Biology subjects

Weaver, M. E.

Publications and source records attributed to Weaver, M. E..

4 recordsLinked to original sources

bioRxiv2026

Redirecting carbon and electron flow in methanogenic laboratory scale anaerobic digestors with hypophosphite

In anaerobic digestion, formate is a central electron carrier linking primary and secondary fermentation to methanogenesis. Efforts to alter methane production have largely focused on directly targeting methanogens, while disruption of other trophic levels is underexplored. We recently demonstrated that hypophosphite is a naturally occurring inhibitor of formate exchange in syntrophic methanogenic systems. Here, we investigated whether intercepting formate exchange using hypophosphite can modulate methane production in a complex fermentative methanogenic system and what the longer-term consequences are for the structure and function of the microbiome. Using continuous up-flow anaerobic sludge blanket (UASB) columns fed with whey, we found that 100 M hypophosphite resulted in a transient (17 days) reduction in methane production by 20% to 50%, while carbon and electron flow was redirected towards hydrogen and volatile fatty acids. Accumulation of propionate, butyrate, branched-chain fatty acids, and not acetate indicated disruption of syntrophic formate metabolism. Following recovery of methane production in hypophosphite treated columns, we increased hypophosphite concentrations to millimolar levels and saw no repeated suppression of methane production. 16S rDNA amplicon sequencing revealed that hypophosphite treatment did not cause significant changes to microbiome composition. Methanogenic activity assays revealed a loss of formatotrophic methanogenic capacity in hypophosphite treated columns. Together, these results show that specific inhibition of formate exchange between syntrophs and methanogens decouples fermentative and methanogenic processes without altering microbiome composition with carbon and electron flow to methane ultimately redirected through hydrogen or acetate. This work demonstrates that hypophosphite can intercept syntrophic formate exchange in an engineered system and that long- term treatment with hypophosphite redirects electron flow towards electron carriers other than formate.

microbiology↗

bioRxiv2026

Hypophosphite is a naturally-occurring selective inhibitor of syntrophic methanogenesis

Microbial methanogenesis is a major contributor to global warming and methane fluxes represent a loss of energy and electrons from industrial ecosystems. The chemical space of methane control strategies is still under-explored. Most known methanogenesis inhibitors target methanogenic archaeal enzymes. However, interference with syntrophic electron exchange in methanogenic systems presents an additional target for methane control. Here we show that hypophosphite (H2PO2-), an inorganic formate analog, is a potent and selective inhibitor of syntrophic methanogenesis versus primary fermentation in rice field sediments and cattle rumens. Hypophosphite is also generally recognized as safe and relatively non-toxic to plants and animals. Genetic screens and physiological assays in the model methanogen Methanococcus maripaludis S2 implicate formate metabolism as the target of hypophosphite inhibition. Currently, there is no known biological pathway for anaerobic hypophosphite oxidation and hypophosphite is stable in anoxic sediments for weeks to months. Given its widespread natural occurrence, we propose that hypophosphite may modulate carbon cycling in natural environments. Taken together, our results suggest that hypophosphite could be used as a safe, inexpensive, strategy for methane control in syntrophic methanogenic ecosystems.

microbiology↗

bioRxiv2025

Lithosyntrophy: Obligate syntrophy in a phosphite-oxidizing, methanogenic culture

The anaerobic conversion of organic matter to methane and carbon dioxide typically relies on obligate syntrophic interactions between bacteria and methanogenic archaea, where interspecies hydrogen (H2) transfer enables thermodynamically constrained reactions to proceed near equilibrium. Syntrophs couple the oxidation of fermentation products such as fatty acids and alcohols to the reduction of protons to form H2. These reactions can only proceed if low H2 concentrations are maintained by H2-consuming syntrophic partners. Here, we describe "lithosyntrophy," a novel mode of syntrophic interaction in which electrons that drive hydrogenotrophic methanogenesis originate from an inorganic compound rather than from the canonical organic substrates. Candidatus Phosphitivorax anaerolimi strain Phox-21 oxidizes phosphite (HPO32-, oxidation state +3) to phosphate coupled to hydrogenogenesis in an obligate energetic dependency on a hydrogenotrophic methanogen, Methanoculleus sp. Physiology experiments, thermodynamic calculations, genomic annotation, and metaproteomics analysis collectively revealed a mechanism for syntrophic phosphite oxidation in Phox-21, which requires phosphite, acetate, and CO2 as co-substrates. In this pathway, electrons derived from phosphite drive H2 production via an electron-confurcating hydrogenase. Unlike previously characterized acetogenic phosphite oxidizers that grow without exogenous acetate, Phox-21 requires acetate to regenerate AMP, a cofactor required by the phosphite dehydrogenase, PtdF. Lithosyntrophic phosphite oxidizers may play important roles both in transferring reducing equivalents as well as biologically available phosphorus to other members of their surrounding microbial communities. We infer that lithosyntrophic DPO emerged before acetoclastic methanogenesis and was a major sink for acetate in the Archaean when phosphite was more abundant. Significance statementDissimilatory phosphite-oxidizing microorganisms (DPOM) use phosphite as an energy source, producing phosphate. While the two previously isolated DPOM couple phosphite oxidation to carbon fixation via the Wood-Ljungdahl pathway, Candidatus Phosphitivorax anaerolimi strain Phox-21 instead performs lithosyntrophic metabolism, coupling DPO to proton reduction in obligate partnership with a hydrogenotrophic methanogen. This establishes a novel link between phosphorus and carbon redox cycles: like organosyntrophy, DPO can fuel methanogenesis. Lithosyntrophy expands our understanding of syntrophic interactions and suggests similar processes may occur with other inorganic substrates in anoxic ecosystems. We propose lithosyntrophic DPO predates acetoclastic methanogenesis, serving as an early acetate sink during the Archaean. Following Earths oxygenation, phosphite depletion likely reduced competition for acetate, enabling the later evolution of acetoclastic methanogenesis.

microbiology↗

bioRxiv2025

Organic carbon oxidation state shapes fermentative methanogenic microbiomes and controls greenhouse gas fluxes

Organic compounds with a negative nominal oxidation state of carbon (NOSC) are thermodynamically recalcitrant in anaerobic ecosystems, but few studies have measured the influence of NOSC on carbon degradation rates, gaseous product yields, or microbiome composition. We amended anaerobic rice paddy sediment microcosms with monomeric organic carbon compounds varying in NOSC. Consistent with thermodynamic and stoichiometric predictions, negative NOSC compounds are catabolized more slowly but produce more methane per mole of carbon. Negative NOSC microbiomes have higher alpha diversity, more syntrophs and methanogens, and fewer fermentative bacteria. Strikingly, fermentative bacterial taxa display genomically encoded NOSC catabolic preferences both in the lab and field. Negative NOSC- preferring fermenters have longer predicted doubling times, consistent with the thermodynamic recalcitrance of their preferred substrates. We propose that microbial NOSC preference can be leveraged for predicting and engineering greenhouse gas fluxes and understanding bacterial population dynamics and trait evolution across redox gradients.

microbiology↗