Ontology highlight
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PROVIDER: PRJNA1273842 | ENA |
REPOSITORIES: ENA
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Project description:Widespread organic pollutants such as BTEX (benzene, toluene, ethylbenzene, and xylene) are traditionally considered to enhance soil carbon loss through mineralization and ecotoxicity. Challenging this paradigm, we reveal that BTEX can stimulate microbial carbon chain elongation (CE)—a previously overlooked carbon fixation pathway—thereby reshaping soil carbon dynamics. Through phased amplicon sequencing, metagenomics, and metaproteomics, we demonstrate that BTEX exerts bidirectional regulation on CE at both taxonomic and molecular levels. Specifically, BTEX selectively enriches Clostridium_sensu_stricto_12 and Rummelibacillus, while suppressing Acinetobacter, a key CE contributor in natural soils. BTEX also inhibits Petrimonas, a syntrophic degrader of medium-chain fatty acids (MCFAs), promoting MCFAs accumulation. Moreover, BTEX-degrading bacteria establish cooperative interactions with CE bacteria, facilitating the sequestration of carbon as MCFAs rather than complete mineralization to CO₂, with Bacillus bridging both metabolic roles. At the molecular level, BTEX enhances CE by accelerating substrate uptake and acetyl-CoA flux into the reverse β-oxidation (RBO) pathway. Multi-omics analysis revealed that BTEX downregulates fatty acid biosynthesis (FAB), another pathway of CE, through fabR, acrR, and fadR while maintaining NADH availability to relieve Rex-mediated inhibition of the key RBO enzyme gene bcd. However, excessive BTEX disrupts metabolic homeostasis and suppresses CE activity. Collectively, our findings redefine the ecological implications of aromatic hydrocarbon contamination by uncovering its capacity to modulate anaerobic carbon fixation and retention in soil microbial communities. This work highlights a previously unrecognized link between pollutant degradation and biogenic carbon sequestration, with broader implications for understanding soil biogeochemical resilience under anthropogenic pressure.
| PXD064805 |
Project description:Carbon fixation and chain elongation during mixotrophic fermentation of biomass
| PRJEB88737 | ENA
Project description:Biological carbon fixation is foundational to the biosphere. Most autotrophs are thought to possess one carbon fixation pathway. The hydrothermal vent tubeworm Riftia pachyptila’s chemoautotrophic symbionts, however, possess two functional pathways: the Calvin Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycles. Little is known about how Riftia’s symbionts and related organisms coordinate the functioning of these two pathways. Here we investigated net carbon fixation rates, transcriptional/metabolic responses, and transcriptional co-expression patterns of Riftia pachyptila’s endosymbionts by incubating tubeworms at environmental pressures, temperature, and geochemistry. Results showed that rTCA and CBB transcriptional patterns varied in response to different geochemical regimes and that each pathway is allied to specific metabolic processes, suggesting distinctive yet complementary roles in metabolic function. Net carbon fixation rates were also exemplary, and accordingly we propose that co-activity of CBB and rTCA may be an adaptation for maintaining high carbon fixation rates, conferring a fitness advantage in dynamic vent environments.
2024-03-28 | GSE249345 | GEO
Project description:Seven carbon autotrophic fixation pathways were described so far. However, it is not common to find the co-existence of more than one cycle in a single cell. Here, we describe a thermophilic bacterium Carbonactinospora thermoautotrophica StC with a unique and versatile carbon metabolism. StC was isolated from a consortium found in a burning organic pile that exhibits an optimal growth temperature between 55° and 65° C. The genome analyses suggested that the strain StC potentially performs two-carbon fixation pathways, Calvin-Benson-Bassham (CBB) cycle and the Reductive citrate cycle (rTCA) and preserve a microcompartment related with CO2 concentration. To better understand the carbon fixation in StC strain, the expression of the genes of bacterial cells grown autotrophically and heterotrophically were analyzed. For our surprise the data showed the co-existing of the both carbon fixation pathways - CBB and rTCA cycles - in a cultivable thermophilic chemoautotrophic bacterium Carbonactinospora thermoautotrophica strain StC, based on integrated omics of genomics, transcriptomics, and proteomics. These two cycles working together may help microorganisms to improve the CO2 fixation. The knowledge about the co-occurrence of carbon cycle in a single cell leads open a question ‘why microorganisms use multiple pathways to fix carbon and what the advantage for this strategy?’. Advancing on this is a key to better understand the biological carbon fixation mechanism in thermophiles and prospecting the repurposing of enzymes in synthetic biology for biotechnological applications.
2024-04-09 | GSE263135 | GEO
Project description:Food waste is a major source of environmental pollution, as its landfills attribute to greenhouse gas emissions. This study developed a robust upcycling bioprocess that converts food waste into lactic acid through autochthonous fermentation and further produces biodegradable polymer polyhydroxybutyrate (PHB). Food can be stored without affecting its bioconversion to lactic acid, making it feasible for industrial application. Mapping autochthonous microbiota in the food waste fermentation before and after storage revealed lactic-acid-producing microorganisms dominate during the indigenous fermentation. Furthermore, through global transcriptomic and gene set enrichment analyses, it was discovered that coupling lactic acid as carbon source with ammonium sulfate as nitrogen source in Cupriavidus necator culture upregulates pathways, including PHB biosynthesis, CO2 fixation, carbon metabolism, pyruvate metabolism, and energy metabolism compared to pairing with ammonium nitrate. There was ∼90 % PHB content in the biomass. Overall, the study provides crucial insights into establishing a bioprocess for food waste repurposing.
2025-06-16 | GSE296860 | GEO
Project description:Diatoms played an essential role in marine primary productivity. Polysaccharide chrysolaminarin and neutral lipid, mainly TAG, were necessary carbon fixation in diatom Phaeodactylum tricornutum. Our study speculated on the metabolism pathway of chrysolaminarin, fatty acid, fatty acid β-oxidation and TAG. Transcriptional levels coordinated with carbon fixation metabolism pathway were conjoint analysis in this study.
2022-08-03 | GSE210141 | GEO