Indirect Evidence Link PCB Dehalogenation with Geobacteraceae in Anaerobic Sediment-Free Microcosms

Unlocking the potential of resuscitation-promoting factor for enhancing anaerobic microbial dechlorination of polychlorinated biphenyls

Microbial dechlorination of polychlorinated biphenyls (PCBs) is limited by the slow growth rate and low activity of dechlorinators. Resuscitation promoting factor (Rpf) of Micrococcus luteus, has been demonstrated to accelerate the enrichment of highly active PCB-dechlorinating cultures. However, it remains unclear whether the addition of Rpf can further improve the dechlorination performance of anaerobic dechlorination cultures. In this study, the effect of Rpf on the performance of TG4, an enriched PCB-dechlorinating culture obtained by Rpf amendment, for reductive dechlorination of four typical PCB congeners (PCBs 101, 118, 138, 180) was evaluated. The results indicated that Rpf significantly enhanced the dechlorination of the four PCB congeners, with residual mole percentages of PCBs 101, 118, 138 and 180 in Rpf-amended cultures being 16.2-29.31 %, 13.3-20.1 %, 11.9-14.4 % and 9.4-17.3 % lower than those in the corresponding cultures without Rpf amendment after 18 days of incubation. Different models were identified as appropriate for elucidating the dechlorination kinetics of distinct PCB congeners, and it was observed that the dechlorination rate constant is significantly influenced by the PCB concentration. The supplementing Rpf did not obviously change dechlorination metabolites, and the removal of chlorines occurred mainly at para- and meta- positions. Analysis of microbial community and functional gene abundance suggested that Rpf-amended cultures exhibited a significant enrichment of Dehalococcoides, Dehalogenimonas and Desulfitobacterium, as well as non-dechlorinators belonging to Desulfobacterota and Bacteroidetes. These findings highlight the potential of Rpf as an effective additive for enhancing PCB dechlorination, providing new insights into the survival of functional microorganisms involved in anaerobic reductive dechlorination.

Resuscitation-Promoting Factor Accelerates Enrichment of Highly Active Tetrachloroethene/Polychlorinated Biphenyl-Dechlorinating Cultures

The anaerobic bioremediation of polychlorinated biphenyls (PCBs) is largely impeded by difficulties in massively enriching PCB dechlorinators in short periods of time. Tetrachloroethene (PCE) is often utilized as an alternative electron acceptor to preenrich PCB-dechlorinating bacteria. In this study, resuscitation promoting factor (Rpf) was used as an additive to enhance the enrichment of the microbial communities involved in PCE/PCBs dechlorination. The results indicated that Rpf accelerates PCE dechlorination 3.8 to 5.4 times faster than control cultures. In Aroclor 1260-fed cultures, the amendment of Rpf enables significantly more rapid and extensive dechlorination of PCBs. The residual high-chlorinated PCB congeners (≥5 Cl atoms) accounted for 36.7% and 59.8% in the Rpf-amended cultures and in the corresponding controls, respectively. This improvement was mainly attributed to the enhanced activity of the removal of meta-chlorines (47.7 mol % versus 14.7 mol %), which did not appear to affect dechlorination pathways. The dechlorinators, including Dehalococcoides in Chloroflexi and Desulfitobacterium in Firmicutes, were greatly enriched via Rpf amendment. The abundance of nondechlorinating populations, including Methanosarcina, Desulfovibrio, and Bacteroides, was also greatly enhanced via Rpf amendment. These results suggest that Rpf serves as an effective additive for the rapid enrichment of active dechlorinating cultures so as to provide a new approach by which to massively cultivate bioinoculants for accelerated in situ anaerobic bioremediation. IMPORTANCE The resuscitation promoting factor (Rpf) of Micrococcus luteus has been reported to resuscitate and stimulate the growth of functional microorganisms that are involved in the aerobic degradation of polychlorinated biphenyls (PCBs). However, few studies have been conducted to investigate the role of Rpf on anaerobic microbial populations. In this study, the enhancement of Rpf on the anaerobic microbial dechlorination of PCE/PCBs was discovered. Additionally, the Rpf-responsive populations underlying the enhanced dechlorination were uncovered. This report reveals the rapid enrichment of active dechlorinating cultures via Rpf amendment, and this sheds light on massively enriching PCB dechlorinators in short periods of time. The enhanced in situ anaerobic bioremediation of PCBs could be expected by supplementing Rpf.

mibPOPdb: An online database for microbial biodegradation of persistent organic pollutants

Microbial biodegradation of persistent organic pollutants (POPs) is an attractive, ecofriendly, and cost-efficient clean-up technique for reclaiming POP-contaminated environments. In the last few decades, the number of publications documenting POP-degrading microbes, enzymes, and experimental data sets has continuously increased, necessitating the development of a dedicated web resource that catalogs consolidated information on POP-degrading microbes and tools to facilitate integrative analysis of POP degradation data sets. To address this knowledge gap, we developed the Microbial Biodegradation of Persistent Organic Pollutants Database (mibPOPdb) by accumulating microbial POP degradation information from the public domain and manually curating published scientific literature. Currently, in mibPOPdb, there are 9215 microbial strain entries, including 184 gene (sub)families, 100 enzymes, 48 biodegradation pathways, and 593 intermediate compounds identified in POP-biodegradation processes, and information on 32 toxic compounds listed under the Stockholm Convention environmental treaty. Besides the standard database functionalities, which include data searching, browsing, and retrieval of database entries, we provide a suite of bioinformatics services to facilitate comparative analysis of users' own data sets against mibPOPdb entries. Additionally, we built a Graph Neural Network-based prediction model for the biodegradability classification of chemicals. The predictive model exhibited a good biodegradability classification performance and high prediction accuracy. mibPOPdb is a free data-sharing platform designated to promote research in microbial-based biodegradation of POPs and fills a long-standing gap in environmental protection research. Database URL: http://mibpop.genome-mining.cn/.

DNA stable isotope probing on soil treated by plant biostimulation and flooding revealed the bacterial communities involved in PCB degradation

Polychlorinated biphenyl (PCB)-contaminated soils represent a major treat for ecosystems health. Plant biostimulation of autochthonous microbial PCB degraders is a way to restore polluted sites where traditional remediation techniques are not sustainable, though its success requires the understanding of site-specific plant-microbe interactions. In an historical PCB contaminated soil, we applied DNA stable isotope probing (SIP) using ¹³C-labeled 4-chlorobiphenyl (4-CB) and 16S rRNA MiSeq amplicon sequencing to determine how the structure of total and PCB-degrading bacterial populations were affected by different treatments: biostimulation with Phalaris arundinacea subjected (PhalRed) or not (Phal) to a redox cycle and the non-planted controls (Bulk and BulkRed). Phal soils hosted the most diverse community and plant biostimulation induced an enrichment of Actinobacteria. Mineralization of 4-CB in SIP microcosms varied between 10% in Bulk and 39% in PhalRed soil. The most abundant taxa deriving carbon from PCB were Betaproteobacteria and Actinobacteria. Comamonadaceae was the family most represented in Phal soils, Rhodocyclaceae and Nocardiaceae in non-planted soils. Planted soils subjected to redox cycle enriched PCB degraders affiliated to Pseudonocardiaceae, Micromonosporaceae and Nocardioidaceae. Overall, we demonstrated different responses of soil bacterial taxa to specific rhizoremediation treatments and we provided new insights into the populations active in PCB biodegradation.

Response surface methodology (RSM) and artificial neural network (ANN) approach to optimize the photocatalytic conversion of rice straw hydrolysis residue (RSHR) into vanillin and 4-hydroxybenzaldehyde

Effective use of waste lignin is always a challenging task, technologies have been applied in the past to get value-added compounds from waste lignin. However, the existing technologies are not economical and efficient to produce the value-added chemicals. Alkali soluble lignin from rice straw hydrolysis residue (RSHR) is subjected to photocatalytic conversion into value-added compounds. Photocatalysis is one of the multifarious advanced oxidation processes (AOPs), carried out with TiO2 nanoparticles under a 125 W UV bulb. Gas chromatography mass spectroscopy (GCMS) confirmed the formation of vanillin and 4-hydroxybenzaldehyde. RSM and ANN techniques are adopted to optimize the process conditions for the maximization of the products. The response one (Y 1) vanillin (24.61 mg) and second response (Y 2) 4-hydroxybenzaldehyde (19.51 mg) is obtained at the optimal conditions as 7.0 h irradiation time, 2.763 g/L catalyst dose, 15 g/L lignin concentration, and 14.26 g/L NaOH dose for alkali treatment, suggested by face-centered central composite design (CCD). RSM and ANN models are statistically analyzed in terms of RMSE, R 2 and AAD. For RSM the R 2 0.9864 and 0.9787 while for ANN 0.9875 and 0.9847, closer to one warrant the good fitting of the models. Therefore, in terms of higher precision and predictive ability of both models the ANN model showed excellence for both responses as compared to the RSM model.

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.

A global survey reveals a divergent extradiol dioxygenase clade as a widespread complementary contributor to the biodegradation of mono- and polycyclic aromatic hydrocarbons

Extradiol dioxygenation is a key reaction in the microbial aerobic degradation of mono- and polycyclic aromatic hydrocarbon catecholic derivatives. It has been reported that many bacterial enzymes exhibiting such converging functions act on a wide range of catecholic substrates. The present study reports a new subfamily of extradiol dioxygenases (EXDOs) with broad substrate specificity, the HrbC EXDOs. The new clade belongs to the XII cluster within family 2 of the vicinal oxygen chelate superfamily (EXDO-VC2), which is typically characterized by a preference for bicyclic substrates. Coding hrbC orthologs were isolated by activity-based screening of fosmid metagenomic libraries from large DNA fragments derived from heavily PAH-contaminated soils. They occurred as solitary genes within conserved sequences encoding enzymes for amino acid metabolism and were stably maintained in the chromosomes of the Betaproteobacteria lineages harboring them. Analysis of contaminated aquifers revealed coexpression of hrbC as a polycistronic mRNA component. The predicted open reading frames were verified by cloning and heterologous expression, confirming the expected molecular mass and meta-cleavage activity of the recombinant enzymes. Evolutionary analysis of the HrbC protein sequences grouped them into a discrete cluster of 1,2-dihydroxynaphthalene dioxygenases represented by a cultured PAH degrader, Rugosibacter aromaticivorans strain Ca6. The ecological importance and relevance of the new EXDO genes were confirmed by PCR-based mapping in different biogeographical localities contaminated with a variety of mono- and polycyclic aromatic compounds. The cosmopolitan distribution of hrbC in PAH-contaminated aquifers supports our hypothesis about its auxiliary role in the degradation of toxic catecholic intermediates, contributing to the composite EXDO catabolic capacity of the world's microbiomes.

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.

Effects of iron-carbon materials on microbial-catalyzed reductive dechlorination of polychlorinated biphenyls in Taihu Lake sediment microcosms: Enhanced chlorine removal, detoxification and shifts of microbial community

Nano zero-valent iron particles (nZVI, 0.09 wt%), micro zero-valent iron particles (mZVI, 0.09 wt%), granular activated carbon (GAC, 3.03 wt%), GAC supported nZVI (nZVI/GAC, 3.12 wt%) and nZVI&GAC (nZVI 0.09 wt%, GAC 3.03 wt%) were evaluated for their effects on polychlorinated biphenyls (PCBs) anaerobic reductive dechlorination, detoxification, as well as microbial community structure in Taihu Lake (China) sediment microcosms. The results showed that all of these five materials could stimulate PCBs reductive dechlorination, especially for dioxin-like PCB congeners, and nZVI&GAC had the best removal effect on PCBs. The reduction of total PCBs increased from 13.5% to 33.2%. H₂ generated by zero-valent iron corrosion was utilized by organohalide-respiring bacteria (OHRB) to enhance the dechlorination of PCBs predominantly via meta chlorine removal in the short term. The addition of ZVI had little impact on the total bacterial abundance and the microbial community structure. The adsorption of GAC and potential bioremediation properties of attached biofilm could promote the long-term removal of PCBs. GAC, nZVI/GAC, nZVI&GAC had different influences on the microbial structure. These findings provide insights into the biostimulation technique for in situ remediations of PCBs contaminated sediments.

Organochlorines and Polycyclic Aromatic Hydrocarbons as fingerprint of exposure pathways from marine sediments to biota

To elucidate the dynamics of a suite of organochlorine contaminants (PCBs, HCB), PAHs and Hg and verify the potential of these pollutants as reliable fingerprints of sources, an ensemble of marine sediments and organisms (finfish, shellfish species and Mytilus galloprovincialis) were analysed from the contaminated Augusta Bay (Southern Italy). The Hg and HCB concentration in the sediments exceeded the EQS of the Directive 2000/60/EU. Similarly, ∑PCB and selected PAHs were above the threshold limit set by regulation. The marine organisms showed Hg concentrations above CE 1881/2006. Contaminants in transplanted mussel evidenced an increased accumulation overtime and different distribution patterns between sampling sites. Analysis of the homolog composition of PCB congeners revealed comparable patterns between sediments and marine organisms and offered the opportunity to define a robust fingerprint for tracing contaminants transfer from the abiotic to the biotic compartments. These results were confirmed by the Fluoranthene/Pyrene, Hg and HCB distribution modes.

'Cry-for-help' in contaminated soil: a dialogue among plants and soil microbiome to survive in hostile conditions

An open question in environmental ecology regards the mechanisms triggered by root chemistry to drive the assembly and functionality of a beneficial microbiome to rapidly adapt to stress conditions. This phenomenon, originally described in plant defence against pathogens and predators, is encompassed in the ‘cry‐for‐help’ hypothesis. Evidence suggests that this mechanism may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Polychlorinated biphenyls (PCBs) were considered as model pollutants due to their toxicity, recalcitrance and poor phyto‐extraction potential, which lead to a plethora of phytotoxic effects and rise environmental safety concerns. Plants have inefficient detoxification processes to catabolize PCBs, even leading to by‐products with a higher toxicity. We propose that the ‘cry‐for‐help’ mechanism could drive the exudation‐mediated recruitment and sustainment of the microbial services for PCBs removal, exerted by an array of anaerobic and aerobic microbial degrading populations working in a complex metabolic network. Through this synergistic interaction, the holobiont copes with the soil contamination, releasing the plant from the pollutant stress by the ecological services provided by the boosted metabolism of PCBs microbial degraders. Improving knowledge of root chemistry under PCBs stress is, therefore, advocated to design rhizoremediation strategies based on plant microbiome engineering.

Illumina sequencing of 16S rRNA genes reveals a unique microbial community in three anaerobic sludge digesters of Dubai

Understanding the microbial communities in anaerobic digesters, especially bacteria and archaea, is key to its better operation and regulation. Microbial communities in the anaerobic digesters of the Gulf region where climatic conditions and other factors may impact the incoming feed are not documented. Therefore, Archaeal and Bacterial communities of three full-scale anaerobic digesters, namely AD1, AD3, and AD5 of the Jebel Ali Sewage water Treatment Plant (JASTP) were analyzed by Illumina sequencing of 16S rRNA genes. Among bacteria, the most abundant genus was fermentative bacteria Acetobacteroides (Blvii28). Other predominant bacterial genera in the digesters included thermophilic bacteria (Fervidobacterium and Coprothermobacter) and halophilic bacteria like Haloterrigena and Sediminibacter. This can be correlated with the climatic condition in Dubai, where the bacteria in the incoming feed may be thermophilic or halophilic as much of the water used in the country is desalinated seawater. The predominant Archaea include mainly the members of the phyla Euryarchaeota and Crenarchaeota belonging to the genus Methanocorpusculum, Metallosphaera, Methanocella, and Methanococcus. The highest population of Methanocorpusculum (more than 50% of total Archaea), and other hydrogenotrophic archaea, is in agreement with the high population of bacterial genera Acetobacteroides (Blvii28) and Fervidobacterium, capable of fermenting organic substrates into acetate and H₂. Coprothermobacter, which is known to improve protein degradation by establishing syntrophy with hydrogenotrophic archaea, is also one of the digesters’ dominant genera. The results suggest that the microbial community in three full-scale anaerobic digesters is different. To best of our knowledge this is the first detailed report from the UAE.

Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors

Although microbial communities of anaerobic bioreactors have been extensively studied using DNA-based tools, there are still several knowledge gaps regarding the microbiology of the process, in particular integration of all generated data is still limited. One understudied core phylum within anaerobic bioreactors is the phylum Chloroflexi, despite being one of the most abundant groups in anaerobic reactors. In order to address the abundance, diversity and phylogeny of this group in full-scale methanogenic reactors globally distributed, a compilation of 16S ribosomal RNA gene sequence data from 62 full-scale methanogenic reactors studied worldwide, fed either with wastewater treatment anaerobic reactors (WTARs) or solid-waste treatment anaerobic reactors (STARs), was performed. One of the barriers to overcome was comparing data generated using different primer sets and different sequencing platforms. The sequence analysis revealed that the average abundance of Chloroflexi in WTARs was higher than in STARs. Four genera belonging to the Anaerolineae class dominated both WTARs and STARs but the core populations were different. According to the phylogenetic analysis, most of the sequences formed clusters with no cultured representatives. The Anaerolineae class was more abundant in reactors with granular biomass than in reactors with disperse biomass supporting the hypothesis that Anaerolineae play an important role in granule formation and structure due to their filamentous morphology. Cross-study comparisons can be fruitfully used to understand the complexity of the anaerobic digestion process. However, more efforts are needed to standardize protocols and report metadata information.

Bacterial communities as indicators of environmental pollution by POPs in marine sediments

Decades of intensive discharge from industrial activities into coastal systems has resulted in the accumulation of a variety of persistent organic pollutants (POPs) in marine waters and sediments, having detrimental impacts on aquatic ecosystems and the resident biota. POPs are among the most hazardous chemicals originating from industrial activities due to their biotoxicity and resistance to environmental degradation. Bacterial communities are known to break down many of these aromatic compounds, and different members of naturally occurring bacterial consortia have been described to work in syntrophic association to thrive in heavily contaminated waters and sediments, making them potential candidates as bioindicators of environmental pollution. In this study environmental, sampling was combined with chemical analysis of pollutants and high-resolution sequencing of bacterial communities using Next Generation Sequencing molecular biology tools. The aim of the present study was to describe the bacterial communities from marine sediments containing high loads of POPs and to identify relevant members of the resident microbial communities that may act as bioindicators of contamination. Marine sediments were collected from a coastal bay area of the Baltic Sea historically influenced by intense industrial activity, including metal smelting, oil processing, and pulp and paper production. Different types of POPs were detected at high concentrations. Fiberbank sediments, resulting from historic paper industry activity, were found to harbour a clearly distinct bacterial community including a number of bacterial taxa capable of cellulolytic and dechlorination activities. Our findings indicate that specific members of the bacterial communities thrive under increasing levels of POPs in marine sediments, and that the abundances of certain taxa correlate with specific POPs (or groups), which could potentially be employed in monitoring, status assessment and environmental management purposes.

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.

Characterization of the Belowground Microbial Community in a Poplar-Phytoremediation Strategy of a Multi-Contaminated Soil

Due to their widespread use in industrial applications in recent decades, Polychlorobiphenyls (PCBs) and heavy metals (HMs) are the most common soil contaminants worldwide, posing a risk for both ecosystems and human health. In this study, a poplar-assisted bioremediation strategy has been applied for more than 4 years to a historically contaminated area (PCBs and HMs) in Southern Italy using the Monviso poplar clone. This clone was effective in promoting a decrease in all contaminants and an increase in soil quality in terms of organic carbon and microbial abundance. Moreover, a significant shift in the structure and predicted function of the belowground microbial community was also observed when analyzing both DNA and cDNA sequencing data. In fact, an increase in bacterial genera belonging to Proteobacteria able to degrade PCBs and resist HMs was observed. Moreover, the functional profiling of the microbial community predicted by PICRUSt2 made it possible to identify several genes associated with PCB transformation (e.g., bphAa, bphAb, bphB, bphC), response to HM oxidative stress (e.g., catalase, superoxide reductase, peroxidase) and HM uptake and expulsion (e.g., ABC transporters). This work demonstrated the effectiveness of the poplar clone Monviso in stimulating the natural belowground microbial community to remove contaminants and improve the overall soil quality. It is a practical example of a nature based solution involving synergic interactions between plants and the belowground microbial community.

Long-term microbial community dynamics in a pilot-scale gas sparged anaerobic membrane bioreactor treating municipal wastewater under seasonal variations

This study evaluates the microbial community development in the suspended sludge within a pilot-scale gas sparged Anaerobic membrane bioreactor (AnMBR) under ambient conditions, as well as understand the influence of microbial signatures in the influent municipal wastewater on the bioreactor using amplicon sequence analysis. The predominant bacterial phyla comprised of Bacteroidetes, Proteobacteria, Firmicutes, and Chloroflexi demonstrated resiliency with ambient temperature operation over a period of 472 days. Acetoclastic Methanosaeta were predominant during most of the AnMBR operation. Beta diversity analysis indicated that the microbial communities present in the influent wastewater did not affect the AnMBR core microbiome. Syntrophic microbial interactions were evidenced by the presence of the members from Synergistales, Anaerolineales, Clostridiales, and Syntrophobacterales. The proliferation of sulfate reducing bacteria (SRB) along with sulfate reduction underscored the competition of SRB in the AnMBR. Operational and environmental variables did not greatly alter the core bacterial population based on canonical correspondence analysis.

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.

Predicting the potential for organohalide respiration in wastewater: Comparison of intestinal and wastewater microbiomes

Halogenated compounds such as polychlorinated biphenyl (PCBs) and polybrominated diphenyl ethers (PBDEs) enter wastewater treatment plants (WWTPs) via the sewage system. These organic contaminants partition between the aqueous and the biosolid phase, where the former is discharged as wastewater effluent. Biosolids from a WWTP provide a hydrophobic surface for adsorption and thus the presence and potential growth of organohalide respiring (OHR) bacteria. In this study, the aim was to assess the potential organohalide respiration capacity in wastewater biosolids by investigating actively organohalide respiring bacteria with a focus on organohalide respiration of PCBs and PCE. The results of the biosolids analysis showed increased amounts of products from PCB respiration. Simultaneously, experiments with organohalide respiration of PCE in biosolids samples showed significant decreases PCE concentration after 46 days (28-92%). Subsequently, it was evaluated if the OHR microbial populations in biosolids were similar to those present in intestinal human biofilms by applying a bioinformatic approach. The OHR populations of the communities were analyzed from existing American and Chinese human intestinal microbiomes. The overall groups Proteobacteria, Bacteroides, Actinobacteria, and Firmicutes phyla dominated the microbiomes in all datasets. The OHR groups in biosolids and intestinal biofilms included Dehalogenimonas, Dehalobacter, Desulfitibacter, Desulfovibrio, Sulfurospirillum, Clostridium, and Comamonas. The results of this study showed that several OHR phyla were present in all samples independent of origin. Wastewater and intestinal microbiomes also contained OHR phyla. Overall, the results points towards using bacterial communities in biosolids as indicators of organohalide respiration in wastewater and intestinal microbiomes, which is related to ingestion or halogenated compounds.

How wastewater with different nutrient levels influences microbial degradation of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) in anaerobic sediments

While wastewater and polybrominated diphenyl ethers (PBDEs) are commonly both discharged into aquatic ecosystems, little information is known about how wastewaters with different nutrient levels impact on microbial degradation of PBDEs. In this study, we used an anaerobic microcosm experiment to examine how the removal rates of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) from contaminated sediment varied when exposed to three wastewaters with different nutrient properties, namely livestock wastewater (LS), municipal sewage (MS), and shrimp pond wastewater (SP), and to determine the microbial controls on removal processes. We found that BDE-47 degraded relatively rapidly in MS, which had low carbon and nitrogen concentrations, but degraded much more slowly in LS and SP, which had relatively high nutrient concentrations. The variations in BDE-47 removal in different wastewater were related to iron reduction rates and the abundances of organohalide-respiring bacteria (OHRB). The community compositions of both total bacteria and OHRB from the family Dehalococcoidaceae differed significantly among the wastewater treatments. Compared with other treatments, some bacterial groups with PBDE degradation abilities were more abundant in MS where the PBDE-degradation efficiencies were higher. Our results should help support evaluations of the bioremediation potential of sites that are contaminated with both halogenated organic compounds and nutrient-rich wastewater.

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.

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.

Biochar accelerates microbial reductive debromination of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) in anaerobic mangrove sediments

A common congener of polybrominated diphenyl ethers, 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), is a prevalent, persistent and toxic pollutant. It could be removed by reduction debromination by microorganisms but the rate is often slow. The study hypothesized that spent mushroom substrate derived biochar amendment could accelerate the microbial reductive debromination of BDE-47 in anaerobic mangrove sediment slurries and evaluated the mechanisms behind. At the end of 20-week experiment, percentages of residual BDE-47 in slurries amended with biochar were significantly lower but debromination products were higher than those without biochar. Such stimulatory effect on debromination was dosage-dependent, and debromination was coupled with iron (Fe) reduction. Biochar amendment significantly enhanced the Fe(II):Fe(III) ratio, Fe(III) reduction rate and the abundance of iron-reducing bacteria in genus Geobacter, thus promoting bacterial iron-reducing process. The abundances of dehalogenating bacteria in genera Dehalobacter, Dehalococcoides, Dehalogenimonas and Desulfitobacterium were also stimulated by biochar. Biochar as an electron shuttle might increase electron transfer from iron-reducing and dehalogenating bacteria to PBDEs for their reductive debromination. More, biochar shifted microbial community composition in sediment, particularly the enrichment of potential PBDE-degrading bacteria including organohalide-respiring and sulfate-reducing bacteria, which in turn facilitated the reductive debromination of BDE-47 in anaerobic mangrove sediment slurries.