Draft Genome Sequence of Exophiala Strain HKRS030, a Fungus Capable of Reducing Iron but Not Nitrate.

Exophiala strain HKRS030 was isolated from a cryptoendolithic community found in the Grand Staircase-Escalante National Monument (GSENM) in southern Utah, USA. Exophiala strain HKRS030 was observed to dissimilatorily reduce iron(III) while being unable to reduce nitrate.

Composition, diversity, and activity of aerobic ammonia-oxidizing Bacteria and Archaea in the intertidal sands of a grand strand South Carolina beach.

Aerobic ammonia oxidation to nitrite has been established as an important ecosystem process in regulating the level of nitrogen in marine ecosystems. This process is carried out by ammonia-oxidizing bacteria (AOB) within the classes Betaproteobacteria and Gammaproteobacteria and ammonia-oxidizing Archaea (AOA) from the phylum Thaumarchaeota, and the latter of which has been established as more prevalent in marine systems. This study investigated the presence, abundance, and activity of these groups of microbes at a beach near Springmaid Pier in Myrtle Beach, South Carolina, through the implementation of next generation sequencing, quantitative PCR (qPCR), and microcosm experiments to monitor activity. Sequencing analysis revealed a diverse community of ammonia-oxidizing microbes dominated by AOA classified within the family Nitrosopumilaceae, and qPCR revealed the abundance of AOA amoA genes over AOB by at least an order of magnitude in most samples. Microcosm studies indicate that the rates of potential ammonia oxidation in these communities satisfy Michaelis-Menten substrate kinetics and this process is more active at temperatures corresponding to summer months than winter. Potential rates in AOA medium were higher than that of AOB medium, indicating a potentially greater contribution of AOA to this process in this environment. In conclusion, this study provides further evidence of the dominance of AOA in these environments compared with AOB and highlights the overall efficiency of this process at turning over excess ammonium that may be present in these environments.

Microbial community structure shows differing levels of temporal stability in intertidal beach sands of the grand strand region of South Carolina.

Studies of microbial community structure in intertidal and supratidal beach sands along the California and Gulf of Mexico coasts have begun to reveal geographical patterns in microbial diversity through the use of next generation sequencing technology. Only a few studies have targeted communities along the Eastern seaboard, leaving a variety of microbial ecosystems uncharacterized. In this study, we examine the microbial community structure within three South Carolina beaches along the Grand Strand via sequencing of the V4 region of the 16S rRNA gene to discern relationships between diversity and temporal or regional factors. Gammaproteobacteria, Planctomycetes, Acidobacteria, and Actinobacteria dominated the composition of these beaches. Diversity analyses revealed that highly diverse communities were similar in overall composition and diversity but showed different levels of community structure stability over time. The community structure in Pawleys Island sands showed no significant change over time, while Garden City experienced significant shifts between each sampling date. Community structure also differed between beaches and, to a lesser degree, sampling date. These data provide evidence of the high microbial diversity within these beach sands and suggest that even though beaches of the same geographic region can show similarity in composition and diversity at a particular timepoint, the nature of their community structure and underlying diversity may differ comparatively and over time.

Use of γ-hexachlorocyclohexane as a terminal electron acceptor by an anaerobic enrichment culture.

The use of γ-hexachlorocyclohexane (HCH) as a terminal electron acceptor via organohalide respiration was demonstrated for the first time with an enrichment culture grown in a sulfate-free HEPES-buffered anaerobic mineral salts medium. The enrichment culture was initially developed with soil and groundwater from an industrial site contaminated with HCH isomers, chlorinated benzenes, and chlorinated ethenes. When hydrogen served as the electron donor, 79-90% of the electron equivalents from hydrogen were used by the enrichment culture for reductive dechlorination of the γ-HCH, which was provided at a saturation concentration of approximately 10 mg/L. Benzene and chlorobenzene were the only volatile transformation products detected, accounting for 25% and 75% of the γ-HCH consumed (on a molar basis), respectively. The enrichment culture remained active with only hydrogen as the electron donor and γ-HCH as the electron acceptor through several transfers to fresh mineral salts medium for more than one year. Addition of vancomycin to the culture significantly slowed the rate of γ-HCH dechlorination, suggesting that a Gram-positive organism is responsible for the reduction of γ-HCH. Analysis of the γ-HCH dechlorinating enrichment culture did not detect any known chlororespiring genera, including Dehalobacter. In bicarbonate-buffered medium, reductive dechlorination of γ-HCH was accompanied by significant levels of acetogenesis as well as methanogenesis.

Aerobic cometabolism of trichloroethene and cis-dichloroethene with benzene and chlorinated benzenes as growth substrates.

Using inoculum from a microcosm study that exhibited aerobic transformation of cis-1,2-dichloroethene (cDCE) and trichloroethene (TCE) commensurate with biodegradation of monoaromatic compounds, enrichment cultures were developed by providing benzene, chlorobenzene (CB), dichlorobenzene (DCB) isomers and 1,2,4-trichlorobenzene as carbon and energy sources. Isolates that grow on benzene, CB, 1,2-DCB and 1,3-DCB were identified as Rhodococcus, Ralstonia, Variovorax and Ralstonia spp., respectively. Cometabolic transformation of cDCE and TCE by resting cells was demonstrated. Transformation capacities (T(c)=0.47-1.0 µg TCE mg(-1)biomass; 1.3-5.3 µg cDCE mg(-1)biomass), transformation yields (T(y)=0.18-0.27 µg TCE mg(-1)substrate; 0.46-2.1 µg cDCE mg(-1)substrate), and pseudo-first-order cometabolic degradation rate constants (0.00081-0.0031 L mg TCE(-1)d(-1); 0.0012-0.030 L mg cDCE(-1)d(-1)) for resting cells grown on benzene, CB, 1,2-DCB and 1,3-DCB were generally lower in comparison to phenol and toluene-grown isolates. Cometabolic transformation of cDCE and TCE also occurred while the cultures concurrently consumed their growth substrate (T(c)(')=0.15-0.33 µg TCE mg(-1)biomass; 4.9-11 µg cDCE mg(-1)biomass; T(y)(')=0.06-0.11 µg TCE mg(-1)substrate; 1.7-4.6 µg cDCE mg(-1)substrate), a condition that is more likely to be encountered in situ compared to cometabolic transformations by resting cells. This study is the first to report transformation rates, capacities, and yields for cometabolism of cDCE and TCE during aerobic growth on benzene, CB, 1,2-DCB and 1,3-DCB. This type of information is needed to predict the potential for natural attenuation when these compounds occur as co-contaminants.

Anaerobic biotransformation of high concentrations of chloroform by an enrichment culture and two bacterial isolates.

A fermentative enrichment culture (designated DHM-1) was developed that is capable of cometabolically biotransforming high concentrations of chloroform (CF) to nontoxic end products. Two Pantoea spp. were isolated from DHM-1 that also possess this dechlorination capability. Following acclimation to increasing levels of CF, corn syrup-grown DHM-1 was able to transform over 500 mg/liter CF in the presence of vitamin B(12) (approximately 3% of CF on a molar basis) at a rate as high as 22 mg/liter/day in a mineral salts medium. CO, CO(2), and organic acids were the predominant biodegradation products, suggesting that hydrolytic reactions predominate during CF transformation. DHM-1 was capable of growing on corn syrup in the presence of high concentrations of CF (as may be present near contaminant source zones in groundwater), which makes it a promising culture for bioaugmentation. Strains DHM-1B and DHM-1T transform CF at rates similar to that of the DHM-1 enrichment culture. The ability of these strains to grow in the presence of high concentrations of CF appears to be related to alteration of membrane fluidity or homeoviscous and homeophasic adaptation.

Evaluation of strategies for anaerobic bioremediation of high concentrations of halomethanes.

Bioremediation is being considered for groundwater at an industrial site contaminated with carbon tetrachloride (CT), trichlorofluoromethane (CFC-11), and chloroform (CF), at concentrations typically considered too high for biological treatment. 1,1-Dichloroethene is also present. The objective of this study was to evaluate in situ anaerobic remediation by biostimulation alone (lactate, emulsified vegetable oil, and corn syrup), biostimulation (corn syrup) supplemented with vitamin B(12) (cyanocobalamin), and bioaugmentation in combination with catalytic levels of B(12). Three cultures were evaluated for enhancing biotransformation of CT, CFC-11 and CF: two were sulfate reducing enrichments (grown on lactate and ethanol, respectively), based on a high concentration of sulfate in the groundwater; the other was a fermentative enrichment grown on corn syrup. A microcosm study with soil and groundwater (neutralized to pH 7) from the site revealed that bioaugmentation is a potentially feasible treatment approach, with complete biotransformation of 8.8mg/L CT, 26mg/L CFC-11, and 500mg/L of CF in approximately 500days. The lactate-grown sulfate reducing culture and the corn syrup-grown fermentative culture were the most effective. Subsequent bioaugmentation with a chloroethene-respiring culture yielded rapid reduction of 1,1-dichloroethene (9.1mg/L) to ethene. Complete transformation of CT, CFC-11 and CF was also observed with corn syrup+B(12), although the time required was twice as long compared to bioaugmentation. In the presence of B(12), biotransformation of [(14)C]CT and [(14)C]CF yielded mainly CO, CO(2), and organic acids. CT was consistently transformed first, followed by CFC-11 and then CF. Corn syrup was only partially effective for halomethane removal without B(12), but was more effective than emulsified vegetable oil or lactate.

Characterization of the Caulobacter crescentus holdfast polysaccharide biosynthesis pathway reveals significant redundancy in the initiating glycosyltransferase and polymerase steps.

Caulobacter crescentus cells adhere to surfaces by using an extremely strong polar adhesin called the holdfast. The polysaccharide component of the holdfast is comprised in part of oligomers of N-acetylglucosamine. The genes involved in the export of the holdfast polysaccharide and the anchoring of the holdfast to the cell were previously discovered. In this study, we identified a cluster of polysaccharide biosynthesis genes (hfsEFGH) directly adjacent to the holdfast polysaccharide export genes. Sequence analysis indicated that these genes are involved in the biosynthesis of the minimum repeat unit of the holdfast polysaccharide. HfsE is predicted to be a UDP-sugar lipid-carrier transferase, the glycosyltransferase that catalyzes the first step in polysaccharide biosynthesis. HfsF is predicted to be a flippase, HfsG is a glycosyltransferase, and HfsH is similar to a polysaccharide (chitin) deacetylase. In-frame hfsG and hfsH deletion mutants resulted in severe deficiencies both in surface adhesion and in binding to the holdfast-specific lectin wheat germ agglutinin. In contrast, hfsE and hfsF mutants exhibited nearly wild-type levels of adhesion and holdfast synthesis. We identified three paralogs to hfsE, two of which are redundant to hfsE for holdfast synthesis. We also identified a redundant paralog to the hfsC gene, encoding the putative polysaccharide polymerase, and present evidence that the hfsE and hfsC paralogs, together with the hfs genes, are absolutely required for proper holdfast synthesis.