Impact of yeast extract and basal salts medium on 1,4-dioxane biodegradation rates and the microorganisms involved in carbon uptake from 1,4-dioxane.

Conventional physical and chemical treatment technologies for 1,4-dioxane can be ineffective and consequently attention has focused on bioremediation. Towards this, the current research investigated the impact of basal salts medium (BSM) and yeast extract on 1,4-dioxane biodegradation rates in microcosms with different soil or sediment (agricultural soil, wetland sediment, sediment from an impacted site). Phylotypes responsible for carbon uptake from 1,4-dioxane were determined using stable isotope probing (SIP), both with and without BSM and yeast extract.

Comprehensive model for predicting toxic equivalents (TEQ) reduction due to dechlorination of polychlorinated dibenzo-p-dioxin and dibenzofurans (PCDD/F congeners).

Remediation-focused predictive tools for polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) rely on transformation models to evaluate the reduction in total contaminant load and toxic equivalency (TEQ). In this study, a comprehensive model predicting the profiles of PCDD/F congeners and the associated TEQs was developed. The model employs first-order kinetics to describe the transformation of 256 reactions for 75 PCDD congeners and 421 reactions for 135 PCDF congeners.

Electrochemical Detection of Nucleic Acids Using Three-Dimensional Graphene Screen-Printed Electrodes.

Electrochemical approaches, along with miniaturization of electrodes, are increasingly being employed to detect and quantify nucleic acid biomarkers. Miniaturization of the electrodes is achieved through the use of screen-printed electrodes (SPEs), which consist of one to a few dozen sets of electrodes, or by utilizing printed circuit boards. Electrode materials used in SPEs include glassy carbon (Chiang H-C, Wang Y, Zhang Q, Levon K, Biosensors (Basel) 9:2-11, 2019), platinum, carbon, and graphene (Cheng FF, He TT, Miao HT, Shi JJ, Jiang LP, Zhu JJ, ACS Appl Mater Interfaces 7:2979-2985, 2015).

Propane Monooxygenases in Soil Associated Metagenomes Align Most Closely to those in the Genera Kribbella, Amycolatopsis, Bradyrhizobium, Paraburkholderia and Burkholderia.

Propanotrophs are a focus of interest because of their ability to degrade numerous environmental contaminants. To explore the phylogeny of microorganisms containing the propane monooxygenase gene cluster (prmABCD), NCBI bacterial genomes and publicly available soil associated metagenomes (from soils, rhizospheres, tree roots) were both examined. Nucleic acid sequences were collected only if all four subunits were located together, were of the expected length and were annotated as propane monooxygenase subunits.

An investigation of soil and groundwater metagenomes for genes encoding soluble and particulate methane monooxygenase, toluene-4-monoxygenase, propane monooxygenase and phenol hydroxylase.

Soil and groundwater were investigated for the genes encoding soluble and particulate methane monooxygenase/ammonia monooxygenase (sMMO, pMMO/AMO), toluene 4-monooxygenase (T4MO), propane monooxygenase (PMO) and phenol hydroxylase (PH). The objectives were (1) to determine which subunits were present, (2) to examine the diversity of the phylotypes associated with the biomarkers and (3) to identify which metagenome associated genomes (MAGs) contained these subunits. All T4MO and PH subunits were annotated in the groundwater metagenomes, while few were annotated in the soil metagenomes.

Composition and metabolism of microbial communities in soil pores.

Delineation of microbial habitats within the soil matrix and characterization of their environments and metabolic processes are crucial to understand soil functioning, yet their experimental identification remains persistently limited. We combined single- and triple-energy X-ray computed microtomography with pore specific allocation of C labeled glucose and subsequent stable isotope probing to demonstrate how long-term disparities in vegetation history modify spatial distribution patterns of soil pore and particulate organic matter drivers of microbial habitats, and to probe bacterial communities populating such habitats. Here we show striking differences between large (30-150 µm Ø) and small (4-10 µm Ø) soil pores in (i) microbial diversity, composition, and life-strategies, (ii) responses to added substrate, (iii) metabolic pathways, and (iv) the processing and fate of labile C.

Occurrence of Rhodococcus sp. RR1 prmA and Rhodococcus jostii RHA1 prmA across microbial communities and their enumeration during 1,4-dioxane biodegradation.

1,4-Dioxane, a likely human carcinogen, is a co-contaminant at many chlorinated solvent contaminated sites. Conventional treatment technologies, such as carbon sorption or air stripping, are largely ineffective, and so many researchers have explored bioremediation for site clean-up. An important step towards this involves examining the occurrence of the functional genes associated with 1,4-dioxane biodegradation.

In silico analysis of soil, sediment and groundwater microbial communities to predict biodegradation potential.

This study examined soil, sediment and groundwater microbial communities for a set of key functional genes important for contaminant biodegradation. This involved PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) predictions based on 16S rRNA gene amplicon datasets from three separate studies with different inocula and incubation conditions, as follows: aerobic soils, oxygen-limited microcosms containing sediments and groundwater, as well as methanogenic microcosms with different inocula. PICRUSt2 predicts functional profiles of microbial communities based on marker gene (16S rRNA gene) data.

Predicted functional genes for the biodegradation of xenobiotics in groundwater and sediment at two contaminated naval sites.

The goals of this study were to predict the genes associated with the biodegradation of organic contaminants and to examine microbial community structure in samples from two contaminated sites. The approach involved a predictive bioinformatics tool (PICRUSt2) targeting genes from twelve KEGG xenobiotic biodegradation pathways (benzoate, chloroalkane and chloroalkene, chlorocyclohexane and chlorobenzene, toluene, xylene, nitrotoluene, ethylbenzene, styrene, dioxin, naphthalene, polycyclic aromatic hydrocarbons, and metabolism of xenobiotics by cytochrome P450). Further, the predicted phylotypes associated with functional genes early in each pathway were determined.

Predicting the occurrence of monooxygenases and their associated phylotypes in soil microcosms.

Cometabolic oxidation involves the oxidation of chemicals often by monooxygenases or dioxygenases and can be a removal process for environmental contaminants such as trichloroethene (TCE) or 1,4-dioxane. Information on the occurrence of these genes and their associated microorganisms in environmental samples has the potential to enhance our understanding of contaminant removal. The overall aims were to 1) ascertain which genes encoding for monooxygenases (from methanotrophs, ammonia oxidizing bacteria and toluene/phenol oxidizers) and other key enzymes are present in soil microcosms and 2) determine which phylotypes are associated with those genes.

Diversity and abundance of the functional genes and bacteria associated with RDX degradation at a contaminated site pre- and post-biostimulation.

Bioremediation is becoming an increasingly popular approach for the remediation of sites contaminated with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Multiple lines of evidence are often needed to assess the success of such approaches, with molecular studies frequently providing important information on the abundance of key biodegrading species. Towards this goal, the current study utilized shotgun sequencing to determine the abundance and diversity of functional genes (xenA, xenB, xplA, diaA, pnrB, nfsI) and species previously associated with RDX biodegradation in groundwater before and after biostimulation at an RDX-contaminated Navy Site.

Identification of the phylotypes involved in cis-dichloroethene and 1,4-dioxane biodegradation in soil microcosms.

Co-contamination with chlorinated compounds and 1,4-dioxane has been reported at many sites. Recently, there has been an increased interest in bioremediation because of the potential to degrade multiple contaminants concurrently. Towards improving bioremediation efficacy, the current study examined laboratory microcosms (inoculated separately with two soils) to determine the phylotypes and functional genes associated with the biodegradation of two common co-contaminants (cis-dichloroethene [cDCE] and 1,4-dioxane).

Diversity of nitrogen cycling genes at a Midwest long-term ecological research site with different management practices.

Nitrogen fertilizer results in the release of nitrous oxide (NO), a concern because NO is an ozone-depleting substance and a greenhouse gas. Although the reduction of NO to nitrogen gas can control emissions, the factors impacting the enzymes involved have not been fully explored. The current study investigated the abundance and diversity of genes involved in nitrogen cycling (primarily denitrification) under four agricultural management practices (no tillage [NT], conventional tillage [CT], reduced input, biologically-based).

Anaerobic 1,4-dioxane biodegradation and microbial community analysis in microcosms inoculated with soils or sediments and different electron acceptors.

1,4-Dioxane, a probable human carcinogen, is a co-contaminant at many chlorinated solvent-contaminated sites. Although numerous 1,4-dioxane-degrading aerobic bacteria have been isolated, almost no information exists on the microorganisms able to degrade this chemical under anaerobic conditions. Here, the potential for 1,4-dioxane biodegradation was examined using multiple inocula and electron acceptor amendments.

Enrichment of novel Actinomycetales and the detection of monooxygenases during aerobic 1,4-dioxane biodegradation with uncontaminated and contaminated inocula.

1,4-Dioxane, a co-contaminant at many chlorinated solvent sites, is a problematic groundwater pollutant because of risks to human health and characteristics which make remediation challenging. In situ 1,4-dioxane bioremediation has recently been shown to be an effective remediation strategy. However, the presence/abundance of 1,4-dioxane degrading species across different environmental samples is generally unknown.

Influence of terminal electron-accepting conditions on the soil microbial community and degradation of organic contaminants of emerging concern.

Better understanding of the fate and persistence of trace organic contaminants of emerging concern (CEC) in agricultural soils is critical for assessing the risks associated with using treated wastewater effluent to irrigate crops and land application of wastewater biosolids. This study reports on the influence of prevailing terminal electron-accepting processes (TEAPs, i.e.

High throughput quantification of the functional genes associated with RDX biodegradation using the SmartChip real-time PCR system.

The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a contaminant at many military sites. RDX bioremediation as a clean-up approach has been gaining popularity because of cost benefits compared to other methods. RDX biodegradation has primarily been linked to six functional genes (diaA, nfsI, pnrB, xenA, xenB, xplA).

Carbamazepine, triclocarban and triclosan biodegradation and the phylotypes and functional genes associated with xenobiotic degradation in four agricultural soils.

Pharmaceuticals and personal care products (PPCPs) are released into the environment due to their poor removal during wastewater treatment. Agricultural soils subject to irrigation with wastewater effluent and biosolids application are possible reservoirs for these chemicals. This study examined the impact of the pharmaceutical carbamazepine (CBZ), and the antimicrobial agents triclocarban (TCC) and triclosan (TCS) on four soil microbial communities using shotgun sequencing (HiSeq Illumina) with the overall aim of determining possible degraders as well as the functional genes related to general xenobiotic degradation.

Abundance of Chlorinated Solvent and 1,4-Dioxane Degrading Microorganisms at Five Chlorinated Solvent Contaminated Sites Determined via Shotgun Sequencing.

Shotgun sequencing was used for the quantification of taxonomic and functional biomarkers associated with chlorinated solvent bioremediation in 20 groundwater samples (five sites), following bioaugmentation with SDC-9. The analysis determined the abundance of (1) genera associated with chlorinated solvent degradation, (2) reductive dehalogenase (RDases) genes, (3) genes associated with 1,4-dioxane removal, (4) genes associated with aerobic chlorinated solvent degradation, and (5) D. mccartyi genes associated with hydrogen and corrinoid metabolism.

Diclofenac, carbamazepine and triclocarban biodegradation in agricultural soils and the microorganisms and metabolic pathways affected.

The incomplete elimination of pharmaceuticals and personal care products (PPCPs) during wastewater treatment has resulted in their detection in the environment. PPCP biodegradation is a potential removal mechanism; however, the microorganisms and pathways involved in soils are generally unknown. Here, the biodegradation of diclofenac (DCF), carbamazepine (CBZ) and triclocarban (TCC) in four agricultural soils at concentrations typically detected in soils and biosolids (50 ng g) was examined.

Integrated methodological approach reveals microbial diversity and functions in aerobic groundwater microcosms adapted to vinyl chloride.

Vinyl chloride (VC), a known human carcinogen, is often formed in groundwater (GW) by incomplete reductive dechlorination of chlorinated ethenes. An integrated microbial ecology approach involving bacterial enrichments and isolations, carbon stable-isotope probing (SIP) and metagenome and genome sequencing was applied to ethene-fed GW microcosms that rapidly transitioned to aerobic growth on VC. Actinobacteria, Proteobacteria and Bacteroidetes dominated the microbial communities in ethene- and VC-grown cultures.

Most probable number with visual based LAMP for the quantification of reductive dehalogenase genes in groundwater samples.

The remediation of chlorinated solvent contaminated sites frequently involves bioaugmentation with mixed cultures containing Dehalococcoides mccartyi. Their activity is then examined by quantifying reductive dehalogenase (RDase) genes. Recently, we described a rapid, low cost approach, based on loop mediated isothermal amplification (LAMP), which allowed for the visual detection of RDase genes from groundwater.

Development and application of a rapid, user-friendly, and inexpensive method to detect Dehalococcoides sp. reductive dehalogenase genes from groundwater.

TaqMan probe-based quantitative polymerase chain reaction (qPCR) specific to the biomarker reductive dehalogenase (RDase) genes is a widely accepted molecular biological tool (MBT) for determining the abundance of Dehalococcoides sp. in groundwater samples from chlorinated solvent-contaminated sites. However, there are significant costs associated with this MBT.

Most probable number - loop mediated isothermal amplification (MPN-LAMP) for quantifying waterborne pathogens in <25min.

We are reporting a most probable number approach integrated to loop mediated isothermal technique (MPN-LAMP) focusing on Gram-negative Escherichia coli and Gram-positive Enterococcus faecalis bacterial cells without nucleic acids extraction. LAMP assays for uidA from E. coli and gelE from E.

Direct loop mediated isothermal amplification on filters for quantification of Dehalobacter in groundwater.

Nucleic acid amplification of biomarkers is increasingly used to monitor microbial activity and assess remedial performance in contaminated aquifers. Previous studies described the use of filtration, elution, and direct isothermal amplification (i.e.