Biology subjects

Coates, J. D.

Publications and source records attributed to Coates, J. D..

7 recordsLinked to original sources

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

Bioplastic Production Potential of Azospira suillum PS: Growth-Associated PHB Production Under Aerobic and Anaerobic Conditions

Plastics are indispensable in modern society, yet less than 10% of the 380 million tons produced annually are recycled. This accumulation of non-degradable waste has intensified the search for sustainable alternatives. Polyhydroxyalkanoates (PHAs), particularly polyhydroxybutyrate (PHB), are biodegradable polymers produced by microorganisms. Here, we investigate the capacity of Azospira suillum PS, a model facultative perchlorate-reducing bacterium, to synthesize PHB. We show that unlike most organisms, PHB production is growth-associated both aerobically, and anaerobically with perchlorate as an electron acceptor under moderate nitrogen deplete conditions. Genomic analysis revealed four phaC homologs, with one, phaC4, co-localized with phaB and phaR, suggesting a conserved operon. While three of the phaC genes were successfully deleted, phaC4 could not be disrupted, indicating an essential role for growth. Redox profiling revealed a positive correlation between PHB accumulation and NADPH/NADP+ ratios, supporting the role of cytoplasmic reducing equivalents in PHB synthesis. This study presents the first demonstration of PHA production under perchlorate-respiring conditions and one of the few documented cases of growth-associated PHA synthesis. It offers new insights into the genetic and metabolic basis of PHB production in A. suillum PS, underscoring its potential as a platform organism for sustainable, growth-coupled bioplastic production.

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↗

bioRxiv2024

Polyhydroxybutyrate production in freshwater SAR11 (LD12)

SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate (PHA) polymers. Here, we investigated the relevance of PHA production to SAR11 biology. Phylogenetics showed that Pha proteins occurred on a long branch and provided evidence for origin at the common ancestor of the brackish IIIa and freshwater LD12 subclades, followed by horizontal transfer within SAR11. Using the LD12 representative "Candidatus Fonsibacter ubiquis" strain LSUCC0530, we found that a large minority of LSUCC0530 cells contained a single Nile red-staining granule, confirmed that the cells produced polyhydroxybutyrate (PHB), and estimated the total PHB content in the cells. We heterologously expressed the LSUCC0530 phaCAB locus in Escherichia coli, finding it to be functional and the likely origin of the PHB. We also determined that, irrespective of changes to carbon, nitrogen, and phosphorus concentrations, a similar fraction of LSUCC0530 cells generated PHB granules and expression of the phaCAB locus remained constant. We suggest that PHB synthesis in LSUCC0530 may be constitutively active due to the slow growth dynamics and minimal regulation that characterize SAR11 bacteria. This is the first characterization of polymer storage in SAR11, providing new insights into the likely fitness advantage for cells harboring this metabolism.

microbiology↗

bioRxiv2021

Chlorine redox chemistry is not rare in biology

Chlorine is abundant in cells and biomolecules, yet the biology of chlorine oxidation and reduction is poorly understood. Some bacteria encode the enzyme chlorite dismutase (Cld), which detoxifies chlorite (CIO2-) by converting it to chloride (Cl-) and molecular oxygen (O2). Cld is highly specific for chlorite and aside from low hydrogen peroxide activity has no known alternative substrate. Here, we reasoned that because chlorite is an intermediate oxidation state of chlorine, Cld can be used as a biomarker for oxidized chlorine species in microorganisms and microbial habitats. Cld was abundant in metagenomes from soils and freshwater to water treatment systems. About 5% of bacterial and archaeal genera contain an organism encoding Cld in its genome, and within some genera Cld is nearly conserved. Cld has been subjected to extensive horizontal gene transfer, suggesting selection by chlorite is episodic yet strong. Cld was also used as a biomarker to predict genes related to chlorine redox chemistry. Genes found to have a genetic association with Cld include known genes for responding to reactive chlorine species and uncharacterized genes for transporters, regulatory elements, and putative oxidoreductases that present targets for future research. Cld was repeatedly co-located in genomes with genes for enzymes that can inadvertently reduce perchlorate (CIO4-) or chlorate (CIO3-), confirming that in nature (per)chlorate reduction does not only occur in specialized anaerobic respiratory metabolisms. The presence of Cld in genomes of obligate aerobes without such enzymes suggested that chlorite, like hypochlorous acid (HOCl), might be formed by oxidative processes within natural habitats. In summary, the comparative genomics of Cld has provided an atlas for a deeper understanding of chlorine oxidation and reduction reactions that are an underrecognized feature of biology.

microbiology↗

bioRxiv2019

Identification of a parasitic symbiosis between respiratory metabolisms in the biogeochemical chlorine cycle

A key step in the chlorine cycle is the reduction of perchlorate (ClO4-) and chlorate (ClO3-) to chloride by microbial respiratory pathways. Perchlorate-reducing bacteria and chlorate-reducing bacteria differ in that the latter cannot use perchlorate, the most oxidized chlorine compound. However, a recent study identified a bacterium with the chlorate reduction pathway dominating a community provided only perchlorate. Here we confirm a metabolic interaction between perchlorate- and chlorate-reducing bacteria and define its mechanism. Perchlorate-reducing bacteria supported the growth of chlorate-reducing bacteria to up to 90% of total cells in communities and co-cultures. Chlorate-reducing bacteria required the gene for chlorate reductase to grow in co-culture with perchlorate-reducing bacteria, demonstrating that chlorate is responsible for the interaction, not the subsequent intermediates chlorite and oxygen. Modeling of the interaction suggested that cells specialized for chlorate reduction have a competitive advantage for consuming chlorate produced from perchlorate, especially at high concentrations of perchlorate, because perchlorate and chlorate compete for a single enzyme in perchlorate-reducing cells. We conclude that perchlorate-reducing bacteria inadvertently support large populations of chlorate-reducing bacteria in a parasitic relationship through the release of the intermediate chlorate. An implication of these findings is that undetected chlorate-reducing bacteria have likely negatively impacted efforts to bioremediate perchlorate pollution for decades.

microbiology↗