Metagenomic analysis of Fe(II)-oxidizing bacteria for Fe(III) mineral formation and carbon assimilation under microoxic conditions in paddy soil.

Microbially mediated Fe(II) oxidation is prevalent and thought to be central to many biogeochemical processes in paddy soils. However, we have limited insights into the Fe(II) oxidation process in paddy fields, considered the world's largest engineered wetland, where microoxic conditions are ubiquitous. In this study, microaerophilic Fe(II) oxidizing bacteria (FeOB) from paddy soil were enriched in gradient tubes with FeS, FeCO, and Fe(PO) as iron sources to investigate their capacity for Fe(II) oxidation and carbon assimilation.

Microbial transformation of widely used pharmaceutical and personal care product compounds.

Pharmaceutical and personal care products (PPCPs) are commonly used chemicals that are increasingly detected in urban-impacted environments, particularly those receiving treated wastewater. PPCPs may have toxicological effects on the macrofauna that are exposed through contaminated water; thus, there is interest in microbially mediated transformations that may degrade PPCPs. This review discusses specific examples of PPCP transformations that may occur in anoxic environments, including O-methylation and O-demethylation.

Bacterial response to sharp geochemical gradients caused by acid mine drainage intrusion in a terrace: Relevance of C, N, and S cycling and metal resistance.

A unique terrace with sharp gradient of environmental conditions was selected to study the microbial response and survival strategies to the extreme environments introduced by acid mine drainage (AMD) contamination. A combination of geochemical analyses, metagenomic sequencing, ex-situ microcosm setups, and statistical analyses were used to investigate the environment-microbe interactions. The microbial communities and metabolic potentials along the terrace were studied by focusing on the genes associated with important biogeochemical processes (i.

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage.

Acid mine drainage (AMD) is harmful to the environment and human health. Microorganisms-mineral interactions are responsible for AMD generation but can also remediate AMD contamination. Understanding the microbial response to AMD irrigation will reveal microbial survival strategies and provide approaches for AMD remediation.

Humic Substances Facilitate Arsenic Reduction and Release in Flooded Paddy Soil.

Organic matter is important for controlling arsenic reduction and release under anoxic conditions. Humic substances (HS) represent an important fraction of natural organic matter, yet the manner in which HS affect arsenic transformation in flooded paddy soil has not been thoroughly elucidated. In this study, anaerobic microcosms were established with arsenic-contaminated paddy soil and amended with three extracted humic fractions (fulvic acid, FA; humic acid, HA; and humin, HM).

Diastereoisomer-Specific Biotransformation of Hexabromocyclododecanes by a Mixed Culture Containing Strain 195.

Hexabromocyclododecane (HBCD) stereoisomers may exhibit substantial differences in physicochemical, biological, and toxicological properties. However, there remains a lack of knowledge about stereoisomer-specific toxicity, metabolism, and environmental fate of HBCD. In this study, the biotransformation of (±)α-, (±)β-, and (±)γ-HBCD contained in technical HBCD by a mixed culture containing the organohalide-respiring bacterium strain 195 was investigated.

Sulfate-Reducing Naphthalene Degraders Are Picky Eaters.

Polycyclic aromatic hydrocarbons (PAHs) are common organic contaminants found in anoxic environments. The capacity for PAH biodegradation in unimpacted environments, however, has been understudied. Here we investigate the enrichment, selection, and sustainability of a microbial community from a pristine environment on naphthalene as the only amended carbon source.

Draft genome sequence of sp. WAO an arsenite and sulfide oxidizer isolated from a pyrite rock outcrop in New Jersey.

This genome report describes the draft genome and physiological characteristics of sp. WAO (=DSM 102914), a novel strain of the genus in the family . sp.

The antihistamine diphenhydramine is demethylated by anaerobic wastewater microorganisms.

While emerging pharmaceutical contaminants are monitored in wastewater treatment and the environment, there is little information concerning their microbial metabolites. The transformation of diphenhydramine by microorganisms in anaerobic digester sludge was investigated using anaerobic cultures amended with 1 mM diphenhydramine as the sole carbon source. Complete transformation of the parent compound to a persistent metabolite occurred within 191 days.

Naproxen Is Transformed Via Acetogenesis and Syntrophic Acetate Oxidation by a Methanogenic Wastewater Consortium.

Over-the-counter pharmaceutical compounds can serve as microbial substrates in wastewater treatment processes as well as in the environment. The metabolic pathways and intermediates produced during their degradation, however, are poorly understood. In this study, we investigate an anaerobic wastewater community that metabolizes naproxen via demethylation.

Transcriptional Activity of Arsenic-Reducing Bacteria and Genes Regulated by Lactate and Biochar during Arsenic Transformation in Flooded Paddy Soil.

Organic substrates and biochar are important in controlling arsenic release from sediments and soils; however, little is known about their impact on arsenic-reducing bacteria and genes during arsenic transformation in flooded paddy soils. In this study, microcosm experiments were established to profile transcriptional activity of As(V)-respiring gene (arrA) and arsenic resistance gene (arsC) as well as the associated bacteria regulated by lactate and/or biochar in anaerobic arsenic-contaminated paddy soils. Chemical analyses revealed that lactate as the organic substrate stimulated microbial reduction of As(V) and Fe(III), which was simultaneously promoted by lactate+biochar, due to biochar's electron shuttle function that facilitates electron transfer from bacteria to As(V)/Fe(III).

Benzoyl-CoA, a universal biomarker for anaerobic degradation of aromatic compounds.

Aromatic compounds are a major component of the global carbon pool and include a diverse range of compounds such as humic acid, lignin, amino acids, and industrial contaminants. Due to the prevalence of aromatic compounds in the environment, aerobic and anaerobic microorganisms have evolved mechanisms by which to metabolize that available carbon. Less well understood are the anaerobic pathways.

The bamA gene for anaerobic ring fission is widely distributed in the environment.

Benzoyl-CoA is the signature central metabolite associated with the anaerobic metabolism of a diverse range of compounds such as humic acid, lignin, amino acids, and industrial chemicals. Aromatic chemicals with different upstream degradation pathways all funnel into the downstream benzoyl-CoA pathway. Different genes encoding enzymes of the benzoyl-CoA pathway could be used as biomarkers for the anaerobic benzoyl-CoA pathway, however, the ring opening hydrolase, encoded by the bamA gene, is ideal because it is detected under a range of respiratory conditions, including under denitrifying, iron-reducing, sulfate-reducing, and fermentative conditions.

Precipitation of alacranite (As8S9) by a novel As(V)-respiring anaerobe strain MPA-C3.

Strain MPA-C3 was isolated by incubating arsenic-bearing sediments under anaerobic, mesophilic conditions in minimal media with acetate as the sole source of energy and carbon, and As(V) as the sole electron acceptor. Following growth and the respiratory reduction of As(V) to As(III), a yellow precipitate formed in active cultures, while no precipitate was observed in autoclaved controls, or in uninoculated media supplemented with As(III). The precipitate was identified by X-ray diffraction as alacranite, As8 S9 , a mineral previously only identified in hydrothermal environments.

Impact of mercury on denitrification and denitrifying microbial communities in nitrate enrichments of subsurface sediments.

The contamination of groundwater with mercury (Hg) is an increasing problem worldwide. Yet, little is known about the interactions of Hg with microorganisms and their processes in subsurface environments. We tested the impact of Hg on denitrification in nitrate reducing enrichment cultures derived from subsurface sediments from the Oak Ridge Integrated Field Research Challenge site, where nitrate is a major contaminant and where bioremediation efforts are in progress.

Pathways for arsenic from sediments to groundwater to streams: biogeochemical processes in the Inner Coastal Plain, New Jersey, USA.

The Cretaceous and Tertiary sediments that underlie the Inner Coastal Plain of New Jersey contain the arsenic-rich mineral glauconite. Streambed sediments in two Inner Coastal Plain streams (Crosswicks and Raccoon Creeks) that traverse these glauconitic deposits are enriched in arsenic (15-25mg/kg), and groundwater discharging to the streams contains elevated levels of arsenic (>80μg/L at a site on Crosswicks Creek) with arsenite generally the dominant species. Low dissolved oxygen, low or undetectable levels of nitrate and sulfate, detectable sulfide concentrations, and high concentrations of iron and dissolved organic carbon (DOC) in the groundwater indicate that reducing environments are present beneath the streambeds and that microbial activity, fueled by the DOC, is involved in releasing arsenic and iron from the geologic materials.

Characterization of the microbial community from the marine sediment of the Venice lagoon capable of reductive dechlorination of coplanar polychlorinated biphenyls (PCBs).

The native microbial community of a contaminated sediment from Brentella Canal (Venice Lagoon, Italy) was enriched in slurry microcosms consisting of sterile sediment suspended in sterile site water in the presence of 3,3',4,4'-tetrachlorobiphenyl, 3,3',4,4',5- and 2,3',4,4',5-pentachlorobiphenyls, 3,3',4,4',5,5'- and 2,3,3',4,4',5-hexachlorobiphenyls. The enrichment cultures were characterized at each subculturing step by 16S rRNA gene Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE) analysis. About 90% of spiked polychlorinated biphenyls (PCBs) were stoichiometrically converted into di- and tri-chlorinated congeners by each enriched culture via dechlorination of flanked para chlorines and ortho-flanked meta chlorines.

Detection of 2,4,6-trinitrotoluene-utilizing anaerobic bacteria by 15N and 13C incorporation.

2,4,6-Trinitrotoluene ((15)N or (13)C labeled) was added to Norfolk Harbor sediments to test whether anaerobic bacteria use TNT for growth. Stable-isotope probing (SIP)-terminal restriction fragment length polymorphism (TRFLP) detected peaks in the [(15)N]TNT cultures (60, 163, and 168 bp). The 60-bp peak was also present in the [(13)C]TNT cultures and was related to Lysobacter taiwanensis.

Novel autotrophic arsenite-oxidizing bacteria isolated from soil and sediments.

Arsenic oxidation is recognized as being mediated by both heterotrophic and chemoautotrophic microorganisms. Enrichment cultures were established to determine whether chemoautotrophic microorganisms capable of oxidizing arsenite As(III) to arsenate As(V) are present in selected contaminated but nonextreme environments. Three new organisms, designated as strains OL-1, S-1 and CL-3, were isolated and found to oxidize 10 mM arsenite to arsenate under aerobic conditions using CO2-bicarbonate (CO2/HCO3-) as a carbon source.

Anaerobic alkane-degrading strain AK-01 contains two alkylsuccinate synthase genes.

The sulfate-reducing strain AK-01 activates alkanes via addition of the subterminal carbon to the double bond of fumarate. This reaction is similar to the action of the glycyl radical enzyme benzylsuccinate synthase (Bss). It was hypothesized that strain AK-01 possesses a similar enzyme.

Comparison of mechanisms of alkane metabolism under sulfate-reducing conditions among two bacterial isolates and a bacterial consortium.

Recent studies have demonstrated that fumarate addition and carboxylation are two possible mechanisms of anaerobic alkane degradation. In the present study, we surveyed metabolites formed during growth on hexadecane by the sulfate-reducing isolates AK-01 and Hxd3 and by a mixed sulfate-reducing consortium. The cultures were incubated with either protonated or fully deuterated hexadecane; the sulfate-reducing consortium was also incubated with [1,2-13C2]hexadecane.

Characterization of Fe(III)-reducing enrichment cultures and isolation of Fe(III)-reducing bacteria from the Savannah River site, South Carolina.

The Savannah River site, South Carolina (SRS), has been subjected to heavy metal and radionuclide contamination. Dissimilatory Fe(III)-reducing bacteria, by reducing insoluble Fe(III) to soluble Fe(II), may enhance contaminant mobility through subsurface environments. In order to investigate populations of the indigenous iron-reducing microbes from the SRS, duplicate enrichment cultures were initiated using a 10% inoculum of 7 sediment/soil samples, and serial dilutions were made into Wolfe's minimal salts media amended with 50 mM Fe(III) floc, 10 mM acetate and 0.

Metabolic biomarkers for monitoring in situ anaerobic hydrocarbon degradation.

During the past 15 years researchers have made great strides in understanding the metabolism of hydrocarbons by anaerobic bacteria. Organisms capable of utilizing benzene, toluene, ethylbenzene, xylenes, alkanes, and polycyclic aromatic hydrocarbons have been isolated and described. In addition, the mechanisms of degradation for these compounds have been elucidated.

Combined effects of contaminant desorption and toxicity on risk from PAH contaminated sediments.

A strong inverse correlation was observed between the polycyclic aromatic hydrocarbon (PAH) mass fraction desorbed, a surrogate measure of bioavailability, and relative carcinogenicity, as quantified by potency equivalency factors (PEFs), for two study sediments from the New York/New Jersey Harbor estuary. Because compounds with the highest toxicity, such as dibenz(a,h)anthracene and benzo(a)pyrene (BAP), also tended to be the least rapidly and least extensively desorbed, the U.S.