Abstract Methane emissions from rice paddies are a major source of greenhouse gases, and silicate fertilizer (SF) derived from blast furnace slag has emerged as an environmentally friendly amendment that reduces methane release. SF modifies the soil redox environment by supplying electron acceptors such as iron, but the microbial mechanisms underlying methane mitigation remain unclear. Here, we combined metagenomic profiling, microbial isolation, and greenhouse experiments to show that SF consistently enriched Burkholderia vietnamiensis together with the methanotrophs in the rice rhizosphere. Inoculation of B. vietnamiensis strain HU01 alone reproduced the methane-suppressing effect of SF and increased methanotroph abundance. Cell-free culture supernatants of HU01 stimulated the growth of Methylococcus geothermalis and Methylocystis parvus through secreted, low-molecular-weight, heat-stable metabolites. Although metabolic modeling predicted primary metabolites such as L-glutamate and cobalamin as candidate cross-feeding factors, LC–MS/MS analysis of the highly active fractions indicated that the robust bioactivity was primarily driven by a chemically complex metabolite mixture rather than these ubiquitous single compounds. These results provide direct evidence that enrichment of a single heterotrophic species can enhance methane oxidation by stimulating methanotroph activity through metabolite exchange. B. vietnamiensis HU01 represents a promising microbial resource for methane mitigation and illustrates how targeted heterotroph–methanotroph interactions can be leveraged for climate-smart rice cultivation.
Abstract Bacterial biofilms are characterized by profound heterogeneity, which is a primary driver of their antibiotic recalcitrance and a major obstacle to clinical infection control. However, how metabolic heterogeneity underpins collective antibiotic tolerance within biofilms remains poorly understood, particularly at single-cell resolution. Here, we apply single-cell RNA sequencing to dissect the response of Staphylococcus aureus ATCC 12600 biofilms to vancomycin. We show that vancomycin induces heterogeneous upregulation of the fructose metabolism genes fruA and fruK, which spatially segregates the biofilm into metabolically active and metabolically reduced subpopulations. Active cells exhibit increased fructose consumption, which fuels peptidoglycan biosynthesis and promotes cell wall thickening, as a mechanism that directly enhances vancomycin tolerance. In contrast, certain metabolically reduced subpopulations potentiate oxidative stress repair programs, representing an alternative survival strategy. In a diabetic mouse model characterized by impaired fructose clearance, elevated systemic fructose levels exacerbate pulmonary S. aureus infection, indicating that fructose utilization may reflect clinically relevant features of host susceptibility. Together, our findings uncover a fundamental link between metabolic heterogeneity and antibiotic tolerance in S. aureus biofilms, opening new avenues for the rational design of anti-biofilm therapeutics.
Abstract Soil is a competitive environment containing a variety of resources used for bacterial growth. Complex polysaccharides, like chitin or starch, require the secretion of enzymes that degrade these resources into smaller units before they can be consumed. However, exoenzymes and the products they create are public goods, meaning they can be used by competitors who consume and benefit from these public goods even if they do not produce enzymes themselves. Here, we test the hypothesis that antibiotics produced by Streptomyces are used to privatize public goods by restricting access to resource exploiters. Using experiments with Streptomyces coelicolor and Bacillus subtilis, we first show that B. subtilis resource exploitation significantly reduces S. coelicolor fitness on a complex resource (starch) but not on a simple carbon source (maltose) which does not require exoenzyme secretion. Next, we show that antibiotics produced by S. coelicolor markedly increase fitness against resource exploiters, despite evidence that antibiotic production is metabolically costly. Finally, we find that the benefits of antibiotic production and the costs of resource exploitation are both higher during growth on lower resource concentrations. Our results provide insights into the context-dependent costs and benefits of antibiotic secretion in Streptomyces and highlight the role of resource complexity and concentration in mediating competitive strategies in bacteria.
Abstract The nutritional symbiosis between corals and their photosynthetic dinoflagellate partners underpins the ecological success of reef-building corals in nutrient-poor environments. Although coral holobionts can assimilate the abundant yet highly variable environmental nitrate, direct insight into how nitrate reductase is regulated in these symbiotic algae has been lacking. Here, nitrate reductase protein abundance and gene expression were characterized in cultured Symbiodiniaceae exposed to different nitrogen regimes and light conditions, revealing the multifactorial nature of its regulation. The results indicate that nitrate reductase behaves as a substrate-induced enzyme: nitrate stimulates protein synthesis in nitrogen-starved cultures, whereas ammonium actively suppresses its expression in a concentration-dependent manner. Light availability and photosynthetic electron transport further modulate protein abundance, suggesting that although nitrate reductase synthesis depends on nitrate availability, its stability may rely on photosynthesis. In hospite, nitrate reductase is synthesized within hours of nitrate exposure by symbionts from nitrogen-starved corals, indicating that nitrate reduction can occur within the host environment. However, this response is transient and reduced relative to free-living cells, suggesting that nitrate reduction may function as a facultative pathway activated when preferred nitrogen sources become limited. Finally, gene expression measurements and pharmacological inhibition experiments are consistent with predominant post-transcriptional regulation of nitrate reductase protein expression, enabling rapid and reversible control of nitrate assimilation. Together, these findings describe a tightly regulated and responsive nitrate reduction system in coral symbionts that provides a flexible mechanism contributing to nitrogen homeostasis under fluctuating nutrient regimes.
Abstract Marine plankton fuel their metabolism through a continuum of trophic strategies, spanning from pure autotrophy to pure heterotrophy, with mixotrophy combining the two modes within a single organism. Different taxa balance these strategies depending on environmental conditions, complicating efforts to link community composition with ecosystem processes. To quantify the transcriptional investment in processes supporting primary production versus respiration along the trophic continuum, we developed the Transcript-informed Productivity (TiP) metric, defined as the ratio of transcripts in photosynthesis-related pathways (e.g., photosynthesis, carbon fixation) to those in both photosynthesis and respiration-related pathways (e.g., respiration, macromolecule degradation). Higher TiP indicates greater transcriptional investment in primary productivity, whereas lower TiP reflects reduced investment in primary productivity and/or increased investment in catabolic activities. We applied TiP across eukaryotic plankton size classes (~1-100 μm) and taxonomic groups using metatranscriptomes collected during three latitudinal expeditions across the North Pacific. By combining TiP with 18S rRNA gene sequence data and cell size characterization via flow cytometry, we show that biomass in more nutrient-rich areas was dominated by larger phototrophic eukaryotic plankton (diatoms) with higher TiP, consistent with elevated net community productivity. In nutrient-limited areas, eukaryotic pico- and nano-phytoplankton were dominated by Haptophyta and Dinophyta and displayed reduced TiP, suggesting greater reliance on energy from respiration rather than photosynthesis, consistent with mixotrophic strategies supporting these taxa under nutrient limitation. The TiP metric provided taxon-resolved indicators of eukaryotic productivity and respiration and can complement bulk Net Community Productivity (NCP) measurements by identifying the taxa contributing most to ecosystem metabolic balance.
