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

Syngas-driven sewage sludge conversion to microbial protein through H2S- and CO-tolerant hydrogen-oxidizing bacteria

Treating excess municipal sewage sludge (MSS) by means of thermochemical processes could enable its conversion into high-value microbial protein (MP) through syngas. Nevertheless, the variable composition and content of inhibitory compounds of the latter hinders the application potential of such a biorefinery scheme. Through a series of short- (48 to 96 h) and long-term (30 days) batch aerobic bioconversion tests, the present study aimed at investigating the potential of a mixed culture of hydrogen-oxidizing bacteria (HOB) to produce MP from a simulated syngas mixture characterized by variable H2 and CO2 concentrations, and different levels of CO and H2S as potential inhibitors of the HOB-driven process. Syngas was converted into MP with a protein content as high as 74 %, reaching biomass yields of 0.25 g VSS/g H2-COD, close to the maximum reported HOB yield of 0.28 g VSS/g H2-COD,  and volumetric productivities of 16 mg VSS/L/h. The potential of the process to provide between 50 and 100 % of the total nitrogen requirement of HOB solely by means of the gaseous ammonia nitrogen recovered through syngas was also preliminarily calculated. The presence of H2S and CO concentrations up to 0.4 % and up to 40 %, respectively, and a wide range of H2/CO2 ratios (2 - 10) had no negative influence on the main process performances. The role played by H2S- and CO-tolerant HOB species was fundamental to guarantee a high tolerance to microbial inhibitors, and demonstrated the high potential of mixed cultures for resource recovery and valorisation.

Direct aerobic oxidation (DAO) of chlorinated aliphatic hydrocarbons: A review of key DAO bacteria, biometabolic pathways and in-situ bioremediation potential

Contamination of aquifers and vadose zones with chlorinated aliphatic hydrocarbons (CAH) is a world-wide issue. Unlike other reactions, direct aerobic oxidation (DAO) of CAHs does not require growth substrates and avoids the generation of toxic by-products. Here, we critically review the current understanding of chlorinated aliphatic hydrocarbons-DAO and its application in bioreactors and at the field scale. According to reports on chlorinated aliphatic hydrocarbons-DAO bacteria, isolates mainly consisted of Methylobacterium and Proteobacterium. Chlorinated aliphatic hydrocarbons-DAO bacteria are characterized by tolerance to a high concentration of CAHs and highly efficient removal of CAHs. Trans-1,2-dichloroethylene (t-DCE) is easily transformed biomass for bacteria, followed by 1,2-dichloroethane (1,2-DCA), dichloromethane (DCM), vinyl chloride (VC) and cis-1,2-dichloroethylene (c-DCE). Significant differences in the maximum specific growth rates were observed with different CAHs and biometabolic pathways for DCM, 1,2-DCA, VC and c-DCE degradation have been successfully parsed. Detection of the functional genes etnC and etnE is useful for the determination of active VC DAO bacteria. Additionally, DAO bacteria have been successfully applied to CAHs in new types of bioreactors with satisfactory results. To the best of the authors' knowledge, only one study on DAO-CAHs was conducted in-situ and resulted in 99% CAH removal. Lastly, we put forward future development prospect of chlorinated aliphatic hydrocarbons-DAO.

Biodegradation of a Complex Phenolic Industrial Stream by Bacterial Strains Isolated from Industrial Wastewaters

Molecular and metabolomic tools were used to design and understand the biodegradation of phenolic compounds in real industrial streams. Bacterial species were isolated from an industrial wastewater treatment plant of a phenol production factory and identified using molecular techniques. Next, the biodegradation potential of the most promising strains was analyzed in the presence of a phenolic industrial by-product containing phenol, alfa-methylstyrene, acetophenone, 2-cumylphenol, and 4-cumylphenol. A bacterial consortium comprising Pseudomonas and Alcaligenes species was assessed for its ability to degrade phenolic compounds from the phenolic industrial stream (PS). The consortium adapted itself to the increasing levels of phenolic compounds, roughly up to 1750 ppm of PS; thus, becoming resistant to them. In addition, the consortium exhibited the ability to grow in the presence of PS in repeated batch mode processes. Results from untargeted metabolomic analysis of the culture medium in the presence of PS suggested that bacteria transformed the toxic phenolic compounds into less harmful molecules as a survival mechanism. Overall, the study demonstrates the usefulness of massive sequencing and metabolomic tools in constructing bacterial consortia that can efficiently biodegrade complex PS. Furthermore, it improves our understanding of their biodegradation capabilities.

Mini Review: Advances in 2-Haloacid Dehalogenases

The 2-haloacid dehalogenases (EC 3.8.1.X) are industrially important enzymes that catalyze the cleavage of carbon-halogen bonds in 2-haloalkanoic acids, releasing halogen ions and producing corresponding 2-hydroxyl acids. These enzymes are of particular interest in environmental remediation and environmentally friendly synthesis of optically pure chiral compounds due to their ability to degrade a wide range of halogenated compounds with astonishing efficiency for enantiomer resolution. The 2-haloacid dehalogenases have been extensively studied with regard to their biochemical characterization, protein crystal structures, and catalytic mechanisms. This paper comprehensively reviews the source of isolation, classification, protein structures, reaction mechanisms, biochemical properties, and application of 2-haloacid dehalogenases; current trends and avenues for further development have also been included.

Water table fluctuations affect dichloromethane biodegradation in lab-scale aquifers contaminated with organohalides

Dichloromethane (DCM) is a toxic industrial solvent frequently detected in multi-contaminated aquifers. It can be degraded biotically or abiotically, and under oxic or anoxic conditions. The extent and pathways of DCM degradation in aquifers may thus depend on water table fluctuations and microbial responses to hydrochemical variations. Here, we examined the effect of water table fluctuations on DCM biodegradation in two laboratory aquifers fed with O₂-depleted DCM-spiked groundwater from a well-characterized former industrial site. Hydrochemistry, stable isotopes of DCM (δ¹³C and δ³⁷Cl), and bacterial community composition were examined to determine DCM mass removal and degradation pathways under steady-state (static water table) and transient (fluctuating water table) conditions. DCM mass removal was more pronounced under transient (95%) than under steady-state conditions (42%). C and Cl isotopic fractionation values were larger under steady-state (ε_bulk^C = -23.6 ± 3.2‰, and ε_bulk^Cl= -8.7 ± 1.6‰) than under transient conditions (ε_bulk^C = -11.8 ± 2.0‰, and ε_bulk^Cl = -3.1 ± 0.6‰). Dual C-Cl isotope analysis suggested the prevalence of distinct anaerobic DCM degradation pathways, with Λ^C/Cl values of 1.92 ± 0.30 and 3.58 ± 0.42 under steady-state and transient conditions, respectively. Water table fluctuations caused changes in redox conditions and oxygen levels, resulting in a higher relative abundance of Desulfosporosinus (Peptococcaceae family). Taken together, our results show that water table fluctuations enhanced DCM biodegradation, and correlated with bacterial taxa associated with anaerobic DCM degradation. Our integrative approach allows to evaluate anaerobic DCM degradation under dynamic hydrogeological conditions, and may help improving bioremediation strategies at DCM contaminated sites.

Novel dichloromethane-fermenting bacteria in the Peptococcaceae family

Dichloromethane (DCM; CH2Cl2) is a toxic groundwater pollutant that also has a detrimental effect on atmospheric ozone levels. As a dense non-aqueous phase liquid, DCM migrates vertically through groundwater to low redox zones, yet information on anaerobic microbial DCM transformation remains scarce due to a lack of cultured organisms. We report here the characterisation of DCMF, the dominant organism in an anaerobic enrichment culture (DFE) capable of fermenting DCM to the environmentally benign product acetate. Stable carbon isotope experiments demonstrated that the organism assimilated carbon from DCM and bicarbonate via the Wood-Ljungdahl pathway. DCMF is the first anaerobic DCM-degrading population also shown to metabolise non-chlorinated substrates. It appears to be a methylotroph utilising the Wood-Ljungdahl pathway for metabolism of methyl groups from methanol, choline, and glycine betaine. The flux of these substrates from subsurface environments may either directly (DCM, methanol) or indirectly (choline, glycine betaine) affect the climate. Community profiling and cultivation of cohabiting taxa in culture DFE without DCMF suggest that DCMF is the sole organism in this culture responsible for substrate metabolism, while the cohabitants persist via necromass recycling. Genomic and physiological evidence support placement of DCMF in a novel genus within the Peptococcaceae family, 'Candidatus Formimonas warabiya'.

Chlorinated ethene biodegradation and associated bacterial taxa in multi-polluted groundwater: Insights from biomolecular markers and stable isotope analysis

Chlorinated ethenes (CEs) are most problematic pollutants in groundwater. Dehalogenating bacteria, and in particular organohalide-respiring bacteria (OHRB), can transform PCE to ethene under anaerobic conditions, and thus contribute to bioremediation of contaminated sites. Current approaches to characterize in situ biodegradation of CEs include hydrochemical analyses, quantification of the abundance of key species (e.g. Dehalococcoides mccartyi) and dehalogenase genes (pceA, vcrA, bvcA and tceA) involved in different steps of organohalide respiration (OHR) by qPCR, and compound-specific isotope analysis (CSIA) of CEs. Here we combined these approaches with sequencing of 16S rRNA gene amplicons to consider both OHRB and bacterial taxa involved in CE transformation at a multi-contaminated site. Integrated analysis of hydrogeochemical characteristics, gene abundances and bacterial diversity shows that bacterial diversity and OHRB mainly correlated with hydrogeochemical conditions, suggesting that pollutant exposure acts as a central driver of bacterial diversity. CSIA, abundances of four reductive dehalogenase encoding genes and the prevalence of Dehalococcoides highlighted sustained PCE, DCE and VC degradation in several wells of the polluted plume. These results suggest that bacterial taxa associated with OHR play an essential role in natural attenuation of CEs, and that representatives of taxa including Dehalobacterium and Desulfosporosinus co-occur with Dehalococcoides. Overall, our study emphasizes the benefits of combining several approaches to evaluate the interplay between the dynamics of bacterial diversity in CE-polluted plumes and in situ degradation of CEs, and to contribute to a more robust assessment of natural attenuation at multi-polluted sites.

Transcriptional regulation of organohalide pollutant utilisation in bacteria

Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.

Proteotyping Environmental Microorganisms by Phylopeptidomics: Case Study Screening Water from a Radioactive Material Storage Pool

The microbial diversity encompassed by the environmental biosphere is largely unexplored, although it represents an extensive source of new knowledge and potentially of novel enzymatic catalysts for biotechnological applications. To determine the taxonomy of microorganisms, proteotyping by tandem mass spectrometry has proved its efficiency. Its latest extension, phylopeptidomics, adds a biomass quantitation perspective for mixtures of microorganisms. Here, we present an application of phylopeptidomics to rapidly and sensitively screen microorganisms sampled from an industrial environment, i.e., a pool where radioactive material is stored. The power of this methodology is demonstrated through the identification of both prokaryotes and eukaryotes, whether as pure isolates or present as mixtures or consortia. In this study, we established accurate taxonomical identification of environmental prokaryotes belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla, as well as eukaryotes from the Ascomycota phylum. The results presented illustrate the potential of tandem mass spectrometry proteotyping, in particular phylopeptidomics, to screen for and rapidly identify microorganisms.

Interspecies interaction and effect of co-contaminants in an anaerobic dichloromethane-degrading culture

An anaerobic stable mixed culture dominated by bacteria belonging to the genera Dehalobacterium, Acetobacterium, Desulfovibrio, and Wolinella was used as a model to study the microbial interactions during DCM degradation. Physiological studies indicated that DCM was degraded in this mixed culture at least in a three-step process: i) fermentation of DCM to acetate and formate, ii) formate oxidation to CO₂ and H₂, and iii) H₂/CO₂ reductive acetogenesis. The 16S rRNA gene sequencing of cultures enriched with formate or H₂ showed that Desulfovibrio was the dominant population followed by Acetobacterium, but sequences representing Dehalobacterium were only present in cultures amended with DCM. Nuclear magnetic resonance analyses confirmed that acetate produced from ¹³C-labelled DCM was marked at the methyl ([2-¹³C]acetate), carboxyl ([1-¹³C]acetate), and both ([1,2-¹³C]acetate) positions, which is in accordance to acetate formed by both direct DCM fermentation and H₂/CO₂ acetogenesis. The inhibitory effect of ten different co-contaminants frequently detected in groundwaters on DCM degradation was also investigated. Complete inhibition of DCM degradation was observed when chloroform, perfluorooctanesulfonic acid, and diuron were added at 838, 400, and 107 μM, respectively. However, the inhibited cultures recovered the DCM degradation capability when transferred to fresh medium without co-contaminants. Findings derived from this work are of significant relevance to provide a better understanding of the synergistic interactions among bacteria to accomplish DCM degradation as well as to predict the effect of co-contaminants during anaerobic DCM bioremediation in groundwater.

Integrative isotopic and molecular approach for the diagnosis and implementation of an efficient in-situ enhanced biological reductive dechlorination of chlorinated ethenes

Based on the previously observed intrinsic bioremediation potential of a site originally contaminated with perchloroethene (PCE), field-derived lactate-amended microcosms were performed to test different lactate isomers and concentrations, and find clearer isotopic and molecular parameters proving the feasibility of an in-situ enhanced reductive dechlorination (ERD) from PCE-to-ethene (ETH). According to these laboratory results, which confirmed the presence of Dehalococcoides sp. and the vcrA gene, an in-situ ERD pilot test consisting of a single injection of lactate in a monitoring well was performed and monitored for 190 days. The parameters used to follow the performance of the ERD comprised the analysis of i) hydrochemistry, including redox potential (Eh), and the concentrations of redox sensitive species, chlorinated ethenes (CEs), lactate, and acetate; ii) stable isotope composition of carbon of CEs, and sulphur and oxygen of sulphate; and iii) 16S rRNA gene sequencing from groundwater samples. Thus, it was proved that the injection of lactate promoted sulphate-reducing conditions, with the subsequent decrease in Eh, which allowed for the full reductive dechlorination of PCE to ETH in the injection well. The biodegradation of CEs was also confirmed by the enrichment in ¹³C and carbon isotopic mass balances. The metagenomic results evidenced the shift in the composition of the microbial population towards the predominance of fermentative bacteria. Given the success of the in-situ pilot test, a full-scale ERD with lactate was then implemented at the site. After one year of treatment, PCE and trichloroethene were mostly depleted, whereas vinyl chloride (VC) and ETH were the predominant metabolites. Most importantly, the shift of the carbon isotopic mass balances towards more positive values confirmed the complete reductive dechlorination, including the VC-to-ETH reaction step. The combination of techniques used here provides complementary lines of evidence for the diagnosis of the intrinsic biodegradation potential of a polluted site, but also to monitor the progress, identify potential difficulties, and evaluate the success of ERD at the field scale.

A multi-path chain kinetic reaction model to predict the evolution of 1,1,1-trichloroethane and its daughter products contaminant-plume in permeable reactive bio-barriers

Permeable reactive bio-barriers (Bio-PRBs) are a new and developing technique for in situ remediation of groundwater contamination. Some remediation technologies have often been impeded by insufficient understanding of contaminant transport and transformation in the subsurface environment. Therefore, advanced knowledge in contaminant transport and reactions in Bio-PRBs will be crucial to the successful practical application of this technique. A two-dimensional reaction model C1 was developed for predicting the multi-path chain kinetic reaction of 1,1,1-trichloroethane (1,1,1-TCA) in Bio-PRBs. This study demonstrates that model C1 is able to predict the 1,1,1-TCA breakthrough time and rapidly evaluate the Bio-PRBs retardation performance. The results show that microbial growth and immobilization are the key factors that affect the retardation and remediation performance of Bio-PRBs. The free growth of microorganisms had significant negative effects on hydraulic conductivity (K) in the zero-valent iron (ZVI) region of free microorganism Bio-PRBs (FM-PRBs). The total head loss in the FM-PRB was 9.0 cm, which was significantly greater than the head loss (6.5 cm) of immobilized microorganism Bio-PRBs (IM-PRBs). Compared to ZVI-PRBs and FM-PRBs, the numerical simulation results reveal that microbial immobilization significantly improves the remediation performance of IM-PRBs by 550.9% and 32.7%, respectively. The dual effect of microorganisms leads to significant differences in the 1,1,1-TCA and daughter products (1,1-dichloroethane, 1,1-dichloroethene, chloroethane and vinyl chloride) contaminant-plume evolution between FM-PRBs and IM-PRBs. In addition, model C1 can be utilized to design standard Bio-PRBs for real site of 1,1,1-TCA contanminated groundwater. To meet the safety standard of groundwater as potable water, the width of IM-PRBs needs to be increased by 24 cm. However, in FM-PRBs, the width needs to be increased by 42 cm. Therefore, IM-PRBs save costs significantly. This work has successfully used a model to optimize Bio-PRBs and to predict 1,1,1-TCA and daughter products contaminant-plume evolution in different Bio-PRBs.

Tracking the Multistep Formation of Ln(III) Complexes with in situ Schiff Base Exchange Reaction and its Highly Selective Sensing of Dichloromethane

Four complexes, namely, [Ln₂(L2)₂(NO₃)₄]. 2CH₃OH (Ln = Tb (1), Dy (2), Ho (3), Er (4), and L2 = (E)-2-methoxy-6-(((pyridin-2-ylmethyl)imino)methyl)phenol), were obtained by reacting (E)-2-((3-methoxy-2-oxidobenzylidene)amino)ethanesulfonate (L1), Ln(NO₃)₃·6H₂O, and 2-aminomethylpyridine at room temperature under solvothermal conditions in methanol for 12 h. The new Schiff base L2 was generated in situ based on the organic ligand L1 and 2-aminomethylpyridine through Schiff base exchange reaction by using lanthanide salts as inductor. A combination of crystallography and mass spectrometry was performed to track the exchange reaction, and the underlying mechanism accompanied by the complex assembly process was clearly presented. The multistep formation mechanism of the above dinuclear complex was also proposed, i.e., [L1] → Dy[L1]/[L2] → Dy[L2] → Dy[L2]₂ → Dy₂[L2]₂. Luminescence test of 1 showed that it had extremely high selectivity to dichloromethane (CH₂Cl₂). Therefore, we established a quick, simple, and efficient method of detecting CH₂Cl₂ that enabled strong-luminescence observation with the naked eye. Tests for small amounts of CH₂Cl₂ in water further indicated the potential of 1 as a test strip for CH₂Cl₂ fluorescence detection in water samples. Alternating-current magnetic susceptibility studies indicated the field-induced single-molecule magnet behavior of 2.

Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds

Organic and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems.

Dual Carbon-Chlorine Isotope Analysis Indicates Distinct Anaerobic Dichloromethane Degradation Pathways in Two Members of Peptococcaceae

Dichloromethane (DCM) is a probable human carcinogen and frequent groundwater contaminant and contributes to stratospheric ozone layer depletion. DCM is degraded by aerobes harboring glutathione-dependent DCM dehalogenases; however, DCM contamination occurs in oxygen-deprived environments, and much less is known about anaerobic DCM metabolism. Some members of the Peptococcaceae family convert DCM to environmentally benign products including acetate, formate, hydrogen (H₂), and inorganic chloride under strictly anoxic conditions. The current study applied stable carbon and chlorine isotope fractionation measurements to the axenic culture Dehalobacterium formicoaceticum and to the consortium RM comprising DCM degrader Candidatus Dichloromethanomonas elyunquensis. Degradation-associated carbon and chlorine isotope enrichment factors (ε_C and ε_Cl) of -42.4 ± 0.7‰ and -5.3 ± 0.1‰, respectively, were measured in D. formicoaceticum cultures. A similar ε_Cl of -5.2 ± 0.1‰, but a substantially lower ε_C of -18.3 ± 0.2‰, were determined for Ca. Dichloromethanomonas elyunquensis. The ε_C and ε_Cl values resulted in distinctly different dual element C-Cl isotope correlations (Λ^C/Cl = Δδ¹³C/Δδ³⁷Cl) of 7.89 ± 0.12 and 3.40 ± 0.03 for D. formicoaceticum and Ca. Dichloromethanomonas elyunquensis, respectively. The distinct Λ^C/Cl values obtained for the two cultures imply mechanistically distinct C-Cl bond cleavage reactions, suggesting that members of Peptococcaceae employ different pathways to metabolize DCM. These findings emphasize the utility of dual carbon-chlorine isotope analysis to pinpoint DCM degradation mechanisms and to provide an additional line of evidence that detoxification is occurring at DCM-contaminated sites.