Dynamics of organohalide-respiring bacteria and their genes following in-situ chemical oxidation of chlorinated ethenes and biostimulation

Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges

Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.

Early stage biofilm formation on bio-based microplastics in a freshwater reservoir

Bio-based plastics (BP) produced from renewable biomass resources, such as high-density polyethylene (HDPE), polylactic acid (PLA) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), is currently increasing in terms of both products and applications. However, their biodegradability and environmental fate are not yet fully understood, especially in freshwaters. Here, we present the results of an in-situ study in a freshwater reservoir, where we submerged HDPE, PLA and PHBV microscale BP (mBP) in dialysis bags to enable exchange of small organic and inorganic molecules, including nutrients, with the surrounding water. After one and two months, the bacterial biofilm that formed on each mBP was characterised by 16S rRNA amplicon sequencing. After two-months, Oxalobacteraceae, Pedosphaeraceae, Flavobacteriaceae (Flavobacterium) and Chitinophagaceae (Ferruginibacter) had increased by up to four times. Both these and other common members (≥1 % relative total biomass) of the microbial community were similarly abundant on all mBP. Low-abundance (0.3-1 %) bacterial taxa, however, were significantly more diverse and differed on each mBP. Notably, some low-abundance families and genera increased on specific materials, e.g. Sphingomonadaceae on HDPE, Sphingobacteriaceae on PHBV, Gemmatimonas and Crenothrix on PLA. Overall, abundant bacteria were regarded as a pioneering community, while low-abundance bacteria were more diverse and preferred mBP types in the early stages of biofilm formation on mBP. It could be influenced by the environmental conditions, where nutrient levels and low temperatures might shape the low-abundance of attached bacterial communities than the plastic material itself.

Field application of glycerol to enhance reductive dechlorination of chlorinated ethenes and its impact on microbial community

Chlorinated ethenes (CEs) are common and persistent contaminants of soil and groundwater. Their degradation is mostly driven by a process of bacterial reductive dechlorination (also called organohalide respiration) in anaerobic conditions. This study summarizes the outcomes of the long-term in-situ application of glycerol for the enhanced reductive dechlorination of CEs on a highly contaminated site. Glycerol injection resulted in an almost immediate increase in the abundance of fermentative Firmicutes, which produce essential sources of carbon (acetate) and electrons (H₂) for organohalide-respiring bacteria (OHRB) and change groundwater conditions to be suitable for OHRB growth. The decreased redox potential of groundwater promoted also the proliferation of sulfate-reducing bacteria, which compete for electron donors with OHRB but at the same time support their growth by producing essential corrinoids and acetate. A considerable increase in the abundance of OHRB Dehalococcoides, concurrently with vinyl chloride (VC) reductase gene levels, was revealed by real time polymerase chain reaction (qPCR) method. Consistent with the shifts in bacterial populations, the concentrations of pollutants tetrachloroethylene and trichloroethylene decreased during the monitoring period, with rising levels of cis-1,2-dichloroethylene, VC, and most importantly, the final CE degradation products: ethene and ethane. Our study implies the importance of syntrophic bacterial interactions for successful and complete CE degradation and evaluates glycerol as convenient substrate to enhance reductive dechlorination and as an effective source of electrons for OHRB.

Cleanup chlorinated ethene-polluted groundwater using an innovative immobilized Clostridium butyricum column scheme: A pilot-scale study

In this study, the developed innovative immobilized Clostridium butyricum (ICB) (hydrogen-producing bacteria) column scheme was applied to cleanup chlorinated-ethene [mainly cis-1,2-dichloroethene (cis-DCE)] polluted groundwater in situ via the anaerobic reductive dechlorinating processes. The objectives were to assess the effectiveness of the field application of ICB scheme on the cleanup of cis-DCE polluted groundwater, and characterize changes of microbial communities after ICB application. Three remediation wells and two monitor wells were installed within the cis-DCE plume. In the remediation well, a 1.2-m PVC column (radius = 2.5 cm) (filled with ICB beads) and 20 L of slow polycolloid-releasing substrate (SPRS) were supplied for hydrogen production enhancement and primary carbon supply, respectively. Groundwater samples from remediation and monitor wells were analyzed periodically for cis-DCE and its degradation byproducts, microbial diversity, reductive dehalogenase, and geochemical indicators. Results reveal that cis-DCE was significantly decreased within the ICB and SPRS influence zone. In a remediation well with ICB injection, approximately 98.4% of cis-DCE removal (initial concentration = 1.46 mg/L) was observed with the production of ethene (end-product of cis-DCE dechlorination) after 56 days of system operation. Up to 0.72 mg/L of hydrogen was observed in remediation wells after 14 days of ICB and SPRS introduction, which corresponded with the increased population of Dehalococcoides spp. (Dhc) (increased from 3.76 × 103 to 5.08 × 105 gene copies/L). Results of metagenomics analyses show that the SPRS and ICB introduction caused significant impacts on the bacterial communities, and increased Bacteroides, Citrobacter, and Desulfovibrio populations were observed, which had significant contributions to the reductive dechlorination of cis-DCE. Application of ICB could effectively result in increased populations of Dhc and RDase genes, which corresponded with improved dechlorination of cis-DCE and vinyl chloride. Introduction of ICB and SPRS could be applied as a potential in situ remedial option to enhance anaerobic dechlorination efficiencies of chlorinated ethenes.

Analysis of nitrifying bacteria growth on two new types of biomass carrier using respirometry and molecular genetic methods

This work addresses the testing of two newly produced biomass carriers (micro- and nanofibers) and one commercially available AnoxKaldnes™ K3 carrier in a laboratory post-nitrification reactor. The carriers were prepared under parameters suitable for high-quality biomass adhesion to their surface, and each was characterized by its specific structures. As part of the evaluation of the biofilms using respirometry and molecular genetic methods, the carriers were assessed in terms of their effectiveness and comparability. The rate of biofilm development was dependent on the structure and surface properties of the individual carriers. The results showed that the biofilm most strongly adhered to nanofiber carriers, where nitrating bacteria's slower but more abundant development occurred. Microfiber carriers were more stable, but a diverse internal structure may be unsuitable in a populated carrier's early stages. The AnoxKaldnes™ K3 carriers showed the slowest growth of biofilm, but the monitored nitrifying bacteria were abundant after an extended time. AOB representatives are likely to prefer an environment with a high amount of biomass and a large active area. Conversely, NOB representatives thrive better in a slowly forming biofilm. The methods used to monitor biofilm are challenging to compare directly, but they do complement each other, which aids in verifying the individual test results. Developing new types of biomass carriers with the potential for high-quality adhesion of microorganisms is a prerequisite for the expansion of highly efficient biotechnological processes, especially for wastewater treatment.

Discovering the potential of an nZVI-biochar composite as a material for the nanobioremediation of chlorinated solvents in groundwater: Degradation efficiency and effect on resident microorganisms

Abiotic and biotic remediation of chlorinated ethenes (CEs) in groundwater from a real contaminated site was studied using biochar-based composites containing nanoscale zero-valent iron (nZVI/BC) and natural resident microbes/specific CE degraders supported by a whey addition. The material represented by the biochar matrix decorated by isolated iron nanoparticles or their aggregates, along with the added whey, was capable of a stepwise dechlorination of CEs. The tested materials (nZVI/BC and BC) were able to decrease the original TCE concentration by 99% in 30 days. Nevertheless, regarding the transformation products, it was clear that biotic as well as abiotic transformation mechanisms were involved in the transformation process when nonchlorinated volatiles (i.e., methane, ethane, ethene, and acetylene) were detected after the application of nZVI/BC and nZVI/BC with whey. The whey addition caused a massive increase in bacterial biomass in the groundwater samples (monitored by 16S rRNA sequencing and qPCR) that corresponded with the transformation of trichloro- and dichloro-CEs, and this process was accompanied by the formation of less chlorinated products. Moreover, the biostimulation step also eliminated the adverse effect caused by nZVI/BC (decrease in microbial biomass after nZVI/BC addition). The nZVI/BC material or its aging products, and probably together with vinyl chloride-respiring bacteria, were able to continue the further reductive dechlorination of dichlorinated CEs into nonhalogenated volatiles. Overall, the results of the present study demonstrate the potential, feasibility, and environmental safety of this nanobioremediation approach.

Application of nanofiber carriers for sampling of microbial biomass from contaminated groundwater

Sampling of microbial biomass is crucial for understanding and controlling remediation processes ongoing at contaminated sites in general, particularly when molecular genetic analyses are employed. In this study, fiber-based carriers with a nanofiber layer were developed and tested as a method to sample microbial biomass in groundwater for molecular genetic analysis. Nanofiber carriers, varying in the shape and the linear density of nanofibers, were examined throughout a 27-month monitoring period in groundwater contaminated with benzene, toluene, ethylbenzene and xylene isomers (BTEX), and chlorinated ethenes. The effect of carrier shape and nanofiber layer density on the microbial surface colonization and composition of the microbial biofilm was determined using real-time PCR and next-generation sequencing (NGS) analysis. Differences in microbial community composition between nanofiber carriers, groundwater, and soil samples were also analyzed to assess the applicability of carriers for biomass sampling at contaminated sites. The nanofiber carriers showed their applicability as a sampling tool, particularly because of their easy manipulation that facilitates DNA isolation. The majority of taxa (Proteobacteria, Firmicutes, and Bacteroidetes) present on the carrier surfaces were also detected in the groundwater. Moreover, the microbial community on all nanofiber carriers reflected the changes in the chemical composition of groundwater. Although the carrier characteristics (shape, nanofiber layer) did not substantially influence the microbial community on the carrier surface, the circular and planar carriers with a nanofiber layer displayed faster microbial surface colonization. However, the circular carrier was the most suitable for biomass sampling in groundwater because of its high contact area and because it does not require pre-treatment prior to DNA extraction.

A Multidisciplinary Approach to Evaluate the Effectiveness of Natural Attenuation at a Contaminated Site

This study evaluates the natural attenuation of chlorinated hydrocarbons as remediation action in a contaminated site downtown the city of Parma (Italy). To achieve this goal, a combination of new investigation methods (bio-molecular analysis, compound specific isotope analysis, phytoscreening) has been proposed. The approach (named circular multi step) allows to: fully understand the phenomena that occur at the study site, design new investigation activities, and manage best practices. Consequently, each step of the approach improves the conceptual and numerical models with new knowledge. The activities carried out at the study site allowed to detect a contamination of perchloroethylene in a large part of the city of Parma and, of main importance, underneath a kindergarten. The results of the study did not show significant natural attenuation of chlorinated hydrocarbons and that the detected contamination could refer to the same unknown contaminant source. Furthermore, the innovative phytoscreening technique was applied to assess the presence of chlorinated hydrocarbons at the ground level. The plume spread was estimated through numerical modeling starting from potential contaminant sources. This study enhances the knowledge of groundwater flow and contamination in Parma and allows authorities to design new investigation/reclamation activities through management actions.

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.

Effect of chelated iron activated peroxydisulfate oxidation on perchloroethene-degrading microbial consortium

In this work, the effect of In-Situ Chemical Oxidation (ISCO) using peroxydisulfate (PDS) on chloroethenes-degrading microbial consortium in the presence of perchloroethene (PCE; tetrachloroethene) was investigated. Degradation of PCE was examined using PDS without an activation, activated with iron Fe(II) chelated by citric acid (CA), and microbial consortium derived from chloroethenes-contaminated site in liquid and sand microcosms. Two different molar ratios of PCE/PDS/(Fe(II)+CA) (1/8/1.6 and 1/16/3.2) were tested. The PCE removal efficiency was the highest in the bacteria-free microcosms. An expected increase in the PCE removal efficiency by coupling PDS and microbial consortium was not confirmed. Surprisingly, the reduced capacity of PDS to remove PCE in the systems containing both PDS and microbial consortium was observed indicating that indigenous microbes may reduce the efficiency of PDS during a remediation. High-throughput 16S rRNA gene sequencing analysis revealed negative effect of PDS on organohalide-respiring bacteria (OHRB), which were not detected after 19 days of the experiment, unlike in biotic control. On the other hand, amplicon sequence variants (ASVs) affiliated with genera Brevundimonas and Pseudomonas that have been described for their capability of aerobic cometabolic/metabolic degradation of chloroethenes (CEs) were among the most frequently detected ASVs after the PDS treatment. Results further showed that the sole Fe(II)-CA affected the diversity of the microbial consortium. Overall, results of this study provide new insight into the coupling ISCO using PDS with in situ bioremediation of CEs.

Biotechnology and nanotechnology for remediation of chlorinated volatile organic compounds: current perspectives

Chlorinated volatile organic compounds (CVOCs) are persistent organic pollutants which are harmful to public health and the environment. Many CVOCs occur in substantial quantities in groundwater and soil, even though their use has been more carefully managed and restricted in recent years. This review summarizes recent data on several innovative treatment solutions for CVOC-affected media including bioremediation, phytoremediation, nanoscale zero-valent iron (nZVI)-based reductive dehalogenation, and photooxidation. There is no optimally developed single technology; therefore, the possibility of using combined technologies for CVOC remediation, for example bioremediation integrated with reduction by nZVI, is presented. Some methods are still in the development stage. Advantages and disadvantages of each treatment strategy are provided. It is hoped that this paper can provide a basic framework for selection of successful CVOC remediation strategies.

Combining nanoscale zero-valent iron with electrokinetic treatment for remediation of chlorinated ethenes and promoting biodegradation: A long-term field study

Nanoscale zero-valent iron (nZVI) is recognized as a powerful tool for the remediation of groundwater contaminated by chlorinated ethenes (CEs). This long-term field study explored nZVI-driven degradation of CEs supported by electrokinetic (EK) treatment, which positively affects nZVI longevity and migration, and its impact on indigenous bacteria. In particular, the impact of combined nZVI-EK treatment on organohalide-respiring bacteria, ethenotrophs and methanotrophs (all capable of CE degradation) was assessed using molecular genetic markers detecting Dehalococcoides spp., Desulfitobacterium spp., the reductive dehalogenase genes vcrA and bvcA and ethenotroph and methanotroph functional genes. The remediation treatment resulted in a rapid decrease of the major pollutant cis-1,2-dichloroethene (cDCE) by 75% in the affected area, followed by an increase in CE degradation products methane, ethane and ethene. The newly established geochemical conditions in the treated aquifer not only promoted growth of organohalide-respiring bacteria but also allowed for the concurrent presence of vinyl chloride- and cDCE-oxidizing methanotrophs and (especially) ethenotrophs, which proliferated preferentially in the vicinity of an anode where low levels of oxygen were produced. The nZVI treatment resulted in a temporary negative impact on indigenous bacteria in the application well close to the cathode; but even there, the microbiome was restored within 15 days. The nZVI-EK treatment proved highly effective in reducing CE contamination and creating a suitable environment for subsequent biodegradation by changing groundwater conditions, promoting transport of nutrients and improving CE availability to soil and groundwater bacteria.

Stratification of chlorinated ethenes natural attenuation in an alluvial aquifer assessed by hydrochemical and biomolecular tools

Biomolecular and hydrochemical tools were used to evaluate natural attenuation of chlorinated ethenes in a Quaternary alluvial aquifer located close to a historical source of large-scale tetrachloroethylene (PCE) contamination. Distinct stratification of redox zones was observed, despite the aquifer's small thickness (2.8 m). The uppermost zone of the target aquifer was characterised by oxygen- and nitrate-reducing conditions, with mixed iron- to sulphate-reducing conditions dominant in the lower zone, along with indications of methanogenesis. Natural attenuation of PCE was strongly influenced by redox heterogeneity, while higher levels of PCE degradation coincided with iron- to sulphate reducing conditions. Next generation sequencing of the middle and/or lower zones identified anaerobic bacteria (Firmicutes, Chloroflexi, Actinobacteria and Bacteroidetes) associated with reductive dechlorination. The relative abundance of dechlorinators (Dehalococcoides mccartyi, Dehalobacter sp.) identified by real-time PCR in soil from the lower levels supports the hypothesis that there is a significant potential for reductive dechlorination of PCE. Local conditions were insufficiently reducing for rapid complete dechlorination of PCE to harmless ethene. For reliable assessment of natural attenuation, or when designing monitoring or remedial systems, vertical stratification of key biological and hydrochemical markers should be analysed as standard, even in shallow aquifers.

Microbial degradation of chloroethenes: a review

Contamination by chloroethenes has a severe negative effect on both the environment and human health. This has prompted intensive remediation activity in recent years, along with research into the efficacy of natural microbial communities for degrading toxic chloroethenes into less harmful compounds. Microbial degradation of chloroethenes can take place either through anaerobic organohalide respiration, where chloroethenes serve as electron acceptors; anaerobic and aerobic metabolic degradation, where chloroethenes are used as electron donors; or anaerobic and aerobic co-metabolic degradation, with chloroethene degradation occurring as a by-product during microbial metabolism of other growth substrates, without energy or carbon benefit. Recent research has focused on optimising these natural processes to serve as effective bioremediation technologies, with particular emphasis on (a) the diversity and role of bacterial groups involved in dechlorination microbial processes, and (b) detection of bacterial enzymes and genes connected with dehalogenation activity. In this review, we summarise the different mechanisms of chloroethene bacterial degradation suitable for bioremediation and provide a list of dechlorinating bacteria. We also provide an up-to-date summary of primers available for detecting functional genes in anaerobic and aerobic bacteria degrading chloroethenes metabolically or co-metabolically.