Microbial Community Changes in a Chlorinated Solvents Polluted Aquifer Over the Field Scale Treatment With Poly-3-Hydroxybutyrate as Amendment

Heterogeneity in the Composition and Catabolism of Indigenous Microbiomes in Subsurface Soils Cocontaminated with BTEX and Chlorinated Aliphatic Hydrocarbons

The effectiveness of in situ bioremediation can be affected by an insufficient understanding of high site/soil heterogeneity, especially in cocontaminated soils and sediments. In this study, samples from multiple locations within a relatively small area (20 × 20 m2) contaminated with benzene, toluene, ethylbenzene, and xylene (BTEX) and chlorinated aliphatic hydrocarbons (CAHs) were compared to examine their physicochemical and microbial properties. Unsupervised clustering analysis of 16S rRNA gene amplicon and metagenome shotgun sequencing data indicates that the indigenous community differentiated into three distinct patterns. In Cluster 1, Pseudomonas, with multiple monooxygenases and glutathione S-transferase (GST), was enriched in samples contaminated with high concentrations of BTEX and CAHs. Cluster 2 contained a high fraction of cometabolic degraders. Cluster 3 was dominated by Ralstonia and organohalide-respiring bacteria (OHRBs) mediating the reductive dechlorination of CAHs. Significant differences in composition and function among microbiomes were attributed to the differential distribution of organic pollutants, even in such a small area. Incorporating genomic features with physicochemical data can significantly enhance the understanding of the heterogeneities in soil and their impacts on microbial communities, thereby providing valuable information for the optimization of bioremediation strategies.

1,2-DCA biodegradation potential of an aquifer assessed in situ and in aerobic and anaerobic microcosms

BACKGROUND

1,2-dichloroethane (1,2-DCA) biodegradation can occur through aerobic or anaerobic pathways that can be exploited in bioremediation strategies. Bioremediation interventions are site specific and generally based on anaerobic pathways, nevertheless expanding knowledge on proper conditions favoring the biodegradation and especially on 1,2-DCA degrading microorganisms is crucial. In this work the intrinsic biodegradation potential of an aquifer impacted by Chlorinated Aliphatic Hydrocarbons (mainly 1,2-DCA) was evaluated by characterizing the aquifer microbiome across space and time and by setting up biostimulation treatments in microcosms under different aerobic and anaerobic conditions, in parallel.

RESULTS

The microbial profiling of the aquifer revealed noticeable alpha and beta diversity across the sampling sites within the aquifer and strong fluctuations over time. Surprisingly both the anaerobic and aerobic biostimulation treatments led to the successful removal of 1,2-DCA in microcosms, the enrichment of known 1,2-DCA degraders and the detection of reductive or hydrolytic dehalogenases. Ancylobacter and Starkeya were enriched in aerobic microcosms. Desulfovibrio and Desulfuromonas, known as perchloroethylene degraders, were enriched in anaerobic microcosms, suggesting they could be yet unknown 1,2-DCA respirers.

CONCLUSIONS

Our results demonstrate the occurrence of both aerobic and anaerobic bioremediation potential in the aquifer despite its negative redox potential. Due to the feasibility of direct oxidation with oxygen insufflation, we propose that an enhanced bioremediation strategy based on direct oxidation of 1,2-DCA could be applied to the contaminated aquifer as an ecofriendly, efficient and cost-effective approach as an alternative to anaerobic biodegradation.

Site-specific response of sediment microbial community to supplementation of polyhydroxyalkanoates as biostimulants for PCB reductive dechlorination

The use of biodegradable plastics is constantly raising, increasing the likeliness for these polymers to end up in the environment. Environmental applications foreseeing the intentional release of biodegradable plastics have been also recently proposed, e.g., for polyhydroxyalkanoates (PHAs) acting as slow hydrogen releasing compounds to stimulate microbial reductive dehalogenation processes. However, the effects of their release into the environment on the ecosystems still need to be thoroughly explored. In this work, the use of PHAs to enhance the microbial reductive dechlorination of polychlorobiphenyls (PCBs) and their impact on the metabolic and compositional features of the resident microbial community have been investigated in laboratory microcosms of a polluted marine sediment from Mar Piccolo (Taranto, Italy), and compared with recent findings on a different contaminated marine sediment from Pialassa della Baiona (Ravenna, Italy). A decreased biostimulation efficiency of PHAs on PCBs reductive dechlorination was observed in the sediment from Mar Piccolo, with respect to the sediment from Pialassa della Baiona, suggesting that the sediments' physical-chemical characteristics and/or the biodiversity and composition of its microbial community might play a key role in determining the outcome of this biostimulation strategy. Regardless of the sediment origin, PHAs were found to have a specific and pervasive effect on the sediment microbial community, reducing its biodiversity, defining a newly arranged microbial core of primary degraders and consequently affecting, in a site-specific way, the abundance of subdominant bacteria, possibly cross-feeders. Such potential to dramatically change the structure of autochthonous microbial communities should be carefully considered, since it might have secondary effects, e.g., on the natural biogeochemical cycles.

Reciprocal Interactions of Abiotic and Biotic Dechlorination of Chloroethenes in Soil

Chloroethenes (CEs) as common organic pollutants in soil could be attenuated via abiotic and biotic dechlorination. Nonetheless, information on the key catalyzing matter and their reciprocal interactions remains scarce. In this study, FeS was identified as a major catalyzing matter in soil for the abiotic dechlorination of CEs, and acetylene could be employed as an indicator of the FeS-mediated abiotic CE-dechlorination. Organohalide-respiring bacteria (OHRB)-mediated dechlorination enhanced abiotic CEs-to-acetylene potential by providing dichloroethenes (DCEs) and trichloroethene (TCE) since chlorination extent determined CEs-to-acetylene potential with an order of trans-DCE > cis-DCE > TCE > tetrachloroethene/PCE. In contrast, FeS was shown to inhibit OHRB-mediated dechlorination, inhibition of which could be alleviated by the addition of soil humic substances. Moreover, sulfate-reducing bacteria and fermenting microorganisms affected FeS-mediated abiotic dechlorination by re-generation of FeS and providing short chain fatty acids, respectively. A new scenario was proposed to elucidate major abiotic and biotic processes and their reciprocal interactions in determining the fate of CEs in soil. Our results may guide the sustainable management of CE-contaminated sites by providing insights into interactions of the abiotic and biotic dechlorination in soil.

Microbial community structure and potential function associated with poly-3-hydroxybutyrate biopolymer-boosted activation of peroxymonosulfate for waste-activated sludge decontamination

Excess waste-activated sludge (WAS) is a major biosolid management problem due to its biohazardous and recalcitrant content of phthalate esters (PAEs). This study aimed to assess the combined use of biopolymer, poly-3-hydroxybutyrate and peroxymonosulfate to degrade PAEs and decontaminate WAS. Poly-3-hydroxybutyrate was biosynthesized by Cupriavidus sp. L7L. The combined poly-3-hydroxybutyrate and peroxymonosulfate process removed 86 % of PAEs from WAS in 12 h. The carbonyl groups of poly-3-hydroxybutyrate were conducive to peroxymonosulfate activation leading to PAE degradation followed the radical pathway and surface-mediated electron transfer. Poly-3-hydroxybutyrate and peroxymonosulfate also enriched the PAE-biodegrading microbes in WAS. The microbial population and the functional composition in response to peroxymonosultate treatment was identified, with the genus Sulfurisoma being the most abundant. This synergistic treatment, i.e., advanced oxidation process, was augmented by highly promising microbial polyesters, exhibited important implications for WAS pretreatment toward circular bioeconomy that encompasses carbon-neutral biorefinery and mitigate pollution.

Effect of polyhydroxyalkanoates on the microbial reductive dechlorination of polychlorinated biphenyls and competing anaerobic respirations in a marine microbial culture

The effect of polyhydroxyalkanoates (PHAs) with different composition on the reductive dechlorination activity of a polychlorinated biphenyls (PCBs) dechlorinating marine microbial community and on the activity of sulfate-reducing (SRB) and methanogenic bacteria (MB), were investigated in marine sediment microcosms and compared with the main monomer, 3-hydroxybutyric acid (3HB). Despite PHAs were fermented more slowly than 3HB, all electron donors stimulated constantly sulfate-reduction, methanogenesis and, only transiently, PCB reductive dechlorination. No relevant differences were observed with different compositions of PHAs. According to electron balances, the majority of the supplied electrons (50 %) were consumed by SRB and to less extent by MB (9-31 %), while a small percentage (0.01 %) was delivered to OHRB. In the studied conditions PHAs were confirmed as potential slow‑hydrogen releasing compounds in marine environment but their fermentation rate was sufficiently high to mainly stimulate the competitors of organohalide respring bacteria for electron donors.

Enhanced Natural Attenuation of Groundwater Cr(VI) Pollution Using Electron Donors: Yeast Extract vs. Polyhydroxybutyrate

Remediation interventions based on the native bacteria’s capability to reduce Cr(VI) represent a valid strategy in terms of economic and environmental sustainability. In this study, a bioremediation test was carried out using viable microcosms set with groundwater and deep soil (4:1), collected from the saturated zone of an industrial site in Southern Italy that was polluted by ~130 µg L−1 of Cr(VI). Conditions simulating the potential natural attenuation were compared to the enhanced natural attenuation induced by supplying yeast extract or polyhydroxybutyrate. Sterile controls were set up to study the possible Cr(VI) abiotic reduction. No pollution attenuation was detected in the unamended viable reactors, whereas yeast extract provided the complete Cr(VI) removal in 7 days, and polyhydroxybutyrate allowed ~70% pollutant removal after 21 days. The incomplete abiotic removal of Cr(VI) was observed in sterile reactors amended with yeast extract, thus suggesting the essential role of native bacteria in Cr(VI) remediation. This was in accordance with the results of Pearson’s coefficient test, which revealed that Cr(VI) removal was positively correlated with microbial proliferation (n = 0.724), and also negatively correlated with pH (n = −0.646), dissolved oxygen (n = −0.828) and nitrate (n = −0.940). The relationships between the Cr(VI) removal and other monitored parameters were investigated by principal component analysis, which explained 76.71% of the total variance.

A Polyhydroxybutyrate (PHB)-Biochar Reactor for the Adsorption and Biodegradation of Trichloroethylene: Design and Startup Phase

In this work, polyhydroxy butyrate (PHB) and biochar from pine wood (PWB) are used in a mini-pilot scale biological reactor (11.3 L of geometric volume) for trichloroethylene (TCE) removal (80 mgTCE/day and 6 L/day of flow rate). The PHB-biochar reactor was realized with two sequential reactive areas to simulate a multi-reactive permeable barrier. The PHB acts as an electron donor source in the first “fermentative” area. First, the thermogravimetric (TGA) and differential scanning calorimetry (DSC) analyses were performed. The PHB-powder and pellets have different purity (96% and 93% w/w) and thermal properties. These characteristics may affect the biodegradability of the biopolymer. In the second reactive zone, the PWB works as a Dehalococcoides support and adsorption material since its affinity for chlorinated compounds and the positive effect of the “coupled adsorption and biodegradation” process has been already verified. A specific dechlorinating enriched culture has been inoculated in the PWB zone to realize a coupled adsorption and biodegradation process. Organic acids were revealed since the beginning of the test, and during the monitoring period the reductive dichlorination anaerobic pathway was observed in the first zone; no chlorinated compounds were detected in the effluent thanks to the PWB adsorption capacity.

3D dynamic model empowering the knowledge of the decontamination mechanisms and controlling the complex remediation strategy of a contaminated industrial site

Knowledge of the geology and hydrogeology of the polluted site emblematize a key requirement for environmental remediation, through assembling and synthesizing findings from various sources of physical evidence. In an increasingly virtual era, digital and geo-referenced metadata may serve as tools for collecting, merging, matching, and understanding multi-source information. The main goal of this paper is to emphasize the significance of a 3D hydrogeochemical model to the portrayal and the understanding of contamination dynamics and decontamination mechanisms at a highly contaminated industrial site. Some remediation measures are active on-site, due to the evidence-based presence of chlorinated solvents in groundwater. These are attributable to a slow-release source of pollutants in the saturated zone associated with very low permeability sediments. Therefore, in this research, a new technique for the remediation of secondary sources of dense non-aqueous phase liquid (DNAPL) contamination was investigated for the first time on a full-scale application. The combination of groundwater circulation wells (IEG-GCW®) and a continuous electron donor production device was set up to boost in situ bioremediation (ISB). A multi-phase approach was followed handling and releasing data during various remediation stages, from site characterization via pilot testing to full-scale remediation, thus allowing users to monitor, analyze, and manipulate information in 3D space-time. Multi-source and multi-temporal scenarios reveal the impact of ongoing hydraulic dynamics and depict the decontamination mechanisms in response to the interventions implemented over time, by quantifying the overall performance of the adopted strategies in terms of removal of secondary sources of pollution still active at the site.

Combined Strategies to Prompt the Biological Reduction of Chlorinated Aliphatic Hydrocarbons: New Sustainable Options for Bioremediation Application

Groundwater remediation is one of the main objectives to minimize environmental impacts and health risks. Chlorinated aliphatic hydrocarbons contamination is prevalent and presents particularly challenging scenarios to manage with a single strategy. Different technologies can manage contamination sources and plumes, although they are usually energy-intensive processes. Interesting alternatives involve in-situ bioremediation strategies, which allow the chlorinated contaminant to be converted into non-toxic compounds by indigenous microbial activity. Despite several advantages offered by the bioremediation approaches, some limitations, like the relatively low reaction rates and the difficulty in the management and control of the microbial activity, can affect the effectiveness of a bioremediation approach. However, those issues can be addressed through coupling different strategies to increase the efficiency of the bioremediation strategy. This mini review describes different strategies to induce the reduction dechlorination reaction by the utilization of innovative strategies, which include the increase or the reduction of contaminant mobility as well as the use of innovative strategies of the reductive power supply. Subsequently, three future approaches for a greener and more sustainable intervention are proposed. In particular, two bio-based materials from renewable resources are intended as alternative, long-lasting electron-donor sources (e.g., polyhydroxyalkanoates from mixed microbial cultures) and a low-cost adsorbent (e.g., biochar from bio-waste). Finally, attention is drawn to novel bio-electrochemical systems that use electric current to stimulate biological reactions.

Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake

The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.

Molecular characterization of microbial communities in a peat-rich aquifer system contaminated with chlorinated aliphatic compounds

In an aquifer-aquitard system in the subsoil of the city of Ferrara (Emilia-Romagna region, northern Italy) highly contaminated with chlorinated aliphatic toxic organics such as trichloroethylene (TCE) and tetrachloroethylene (PCE), a strong microbial-dependent dechlorination activity takes place during migration of contaminants through shallow organic-rich layers with peat intercalations. The in situ microbial degradation of chlorinated ethenes, formerly inferred by the utilization of contaminant concentration profiles and Compound-Specific Isotope Analysis (CSIA), was here assessed using Illumina sequencing of V4 hypervariable region of 16S rRNA gene and by clone library analysis of dehalogenase metabolic genes. Taxon-specific investigation of the microbial communities catalyzing the chlorination process revealed the presence of not only dehalogenating genera such as Dehalococcoides and Dehalobacter but also of numerous other groups of non-dehalogenating bacteria and archaea thriving on diverse metabolisms such as hydrolysis and fermentation of complex organic matter, acidogenesis, acetogenesis, and methanogenesis, which can indirectly support the reductive dechlorination process. Besides, the diversity of genes encoding some reductive dehalogenases was also analyzed. Geochemical and 16S rRNA and RDH gene analyses, as a whole, provided insights into the microbial community complexity and the distribution of potential dechlorinators. Based on the data obtained, a possible network of metabolic interactions has been hypothesized to obtain an effective reductive dechlorination process.

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan

Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.

Assessment of Long-Term Fermentability of PHA-Based Materials from Pure and Mixed Microbial Cultures for Potential Environmental Applications

The use of polyhydroxyalkanoates (PHA) as slow-release electron donors for environmental remediation represents a novel and appealing application that is attracting considerable attention in the scientific community. In this context, here, the fermentation pattern of different types of PHA-based materials has been investigated in batch and continuous-flow experiments. Along with commercially available materials, produced from axenic microbial cultures, PHA produced at pilot scale by mixed microbial cultures (MMC) using waste feedstock have been also tested. As a main finding, a rapid onset of volatile fatty acids (VFA) production was observed with a low-purity MMC-deriving material, consisting of microbial cells containing 56% (on weight basis) of intracellular PHA. Indeed, with this material a sustained, long-term production of organic acids (i.e., acetic, propionic, and butyric acids) was observed. In addition, the obtained yield of conversion into acids (up to 70% gVFA/gPHA) was higher than that obtained with the other tested materials, made of extracted and purified PHA. These results clearly suggest the possibility to directly use the PHA-rich cells deriving from the MMC production process, with no need of extraction and purification procedures, as a sustainable and effective carbon source bringing remarkable advantages from an economic and environmental point of view.

Bioremediation of typical chlorinated hydrocarbons by microbial reductive dechlorination and its key players: A review

Chlorinated hydrocarbon contamination in soils and groundwater has a severe negative impact on the human health. Microbial reductive dechlorination is a major degradation pathway of chlorinated hydrocarbon in anaerobic subsurface environments, has been extensively studied. Recent progress on the diversity of the reductive dechlorinators and the key enzymes of chlororespiration has been well reviewed. Here, we present a thorough overview of the studies related to bioremediation of chloroethenes and polychlorinated biphenyls based on enhanced in situ reductive dechlorination. The major part of this review is to provide an up-to-date summary of functional microorganisms which are either detected during in situ biostimulation or applied in bioaugmentation strategies. The applied biostimulants and corresponding reductive dechlorination products are also summarized and the future research needs are finally discussed.

A selected bacterial strain for the self-healing process in cementitious specimens without cell immobilization steps

The use of microorganisms capable of mediating the bioprecipitation process can be an important application in the self-healing processes of cement specimens. Thus, the present study identified and evaluated five Bacillus strains for potential application in the protocol of self-healing via bioprecipitation. Cell growth, enzyme production, and kinetic parameters conditions were evaluated during the fermentation process. Based on the analysis of 16S rDNA in conjunction with biochemical testing, results demonstrate that the strains are either Bacillus cereus or Bacillus thuringiensis. Strategically it was found that the addition of glycerol to fermentative medium was essential to increase the bacterial concentration (≈ 4.2 × 10⁷ cells mL^-1) and production of the enzyme urease (≈ 3.623,2 U.mL^-1). The addition of this medium after 40 days of fermentation promoted the self-healing of cracks and increased compressive strength in ≈ 14.2% of the cementitious specimens; therefore, increasing the sustainability and engineering properties of cement-based materials.

Diversity of bacteria and archaea in the groundwater contaminated by chlorinated solvents undergoing natural attenuation

Chlorinated solvents (CS)-contaminated groundwater poses serious risks to the environment and public health. Microorganisms play a vital role in efficient remediation of CS. In this study, the microbial community (bacterial and archaeal) composition of three CS-contaminated groundwater wells located at an abandoned chemical factory which covers three orders of magnitude in concentration (0.02-16.15 mg/L) were investigated via 16S rRNA gene high-throughput sequencing. The results indicated that Proteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal groups at the phylum level in groundwater, respectively. The major bacterial genera (Flavobacterium sp., Mycobacterium sp. and unclassified Parcubacteria taxa, etc.) and archaeal genera (Thaumarchaeota Group C3, Miscellaneous Crenarchaeotic Group and Miscellaneous Euryarchaeotic Group, etc.) might be involved in the dechlorination processes. In addition, Pearson's correlation analyses showed that alpha diversity of the bacterial community was not significantly correlated with CS concentration, while alpha diversity of archaeal community greatly decreased with the increased contamination of CS. Moreover, partial Mantel test indicated that oxidation-reduction potential, dissolved oxygen, temperature and methane concentration were major drivers of bacterial and archaeal community composition, whereas CS concentration had no significant impact, indicating that both indigenous bacterial and archaeal community compositions are capable of withstanding elevated CS contamination. This study improves our understanding of how the natural microbial community responds to high CS-contaminated groundwater.

Reductive/Oxidative Sequential Bioelectrochemical Process for Perchloroethylene Removal

An innovative bioelectrochemical reductive/oxidative sequential process was developed and tested on a laboratory scale to obtain the complete mineralization of perchloroethylene (PCE) in a synthetic medium. The sequential bioelectrochemical process consisted of two separate tubular bioelectrochemical reactors that adopted a novel reactor configuration, avoiding the use of an ion exchange membrane to separate the anodic and cathodic chamber and reducing the cost of the reactor. In the reductive reactor, a dechlorinating mixed inoculum received reducing power to perform the reductive dechlorination of perchloroethylene (PCE) through a cathode chamber, while the less chlorinated daughter products were removed in the oxidative reactor, which supported an aerobic dechlorinating culture through in situ electrochemical oxygen evolution. Preliminary fluid dynamics and electrochemical tests were performed to characterize both the reductive and oxidative reactors, which were electrically independent of each other, with each having its own counterelectrode. The first continuous-flow potentiostatic run with the reductive reactor (polarized at −450 mV vs SHE) resulted in obtaining 100% ± 1% removal efficiency of the influent PCE, while the oxidative reactor (polarized at +1.4 V vs SHE) oxidized the vinyl chloride and ethylene from the reductive reactor, with removal efficiencies of 100% ± 2% and 92% ± 1%, respectively.

Tetrachloroethene primes reductive dechlorination of polychlorinated biphenyls in a river sediment microcosm

Halo-priming is an effective approach to initiate microbial reductive dechlorination of polychlorinated biphenyls (PCBs) at contaminated sites, of which the application has been restricted by introducing extra pollutants generated from priming organohalides. In this study, tetrachloroethene (PCE) was demonstrated to be an effective priming compound to enhance PCB dechlorination both in a PCB-dechlorinating pure culture and a river sediment microcosm. In the isolated PCB-dechlorinating Dehalococcoides mccartyi CG1, PCB dechlorination activities were stimulated by adding 0.05-0.2 mM PCE, and were inhibited when further increasing PCE concentrations. Both in vivo and in vitro experiments showed that PCBs and PCE were synchronously dechlorinated in D. mccartyi CG1. In a river sediment microcosm, which was established to mimic in situ biostimulation of PCB dechlorination, 0.2 mM PCE could significantly improve para-chlorine removal from both PCB180 (2345-245-CB) and Aroclor 1260, and increase the relative abundance of indigenous dechlorinating Dehalococcoides for more than 20 times (from <0.1% to 2.3-5.0%). At the same time, PCE as a priming compound was completely dechlorinated to non-toxic ethene. Overall, this study provided an efficient strategy to stimulate in situ bioremediation of PCBs.