Biology subjects

Fenner, K.

Publications and source records attributed to Fenner, K..

4 recordsLinked to original sources

bioRxiv2026

An enzyme-level benchmark based on environmental bacterial laccases for predicting contaminant fate in water

Bacterial laccases are widespread multicopper oxidases whose roles in the fate of anthropogenic chemicals in aquatic environments remain poorly understood. Here, we integrate metagenomic analysis, a miniaturized high-throughput assay and machine learning to establish an enzyme-level benchmark for predicting biotransformation of wastewater-relevant trace organic contaminants by laccase-mediator systems. Using a laccase from an ammonia-oxidizing bacterium as a model enzyme, we screened 183 compounds and identified 38 that underwent significant removal. Following phylogenetic analysis of environmental homologs, we expressed and purified two additional laccases from the bacterial methanotrophic phylum Methylmirabilota and an archaeal phylum Thermoproteota, demonstrating the activity of this enzyme family across domains. Graph convolutional network models trained on the dataset achieved up to 78% accuracy in classifying degradable versus persistent chemicals, while quantum-chemical descriptors highlighted key electronic properties governing oxidation. This bottom-up approach to enzyme-chemical interactions establishes a trajectory towards predicting contaminant persistence in engineered and natural waters.

biochemistry↗

bioRxiv2023

Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase

BackgroundAntibiotic resistance, which is mediated by environmental reservoirs, poses a threat to human and animal health. Aquatic biofilms impacted by treated wastewater (WW) are known environmental reservoirs for antibiotic resistance, however the specific influence of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited as to whether genes with low sequence similarity to reference ARGs actually encode for functional ARGs, particularly within complex aquatic microbial communities. ResultsTo disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or nonultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in metagenomic abundances in biofilms grown with increasing percentages of nonultrafiltered WW. In contrast, sulfonamide and BEL family beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to nonultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs which exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing low sequence identity with known ARGs. ConclusionsThis discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted metagenomic analysis on the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms.

microbiology↗

bioRxiv2023

Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater

Organic contaminants enter aquatic ecosystems from various sources, including wastewater treatment plant effluent. Freshwater biofilms play a major role in the removal of organic contaminants from receiving water bodies, but knowledge of the molecular mechanisms driving contaminant biotransformations in complex stream biofilm (periphyton) communities remains limited. Previously, we demonstrated that biofilms in experimental flume systems grown at higher ratios of treated wastewater (WW) to stream water displayed an increased biotransformation potential for a number of organic contaminants. We identified a positive correlation between WW percentage and biofilm biotransformation rates for the widely-used insect repellent, N,N-diethyl-meta-toluamide (DEET). Here, we conducted deep shotgun sequencing of flume biofilms and identified a positive correlation between WW percentage and metagenomic read abundances of DEET hydrolase (DH) homologs. To test the causality of this association, we constructed a targeted metagenomic library of DH homologs from flume biofilms. We screened our complete metagenomic library for activity with four different substrates and a subset thereof with 183 WW-related organic compounds. The majority of active hydrolases in our library preferred aliphatic and aromatic ester substrates while, remarkably, only a single reference enzyme was capable of DEET hydrolysis. Of the 626 total enzyme-substrate combinations tested, approximately 5% were active enzyme-substrate pairs. Metagenomic DH family homologs revealed a broad substrate promiscuity spanning 22 different compounds when summed across all enzymes tested. We biochemically characterized the most promiscuous and active enzymes identified based on metagenomic analysis from uncultivated Rhodospirillaceae and Planctomycetaceae. In addition to characterizing new DH family enzymes, we exemplified a framework for linking metagenome-guided hypothesis generation with experimental validation. Overall, this study expands the scope of known enzymatic contaminant biotransformations for metagenomic hydrolases from WW-receiving stream biofilm communities. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/559296v2_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1b5cbaforg.highwire.dtl.DTLVardef@4f73f7org.highwire.dtl.DTLVardef@467d16org.highwire.dtl.DTLVardef@1be598d_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMetagenomic DEET hydrolase abundances higher in biofilms grown in treated wastewater. C_LIO_LIEleven out of 64 metagenomic hydrolases tested exhibited hydrolysis activity. C_LIO_LIRelated enzymes in a single family of DEET hydrolases biotransform 20+ contaminants. C_LIO_LIReference DEET hydrolase shows a substrate preference for benzamide moieties. C_LIO_LI True DEET hydrolases are in low abundance even in biofilms that degrade DEET. C_LI

biochemistry↗

bioRxiv2021

enviLink: A database linking contaminant biotransformation rules to enzyme classes in support of functional association mining

MotivationThe ability to assess and engineer biotransformation of chemical contaminants present in the environment requires knowledge on which enzymes can catalyze specific contaminant biotransformation reactions. For the majority of over 100000 chemicals in commerce such knowledge is not available. Enumeration of enzyme classes potentially catalyzing observed or de novo predicted contaminant biotransformation reactions can support research that aims at experimentally uncovering enzymes involved in contaminant biotransformation in complex natural microbial communities. DatabaseenviLink is a new data module integrated into the enviPath database and contains 316 theoretically derived linkages between generalized biotransformation rules used for contaminant biotransformation prediction in enviPath and 3rd level EC classes. Rule-EC linkages have been derived using two reaction databases, i.e., Eawag-BBD in enviPath, focused on contaminant biotransformation reactions, and KEGG. 32.6% of identified rule-EC linkages overlap between the two databases, whereas 40.2% and 27.2%, respectively, are originating from Eawag-BBD and KEGG only. Implementation and availabilityenviLink is encoded in RDF triples as part of the enviPath RDF database. enviPath is hosted on a public webserver (envipath.org) and all data is freely available for non-commercial use. enviLink can be searched online for individual transformation rules of interest (https://tinyurl.com/y63ath3k) and is also fully downloadable from the supporting materials (i.e., Jupyter notebook "enviLink" and tsv files provided through GitHub at https://github.com/emanuel-schmid/enviLink).

bioinformatics↗