Abundance of Chlorinated Solvent and 1,4-Dioxane Degrading Microorganisms at Five Chlorinated Solvent Contaminated Sites Determined via Shotgun Sequencing

Abstract

Shotgun sequencing was used for the quantification of taxonomic and functional biomarkers associated with chlorinated solvent bioremediation in 20 groundwater samples (five sites), following bioaugmentation with SDC-9. The analysis determined the abundance of (1) genera associated with chlorinated solvent degradation, (2) reductive dehalogenase (RDases) genes, (3) genes associated with 1,4-dioxane removal, (4) genes associated with aerobic chlorinated solvent degradation, and (5) D. mccartyi genes associated with hydrogen and corrinoid metabolism. The taxonomic analysis revealed numerous genera previously linked to chlorinated solvent degradation, including Dehalococcoides, Desulfitobacterium, and Dehalogenimonas. The functional gene analysis indicated vcrA and tceA from D. mccartyi were the RDases with the highest relative abundance. Reads aligning with both aerobic and anaerobic biomarkers were observed across all sites. Aerobic solvent degradation genes, etnC or etnE, were detected in at least one sample from each site, as were pmoA and mmoX. The most abundant 1,4-dioxane biomarker detected was Methylosinus trichosporium OB3b mmoX. Reads aligning to thmA or Pseudonocardia were not found. The work illustrates the importance of shotgun sequencing to provide a more complete picture of the functional abilities of microbial communities. The approach is advantageous over current methods because an unlimited number of functional genes can be quantified.

Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9

“…The percentage of relative abundance of the genus Dhc , reported in other PCE-/TCE-dechlorinating microbial consortia (e.g., D2, KB-1, ANAS) (43.7% for KB-1; 31.3% for D2 and 18.2% for ANAS), was between 14% and 19.8% based on the taxonomic profiling methods used in this study (Figure ). These values are somewhat lower than those reported by a recent shotgun sequencing effort, which reported higher relative abundances of 30–31% of Dhc in two samples of SDC-9, suggesting that growth conditions and possibly the timing of biomass collection for DNA extraction (which was conducted at an early stage of PCE dechlorination in this study) influence the relative abundance of Dhc . Of additional interest is the occurrence of Desulfitobacterium , which is in the same Peptococcaceae family as Dehalobacter , with some strains able to dechlorinate PCE to TCE or PCE/TCE to cDCE.…”

“…The other most abundant groups detected were members of the genera Desulfovibrio and Methanocorpusculum , which have been reported in other dechlorinating consortia. , While some members of the genus Desulfovibrio ferment lactate to acetate and H 2 , Methanocorpusculum is comprised of strictly carbon dioxide-reducing methanogens that utilize H 2 and formate as electron donors . This genus was also previously detected in SDC-9 at ∼10% relative abundance . Methanomicrobiales has also been reported as a dominant order in consortium KB-1, unlike other cultures, such as ANAS, which contains methanogens of the family Methanobacteriaceae, or D2 with members of the Methanosarcinaceae and Methanosaetaceae families.…”

“…Taxonomic profiling at the genus level, carried out using the short-read classifying systems Kaiju, Clark and MG-RAST, indicated that 14−19.9% of the metagenomic sequence reads were derived from Dhc , demonstrating that this genus was a major component of the SDC-9 consortium (Figure ). The taxonomic analysis using MG-RAST revealed that Desulfitobacterium (17.4%) was of similar abundance in the SDC-9 community as Dhc . On the basis of Kaiju and Clark, Desulfitobacterium (∼10%) was detected as second most abundant genus in consortium SDC-9.…”

“…11 This genus was also previously detected in SDC-9 at ∼10% relative abundance. 35 Methanomicrobiales has also been reported as a dominant order in consortium KB-1, unlike other cultures, such as ANAS, 39 which contains methanogens of the family Methanobacteriaceae, or D2 11 with members of the Methanosarcinaceae and Methanosaetaceae families. These results indicate that methanogen populations vary between dechlorinating consortia.…”

Synergistic Zerovalent Iron (Fe0) and Microbiological Trichloroethene and Perchlorate Reductions Are Determined by the Concentration and Speciation of Fe

“…The reductively dechlorinating enrichment cultures used in this study were ZARA-10 46–48 and SDC-9 (RNAS Remediation products, Brooklyn Center, MN) . Both cultures are enriched in reductively dechlorinating-, fermenting-, and methanogenic-microorganisms. , ZARA-10 culture contains strains of D. mccartyi with tceA , vcrA , and bvcA reductive dehalogenase genes and Geobacter sp.…”