Biology subjects

Edwards, E. A.

Publications and source records attributed to Edwards, E. A..

31 records · Page 2Linked to original sources

bioRxiv2021

Identification of a fully dechlorinated product of chlordecone in soil microcosms and enrichment cultures

Anaerobic microcosms constructed with soil from Guadeloupe, amended with electron donor (ethanol and acetone) and incubated for more than a decade, transformed chlordecone (CLD) into a suite of progressively more dechlorinated products, including a fully dechlorinated carboxylated indene product. This fully dechlorinated transformation product has never before been observed and indicates that complete dechlorination of CLD is possible. The carboxylated indene was detected by LC-MS and structure was confirmed by LC-MS/MS using a Q-Exactive Orbitrap mass spectrometer.

microbiology↗

bioRxiv2021

Anaerobic Benzene Biodegradation Linked to Growth of Highly Specific Bacterial Clades

Reliance on bioremediation to remove benzene from anoxic environments has proven risky for decades but for unknown reasons. Years of research have revealed a strong link between anaerobic benzene biodegradation and the enrichment of highly specific microbes, namely Thermincola in the family Peptococcaceae and the deltaproteobacterial Candidate Sva0485 clade. Using aquifer material from Canadian Forces Base Borden, we compared five bioremediation approaches in batch microcosms. Under conditions simulating natural attenuation or sulfate biostimulation, benzene was not degraded after 1-2 years of incubation and no enrichment of known benzene-degrading microbes occurred. In contrast, nitrate-amended microcosms reported benzene biodegradation coincident with significant growth of Thermincola spp., along with a functional gene presumed to catalyze anaerobic benzene carboxylation (abcA). Inoculation with 2.5% of a methanogenic benzene-degrading consortium containing Sva0485 (Deltaproteobacteria ORM2) resulted in benzene biodegradation in the presence of sulfate or under methanogenic conditions. The presence of other hydrocarbon co-contaminants decreased rates of benzene degradation by a factor of 2-4. Tracking the abundance of the abcA gene and 16S rRNA genes specific for benzene-degrading Thermincola and Sva0485 is recommended to monitor benzene bioremediation in anoxic groundwater systems to further uncover growth rate limiting conditions for these two intriguing phylotypes. SYNOPSISAnaerobic benzene biodegradation was accelerated by biostimulation with nitrate or by bioaugmentation under methanogenic or sulfate-reducing conditions.

microbiology↗

bioRxiv2020

Longitudinal study of vinyl chloride degrading Dehalococcoides mccartyi-containing cultures to promote horizontal gene transfer

Few strains of Dehalococcoides mccartyi harbour and express the vinyl chloride reductase (VcrA) that catalyzes the dechlorination of vinyl chloride (VC), a carcinogenic soil and groundwater contaminant. The vcrA operon is found on a Genomic Island (GI) and therefore believed to participate in horizontal gene transfer. To try to induce horizontal gene transfer of the vcrA-GI, we blended two enrichment cultures in medium without ammonium while providing VC. We hypothesized that these conditions would select for a mutant strain of D. mccartyi that could both fix nitrogen and respire VC. However, after more than 4 years of incubation, we found no evidence for horizontal gene transfer of the vcrA-GI. Rather, we observed VC-dechlorinating activity attributed to the trichloroethene reductase TceA. Sequencing and protein modelling revealed a mutation in the predicted active site of TceA which may have influenced substrate specificity. We also identified two nitrogen-fixing D. mccartyi strains in the KB-1 culture. The presence of multiple strains of D. mccartyi with distinct phenotypes is a feature of natural environments and certain enrichment cultures (such as KB-1) and may enhance bioaugmentation success. The fact that multiple distinct strains persist in the culture for decades and that we could not induce horizontal gene transfer of the vcrA-GI suggests that it is not as mobile as predicted, or that mobility is restricted in ways yet to be discovered to specific sub-clades of Dehalococcoides. TOC Art O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/423565v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@80423forg.highwire.dtl.DTLVardef@7d6484org.highwire.dtl.DTLVardef@5223b2org.highwire.dtl.DTLVardef@a58aab_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2020

Biotransformation of lindane (γ-hexachlorocyclohexane) to non-toxic end products by sequential treatment with three mixed anaerobic microbial cultures

The {gamma} isomer of hexachlorocyclohexane (HCH), also known as lindane, is a carcinogenic persistent organic pollutant. Lindane was used worldwide as an agricultural insecticide. Legacy soil and groundwater contamination with lindane and other HCH isomers is still a big concern. The biotic reductive dechlorination of HCH to non-desirable and toxic lower chlorinated compounds such as monochlorobenzene (MCB) and benzene, among others, has been broadly documented. Here, we demonstrate for the first time that complete biotransformation of lindane to non-toxic end products is attainable using a sequential treatment approach with three mixed anaerobic microbial cultures referred to as culture I, II, and III. Biaugmentation with culture I achieved dechlorination of lindane to MCB and benzene. Culture II was able to dechlorinate MCB to benzene, and finally, culture III carried out methanogenic benzene degradation. Distinct Dehalobacter populations, corresponding to different 16S rRNA amplicon sequence variants in culture I and culture II, were responsible for lindane and MCB dechlorination, respectively. This study continues to highlight key roles of Dehalobacter spp. as chlorobenzene- and HCH-organohalide-respiring bacteria and demonstrates that sequential treatment with specialized anaerobic cultures may be explored at field sites in order to address legacy soil and groundwater contamination with HCH. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/354597v2_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@16ebd4corg.highwire.dtl.DTLVardef@14dfa8dorg.highwire.dtl.DTLVardef@7c5637org.highwire.dtl.DTLVardef@100634a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2019

Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, β-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene

Intensive historical and worldwide use of the persistent pesticide technical-grade hexachlorocyclohexane (HCH), composed of the active ingredient {gamma}-HCH (called lindane) along with several other HCH isomers, has led to widespread contamination. We derived four anaerobic enrichment cultures from HCH-contaminated soil capable of sustainably dechlorinating each of -, {beta}-, {gamma}-, and {delta}-HCH isomers stoichiometrically and completely to benzene and monochlorobenzene (MCB). For each isomer, the dechlorination rates increased progressively from <3 {micro}M/day to [~]12 {micro}M/day over two years. The molar ratio of benzene to MCB produced was a function of the substrate isomer, and ranged from {beta} (0.77{+/-}0.15), (0.55{+/-}0.09), {gamma} (0.13{+/-}0.02) to {delta} (0.06{+/-}0.02) in accordance with pathway predictions based on prevalence of antiperiplanar geometry. Cultivation with a different HCH isomer resulted in distinct bacterial communities, but similar archaeal communities. Data from 16S rRNA gene amplicon sequencing and quantitative PCR revealed significant increases in the absolute abundance of Pelobacter and Dehalobacter, especially in the -HCH and {delta}-HCH cultures. This study provides the first direct comparison of shifts in anaerobic microbial communities induced by the dechlorination of distinct HCH isomers. It also uncovers candidate microorganisms responsible for the dechlorination of -, {beta}-, {gamma}-, and {delta}-HCH, a key step towards better understanding and monitoring of natural attenuation processes and improving bioremediation technologies for HCH-contaminated sites.

microbiology↗

bioRxiv2019

Evidence for extensive anaerobic dechlorination and transformation of the pesticide chlordecone (C10Cl10O) in soil from Guadeloupe

Chlordecone (C10Cl10O) is a bishomocubane molecule, that has been used as pesticide, in many countries in Europe, America, and Africa, from the 1960s to 1990s. In the French West Indies, the historic use of chlordecone to control banana weevil infestations has resulted in pollution of large land areas. Although currently banned, chlordecone persists because it adsorbs strongly to soil and its complex structure is stable, particularly under aerobic conditions. A leaching model established that CLD pollution will last in French west indies soils several decades to half a millennium depending on soil type. However, abiotic chemical transformation catalyzed by reduced vitamin B12 has been shown to break down chlordecone by opening the cage structure to produce C9 polychloroindenes, and more recently these C9 polychloroindenes were also observed as products of anaerobic microbiological transformation by Citrobacter. To assess the potential for bioremediation, the anaerobic biotransformation of chlordecone by microbes native to soils from the French West Indies was investigated. Anaerobic microcosms were constructed from chlordecone impacted Guadeloupe soil and sludge to mimic natural attenuation and eletron donor-stimulated reductive dechlorination. Original microcosms and transfers were incubated over a period of 8 years, during which they were repeatedly amended with chlordecone and electron donor (ethanol and acetone). Using LC/MS, chlordecone and degradation products were detected in all the biologically active microcosms. Observed products in active incubations included monohydro-, dihydro- and trihydrochlordecone derivatives (C10Cl10-nO2Hn, n= 1,2,3), as well as \"open cage\" C9 polychloroindene compounds (C9Cl5-nH3+n, n=0,1,2) and C10 carboxylated polychloroindene derivatives (C10Cl4-nO2H4+n, n=0-3). Products with as many as 9 chlorine atoms removed were detected. These products were not observed in sterile incubations. Chlordecone concentrations decreased in active microcosms as concentrations of products increased, indicating that anaerobic dechlorination processes have occurred. An crude estimation of partitioning coefficients between soil and water showed that carboxylated intermediates sorb poorly, and as a consequence may be flushed away while polychlorinated indenes sorb strongly to soil. Microbial community analysis in microcosms showed enrichment of anaerobic fermenting and acetogenic microbes possibly involved in anaerobic chlordecone biotransformation. It thus should be possible to stimuilate anaerobic dechlorination through donor amendment to contaminated soils, particularly as some metabolites (in particular pentachloroindene) were already detected in field samples as a result of intrinsic processes. Extensive dechlorination in the microcosms, with evidence for up to 9 Cl atoms removed from the parent molecule is game-changing, giving hope to the possibility of using bioremediation to reduce the impact of CLD contamination.

microbiology↗

bioRxiv2019

Sustained dechlorination of vinyl chloride to ethene in Dehalococcoides-enriched cultures grown without addition of exogenous vitamins and at low pH

Trichloroethene (TCE) is a ubiquitous groundwater pollutant. Successful TCE bioremediation has been demonstrated at field sites using specialized microbial consortia harboring TCE-respiring Dehaloccocoides whose growth is cobalamin (vitamin B12)-dependent. Bioaugmentation cultures grown ex situ with ample exogenous vitamins in the medium and at neutral pH may become vitamin-limited or inhibited by acidic pH once injected into field sites, resulting in incomplete TCE dechlorination and accumulation of more toxic vinyl chloride (VC). Here, we report growth of the Dehalococcoides-containing bioaugmentation culture KB-1 in a TCE-amended mineral medium devoid of vitamins and in a VC-amended mineral medium at low pH (6.0 and 5.5). In cultures grown without exogenous vitamins or cobalamin, Acetobacterium, which can synthesize 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, and Sporomusa are the dominant acetogens. At neutral pH, a growing Acetobacterium population supports complete TCE dechlorination by Dehalococcoides at millimolar levels with a substantial increase in the amount of measured cobalamin (~20-fold). Sustained dechlorination of VC to ethene was achieved at a pH as low as 5.5, yet at low pH Acetobacterium is less abundant, potentially affecting the production of DMB and/or cobalamin. However, dechlorination activity at very low pH (< 5.0) was not stimulated by DMB supplementation, but was restored by raising pH to neutral. Assays in cell extracts revealed that vinyl chloride reductase (VcrA) activity declines significantly below pH 6.0 and is undetectable below pH 5.0. This study highlights the roles of and interplay between vitamin-producing populations and pH in microbial dechlorinating communities, and their importance for successful chlorinated ethenes bioremediation at field sites.

microbiology↗

bioRxiv2019

Reductive dehalogenase gene biomarkers differentiate 1,1,1-trichloroethane from 1,1-dichloroethane dechlorination in microcosms and at a field site treated with granular ZVI and guar gum

Chlorinated ethanes are environmental pollutants found frequently at many contaminated industrial sites. 1,1,1-Trichloroethane (1,1,1-TCA) can be dechlorinated and detoxified via abiotic transformation or biologically by the action of dechlorinating microorganisms such as Dehalobacter (Dhb). At a field site, it is challenging to distinguish abiotic vs biotic mechanisms as both processes share common transformation products. In this study, we evaluated using the Dhb 16S rRNA gene and specific reductive dehalogenase genes as biomarkers for 1,1,1-TCA and 1,1-dichloroethane (1,1-DCA) dechlorination. We analyzed samples from laboratory groundwater microcosms and from an industrial site where a mixture of granular zero valent iron (ZVI) and guar gum was injected for 1,1,1-TCA remediation. Abiotic and biotic transformation products were monitored and the changes in dechlorinating organisms were tracked using quantitative PCR (qPCR) with primers targeting the Dhb 16S rRNA gene and two functional genes cfrA and dcrA encoding enzymes that dechlorinate 1,1,1-TCA to 1,1-DCA and 1,1-DCA to chloroethane (CA), respectively. The abundance of the cfrA- and dcrA-like genes confirmed that the two dechlorination steps were carried out by two distinct Dhb populations at the site. Using cell yields established in laboratory microcosms along with measured abundances of the Dhb 16S rRNA gene in site samples, biotic and abiotic transformation of 1,1,1-TCA at the site was estimated. The biomarkers used in this study proved useful for tracking biodechlorination of 1,1,1-TCA and 1,1-DCA where both abiotic (e.g. with ZVI) and biotic processes co-occur.

microbiology↗

bioRxiv2019

Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

Antimicrobial resistance is a globally recognized public health risk. High incidence of antibiotic resistant bacteria and antibiotic resistance genes (ARGs) in solid organic waste necessitates the development of effective treatment strategies. The objective of this study was to assess ARG diversity and abundance as well as the relationship between resistome and microbial community structure during anaerobic co-digestion (AD) of food waste, paper and cardboard. A lab-scale solid-state AD system consisting of six sequentially fed leach beds (each with a solids retention time of 42 days) and an upflow anaerobic sludge blanket (UASB) reactor was operated under mesophilic conditions continuously for 88 weeks to successfully treat municipal organic waste and produce biogas. A total of ten samples from digester feed and digestion products were collected for microbial community analysis including SSU rRNA gene sequencing, total community metagenome sequencing and quantitative PCR. Taxonomic analyses revealed that AD changed the taxonomic profile of the microbial community: digester feed was dominated by bacterial and eukaryotic taxa while anaerobic digestate possessed a large proportion of archaea mainly belonging to the methanogenic genus Methanosaeta. ARGs were identified in all samples with significantly higher richness and relative abundance per 16S rRNA gene in digester feed compared to digestion products. Multidrug resistance was the most abundant ARG type. AD was not able to completely remove ARGs as shown by ARGs detected in digestion products. Using metagenomic assembly and binning we detected potential bacterial hosts of ARGs in digester feed, that included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. IMPORTANCESolid organic waste is a significant source of antibiotic resistance genes (ARGs) (1) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here we studied the antibiotic resistome and microbial community structure within an anaerobic digester treating a mixture of food waste, paper and cardboard. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. We identified the host organisms of some of the ARGs including potentially pathogenic as well as non-pathogenic bacteria, and we detected mobile genetic elements required for horizontal gene transfer. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

microbiology↗

bioRxiv2019

Solid state anaerobic digestion of mixed organic waste: the synergistic effect of food waste addition on the destruction of paper and cardboard

Full-scale anaerobic digestion processes for organic solid waste are common in Europe, but generally unaffordable in Canada and the United States because of inadequate regulations to restrict cheaper forms of disposal, particularly landfill. We investigated the viability of solid-state anaerobic digestion (SS-AD) as an alternative that reduces the costs of waste pretreatment and subsequent wastewater treatment. A laboratory SS-AD digester, comprising six 10L leach beds and an upflow anaerobic sludge blanket reactor treating the leachate, was operated continuously for 88 weeks, with a mass balance of 101{+/-}2%. The feed was a mixture of cardboard, boxboard, newsprint, and fine paper, and varying amounts of food waste (from 0% to 29% on a COD basis). No process upset or instability was observed. The addition of food waste showed a synergistic effect, raising CH4 production from the fibre mixture from 52.7 L.kg-1COD fibreadded to 152 L.kg-1COD fibreadded, an increase of 190%. Substrate COD destruction efficiency reached 65% and a methane yield of 225 L.kg-1 CODadded was achieved at 29% food waste on a COD basis, and a solids retention time of 42 days. This performance was similar to that of a completely stirred tank reactor digesting similar wastes, but with much lower energy input. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/564203v1_ufig1.gif" ALT="Figure 1"> View larger version (122K): org.highwire.dtl.DTLVardef@15c0e8aorg.highwire.dtl.DTLVardef@beadb3org.highwire.dtl.DTLVardef@7def43org.highwire.dtl.DTLVardef@1e717f5_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2018

Interspecies malate-pyruvate shuttle drives amino acid exchange in organohalide-respiring microbial communities

Most microorganisms in the biosphere live in communities and develop coordinated metabolisms via trading metabolites. In this study, we sought to deconstruct the metabolic interdependency in organohalide-respiring microbial communities enriched with Dehalobacter restrictus (Dhb), using a complementary approach of computational metabolic modeling and experimental validation. Dhb possesses a complete set of genes for amino acid biosynthesis yet requires amino acid supplementation. We reconciled this discrepancy using Flux Balance Analysis with consideration for cofactor availability, enzyme promiscuity, and shared protein expression patterns of several Dhb strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of strain PER-K23 cultures were performed to validate the model predictions. The model resolved that Dhbs amino acid dependency results from restricted NADPH regeneration and diagnosed that malate supplementation can replenish intracellular NADPH using malic enzyme. Interestingly, we observed unexpected export of glutamate and pyruvate in parallel to malate consumption in the strain PER-K23 cultures. Further experiments on Dhb-enriched consortium ACT-3 suggested an interspecies malate-pyruvate shuttle between Dhb and a glutamate-auxotrophic Bacteroides sp., reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study reveals that redox constraints and metabolic complementarity are important driving forces for amino acid exchange in anaerobic microbial communities.

microbiology↗

bioRxiv2018

Eight new genomes of organohalide-respiring Dehalococcoides mccartyi reveal evolutionary trends in reductive dehalogenase enzymes

BackgroundBioaugmentation is now a well-established approach for attenuating toxic groundwater and soil contaminants, particularly for chlorinated ethenes and ethanes. The KB-1 and WBC-2 consortia are cultures used for this purpose. These consortia contain organisms belonging to the Dehalococcoidia, including strains of Dehalococcoides mccartyi in KB-1 and of both D. mccartyi and Dehalogenimonas in WBC-2. These tiny anaerobic bacteria couple respiratory reductive dechlorination to growth and harbour multiple reductive dehalogenase genes (rdhA) in their genomes, the majority of which have yet to be characterized.\n\nResultsUsing a combination of Illumina mate-pair and paired-end sequencing we closed the genomes of eight new strains of Dehalococcoides mccartyi found in three related KB-1 sub-cultures that were enriched on trichloroethene (TCE), 1,2-dichloroethane (1,2-DCA) and vinyl chloride (VC), bringing the total number of genomes available in NCBI to 24. A pangenome analysis was conducted on 24 Dehalococcoides genomes and five Dehalogenimonas genomes (2 in draft) currently available in NCBI. This Dehalococcoidia pangenome generated 2875 protein families comprising of 623 core, 2203 accessory, and 49 unique protein families. In Dehalococcoides mccartyi the complement of reductive dehalogenase genes varies by strain, but what was most surprising was how the majority of rdhA sequences actually exhibit a remarkable degree of synteny across all D. mccartyi genomes. Several homologous sequences are also shared with Dehalogenimonas genomes. Nucleotide and predicted protein sequences for all reductive dehalogenases were aligned to begin to decode the evolutionary history of reductive dehalogenases in the Dehalococcoidia.\n\nConclusionsThe conserved synteny of the rdhA genes observed across Dehalococcoides genomes indicates that the major differences between strain rdhA gene complement has resulted from gene loss rather than recombination. These rdhA have a long evolutionary history and trace their origin in the Dehalococcoidia prior to the speciation of Dehalococcoides and Dehalogenimonas. The only rdhA genes suspected to have been acquired by lateral gene transfer are protein-coding rdhA that have been identified to catalyze dehalogenation of industrial pollutants. Sequence analysis suggests that evolutionary pressures resulting in new rdhA genes involve adaptation of existing dehalogenases to new substrates, mobilization of rdhA between genomes or within a genome, and to a lesser degree manipulation of regulatory regions to alter expression.

bioinformatics↗

bioRxiv2017

Chlorinated electron acceptor availability selects for specific Dehalococcoides populations in dechlorinating enrichment cultures and in groundwater

Individual Dehalococcoides mccartyi (Dhc) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes contained within their respective genomes. While thousands of rdhA genes have been sequenced, the activity of the corresponding proteins have been identified in only a handful of cases. Most effort has focused on identifying the enzymes that dechlorinate substrates including trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC) relevant to groundwater remediation. The associated rdhA genes, namely tceA, bvcA, and vcrA, along with the D. mccartyi 16S rRNA gene are often used to track growth and dechlorinating activity in DNA extracted from field samples. In this study, we augmented the typical suite of three characterized rdhA genes to include an additional 12 uncharacterized rdhA sequences identified in the metagenome in the mixed Dhc-containing culture KB-1 to track population shifts within the culture and at two bioaugmented field sites. Quantitative PCR assays were developed for the 15 selected D. mccartyi rdhA genes and evaluated using 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion of rdhA gene copies relative to Dhc 16S gene copies indicated the presence of multiple distinct Dhc populations in each culture. The specific electron acceptor amended to each culture had a major influence on the distribution of D. mccartyi populations and their associated rdhA genes. We also surveyed the abundance of rdhA genes in samples obtained from two bioaugmented field sites. Growth of the dominant D. mccartyi population in the KB-1 inoculum was detected in the UK site samples. At both field sites, the measurement of relative rdhA abundances revaled significant D. mccartyi population shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene, indicating that the selective pressure of the most abundant chlorinated electron acceptor that was observed in lab cultures was also occurring in the populations in the field. Understanding driving forces behind D. mccartyi population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.

microbiology↗