atmospheric hydrogen or other external electron donors, whereas it was taken up and fixed by bacteria at all other stainless steel surfaces in the presence of atmospheric hydrogen. This indicates that the bacteria utilized electrons originating from the corrosion sites due to the ongoing corrosion (cathodic depolarization).

CONCLUSION

Under in situ conditions, bacteria were fixating (14)C-labelled bicarbonate at corrosion sites in the absence of atmospheric hydrogen. This indicates that electrons transferred to the bacteria provided energy for bicarbonate fixation due to cathodic depolarization.

SIGNIFICANCE AND IMPACT OF THE STUDY

Application of the MAR method showed ongoing biocorrosion in the applied in situ model system and allowed in situ examination of bacterial activity on a single cell level directly on a metal surface providing information about potential corrosion mechanisms. Furthermore, application of fluorescence in situ hybridization in combination with MAR allows for identification of the active bacteria.

Microbial reductive dechlorination of aroclor 1260 in Baltimore harbor sediment microcosms is catalyzed by three phylotypes within the phylum Chloroflexi

The specific dechlorination pathways for Aroclor 1260 were determined in Baltimore Harbor sediment microcosms developed with the 11 most predominant congeners from this commercial mixture and their resulting dechlorination intermediates. Most of the polychlorinated biphenyl (PCB) congeners were dechlorinated in the meta position, and the major products were tetrachlorobiphenyls with unflanked chlorines. Using PCR primers specific for the 16S rRNA genes of known PCB-dehalogenating bacteria, we detected three phylotypes within the microbial community that had the capability to dechlorinate PCB congeners present in Aroclor 1260 and identified their selective activities. Phylotype DEH10, which has a high level of sequence identity to Dehalococcoides spp., removed the double-flanked chlorine in 234-substituted congeners and exhibited a preference for para-flanked meta-chlorines when no double-flanked chlorines were available. Phylotype SF1 had similarity to the o-17/DF-1 group of PCB-dechlorinating bacteria. Phylotype SF1 dechlorinated all of the 2345-substituted congeners, mostly in the double-flanked meta position and 2356-, 236-, and 235-substituted congeners in the ortho-flanked meta position, with a few exceptions. A phylotype with 100% sequence identity to PCB-dechlorinating bacterium o-17 was responsible for an ortho and a double-flanked meta dechlorination reaction. Most of the dechlorination pathways supported the growth of all three phylotypes based on competitive PCR enumeration assays, which indicates that PCB-impacted environments have the potential to sustain populations of these PCB-dechlorinating microorganisms. The results demonstrate that the variation in dechlorination patterns of congener mixtures typically observed at different PCB impacted sites can potentially be mediated by the synergistic activities of relatively few dechlorinating species.

Stimulatory and inhibitory effects of organohalides on the dehalogenating activities of PCB-dechlorinating bacterium o-17

Bacterium o-17, a microorganism capable of the ortho dechlorination of 2,3,5,6-polychlorinated biphenyl (PCB), is a member of a sediment-free, nonmethanogenic mixed culture. The culture was examined for the ability to dechlorinate 26 PCB congeners, 12 chlorobenzenes (CBZs), and 6 chlorinated ethenes (CEs). Eight of the PCBs and 4 of the CBZs were dechlorinated including single-flanked ortho PCB chlorines, but double-flanked chlorines of PCBs and CBZs were preferentially dechlorinated. The dechlorination of three of the PCBs (2,3,4,5,6-, 2,3,4,6-, and 2,3,5,6-PCB), three of the CBZs (hexa-, penta-, and 1,2,3-CBZ), and PCE could be sustained for three or more sequential transfers of the bacterial community. Two PCBs (2,3,4- and 2,3,5-PCB), two CBZs (1,2,3,5- and 1,2,4,5-CBZ), and trichloroethene were dechlorinated only when a more extensively chlorinated parent compound was present. Aroclor 1260 and 2,4,6-PCB, not dechlorinated by the culture, inhibited the dechlorination of 2,3,5,6-PCB. Within the culture only bacterium o-17 was linked to dechlorination by PCR-DGGE analysis, confirming that this dehalogenating species was the catalyst for the dechlorination of the compounds tested. The microorganism is capable of dechlorinating several different congeners of PCBs, CBZs, and CEs, and it remains a rare example of an ortho-PCB dechlorinator. However, its limited ability to dechlorinate more extensively chlorinated congeners and Aroclor plus the inhibitory effects of some PCB congeners upon the bacterium is consistent with the observed infrequency of this reaction in the environment. An assessment of bioremediation potential of this microorganism in situ will require a greater understanding of the synergistic, cometabolic and competitive interactions of PCB dechlorinating microbial communities.

The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes

We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. The genome of M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcina spp. in the region proximal to the origin of replication, with interspecies gene similarities as high as 95%. However, it is disordered and marked by increased transposase frequency and decreased gene synteny and gene density in the distal semigenome. Of the 3,680 open reading frames (ORFs) in M. barkeri, 746 had homologs with better than 80% identity to both M. acetivorans and M. mazei, while 128 nonhypothetical ORFs were unique (nonorthologous) among these species, including a complete formate dehydrogenase operon, genes required for N-acetylmuramic acid synthesis, a 14-gene gas vesicle cluster, and a bacterial-like P450-specific ferredoxin reductase cluster not previously observed or characterized for this genus. A cryptic 36-kbp plasmid sequence that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143-nucleotide motif was detected in M. barkeri. Three-way comparison of these genomes reveals differing mechanisms for the accrual of changes. Elongation of the relatively large M. acetivorans genome is the result of uniformly distributed multiple gene scale insertions and duplications, while the M. barkeri genome is characterized by localized inversions associated with the loss of gene content. In contrast, the short M. mazei genome most closely approximates the putative ancestral organizational state of these species.

Sequential reductive dechlorination of meta-chlorinated polychlorinated biphenyl congeners in sediment microcosms by two different Chloroflexi phylotypes

Three species within a deeply branching cluster of the Chloroflexi are the only microorganisms currently known to anaerobically transform polychlorinated biphenyls (PCBs) by the mechanism of reductive dechlorination. A selective PCR primer set was designed that amplifies the 16S rRNA genes of a monophyletic group within the Chloroflexi including Dehalococcoides spp. and the o-17/DF-1 group. Assays for both qualitative and quantitative analyses by denaturing gradient gel electrophoresis and most probable number-PCR, respectively, were developed to assess sediment microcosm enrichments that reductively dechlorinated PCBs 101 (2,2',4,5,5'-CB) and 132 (2,2',3,3',4,6'-CB). PCB 101 was reductively dechlorinated at the para-flanked meta position to PCB 49 (2,2',4,5'-CB) by phylotype DEH10, which belongs to the Dehalococcoides group. This same species reductively dechlorinated the para- and ortho-flanked meta-chlorine of PCB 132 to PCB 91 (2,2',3',4,6'-CB). However, another phylotype designated SF1, which is more closely related to the o-17/DF-1 group, was responsible for the subsequent dechlorination of PCB 91 to PCB 51 (2,2',4,6'-CB). Using the selective primer set, an increase in 16S rRNA gene copies was observed only with actively dechlorinating cultures, indicating that PCB-dechlorinating activities by both phylotype DEH10 and SF1 were linked to growth. The results suggest that individual species within the Chloroflexi exhibit a limited range of congener specificities and that a relatively diverse community of species within a deeply branching group of Chloroflexi with complementary congener specificities is likely required for the reductive dechlorination of different PCBs congeners in the environment.

Development of a plasmid-mediated reporter system for in vivo monitoring of gene expression in the archaeon Methanosarcina acetivorans

A plasmid-based gene reporter system has been developed to construct lacZ gene fusions for monitoring intrinsic promoter expression in Methanosarcina acetivorans. Constructs transform with high efficiency that can be readily screened by color selection on plates and exhibit a consistent copy number on different substrates negating the need for gene copy normalization. Expression of the CO dehydrogenase-acetyl coenzyme A synthase promoter fusion to lacZ revealed 18- to 54-fold down-regulation in cells grown on methylotrophic substrates compared with acetate-grown cells, which is up to an order of magnitude greater than the range of regulation previously reported by enzyme activity assays. This system complements and expands the current techniques for studying genetics of the methanosarcinal Archaea by providing a rapid method for monitoring and quantifying gene expression.

A PCR-based specific assay reveals a population of bacteria within the Chloroflexi associated with the reductive dehalogenation of polychlorinated biphenyls

Polychlorinated biphenyls (PCBs) accumulate and persist in sediments posing a risk to human health and the environment. Highly chlorinated PCBs are reductively dechlorinated in anaerobic sediments and two bacteria, designated o-17 and DF-1, from a novel phylogenetic group that reductively dechlorinate PCBs have recently been identified. However, there is a paucity of knowledge about the distribution, diversity and ecology of PCB-dechlorinating bacteria due to difficulty in obtaining pure cultures and the lack of detection by universal PCR 16S rRNA gene primer sets in sediments. A specific PCR primer was developed and optimized for detection of o-17/DF-1 and other closely related bacteria in the environment. Using this primer set it was determined that bacteria of this group were enriched in sediment microcosms from Baltimore Harbour concurrent with active dechlorination of 2,2′,3,4,4′,5′-hexachlorobiphenyl. Additional 16S rRNA gene sequences that had high levels of similarity to described PCB dechlorinators were detected in sediments from the Elizabeth River tributary of Chesapeake Bay, which had confirmed PCB-dechlorinating activities. Phylogenetic comparison of these detected 16S rRNA gene sequences revealed a relatively diverse group of organisms within the dehalogenating Chloroflexi that are distinct from the Dehalococcoides spp. Results from this study indicate that reductive PCB dechlorination activity may be catalysed by a previously undescribed group of micro-organisms that appear to be prevalent in PCB-impacted sites.

Reductive dechlorination of tetrachloroethene to trans-dichloroethene and cis-dichloroethene by PCB-dechlorinating bacterium DF-1

Polychlorinated biphenyls (PCBs) and chlorinated ethenes (CEs) are known to pollute sediment, soil, and groundwater. The anaerobic dechlorination of these compounds is an integral part of their biodegradation in polluted environments. We report for the first time the dechlorination of tetrachloroethene (PCE) and trichloroethene (TCE) by bacterium DF-1. This PCB and chlorobenzene dechlorinating bacterium dechlorinated PCE to TCE, which was then converted into trans-1,2-dichloroethene (trans-DCE) and cis-1,2-dichloroethene (cis-DCE). The ratio of trans-DCE to cis-DCE produced by the culture had a range of 1.2-1.7. Bacterium DF-1 has been enriched in co-culture with a desulfovibrio-like microorganism. PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of the 16S rRNA genes of the co-culture demonstrated that DF-1 was enriched during the dechlorination of PCE, PCB, and chlorobenzene. DF-1 was not detected in the absence of PCE dechlorination and the desulfovibrio-like organism, isolated in pure culture, did not dechlorinate PCE. This is the first identification of a microorganism capable of producing high amounts of trans-DCE from PCE and indicates that microorganisms such as DF-1 are a possible biological source of trans-DCE in the environment.

Development of two PCR-based techniques for detecting helical and coccoid forms of Helicobacter pylori

The primary mode of transmission of Helicobacter pylori, a human pathogen carried by more than half the population worldwide, is still unresolved. Some epidemiological data suggest water as a possible transmission route. H. pylori in the environment transforms into a nonculturable, coccoid form, which frequently results in the failure to detect this bacterium in environmental samples by conventional culture techniques. To overcome limitations associated with culturing, molecular approaches based on DNA amplification by PCR have been developed and used for the detection of H. pylori in clinical and environmental samples. Our results showed the glmM gene as the most promising target for detection of H. pylori by PCR amplification. Under optimal amplification conditions, glmM-specific primers generated PCR-amplified products that were specific for H. pylori and some other Helicobacter species. Genome sequence analysis revealed the existence of a conserved region linked to a hypervariable region upstream of the 16S rRNA gene of H. pylori. Selective PCR primer sets targeting this sequence were evaluated for the specific detection of H. pylori. One primer set, Cluster2 and B1J99, were shown to be highly specific for H. pylori strains and did not produce any PCR products when other Helicobacter species and other bacterial species were analyzed. In tests with 32 strains of H. pylori, 6 strains of other Helicobacter species, 8 strains of Campylobacter jejuni, and 21 strains belonging to different genera, the primers for glmM were selective for the Helicobacter genus and the primers containing the region flanking the 16S rRNA gene were selective for H. pylori species only. The combination of two sensitive PCR-based methods, one targeting the glmM gene and the other targeting a hypervariable flanking region upstream of the 16S rRNA gene, are complementary to each other. Whereas the glmM-specific primers provide a rapid, sensitive presumptive assay for the presence of H. pylori and closely related Helicobacter spp., the primers for sequences flanking the 16S rRNA gene can confirm the presence of H. pylori and locate the potential source of this bacterium.

Chlorophenol production by anaerobic microorganisms: transformation of a biogenic chlorinated hydroquinone metabolite

Chlorinated hydroquinones of biological origin are fully dechlorinated to 1,4-dihydroquinone by anaerobic bacteria such as Desulfitobacterium spp. (C. E. Milliken, G. P. Meier, J. E. M. Watts, K. R. Sowers, and H. D. May, Appl. Environ. Microbiol. 70:385-392, 2004). In the present study, mixed microbial communities from Baltimore Harbor sediment and a pure culture of Desulfitobacterium sp. strain PCE1 were discovered to demethylate, reductively dehydroxylate, and dechlorinate chlorinated hydroquinones into chlorophenols. Mixed microbial cultures from a freshwater source and several other desulfitobacteria in pure culture did not perform these reactions. Desulfitobacterium sp. strain PCE1 degraded 2,3,5,6-tetrachloro-4-methoxyphenol, a metabolite of basidiomycete fungi, to 2,3,5,6-tetrachlorophenol and 2,3,5-trichlorophenol, recalcitrant compounds that are primarily synthesized anthropogenically.

Microbial anaerobic demethylation and dechlorination of chlorinated hydroquinone metabolites synthesized by basidiomycete fungi

The synthesis and degradation of anthropogenic and natural organohalides are the basis of a global halogen cycle. Chlorinated hydroquinone metabolites (CHMs) synthesized by basidiomycete fungi and present in wetland and forest soil are constituents of that cycle. Anaerobic dehalogenating bacteria coexist with basidiomycete fungi in soils and sediments, but little is known about the fate of these halogenated fungal compounds. In sediment microcosms, the CHMs 2,3,5,6-tetrachloro-1,4-dimethoxybenzene and 2,3,5,6-tetrachloro-4-methoxyphenol (TCMP) were anaerobically demethylated to tetrachlorohydroquinone (TCHQ). Subsequently, TCHQ was converted to trichlorohydroquinone and 2,5-dichlorohydroquinone (2,5-DCHQ) in freshwater and estuarine enrichment cultures. Screening of several dehalogenating bacteria revealed that Desulfitobacterium hafniense strains DCB2 and PCP1, Desulfitobacterium chlororespirans strain Co23, and Desulfitobacterium dehalogenans JW/DU1 sequentially dechlorinate TCMP to 2,3,5-trichloro-4-methoxyphenol and 3,5-dichloro-4-methoxyphenol (3,5-DCMP). After a lag, these strains demethylate 3,5-DCMP to 2,6-DCHQ, which is then completely dechlorinated to 1,4-dihydroquinone (HQ). 2,5-DCHQ accumulated as an intermediate during the dechlorination of TCHQ to HQ by the TCMP-degrading desulfitobacteria. HQ accumulation following TCMP or TCHQ dechlorination was transient and became undetectable after 14 days, which suggests mineralization of the fungal compounds. This is the first report on the anaerobic degradation of fungal CHMs, and it establishes a fundamental role for microbial reductive degradation of natural organochlorides in the global halogen cycle.

Invariant chlorine isotopic signatures during microbial PCB reductive dechlorination

In order to develop more robust insight into the natural attenuation of polychlorinated biphenyls (PCBs), the chlorine isotopic composition of residual 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-CB) was monitored as it underwent microbial reductive dechlorination to 2,3,5-trichlorobiphenyl (2,3,5-CB) in laboratory cultures. Reverse-phase high performance liquid chromatography (HPLC) was employed to isolate the former compound from the experimental matrix for delta37Cl measurement. No detectable isotopic fractionation was observed over the 90 day incubation with sterile control, standard, and inoculated samples all exhibiting delta37Cl values with a range of approximately 0.5 per thousand. These results show that this type of biological activity can be discriminated from other transformations by the absence of a measurable isotope effect during microbial reductive dechlorination. The utility of HPLC isolation for compound-specific delta37Cl analyses of environmentally relevant species is also demonstrated.

Dechlorination of chlorobenzenes by a culture containing bacterium DF-1, a PCB dechlorinating microorganism

Polychlorinated benzenes were reductively dechlorinated by an enrichment culture containing the polychlorinated biphenyl (PCB) dechlorinating bacterium DF-1. The culture dechlorinated hexachlorobenzene (hexa-CB) --> pentachlorobenzene (penta-CB) --> 1,2,3,5-tetrachlorobenzene (1,2,3,5-CB) --> 1,3,5-trichlorobenzene (1,3,5-CB) and did not dechlorinate other tetrachlorobenzenes or any trichlorobenzenes. This restricted series of reactions is the most predominant and frequently reported pathway for the dechlorination of hexa-CB and penta-CB by enrichment cultures inoculated with either freshwater or estuarine sediments. The culture did not dechlorinate hydroxylated and methoxylated polychlorinated benzenes or a hydroxylated PCB. Bacterium DF-1 was detected by PCR/DGGE analysis following dechlorination of penta-CB but was not detected when a chlorinated benzene (CB) was not dechlorinated; detection of other members in the communitywas unaffected by the presence or absence of CB dechlorination. This is the first report of a bacterium that reductively dechlorinates both PCBs and CBs and the first identification of an organism that can dechlorinate a CB with more than four chlorines.

Low-temperature extremophiles and their applications

Psychrophilic (cold-adapted) organisms and their products have potential applications in a broad range of industrial, agricultural and medical processes. In order for growth to occur in low-temperature environments, all cellular components must adapt to the cold. This fact, in combination with the diversity of Archaea, Bacteria and Eucarya isolated from cold environments, highlights the breadth and type of biological products and processes that might be exploited for biotechnology. Relative to this undisputed potential, psychrophiles and their products are under-utilised in biotechnology; however, recent advances, particularly with cold-active enzymes, herald rapid growth for this burgeoning field.

The genome of M. acetivorans reveals extensive metabolic and physiological diversity

Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived from acetate. Here we report the complete genome sequence of an acetate-utilizing methanogen, Methanosarcina acetivorans C2A. Methanosarcineae are the most metabolically diverse methanogens, thrive in a broad range of environments, and are unique among the Archaea in forming complex multicellular structures. This diversity is reflected in the genome of M. acetivorans. At 5,751,492 base pairs it is by far the largest known archaeal genome. The 4524 open reading frames code for a strikingly wide and unanticipated variety of metabolic and cellular capabilities. The presence of novel methyltransferases indicates the likelihood of undiscovered natural energy sources for methanogenesis, whereas the presence of single-subunit carbon monoxide dehydrogenases raises the possibility of nonmethanogenic growth. Although motility has not been observed in any Methanosarcineae, a flagellin gene cluster and two complete chemotaxis gene clusters were identified. The availability of genetic methods, coupled with its physiological and metabolic diversity, makes M. acetivorans a powerful model organism for the study of archaeal biology. [Sequence, data, annotations and analyses are available at http://www-genome.wi.mit.edu/.]

Identification of a bacterium that specifically catalyzes the reductive dechlorination of polychlorinated biphenyls with doubly flanked chlorines

A microorganism whose growth is linked to the dechlorination of polychlorinated biphenyls (PCBs) with doubly flanked chlorines was identified. Identification was made by reductive analysis of community 16S ribosomal DNA (rDNA) sequences from a culture enriched in the presence of 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-CB), which was dechlorinated at the para position. Denaturing gradient gel electrophoresis (DGGE) analysis of total 16S rDNA extracted from the culture led to identification of three operational taxonomic units (OTUs 1, 2, and 3). OTU 1 was always detected when 2,3,4,5-CB or other congeners with doubly flanked chlorines were present and dechlorinated. Only OTUs 2 and 3 were detected in the absence of PCBs and when other PCBs (i.e., PCBs lacking doubly flanked chlorines) were not dechlorinated. Partial sequences of OTUs 2 and 3 exhibited 98.2% similarity to the sequence of "Desulfovibrio caledoniensis" (accession no. DCU53465). A sulfate-reducing vibrio isolated from the culture generated OTUs 2 and 3. This organism could not dechlorinate 2,3,4,5-CB. From these results we concluded that OTU 1 represents the dechlorinating bacterium growing in a coculture with a Desulfovibrio sp. The 16S rDNA sequence of OTU 1 is most similar to the 16S rDNA sequence of bacterium o-17 (89% similarity), an ortho-PCB-dechlorinating bacterium. The PCB dechlorinator, designated bacterium DF-1, reductively dechlorinates congeners with doubly flanked chlorines when it is supplied with formate or H(2)-CO(2) (80:20).

Prevention of mis-aminoacylation of a dual-specificity aminoacyl-tRNA synthetase

Accurate aminoacylation of tRNAs by aminoacyl-tRNA synthetase is essential for the fidelity of protein synthesis. For Methanococcus jannaschii tRNA(Pro), accuracy is difficult because the cognate prolyl-tRNA synthetase also recognizes and aminoacylates tRNA(Cys) with cysteine. We show here that the unmodified transcript of M. jannaschii tRNA(Pro) is indeed mis-acylated with cysteine. However, the origin of mis-charging is not at the anticodon or acceptor stem, the two hotspots for tRNA(Pro) and tRNA(Cys) identity determinants. Instead, replacement of the D loop in the tRNA core with that of tRNA(Cys) suppresses mis-charging with cysteine without compromising the activity of aminoacylation with proline. The reduced level of cysteine activity of the chimera is not due an editing response of the synthetase and is consistent with a relaxed sensitivity of the tRNA to the analog thiaproline in aminoacylation with cysteine. We suggest that mis-acylation is not due to the presence of cysteine determinants, but to a mis-placed 3' end into the cysteine catalytic site that activates and transfers cysteine to the tRNA. Prevention of mis-placement by alteration of the core structure or by nucleotide modifications in the tRNA illustrates a novel strategy of the dual-specificity synthetase.

Identification of a microorganism that links its growth to the reductive dechlorination of 2,3,5,6-chlorobiphenyl

Anaerobic bacteria reductively dechlorinate polychlorinated biphenyls (PCBs) in aquatic sediments, but these microorganisms remain uncultured and, until now, unidentified. Through denaturing gradient gel electrophoresis (DGGE) of 16S rDNA from a highly enriched ortho-PCB dechlorinating culture, the growth of a single microorganism was shown to be dependent upon the presence and dechlorination of 2,3,5,6-tetrachlorobiphenyl. This is the first identification of a microorganism that catalyses the reductive dechlorination of a PCB. The organism, bacterium o-17, has high sequence similarity with the green non-sulphur bacteria and with a group that includes Dehalococcoides ethenogenes. Bacterium o-17 required acetate for dechlorination and growth. H2:CO2 (80:20 at 101 kPa) did not support dechlorination or growth of the dechlorinator. Archaeal 16S rDNA was not detected in actively dechlorinating bromoethanesulphonate-treated non-methanogenic cultures, which indicated that methanogenic Archaea were not required for dechlorination. The consistent association with dechlorinating activity combined with high similarity to other known dechlorinating microorganisms indicates that bacterium o-17 catalyses the reductive ortho-dechlorination of 2,3,5,6-tetrachlorobiphenyl.

Comparative analysis of polychlorinated biphenyl-dechlorinating communities in enrichment cultures using three different molecular screening techniques

The catalysts for many microbially mediated environmental processes such as the dechlorination of polychlorinated biphenyls (PCBs) have been difficult to identify by traditional isolation techniques. Numerous, as yet unsuccessful, attempts have been made to isolate and culture the dechlorinating species. To overcome this limitation, amplified rDNA restriction analysis (ARDRA) of a clone library, denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (TRFLP) were used concurrently to compare their effectiveness for characterizing an enriched microbial community. These methods were applied to enrichment cultures that selectively dechlorinated double-flanked chlorines in the PCB congener 2,3,4,5 chlorinated biphenyl. The methods have different biases, which were apparent from discrepancies in the relative clone frequencies (ARDRA), band intensities (DGGE) or peak heights (TRFLP) from the same enrichment culture. However, each method was effectively qualitative and identified the same organisms: a low G + C Gram-positive eubacterium, an organism most similar to the green non-sulphur bacteria, an Aminobacterium sp. and a Desulfovibrio sp. Overall, in community fingerprinting and preliminary identification, DGGE proved to be the most rapid and effective tool for the monitoring of microorganisms within a highly enriched culture. TRFLP results corroborated DGGE fingerprint analysis; however, identification required the additional step of creating a clone library. ARDRA provided an in-depth analysis of the community and this technique detected slight intraspecies sequence variation in 16S rDNA. These molecular methods are common in environmental microbiology, but rarely are they compared with the same sample site or culture. In general, all three methods detected similar community profiles, but inherent biases resulted in different detection limits for individual OTUs (operational taxonomic units).

The absence and application of stable carbon isotopic fractionation during the reductive dechlorination of polychlorinated biphenyls

A bacterial enrichment culture (specific to doubly flanked chlorine removal) reductively dechlorinated 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-CB) to 2,3,5-trichlorobiphenyl (2,3,5-CB) in aqueous media. Approximately 90% conversion to 2,3,5-CB occurred after 90 days, with no other products formed. The delta13C values of 2,3,4,5-CB and 2,3,5-CB were relatively constant over the course of the reaction, indicating a very small or no isotope effect. In addition, compound-specific delta13C analysis performed for every congener in three different lots of Aroclor 1268 showed an intrinsic isotopic trend of decreasing 13C abundance with increasing chlorine content, similar to observations in other commercial mixtures of polychlorinated biphenyls (PCBs). The results of this laboratory study suggest that microbial reductive dechlorination of PCBs in contaminated sediments will create congeners with more depleted delta13C values than native PCBs of similar chlorination. Such information may provide additional evidence for the occurrence of this process and aid in further understanding the biogeochemistry of these compounds.

Synthesis of cysteinyl-tRNA(Cys) by a genome that lacks the normal cysteine-tRNA synthetase

Synthesis of cysteinyl-tRNA(Cys) by cysteine-tRNA synthetase is required for decoding cysteine codons in all known organisms. The genome of the archaeon Methanococcus jannaschii lacks the gene for a normal cysteine-tRNA synthetase. The activity of the enzyme, however, was identified recently, and it allowed the purification of the enzyme and cloning of its gene. Sequence analysis of the gene showed that it encodes proline-tRNA synthetase and, thus, raised the possibility of dual activities in a single aminoacyl-tRNA synthetase. Assays of aminoacyl-adenylate synthesis confirmed the ability of the enzyme to activate proline and cysteine and showed that both activities were independent of tRNA. Assays of tRNA aminoacylation established the specific attachment of proline to tRNA(Pro) and cysteine to tRNA(Cys). However, in contrast to a recent report of comparable activities with cysteine and proline, results here indicate that the adenylate synthesis and aminoacylation activities with cysteine are significantly lower than the respective activity with proline. In addition, there is evidence of overlapping amino acid-binding sites and tRNA-binding sites. These considerations, among others, raised the distinct possibility that the M. jannaschii proline-tRNA synthetase may recruit additional protein or RNA factors to facilitate the synthesis of cysteinyl-tRNA(Cys).

Cellulomonas persica sp. nov. and Cellulomonas iranensis sp. nov., mesophilic cellulose-degrading bacteria isolated from forest soils

Two newly described species of mesophilic, cellulose-degrading, aerobic bacteria were isolated from forest humus soils along the southern border of the Caspian Sea. Cellulomonas persica and Cellulomonas iranensis are proposed as new specific epithets based on comparative sequence analyses of 16S rDNA, DNA-DNA hybridization and phenotypic characteristics. Formal species descriptions are provided.

Establishment of a polychlorinated biphenyl-dechlorinating microbial consortium, specific for doubly flanked chlorines, in a defined, sediment-free medium

Estuarine sediment from Charleston Harbor, South Carolina, was used as inoculum for the development of an anaerobic enrichment culture that specifically dechlorinates doubly flanked chlorines (i.e., chlorines bound to carbon that are flanked on both sides by other chlorine-carbon bonds) of polychlorinated biphenyls (PCBs). Dechlorination was restricted to the para chlorine in cultures enriched with 10 mM fumarate, 50 ppm (173 microM) 2,3,4, 5-tetrachlorobiphenyl, and no sediment. Initially the rate of dechlorination decreased upon the removal of sediment from the medium. However, the dechlorinating activity was sustainable, and following sequential transfer in a defined, sediment-free estuarine medium, the activity increased to levels near that observed with sediment. The culture was nonmethanogenic, and molybdate, ampicillin, chloramphenicol, neomycin, and streptomycin inhibited dechlorination activity; bromoethanesulfonate and vancomycin did not. Addition of 17 PCB congeners indicated that the culture specifically removes double flanked chlorines, preferably in the para position, and does not attack ortho chlorines. This is the first microbial consortium shown to para or meta dechlorinate a PCB congener in a defined sediment-free medium. It is the second PCB-dechlorinating enrichment culture to be sustained in the absence of sediment, but its dechlorinating capabilities are entirely different from those of the other sediment-free PCB-dechlorinating culture, an ortho-dechlorinating consortium, and do not match any previously published Aroclor-dechlorinating patterns.