bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.10.12.758446

TFA-defluorinating microbial consortium achieved with analogue enrichment

Jensen, E. H.·Forouzandeh, A.·Trier, X.·Gotfredsen, C. H.·Enemark-Rasmussen, K.·Ahmad, S.·Nielsen, T. K.
View original source ↗Export metadata ↓

Abstract

Trifluoroacetate (TFA) is an ultra-short chain perfluoroalkyl substance (PFAS) and a pollutant of global significance; it is persistent and ubiquitous in the environment across compartments, including food, drinking water, animals, and humans. Concentrations in the environment are rising, concerns over the toxicity of the compound are increasing, and there are currently no efficient ways to remediate TFA pollution, as conventional methods are ineffective at scale under environmental conditions. Microorganisms possessing dehalogenating enzymes targeting the structurally analogous compound monofluoroacetate (MFA) present a potential solution to degrade TFA microbiologically. Due to previously demonstrated dehalogenation of difluoroacetate (DFA) by dehalogenases, the promiscuity of such enzymes was hypothesized to be extendable to TFA as well. In this study cultures obtained from an environmental sample of PFAS contaminated wastewater sludge were incubated in M9 minimal media supplied with 33 mM acetate and either 33 mM TFA, DFA, or MFA in an iterative manner, followed by testing in a 30-day experiment. Free fluoride (F-) was measured at 5 timepoints using a fluoride ion specific electrode (ISE). One culture designated MFA1C significantly degraded MFA, DFA, and TFA (two-way ANOVA mixed model, p < 0.05). MFA1C released 11.2 {+/-} 0.7 M F- which constitutes approximately 0.01% of the potential fluoride release from the total 33 mM TFA applied and with the greatest defluorination activity in the first 9 days of incubation. Fluoride release from TFA and formation of DFA and MFA was confirmed with 19F-NMR. Genetic sequencing and protein-ligand modelling identified two candidate dehalogenase enzymes from Achromobacter denitrificans and Stenotrophomonas sp., respectively, with potential capacity to degrade TFA. The findings of this study are a crucial first step towards future potential bioremediation of TFA, and are, to the best of our knowledge, the first to identify a TFA-degrading consortium of microorganisms.

Explore related subjects

microbiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Jensen, E. H., Forouzandeh, A., Trier, X., Gotfredsen, C. H., Enemark-Rasmussen, K., Ahmad, S., Nielsen, T. K.. 2026-10-12. TFA-defluorinating microbial consortium achieved with analogue enrichment. https://doi.org/10.64898/2026.10.12.758446

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Effects of Alternating Polarity Frequency on the Assembly of Electro-Methanogenic Microbial Communities

Electro-methanogenesis can enhance methane production and has attracted extensive interest, but the current strategies for building electro-methanogenic microbial communities suffer from several limitations. Alternating polarity has been shown as a new strategy to build electro-methanogenic communities, but the impact of alternation frequency on community assembly remains to be understood. In this study, the impact was evaluated using bioelectrochemical systems amended with granular activated carbon, and the working-electrode potential was alternated between +0.4 and -0.4 V vs. SHE at six frequencies ranging from 0.5 to 12 days. Among the tested conditions, 4-d alternation led to the best overall performance, producing approximately 250 L/L/kg cumulative biogas, 96% methane content, and a 45% methane yield, while preserving a stable and reproducible community structure. The community contained two Methanobacterium populations, two putatively electroactive Geobacter populations, and one putatively electroactive Pseudomonas population, together with diverse fermentative and syntrophic bacteria. Transcript-based analyses revealed clear frequency- and potential-dependent shifts in the activity of these functional groups. Redundancy analysis associated the Methanobacterium formicicum-related population with cathodic current and methane production, whereas the Geobacter sulfurreducens-related population was linked to anodic current and methane production. Bayesian and local-similarity networks further connected methanogen dynamics with specific electroactive, fermentative, and syntrophic partners. Collectively, these results establish alternating polarity frequency as a critical parameter for building robust communities capable of high-rate, high-quality methane production.

microbiology↗
bioRxiv2026

Benchmarking Microbiome Methods for Improved Metagenomic Sequencing of Lower Respiratory Tract Samples

Bronchoalveolar lavage is a common diagnostic strategy used to sample immune cells and microbiota of the lower respiratory tract. Metagenomic sequencing of raw bronchoalveolar lavage fluid reveals a low biomass microbial community often obscured by abundant host DNA. Here, we set out to determine an optimal strategy to robustly purify microbial DNA in excess of human DNA using a combinatorial lysis, host-depletion, DNA extraction approach. We identify strategies that improve metagenomic sequencing success that are commensurate with purification challenges that reduce signal from respiratory microbiota. Finally, we present a general framework to further improve microbial sequencing of lower respiratory tract samples in a robust and reproducible manner.

microbiology↗
bioRxiv2026

Shared genomic features of oral bacterial habitat specialization

The oral microbiome exhibits spatial organization, with related bacteria occupying different surfaces despite continual dispersal between habitats. Whether this ecological partitioning is accompanied by genomic functions that recur across evolutionarily divergent lineages remains unclear. Here we compared plaque- and mucosa-associated bacteria representing 47 human microbial taxa, 13 genera and six phyla, using 1,121 reference genome assemblies and habitat-affinity estimates assembled from six oral microbiome abundance summaries. Across 13 genera, a genus-balanced screen of 13,917 nonredundant genomic profiles prioritised 14 exploratory annotations with nominal associations in the same direction before and after adjustment for genome composition with none passing genome-wide family-wise error correction. Proteins carrying recurrent domains belonged to multiple sequence clusters. Closely spaced, divergently oriented HxlR-SnoaL_2 gene pairs occurred in 66 genomes associated with plaque biofilms across four genera, although overall HxlR-SnoaL_2 linkage was not significantly associated with plaque preference. Using source-family-balanced habitat scores, nested cross-validation with entire genera held out supported prediction of habitat preference (macro-average within-genus AUC, 0.821; empirical P = 0.010). Predictive performance was lower after adjustment for genome size, GC content and coding-sequence number (AUC, 0.776; empirical P = 0.059). These findings reveal partial recurrence of habitat-associated genomic annotations amid lineage-dependent protein repertoires and genetic arrangements. They provide a comparative framework for distinguishing broadly shared ecological genomic signatures from alternative, potentially lineage-specific routes to oral habitat specialization.

microbiology↗