Biology subjects

Loeffler, F. E.

Publications and source records attributed to Loeffler, F. E..

4 recordsLinked to original sources

bioRxiv2026

Cobamide-Dependent Dichloromethane Fermentation by Dehalobacter Reveals a Hidden Acetogenic Route for Organohalide Biotransformation

Halogenated one-carbon (C1) compounds, such as dichloromethane (DCM), drive critical fluxes in global carbon and halogen cycles. While the genus Dehalobacter is canonically defined by obligate organohalide respiration, its physiological and ecological roles in anaerobic C1 metabolism have remained fundamentally ambiguous. Here, we document a paradigm-shifting metabolic capacity within a sediment-derived microbial consortium: the autonomous fermentation of DCM by a novel population, Candidatus Dehalobacter formatiformans strain J1. Over successive transfers, strain J1 outcompeted co-existing Dehalobacterium formicoaceticum to become the overwhelmingly dominant population (>80% relative abundance), converting DCM stoichiometrically to acetate and formate (4:1) without auxiliary substrates. Genome-resolved metagenomics revealed that strain J1 couples a distinct mec gene cassette--mediating methyl-transfer reactions during DCM activation--to a complete Wood-Ljungdahl pathway for efficient C1 assimilation. Crucially, strain J1 lacks the complete genetic repertoire for de novo cobamide biosynthesis. Physiological validation confirmed that this fermentative pathway is strictly dependent on exogenous cobamides, exposing a profound reliance on community cross-feeding. These findings reveal an unexpected acetogenic lifestyle within Dehalobacter, a lineage historically viewed as comprising obligate organohalide-respiring bacteria. More broadly, this work identifies cobamide-dependent methyl-transfer metabolism as an ecological control on anaerobic DCM fermentation and expands the known roles of Dehalobacter in carbon-halogen cycling in anoxic environments.

microbiology↗

bioRxiv2024

Nitrous Oxide Formation and Consumption in Thawing Permafrost: A Microcosm Study

Nitrous oxide (N2O) emissions contribute to stratospheric ozone depletion and global warming. Climate warming causes permafrost thawing and decomposition of the dormant nitrogenous compounds, releasing N2O; however, understanding of the microbial formation and consumption of N2O in permafrost is still limited. Permafrost soils collected at two depths (5.4 m and 16.9 m) from the East Siberian Sea coast of Russia were used to establish microcosms assessing N2O formation and consumption in the presence of either nitrate (NO3-, 1 mM) or N2O (1 mM), respectively, during incubation at 4 and 20{degrees}C. Rapid N2O formation was observed in NO3--amended microcosms, but N2O consumption was slow and incomplete over a 1-year incubation period in all microcosms. Twenty-six quality-filtered metagenome-assembled genomes (MAGs) harboring genes involved in the reduction of NO3- and/or N2O were recovered from 16 metagenomes obtained from duplicate NO3-- and N2O-amended microcosms. None of the MAGs carried a complete set of genes to perform canonical denitrification (i.e., NO3-[->]N2) indicating N2O formation and consumption is likely driven by non-denitrifying bacteria. While coastal permafrost microbiomes harbor nosZ genes, activity monitored in the microcosms indicates N2O formation exceeds N2O consumption, emphasizing the need for integrated approaches to assess and predict N turnover in thawing permafrost.

microbiology↗

bioRxiv2023

pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms

Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH<5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02mM) and high (2mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, but long lag times of up to 7 months were observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. In acidic microcosms, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen metagenome-assembled genomes (MAGs) recovered from these microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the clade II type nosZ, lacking nitrite reductase genes (nirS, nirK). Five of these MAGs represented novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.

microbiology↗

bioRxiv2021

Global distribution of anaerobic dichloromethane degradation potential

Anthropogenic activities and natural processes release dichloromethane (DCM), a toxic chemical with substantial ozone-depleting capacity. Specialized anaerobic bacteria metabolize DCM; however, the genetic basis for this process has remained elusive. Comparative genomics of the three known anaerobic DCM-degrading bacterial species revealed a homologous gene cluster, designated the methylene chloride catabolism (mec) gene cassette, comprising eight to ten genes with predicted 79.6 - 99.7% amino acid identity. Functional annotation identified genes encoding a corrinoid-dependent methyltransferase system, and shotgun proteomics applied to two DCM-catabolizing cultures revealed high expression of proteins encoded on the mec gene cluster during anaerobic growth with DCM. In a DCM-contaminated groundwater plume, the abundance of mec genes strongly correlated with DCM concentrations (R2 = 0.71 - 0.85) indicating their value as process-specific bioremediation biomarkers. mec gene clusters were identified in metagenomes representing peat bogs, the deep subsurface, and marine ecosystems including oxygen minimum zones (OMZs), suggesting DCM turnover in diverse habitats. The broad distribution of anaerobic DCM catabolic potential suggests a relevant control function for emissions to the atmosphere, and a role for DCM as a microbial energy source in critical zone environments. The findings imply that the global DCM flux might be far greater than emission measurements suggest. ImportanceDichloromethane (DCM) is an increasing threat to stratospheric ozone with both anthropogenic and natural emission sources. Anaerobic bacterial metabolism of DCM has not yet been taken into consideration as a factor in the global DCM cycle. The discovery of the mec gene cassette associated with anaerobic bacterial DCM metabolism and its widespread distribution in environmental systems highlight a strong attenuation potential for DCM. Knowledge of the mec cassette offers new opportunities to delineate DCM sources, enables more robust estimates of DCM fluxes, supports refined DCM emission modeling and simulation of the stratospheric ozone layer, reveals a novel, ubiquitous C1 carbon metabolic system, and provides prognostic and diagnostic tools supporting bioremediation of groundwater aquifers impacted by DCM.

microbiology↗