Tetrachloromethane-Degrading Bacterial Enrichment Cultures and Isolates from a Contaminated Aquifer

A microbial consortium led by a novel Pseudomonas species enables degradation of carbon tetrachloride under aerobic conditions

Carbon tetrachloride (CT) is a recalcitrant and high priority pollutant known for its toxicity, environmental prevalence, and inhibitory activities. Although much is known about anaerobic CT biodegradation, microbial degradation of CT under aerobic conditions has not yet been reported. This study reports for the first time the enrichment of a stable aerobic CT-degrading bacterial consortium, from a CT-contaminated groundwater sample, capable of co-metabolically degrading 30 μM of CT within a week. A Pseudomonas strain (designated as Stari2) that is the predominant bacterium in this consortium was isolated, and further characterization showed that this bacterium can tolerate and co-metabolically degrade up to 5 mM of CT under aerobic conditions in the presence of different carbon/energy sources. The CT biodegradation profiles of strain Stari2 and the consortium were found to be identical, while no significant positive correlation between strain Stari2 and other bacteria was observed in the consortium during the period of higher CT biodegradation. These results confirmed that the isolated Pseudomonas strain Stari2 is the key player in the consortium catalyzing the biodegradation of CT. No chloroform (CF) or other chlorinated compound was detected during the cometabolism of CT. The whole genome sequencing of strain Stari2 showed that it is a novel Pseudomonas species. The findings demonstrated that biodegradation of CT under aerobic conditions is feasible, and the isolated CT-degrader Pseudomonas sp. strain Stari2 has a great potential for in-situ bioremediation of CT-contaminated environments.

Reductive dehalogenation in groundwater by Si-Fe(II) co-precipitates enhanced by internal electric field and low vacancy concentrations

Fe(II) and silicate can form Si-Fe(II) co-precipitates in anoxic groundwater and sediments, but their phase composition and reactivity towards subsurface pollutants are largely unknown. Three types of Si-Fe(II) co-precipitations with the same chemical composition, namely Si-Fe(II)-I, Si-Fe(II)-II, and Si-Fe(II)-III, have been synthesized by different hydroxylation sequences in this work. It was found that Si-Fe(II)-III reduce carbon tetrachloride (CT) much faster (k₁=0.04419 min^-1) than Si-Fe(II)-I (0 min^-1) and Si-Fe(II)-II (7.860 × 10^-4 min^-1). XRD results show that the main component of Si-Fe(II)-III is ferrous silicate (FeSiO₃), which is quite different from that of Si-Fe(II)-I and Si-Fe(II)-II. The unique arrangement of hydroxyl coordination, the less distorted octahedral structure, the polyhedral morphology and the absence of Si-A center vacancies in Si-Fe(II)-III are responsible for its high reductive dehalogenation reactivity. The highest redox activity of Si-Fe(II)-III was shown by electrochemical characterization. The [Fe^II-O-Si]⁺ in Si-Fe(II)-III may stabilize the dichlorocarbene anion (˸CCl₂^-), which favors the transformation of CT to methane (9.2%). The Si-Fe(II) co-precipitates consist of countless internal electric fields, and the transformation of hydroxyl and CT both consumed electrons. The coexistence of hydroxyl and CT increases the electron density in the electron-rich region due to their electronegativity, enhancing their electron-accepting capabilities. This study deepens our understanding of the phase composition and electronic structure of Si-Fe(II) co-precipitates, which fills the gap in the reductive dehalogenation of halides by Si-Fe(II) co-precipitates.

Degradation Characteristics of Carbon Tetrachloride by Granular Sponge Zero Valent Iron

Granular sponge zero valent iron (ZVI) was employed to degrade carbon tetrachloride (CCl₄). The effects of acidic washing, initial solution pH, and ZVI dosage on CCl₄ degradation were investigated. Results showed that CCl₄ was effectively removed by ZVI and approximately 75% of CCl₄ was transformed into chloroform through hydrogenolysis. The rate of chloroform transformation was slower compared to that of CCl₄, resulting in chloroform accumulation. CCl₄ degradation was a pseudo first-order process. The observed pseudo first-order reaction rate constant (k_obs) for CCl₄ and chloroform were 0.1139 and 0.0109 h⁻¹, respectively, with a ZVI dosage of 20 g/L and an initial CCl₄ concentration of 20 mg/L. Surface acidic washing had a negligible effect on CCl₄ degradation with ZVI. The k_obs for CCl₄ degradation increased linearly with increasing ZVI dosage and the optimal dosage of ZVI was 20 g/L based on the surface area-normalized rate constants. The negative relationship between k_obs and the solution pH indicated that the degradation of CCl₄ by ZVI performed better under weakly acidic conditions.

Natural attenuation of pools and plumes of carbon tetrachloride and chloroform in the transition zone to bottom aquitards and the microorganisms involved in their degradation

In the transition zone between aquifers and aquitards, DNAPL pools of carbon tetrachloride and chloroform accumulate because of heterogeneity in this zone. Natural attenuation occurs at pools and plumes, indicating that remediation might be possible. The aims of the study were: i) to assess the role of heterogeneity in the natural attenuation of these compounds, ii) determine degradation processes within this zone, and iii) identify dechlorinating microorganisms. For this, groundwater concentrations, redox-sensitive parameters, CSIA isotopic and DGGE molecular techniques were used. The main findings at depth of the transition zone were: (1) the important key control played by heterogeneity on natural attenuation of contaminants. (2) Heterogeneity caused the highly anoxic environment and dominant sulfate-reducing conditions, which accounts for more efficient natural attenuation. (3) Heterogeneity also explains that the transition zone constitutes an ecotone. (4) The bacteria size exclusion is governed by the pore throat threshold and determines the penetration of dechlorinating microorganisms into the finest sediments, which is relevant, since it implies the need to verify whether microorganisms proposed for bioremediation can penetrate these materials. (5) Reductive dechlorination caused the natural attenuation of contaminants in groundwater and porewater of fine sediments. In the case of carbon tetrachloride, it was an abiotic process biogenically mediated by A. suillum, a bacterium capable of penetrating the finest sediments. In the case of chloroform, it was a biotic process performed by a Clostridiales bacterium, which is unable to penetrate the finest materials. (6) Both microorganisms have potential to be biostimulated to dechlorinate contaminants in the source and the plume in the transition zone. These outcomes are particularly relevant given the longevity of DNAPL sources and have considerable environmental implications as many supply wells in industrial areas exploit aquifers contaminated by chlorinated solvents emerging from DNAPL pools accumulated on the low-conductivity layers in transition zones.

Dichloromethane biodegradation in multi-contaminated groundwater: Insights from biomolecular and compound-specific isotope analyses

Dichloromethane (DCM) is a widespread and toxic industrial solvent which often co-occurs with chlorinated ethenes at polluted sites. Biodegradation of DCM occurs under both oxic and anoxic conditions in soils and aquifers. Here we investigated in situ and ex situ biodegradation of DCM in groundwater sampled from the industrial site of Themeroil (France), where DCM occurs as a major co-contaminant of chloroethenes. Carbon isotopic fractionation (ε_C) for DCM ranging from -46 to -22‰ were obtained under oxic or denitrifying conditions, in mineral medium or contaminated groundwater, and for laboratory cultures of Hyphomicrobium sp. strain GJ21 and two new DCM-degrading strains isolated from the contaminated groundwater. The extent of DCM biodegradation (B%) in the aquifer, as evaluated by compound-specific isotope analysis (δ¹³C), ranged from 1% to 85% applying DCM-specific ε_C derived from reference strains and those determined in this study. Laboratory groundwater microcosms under oxic conditions showed DCM biodegradation rates of up to 0.1 mM·day^-1, with concomitant chloride release. Dehalogenase genes dcmA and dhlA involved in DCM biodegradation ranged from below 4 × 10² (boundary) to 1 × 10⁷ (source zone) copies L^-1 across the contamination plume. High-throughput sequencing on the 16S rrnA gene in groundwater samples showed that both contaminant level and terminal electron acceptor processes (TEAPs) influenced the distribution of genus-level taxa associated with DCM biodegradation. Taken together, our results demonstrate the potential of DCM biodegradation in multi-contaminated groundwater. This integrative approach may be applied to contaminated aquifers in the future, in order to identify microbial taxa and pathways associated with DCM biodegradation in relation to redox conditions and co-contamination levels.

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

The aim of this study is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.IMPORTANCE The key chloroethene-dechlorinating bacterium Dehalococcoides mccartyi is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between Dehalococcoides and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of Veillonellaceae species in the communities compared to other coexisting community members in producing and providing corrinoids for Dehalococcoides species under cobalamin-limited conditions.

Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum

The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45.