Thelusmond, J. 2018. Biodegradation of emergin contaminants in agricultural soils and thier impact on soil microbial communities. Dissertation, Michigan State University, East Lansing, MI.
The incomplete elimination of pharmaceuticals and personal care products (PPCPs) during wastewater treatment has resulted in their dissemination in agricultural soils. Biodegradation is a potential removal mechanism; however, the microorganisms and pathways involved are generally unknown. The current work examined the biodegradation of carbamazepine (CBZ), diclofenac (DCF), triclocarban (TCC), and triclosan (TCS) in agricultural soils under aerobic and anaerobic conditions. Solid phase extraction and liquid chromatography tandem mass spectrometry were used for PPCP extraction and analysis. The soil microbial communities were investigated using 16S rRNA gene amplicon and shotgun sequencing.
The first study examined CBZ biodegradation at three concentrations (50, 500, 5000 ng/g), under aerobic and anaerobic conditions, in two soils, using 16S rRNA gene amplicon sequencing and an approach to predict metagenomes (phylogenetic investigation of communities by reconstruction of unobserved states, PICRUSt). The most significant CBZ biodegradation occurred under aerobic conditions. PICRUSt revealed that one soil contained a greater abundance of xenobiotic degrading genes. Several phylotypes were enriched following CBZ degradation, including unclassified Sphingomonadaceae, Xanthomonadaceae and Rhodobacteraceae, as well as Sphingomonas, Aquicella and Microvirga. These phylotypes are considered putative CBZ degraders as they appear to be benefiting from CBZ biodegradation.
The second study focused on DCF, CBZ and TCC biodegradation in four soils at concentrations typically detected in soils and biosolids (50 ng g -1) using 16S rRNA gene amplicon sequencing and PICRUSt. Rapid DCF removal (<7 days) was observed under aerobic conditions, with limited biodegradation under other conditions. CBZ and TCC degradation was slow (half-lives of 128-241 days and 165-190 days for CBZ and TCC). Phylotypes in the Proteobacteria, Gemmatimonadales and Actinobacteria were more abundant during DCF biodegradation. For CBZ, those in the Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia were enriched during biodegradation. Actinobacteria and Proteobacteria were also enriched during TCC biodegradation. Such differences could indicate these microorganisms are associated with biodegradation. The impact on KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolism pathways was also examined. Four pathways were positively impacted during DCF biodegradation. CBZ had a limited impact on the metabolic pathways. TCC removal was linked to genes associated with the degradation of simple and complex substrates.
The third study examined CBZ, TCC and TCS biodegradation using shotgun sequencing and MG-RAST analysis. CBZ and TCC biodegradation was again slow, and TCS biodegradation was rapid. For each chemical, between three and ten phylotypes were enriched during biodegradation. The genera of previously reported CBZ, TCC or TCS degrading isolates were present; Rhodococcus (CBZ), Streptomyces (CBZ), Pseudomonas (CBZ, TCC, TCS), Sphingomonas (TCC, TCS), Methylobacillus (TCS) and Stenotrophomonas (TCS). From the analysis of xenobiotic degrading pathways, five KEGG pathways were the most dominant.
This research indicates a number of phylotypes are likely involved in PPCP biodegradation in agricultural soils. Also, the work suggests that the phylotypes impacted are affected by the experimental conditions (e.g. PPCP concentration, soil type, incubation time). From the PPCPs examined, CBZ and TCC are highly recalcitrant and will likely remain in agricultural soils for extended periods of time.
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