Microbiome Dynamics of a Polychlorobiphenyl (PCB) Historically Contaminated Marine Sediment under Conditions Promoting Reductive Dechlorination

Microbial and chemically induced reductive dechlorination of polychlorinated biphenyls in the environment

Polychlorinated biphenyls (PCBs) are persistent organic pollutants and are emitted during e-waste activities. Once they enter into the environment, PCBs could pose toxic effects to environmental compartments and public health. Reductive dechlorination offers a sustainable solution to manage the PCBs-contaminated environment. Under anaerobic conditions, reductive dechlorination of PCBs occurs, and PCBs congeners serve as potential electron acceptors which stimulate the growth of PCBs-dechlorinating microorganisms. In this review, microbial and chemically induced reductive dechlorination was summarized. During anaerobic conditions, highly chlorinated PCBs undergo reductive dechlorination and are converted into less chlorinated PCBs. The mechanisms involved in reductive dechlorination are mainly attacks on meta and/or para chlorines of PCBs mixtures in a contaminated environment and ortho dechlorination of PCBs. Based on methods, PCBs removal efficiency was as chemical > biological. Activated carbon (90%) showed more treatment efficiency than bacterial (84%). The review suggested that microbial remediation is a slow process; however, efficiency could be enhanced after amendments. Different microorganisms appear to be responsible for different dechlorination activities and the occurrence of various dehalogenation routes. However, PCBs dechlorination rate, extent, and route are influenced by pH, temperature, availability of carbon sources, and the presence or absence of H2 or competing electron acceptors and other electron donors.

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.

Greenhouse gas emission potential of tropical coastal sediments in densely urbanized area inferred from metabarcoding microbial community data

Although benthic microbial community offers crucial insights into ecosystem services, they are underestimated for coastal sediment monitoring. Sepetiba Bay (SB) in Rio de Janeiro, Brazil, holds long-term metal pollution. Currently, SB pollution is majorly driven by domestic effluents discharge. Here, functional prediction analysis inferred from 16S rRNA gene metabarcoding data reveals the energy metabolism profiles of benthic microbial assemblages along the metal pollution gradient. Methanogenesis, denitrification, and N2 fixation emerge as dominant pathways in the eutrophic/polluted internal sector (Spearman; p < 0.05). These metabolisms act in the natural attenuation of sedimentary pollutants. The methane (CH4) emission (mcr genes) potential was found more abundant in the internal sector, while the external sector exhibited higher CH4 consumption (pmo + mmo genes) potential. Methanofastidiosales and Exiguobacterium, possibly involved in CH4 emission and associated with CH4 consumers respectively, are the main taxa detected in SB. Furthermore, SB exhibits higher nitrous oxide (N2O) emission potential since the norB/C gene proportions surpass nosZ up to 4 times. Blastopirellula was identified as the main responsible for N2O emissions. This study reveals fundamental contributions of the prokaryotic community to functions involved in greenhouse gas emissions, unveiling their possible use as sentinels for ecosystem monitoring.

Integrated transcriptomics and metabolomics analyses reveal the aerobic biodegradation and molecular mechanisms of 2,3',4,4',5-pentachlorodiphenyl (PCB 118) in Methylorubrum sp. ZY-1

2,3',4,4',5-pentachlorodiphenyl (PCB 118), a highly representative PCB congener, has been frequently detected in various environments, garnering much attention across the scientific community. The degradation of highly chlorinated PCBs by aerobic microorganisms is challenging due to their hydrophobicity and persistence. Herein, the biodegradation and adaptation mechanisms of Methylorubrum sp. ZY-1 to PCB 118 were comprehensively investigated using an integrative approach that combined degradation performance, product identification, metabolomic and transcriptomic analyses. The results indicated that the highest degradation efficiency of 0.5 mg L-1 PCB 118 reached 75.66% after seven days of inoculation when the bacteria dosage was 1.0 g L-1 at pH 7.0. A total of eleven products were identified during the degradation process, including low chlorinated PCBs, hydroxylated PCBs, and ring-opening products, suggesting that strain ZY-1 degraded PCB 118 through dechlorination, hydroxylation, and ring-opening pathways. Metabolomic analysis demonstrated that the energy supply and redox metabolism of strain ZY-1 was disturbed with exposure to PCB 118. To counteract this environmental stress, strain ZY-1 adjusted both the fatty acid synthesis and purine metabolism. The analysis of transcriptomics disclosed that multiple intracellular and extracellular oxidoreductases (e.g., monooxygenase, alpha/beta hydrolase and cytochrome P450) participated in the degradation of PCB 118. Besides, active efflux of PCB 118 and its degradation intermediates mediated by multiple transporters (e.g., MFS transporter and ABC transporter ATP-binding protein) might enhance bacterial resistance against these substances. These discoveries provided the inaugural insights into the biotransformation of strain ZY-1 to PCB 118 stress, illustrating its potential in the remediation of contaminated environments.

Core taxa, co-occurrence pattern, diversity, and metabolic pathways contributing to robust anaerobic biodegradation of chlorophenol

It is hard to achieve robustness in anaerobic biodegradation of trichlorophenol (TCP). We hypothesized that specific combinations of environmental factors determine phylogenetic diversity and play important roles in the decomposition and stability of TCP-biodegrading bacteria. The anaerobic bioreactor was operated at 35 °C (H condition) or 30 °C (L condition) and mainly fed with TCP (from 28 μM to 180 μM) and organic material. Metagenome sequencing was combined with 16S rRNA gene amplicon sequencing for the microbial community analysis. The results exhibited that the property of robustness occurred in specific conditions. The corresponding co-occurrence and diversity patterns suggest high collectivization, degree and evenness for robust communities. Two types of core functional taxa were recognized: dechlorinators (unclassified Anaerolineae, Thermanaerothrix and Desulfovibrio) and ring-opening members (unclassified Proteobacteria, Methanosarcina, Methanoperedens, and Rubrobacter). The deterministic process of the expansion of niche of syntrophic bacteria at higher temperatures was confirmed. The reductive and hydrolytic dechlorination mechanisms jointly lead to C-Cl bond cleavage. H ultimately adapted to the stress of high TCP loading, with more abundant ring-opening enzyme (EC 3.1.1.45, ∼55%) and hydrolytic dechlorinase (EC 3.8.1.5, 26.5%) genes than L (∼47%, 10.5%). The functional structure (based on KEGG) in H was highly stable despite the high loading of TCP (up to 60 μM), but not in L. Furthermore, an unknown taxon with multiple functions (dechlorinating and ring-opening) was found based on genetic sequencing; its functional contribution of EC 3.8.1.5 in H (26.5%) was higher than that in L (10.5%), and it possessed a new metabolic pathway for biodegradation of halogenated aromatic compounds. This new finding is supplementary to the robust mechanisms underlying organic chlorine biodegradation, which can be used to support the engineering, regulation, and design of synthetic microbiomes.

Microbial indicators along a metallic contamination gradient in tropical coastal sediments

The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4-V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans, SEEP-SRB1, Spirochaeta 2, among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula, Blastopirellula, Aquibacter, among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment.

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.

Enhancement effects of decabromodiphenyl ether on microbial sulfate reduction in eutrophic lake sediments: A study on sulfate-reducing bacteria using dsrA and dsrB amplicon sequencing

Although sulfate (SO₄^2-) reduction by sulfate-reducing bacteria (SRB) is an important sulfur cycling processes, little is known about how the persistent organic pollutants affect the SO₄^2- reduction process in the eutrophic lake sediments. Here, we carried out a 120-day microcosm experiment to explore the effects of decabromodiphenyl ether (BDE-209) on SO₄^2- reduction mediated by SRB in sediment collected from Taihu Lake, a typical eutrophic lake in China. The results showed that BDE-209 contamination significantly enhanced the activity of dissimilatory sulfite reductase (DSR) (r = 0.83), which led to an increased concentration of sulfide produced by SO₄^2- reduction. This stimulatory effect of BDE-209 on DSR activity was closely related to variations in the dsrA- and dsrB-type SRB communities. The abundances and diversities of the dsrA- and dsrB-containing SRB increased and their community composition varied in response to BDE-209 contamination. The gene copies (r = 0.72), Chao 1 (r = 0.50), Shannon (r = 0.55), and Simpson (r = 0.70) indices of dsrB-containing SRB was positively correlated with BDE-209 contamination. Co-occurrence network analysis revealed that network complexity, connectivity, and the interspecific cooperative relationship in SRB were strengthened by BDE-209 contamination. The keystone species identified in the SRB community mainly belonged to the genera Candidatus Sulfopaludibacter for the dsrA-containing SRB and Desulfatiglans for the dsrB-containing SRB, and their relative abundances were positively correlated with DSR activity in the sediment. The relative abundance of the keystone species and SRB diversity were important microbial factors directly contributing to the variations in DSR activity based on structural equation modeling analysis. Notably, the results of abundance, community structure, and interspecific relationships showed that the dsrB-containing SRB may be more sensitive to the BDE-209 contamination than the dsrA-containing SRB. These results will help us understand the effects of BDE-209 on microbial sulfate reduction in eutrophic lakes.

The amendment of Organic matters enhances the anaerobic dechlorination of Polychlorinated Biphenyls in Paddy Soil

The toxicity of high-chlorinated polychlorinated biphenyls (PCBs) can be efficiently reduced through anaerobic dechlorination. However, this approach suffers a lot in face of in situ microbial remediations, like a shortage of biomass. In this study, we showed that the amendment of organic matters could help microbiota in paddy soil with anaerobic dechlorination and greatly shortened the lag period. The presence of organic matters offered a better environment for dechlorinating bacteria. They provided not only a more strictly anaerobic milieu but also copious carbon sources. By using high-throughput 16S rRNA gene sequencing, genera Dehalobacter, Dehalobacterium, and Desulfitobacterium capable of dechlorination were identified in enriched cultures. Taken together, this study proved that extra organic matters can promote anaerobic dechlorination in paddy soil slurry microcosm systems, which provides new insights into the bioremediation of PCB-contaminated soils.

Organohalide respiration potential in marine sediments from Aarhus Bay

Organohalide respiration (OHR), catalysed by reductive dehalogenases (RDases), plays an important role in halogen cycling. Natural organohalides and putative RDase-encoding genes have been reported in Aarhus Bay sediments, however, OHR has not been experimentally verified. Here we show that sediments of Aarhus Bay can dehalogenate a range of organohalides, and different organohalides differentially affected microbial community compositions. PCE-dechlorinating cultures were further examined by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing. Known organohalide-respiring bacteria (OHRB) including Dehalococcoides, Dehalobacter and Desulfitobacterium decreased in abundance during transfers and serial dilutions, suggesting the importance of yet uncharacterized OHRB in these cultures. Switching from PCE to 2,6-DBP led to its complete debromination to phenol in cultures with and without sulfate. 2,6-DBP debrominating cultures differed in microbial composition from PCE-dechlorinating cultures. Desulfobacterota genera recently verified to include OHRB, including Desulfovibrio and Desulfuromusa, were enriched in all microcosms, whereas Halodesulfovibrio was only enriched in cultures without sulfate. Hydrogen and methane were detected in cultures without sulfate. Hydrogen likely served as electron donor for OHR and methanogenesis. This study shows that OHR can occur in marine environments mediated by yet unknown OHRB, suggesting their role in natural halogen cycling.

Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants

Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.

Occurrence of polychlorinated biphenyls (PCBs) in the sea anemone Bunodosoma zamponii, sediments and seawater from the southwestern Atlantic

Polychlorinated biphenyls (PCBs) are persistent and bioaccumulable organic compounds. The occurrence of PCBs was assessed in two populations of the intertidal sea anemone Bunodosoma zamponii living under different anthropogenic strains. One location was in vicinity to a wastewater plant (Las Delicias, LD), and the other was a preserved location chosen as a reference site (Punta Cantera, PC). Anemone populations were sampled 4 times (spring, summer, autumn and winter) throughout a year, in addition to seawater and sediment from those areas. PCB loadings ranged from 2.89 to 79.41 ng L^-1 in seawater samples and from 0.07 to 6.61 ng g^-1 dry weight in sediment samples. Total PCB levels ranged from 0.22 to 14.94 and 2.79 to 24.69 ng g^-1 wet weight in anemones from PC and LD, respectively. PCBs concentrations in anemones from LD were significantly greater than PC during spring, summer and winter. The congeners 18 and 44 prevailed in seawater samples, 44 and 52 in sediment and 18 and 132+153 in anemones. Redundancy analysis integrated PCB levels from all matrixes and bolstered contrast between sampling sites. Seasonality was also a relevant factor since during winter PCB loading was greater in sediment and anemone samples, coincident with the rainiest season. Disparity between sites could be due to LD's proximity to the wastewater plant, effect of littoral drift direction and/or asymmetries in anemones physiological condition.

Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators

The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.

Long-Term Dechlorination of Polychlorinated Biphenyls (PCBs) in Taihu Lake Sediment Microcosms: Identification of New Pathways, PCB-Driven Shifts of Microbial Communities, and Insights into Dechlorination Potential

Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) is regarded as an alternative approach for in situ remediation and detoxification in the environment. To better understand the process of PCB dechlorination in freshwater lake sediment, a long-term (108 weeks) dechlorination study was performed in Taihu Lake sediment microcosms with nine parent PCB congeners (PCB5, 12, 64, 71, 105, 114, 149, 153, and 170). Within 108 weeks, the total PCBs declined by 32.8%, while parent PCBs declined by 84.8%. PCB dechlorinators preferred to attack meta- and para-chlorines, principally para-flanked meta and single-flanked para chlorines. A total of 58 dechlorination pathways were observed, and 20 of them were not in 8 processes, suggesting the broad spectrum of PCB dechlorination in the environment. Rare ortho dechlorination was confirmed to target the unflanked ortho chlorine, indicating a potential for complete dechlorination. PCBs drove the shifts of the microbial community structures, and putative dechlorinating bacteria were growth-linked to PCB dechlorination. The distinct jump of RDase genes ardA, rdh12, pcbA4, and pcbA5 was found to be consistent with the commencement of dechlorination. The maintained high level of putative dechlorinating phylum Chloroflexi (including Dehalococcoides and o-17/DF-1), genus Dehalococcoides, and four RDase genes at the end of incubation revealed the long-term dechlorination potential. This work provided insights into dechlorination potential for long-term remediation strategies at PCB-contaminated sites.

Recent advances in the biodegradation of polychlorinated biphenyls

Polychlorinated biphenyls (PCBs) are typical lasting organic pollutants. Persistence and recalcitrance to biodegradation of PCBs have hampered the transformation of PCB congeners from the environment. Biological transformation of polychlorinated biphenyls could take place through anaerobic dechlorination, aerobic microbial degradation, and a combination of transformation of anaerobic dechlorination and aerobic degradation. Under anaerobic conditions, microbial dechlorination is an important degradation mode for PCBs, especially high-chlorinated congeners. The low-chlorinated compounds formed after reductive dechlorination could be further aerobically degraded and completely mineralized. This paper reviews the recent advances in biological degradation of PCBs, introduces the functional bacteria and enzymes involved in the anaerobic and aerobic degradation of PCBs, and discusses the synergistic action of anaerobic reduction and aerobic degradation. In addition, the different ways to the microbial remediation of PCBs-contaminated environments are discussed. This review provides a theoretical foundation and practical basis to use PCBs-degrading microorganisms for bioremediation.

Structure and diversity of native bacterial communities in soils contaminated with polychlorinated biphenyls

Persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) are a group of high-risk synthetic substances for human and environmental health. Currently, the study of sites contaminated by the spillage of equipment PCBs containing have been considered targeted areas for the study of bacterial communities with potential for PCBs degradation. There in isolation of bacterial strains is vital for use in biodegradable processes, such as bacterial bioaugmentation, which accelerates the development of phenomena such as natural attenuation of contaminated sites. The objective of this study was to assess biodiversity of bacteria contained in anthropogenic contaminated soils (H_S and H_P) with PCBs compared to a control sample without contaminant and the modified forest (F) and agricultural (A) soil in the laboratory with 100 mg L⁻¹ PCB. For the analysis of 16S rRNA genes amplified from DNA extracted from the soils evaluated, the latest generation of Illumina Miseq and Sanger sequencing for the cultivable strains were detected. The bacteria identified as the most abundant bacterial phyla for H_S and H_P soil was Proteobacteria (56.7%) and Firmicutes (22.9%), which decreased in F and A soils. The most abundant bacterial genera were Burkholderia, Bacillus, Acinetobacter, Comamonas and Cupriavidus. Several species identified in this study, such as Bacillus cereus, Burkholderia cepacia, Comamonas testosteroni and Acinetobacter pittii have been reported as PCBs degraders. Finally, by means of a principal component analysis (PCA), a correlation between the physical and chemical characteristics of the soils in relation to the relative abundances of the bacteria identified was obtained. The C/N ratio was directly related to the control soil (without contaminant), while SOM maintained a relationship with F and A soils and the bacterial abundances were directly related to Hs and Hp soils due to the presence of aroclor 1260. Bacteria with the ability to tolerate high concentrations of this pollutant are considered for future use in biostimulation and bioaugmentation processes in contaminated soils.

Degradation of BDE-47 in mangrove sediments with amendment of extra carbon sources

Polybrominated diphenyl ethers (PBDEs) are widely detected in coastal wetlands but their remediation is still difficult. In this study, different carbon sources, namely formate, acetate, pyruvate, lactate, succinate, methanol and ethanol, were added to mangrove sediments contaminated with BDE-47, a common PBDE congener, to enhance its degradation. After 2-month incubation, all carbon addition significantly enhanced degradation percentages. The residual BDE-47 percentage significantly correlated with the abundance of total bacteria and Dehalococcoides spp. The addition of methanol, acetate and succinate also achieved significantly higher degradation rates and shorter half-lives than sediments without carbon amendment at the end of 5-month incubation, although degradation percentages were comparable between sediments with and without extra carbon. The degradation pathway based on the profiles of degradation products was also similar among treatments. The results indicated the stimulatory effect of extra carbon sources on BDE-47 degradation in contaminated sediments was carbon- and time-specific.

Growth of Dehalococcoides spp. and increased abundance of reductive dehalogenase genes in anaerobic PCB-contaminated sediment microcosms

Polychlorinated biphenyls (PCBs) contaminate 19% of US Superfund sites and represent a serious risk to human and environmental health. One promising strategy to remediate PCB-contaminated sediments utilizes organohalide-respiring bacteria (OHRB) that dechlorinate PCBs.However, functional genes that act as biomarkers for PCB dechlorination processes (i.e., reductive dehalogenase genes) are poorly understood. Here, we developed anaerobic sediment microcosms that harbor an OHRB community dominated by the genus Dehalococcoides. During the 430-day microcosm incubation, Dehalococcoides 16S rRNA sequences increased two orders of magnitude to 10⁷ copies/g of sediment, and at the same time, PCB118 decreased by as much as 70%. In addition, the OHRB community dechlorinated a range of penta- and tetra-chlorinated PCB congeners including PCBs 66, 70 + 74 + 76, 95, 90 + 101, and PCB110 without exogenous electron donor. We quantified candidate reductive dehalogenase (RDase) genes over a 430-day incubation period and found rd14, a reductive dehalogenase that belongs to Dehalococcoides mccartyi strain CG5, was enriched to 10⁷ copies/g of sediment. At the same time, pcbA5 was enriched to only 10⁵ copies/g of sediment. A survey for additional RDase genes revealed sequences similar to strain CG5's rd4 and rd8. In addition to demonstrating the PCB dechlorination potential of native microbial communities in contaminated freshwater sediments, our results suggest candidate functional genes with previously unexplored potential could serve as biomarkers of PCB dechlorination processes.

Biotransformation of hexachlorocyclohexanes contaminated biomass for energetic utilization demonstrated in continuous anaerobic digestion system

Lindane, the γ-hexachlorocyclohexane (HCH) isomer, was among the most used pesticides worldwide. Although it was banned in 2009, residues of Lindane and other HCH-isomers are still found with high concentrations in contaminated fields. For clean-up, phytoremediation combined with anaerobic digestion (AD) of contaminated biomass to produce biogas and fertilizer could be a promising strategy and was tested in two 15 L laboratory-scale continuous stirred tank reactors. During operation over one year by adding HCH isomers (γ, α and β) consecutively, no negative influence on conventional reactor parameters was observed. The γ- and α-HCH isomers were transformed to chlorobenzene and benzene, and transformation became faster along with time, while β-HCH was not removed. Genus Methanosaeta and order Clostridiales, showing significant enhancement on abundance with HCH addition, may be used as bioindicators for HCH dehalogenation in AD process. The potential for HCH degradation in AD system was restricted to axial Cl atoms of HCH and it showed slight enantioselective preference towards transformation of (+) α-HCH. Moreover, metabolite benzene was mineralized to CO₂ and methane, deducing from tracer experiments with benzene-¹³C₆. Overall, AD appears to be a feasible option for treatment of γ and α-HCHs contaminated biomass.

Influence of Human Activities on Broad-Scale Estuarine-Marine Habitats Using Omics-Based Approaches Applied to Marine Sediments

Rapid urban expansion and increased human activities have led to the progressive deterioration of many marine ecosystems. The diverse microbial communities that inhabit these ecosystems are believed to influence large-scale geochemical processes and, as such, analyzing their composition and functional metabolism can be a means to assessing an ecosystem’s resilience to physical and chemical perturbations, or at the very least provide baseline information and insight into future research needs. Here we show the utilization of organic and inorganic contaminant screening coupled with metabolomics and bacterial 16S rRNA gene sequencing to assess the microbial community structure of marine sediments and their functional metabolic output. The sediments collected from Moreton Bay (Queensland, Australia) contained low levels of organic and inorganic contaminants, typically below guideline levels. The sequencing dataset suggest that sulfur and nitrite reduction, dehalogenation, ammonia oxidation, and xylan degradation were the major metabolic functions. The community metabolites suggest a level of functional homogeneity down the 40-cm core depth sampled, with sediment habitat identified as a significant driver for metabolic differences. The communities present in river and sandy channel samples were found to be the most active, with the river habitats likely to be dominated by photoheterotrophs that utilized carbohydrates, fatty acids and alcohols as well as reduce nitrates to release atmospheric nitrogen and oxidize sulfur. Bioturbated mud habitats showed overlapping faunal activity between riverine and sandy ecosystems. Nitrogen-fixing bacteria and lignin-degrading bacteria were most abundant in the sandy channel and bioturbated mud, respectively. The use of omics-based approaches provide greater insight into the functional metabolism of these impacted habitats, extending beyond discrete monitoring to encompassing whole community profiling that represents true phenotypical outputs. Ongoing omics-based monitoring that focuses on more targeted pathway analyses is recommended in order to quantify the flux changes within these systems and establish variations from these baseline measurements.

Bacterial community assemblages in sediments under high anthropogenic pressure at Ichkeul Lake/Bizerte Lagoon hydrological system, Tunisia

Bacterial communities inhabiting sediments in coastal areas endure the effect of strong anthropogenic pressure characterized by the presence of multiple contaminants. Understanding the effect of pollutants on the organization of bacterial communities is of paramount importance in order to unravel bacterial assemblages colonizing specific ecological niches. Here, chemical and molecular approaches were combined to investigate the bacterial communities inhabiting the sediments of the Ichkeul Lake/Bizerte Lagoon, a hydrological system under anthropogenic pressure. Although the microbial community of the Ichkeul Lake sediment was different to that of the Bizerte Lagoon, common bacterial genera were identified suggesting a lake-lagoon continuum probably due to the hydrology of the system exchanging waters according to the season. These genera represent bacterial "generalists" maintaining probably general biogeochemical functions. Linear discriminant analysis effect size (LEfSe) showed significant differential abundance distribution of bacterial genera according to the habitat, the pollution type and level. Further, correlation analyses identified specific bacterial genera which abundance was linked with pesticides concentrations in the lake, while in the lagoon the abundance of specific bacterial genera was found linked with the concentrations of PAHs (Polycyclic aromatic hydrocarbons) and organic forms of Sn. As well, bacterial genera which abundance was not correlated with the concentrations of pollutants were identified in both lake and lagoon. These findings represent valuable information, pointing out specific bacterial genera associated with pollutants, which represent assets for developing bacterial tools for the implementation, the management, and monitoring of bioremediation processes to mitigate the effect of pollutants in aquatic ecosystems.

Effective removal of Aroclor 1254 and hexachlorobenzene in river sediments by coupling in situ phase-inversion emulsification with biological reductive dechlorination

River sediment contamination is a critical environmental problem. Concentrations of certain hydrophobic organic compounds (HOCs) in sediments in Taiwan are ranked at the top in the world. In this study, we proposed a novel in situ phase-inversion emulsification and biological reductive dechlorination (ISPIE/BiRD) method that integrates (1) heating contaminated sediments by hot water-in-oil emulsion to increase the contact between hydrophobic organic contaminants (HOCs), to accelerate the mass transfer between two phases, and to select heat-tolerant hydrogen-producing bacteria, (2) ISPIE forming oil-in-water emulsion to enhance recovery of HOCs by pushing cool water and nutrient buffer through the sediment column, and (3) subsequent BiRD using residual emulsion in sediment. Aroclor 1254 and hexachlorobenzene (HCB) were selected due to significantly higher human health and ecological risks in sediments. Batch biological dechlorination tests were conducted using an L₉(3⁴) orthogonal table according to the Taguchi method. The results showed that significant controlling factors for biological dechlorination were temperature and emulsion concentration. A single operation of ISPIE can achieve the removal of Aroclor 1254 and HCB at as high as 58.2% and 56.5%, respectively. Column study on BiRD further removed about 30% of the residual Aroclor 1254 and HCB at the upper and middle sections of the sediment cores in 35 days. These results supported that ISPIE/BiRD is feasible for HOC-contaminated sediments remediation.

Organic carbon source and salinity shape sediment bacterial composition in two China marginal seas and their major tributaries

Marginal sea sediments receive organic substrates of different origins, but whether and to what extent sediment microbial communities are reflective of the different sources of organic substrates remain unclear. To address these questions, sediment samples were collected in two connected China marginal seas, i.e., Bohai Sea and Yellow Sea, and their two major tributaries (Yellow River and Liao River). Sediment bacterial community composition (BCC) was examined using 16S rRNA gene pyrosequencing. In addition, physicochemical variables that describe environmental conditions and sediment features were measured. Our results revealed that BCCs changed with salinity and organic carbon (OC) content. Members of Gaiellaceae and Comamonadaceae showed a rapid decrease as salinity and phytoplankton-derived OC increased, while Piscirickettsiaceae and Desulfobulbaceae exhibited an opposite distribution pattern. Differences of riverine vs. marginal sea sediment BCCs could be mostly explained by salinity. However, within the marginal seas, sediment BCC variations were mainly explained by OC-related variables, including terrestrial-derived fatty acids (Terr_FA), phytoplankton-derived polyunsaturated fatty acids (Phyto_PUFA), stable carbon isotopes (δ¹³C), and carbon to nitrogen ratio (C/N). In addition to environmental variables, network analysis suggested that interactions among individual bacterial taxa might be important in shaping sediment BCCs in the studied areas.

Effects of Ferric Oxyhydroxide on Anaerobic Microbial Dechlorination of Polychlorinated Biphenyls in Hudson and Grasse River Sediment Microcosms: Dechlorination Extent, Preferences, Ortho Removal, and Its Enhancement

Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) has been observed in many PCB-impacted sediments. However, this biodegradation is relatively site-specific and can be affected by PCB compositions and sediment geochemical conditions. To better understand the influence of a common competing electron acceptor, ferric oxyhydroxide (FeOOH), on dechlorination, two sediments (Hudson River and Grasse River sediments), and two PCB mixtures (PCB 5/12, 64/71, 105/114, and 149/153/170 in Mixture 1 and PCB 5/12, 64/71, 82/97/99, 144/170 in Mixture 2) were used for this microcosm study. The addition of 40 mmole/kg FeOOH completely inhibited PCB dechlorination in the Hudson sediment, but only moderately inhibited PCB dechlorination in the Grasse sediment with a 3-week longer lag time. The inhibitory effect in the Grasse sediment was mainly due to the loss of unflanked para dechlorination activity. Fe(II) analysis showed that dechlorination started prior to the consumption of Fe(III), which indicates PCB reduction and Fe(III) reduction were able to take place concurrently. Dehalococcoides 16S rRNA genes increased with the commencement of dechlorination in the Grasse sediment, but not in the completely inhibited Hudson sediment. Rare ortho dechlorination pathways were identified in FeOOH-amended Grasse sediment microcosms, dominated by transformations of PCB 25(24-3-CB) to PCB 13(3-4-CB) and PCB 28(24-4-CB) to PCB 15(4-4-CB). The addition of carbon sources (acetate or a fatty acid mixture with acetate, propionate, and butyrate) after 27 weeks of incubation reinitiated dechlorination in FeOOH-amended Hudson sediment microcosms. Also, the addition of carbon sources greatly enhanced ortho dechlorination in FeOOH-amended Grasse microcosms, indicating the utilization of acetate and/or the fatty acid mixture for ortho dechlorination-related microorganisms. A dechlorination pathway analysis approach revealed that para-flanked meta dechlorination was primarily preferred followed by ortho-/double-flanked meta dechlorination and single-/double-flanked para dechlorination in the Grasse sediment.

The impact of the Deepwater Horizon blowout on historic shipwreck-associated sediment microbiomes in the northern Gulf of Mexico

More than 2,000 historic shipwrecks spanning 500 years of history, rest on the Gulf of Mexico seafloor. Shipwrecks serve as artificial reefs and hotspots of biodiversity by providing hard substrate, something rare in deep ocean regions. The Deepwater Horizon (DWH) spill discharged crude oil into the deep Gulf. Because of physical, biological, and chemical interactions, DWH oil was deposited on the seafloor, where historic shipwrecks are present. This study examined sediment microbiomes at seven historic shipwrecks. Steel-hulled, World War II-era shipwrecks and wooden-hulled, 19^th century shipwrecks within and outside of the surface oiled area and subsurface plume were examined. Analysis of 16S rRNA sequence libraries, sediment radiocarbon age data, sedimentation rates, and hydrocarbons revealed that the German U-boat U-166 and the wooden-hulled sailing vessel known as the Mardi Gras Wreck, both in the Mississippi Canyon leasing area, were exposed to deposited oil during a rapid sedimentation event. Impacts to shipwreck microbiomes included a significant increase in Piscirickettsiaceae-related sequences in surface sediments, and reduced biodiversity relative to unimpacted sites. This study is the first to address the impact of the spill on shipwreck-associated microbiomes, and to explore how shipwrecks themselves influence microbiome diversity in the deep sea.

PCB dechlorination hotspots and reductive dehalogenase genes in sediments from a contaminated wastewater lagoon

Polychlorinated biphenyls (PCBs) are a class of persistent organic pollutants that are distributed worldwide. Although industrial PCB production has stopped, legacy contamination can be traced to several different commercial mixtures (e.g., Aroclors in the USA). Despite their persistence, PCBs are subject to naturally occurring biodegradation processes, although the microbes and enzymes involved are poorly understood. The biodegradation potential of PCB-contaminated sediments in a wastewater lagoon located in Virginia (USA) was studied. Total PCB concentrations in sediments ranged from 6.34 to 12,700 mg/kg. PCB congener profiles in sediment sample were similar to Aroclor 1248; however, PCB congener profiles at several locations showed evidence of dechlorination. The sediment microbial community structure varied among samples but was dominated by Proteobacteria and Firmicutes. The relative abundance of putative dechlorinating Chloroflexi (including Dehalococcoides sp.) was 0.01-0.19% among the sediment samples, with Dehalococcoides sp. representing 0.6-14.8% of this group. Other possible PCB dechlorinators present included the Clostridia and the Geobacteraceae. A PCR survey for potential PCB reductive dehalogenase genes (RDases) yielded 11 sequences related to RDase genes in PCB-respiring Dehalococcoides mccartyi strain CG5 and PCB-dechlorinating D. mccartyi strain CBDB1. This is the first study to retrieve potential PCB RDase genes from unenriched PCB-contaminated sediments.

Thermally enhanced in situ bioremediation of groundwater contaminated with chlorinated solvents - A field test

In situ bioremediation (ISB) using reductive dechlorination is a widely accepted but relatively slow approach compared to other technologies for the treatment of groundwater contaminated by chlorinated ethenes (CVOCs). Due to the known positive kinetic effect on microbial metabolism, thermal enhancement may be a viable means of accelerating ISB. We tested thermally enhanced ISB in aquifers situated in sandy saprolite and underlying fractured granite. The system comprised pumping, heating and subsequent injection of contaminated groundwater aiming at an aquifer temperature of 20-30°C. A fermentable substrate (whey) was injected in separate batches. The test was monitored using hydrochemical and molecular tools (qPCR and NGS). The addition of the substrate and increase in temperature resulted in a rapid increase in the abundance of reductive dechlorinators (e.g., Dehalococcoides mccartyi, Dehalobacter sp. and functional genes vcrA and bvcA) and a strong increase in CVOC degradation. On day 34, the CVOC concentrations decreased by 87% to 96% in groundwater from the wells most affected by the heating and substrate. On day 103, the CVOC concentrations were below the LOQ resulting in degradation half-lives of 5 to 6days. Neither an increase in biomarkers nor a distinct decrease in the CVOC concentrations was observed in a deep well affected by the heating but not by the substrate. NGS analysis detected Chloroflexi dechlorinating genera (Dehalogenimonas and GIF9 and MSBL5 clades) and other genera capable of anaerobic metabolic degradation of CVOCs. Of these, bacteria of the genera Acetobacterium, Desulfomonile, Geobacter, Sulfurospirillum, Methanosarcina and Methanobacterium were stimulated by the substrate and heating. In contrast, groundwater from the deep well (affected by heating only) hosted representatives of aerobic metabolic and aerobic cometabolic CVOC degraders. The test results document that heating of the treated aquifer significantly accelerated the treatment process but only in the case of an abundant substrate.

Changes in microbial community during removal of BDE-153 in four types of aquatic sediments

Indigenous microorganisms in sediments could degrade polybrominated diphenyl ethers (PBDEs), but how the microbial communities respond to PBDEs was seldom reported. The effect of BDE-153, a common congener in aquatic environments, on the microbial communities in four types of aquatic sediments was evaluated during the 150days' incubation under an anaerobic condition. The intrinsic potential to remove BDE-153 varied significantly among four sediment types, and the removal rates of mangrove, mudflat, marine and freshwater sediments were 0.013, 0.013, 0.011, and 0.009day^-1, respectively. The observed microbial species, Simpson, Shannon, and Chao1 indices in all sediments were rather stable and were not changed significantly by BDE-153 amendment. However, BDE-153 amendment altered the microbial community compositions in three saline sediments at the end of the incubation period. Distance-based multivariate multiple regression analysis revealed that salinity, total organic carbon (TOC) and BDE-52, the major debromination product of BDE-153, were the three main factors explaining the variations in microbial community compositions in BDE-treated sediments; whereas salinity, TOC and pH were the main contributing factors in control sediments without BDE-153. The daughter congeners generated during anaerobic debromination process need more attention, especially their effect on the microbial communities in aquatic sediments.

Time Trends of Persistent Organic Pollutants in Benthic and Pelagic Indicator Fishes from Puget Sound, Washington, USA

We modeled temporal trends in polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and dichlorodiphenyltrichloroethane and its metabolites (DDTs) in two indicator fish species representing benthic and pelagic habitats in Puget Sound, Washington, USA. English sole (Parophrys vetulus, benthic) index sites and larger-scale Pacific herring (Clupea pallasii, pelagic) foraging areas represented a wide range of possible contamination conditions, with sampling locations situated adjacent to watersheds exhibiting high, medium and low development. Consistency in analytical data throughout the study was maintained by either calculating method-bias-correction factors on paired samples as methods evolved or by analyzing older archived samples by current methods. PCBs declined moderately in two herring stocks from a low-development basin (2.3 and 4.0% annual rate of decline) and showed no change in the highly developed and moderately developed basins during a 16- to 21-year period. PCBs increased in English sole from four of ten sites (2.9-7.1%), and the remaining six exhibited no significant change. PBDEs and DDTs declined significantly in all herring stocks (4.2-8.1%), although analytical challenges warrant caution in interpreting DDT results. PBDEs declined in English sole from two high-development and one low-development site (3.7-7.2%) and remained unchanged in the remaining seven. DDTs increased in English sole from one high-development site (Tacoma City Waterway) and declined in two high-development and one low development site. As with herring, analytical challenges warrant caution in interpreting the English sole DDT results. It is likely that source controls and mitigation efforts have contributed to the declines in PBDEs and DDTs overall, whereas PCBs appear to have persisted, especially in the pelagic food web, despite bans in PCB production and use.

Identification of two organohalide-respiring Dehalococcoidia associated to different dechlorination activities in PCB-impacted marine sediments

Background

Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) plays a major role in detoxifying anoxic contaminated freshwater and marine sediments from PCBs. Known members of the phylum Chloroflexi are typically responsible for this activity in freshwater sediments, whereas less is known about the microorganisms responsible for this activity in marine sediments. PCB-respiring activities were detected in PCB-impacted marine sediments of the Venice Lagoon. The aim of this work was to identify the indigenous organohalide-respiring microorganisms in such environments and assess their dechlorination specificity against spiked Aroclor™ 1254 PCBs under laboratory conditions resembling the in situ biogeochemistry.

Results

High PCB dechlorination activities (from 150 ± 7 to 380 ± 44 μmol of chlorine removed kg⁻¹ week⁻¹) were detected in three out of six sediments sampled from different locations of the lagoon. An uncultured non-Dehalococcoides phylotype of the class Dehalococcoidia closely related to Dehalobium chlorocoercia DF-1, namely phylotype VLD-1, was detected and enriched up to 10⁹ 16S rRNA gene copies per gram of sediment where dechlorination activities were higher and 25-4/24-4 and 25-2/24-2/4-4 chlorobiphenyls (CB) accumulated as the main tri-/dichlorinated products. Conversely, a different phylotype closely related to the SF1/m-1 clade, namely VLD-2, also enriched highly where lower dechlorination activity and the accumulation of 25-3 CB as main tri-chlorinated product occurred, albeit in the simultaneous presence of VLD-1. Both phylotypes showed growth yields higher or comparable to known organohalide respirers and neither phylotypes enriched in sediment cultures not exhibiting dechlorination.

Conclusions

These findings confirm the presence of different PCB-respiring microorganisms in the indigenous microbial communities of Venice Lagoon sediments and relate two non-Dehalococcoides phylotypes of the class Dehalococcoidia to different PCB dechlorination rates and specificities.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0743-4) contains supplementary material, which is available to authorized users.

Cable Bacteria and the Bioelectrochemical Snorkel: The Natural and Engineered Facets Playing a Role in Hydrocarbons Degradation in Marine Sediments

The composition and metabolic traits of the microbial communities acting in an innovative bioelectrochemical system were here investigated. The system, known as Oil Spill Snorkel, was recently developed to stimulate the oxidative biodegradation of petroleum hydrocarbons in anoxic marine sediments. Next Generation Sequencing was used to describe the microbiome of the bulk sediment and of the biofilm growing attached to the surface of the electrode. The analysis revealed that sulfur cycling primarily drives the microbial metabolic activities occurring in the bioelectrochemical system. In the anoxic zone of the contaminated marine sediment, petroleum hydrocarbon degradation occurred under sulfate-reducing conditions and was lead by different families of Desulfobacterales (46% of total OTUs). Remarkably, the occurrence of filamentous Desulfubulbaceae, known to be capable to vehicle electrons deriving from sulfide oxidation to oxygen serving as a spatially distant electron acceptor, was demonstrated. Differently from the sediment, which was mostly colonized by Deltaproteobacteria, the biofilm at the anode hosted, at high extent, members of Alphaproteobacteria (59%) mostly affiliated to Rhodospirillaceae family (33%) and including several known sulfur- and sulfide-oxidizing genera. Overall, we showed the occurrence in the system of a variety of electroactive microorganisms able to sustain the contaminant biodegradation alone or by means of an external conductive support through the establishment of a bioelectrochemical connection between two spatially separated redox zones and the preservation of an efficient sulfur cycling.