Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 1, 2024

Abstract Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within are largely unknown, and practical principles tools microbiome engineering still lacking. Here, we present a combinatory top-down bottom-up framework to engineer the construction of function-enhanced synthetic microbiomes. We show that application herbicide herbicide-degrader inoculation drives convergent succession different toward functional (e.g., enhanced bioremediation herbicide-contaminated soils). develop modeling pipeline, SuperCC, can be used document simulate performances Using construct bioremediation-enhanced based on 18 keystone species identified from Our results highlight importance in shaping functions provide guidance

Language: Английский

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Recombinant DNA: unlocking untapped microbial potential for innovation in crop agriculture

Trends in biotechnology, Journal Year: 2025, Volume and Issue: 43(3), P. 533 - 539

Published: Feb. 26, 2025

Language: Английский

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Complete biodegradation of glyphosate with microbial consortium YS622: structural analysis, biochemical pathways, and environmental bioremediation

Journal of environmental chemical engineering, Journal Year: 2024, Volume and Issue: 12(6), P. 114344 - 114344

Published: Oct. 2, 2024

Language: Английский

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Bacterial growth and environmental adaptation via thiamine biosynthesis and thiamine-mediated metabolic interactions

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract Understanding the ancestral transition from anaerobic to aerobic lifestyles is essential for comprehending life’s early evolution. However, biological adaptations occurring during this crucial remain largely unexplored. Thiamine an important cofactor involved in central carbon metabolism and respiration. Here, we explored phylogenetic global distribution of thiamine-auxotrophic thiamine-prototrophic bacteria based on thiamine biosynthetic pathway 154 838 bacterial genomes. We observed strong coincidences origin thiamine-synthetic with “Great Oxygenation Event,” indicating that biosynthesis emerged as adaptation Furthermore, demonstrated thiamine-mediated metabolic interactions are fundamental factors influencing assembly diversity communities by a survey across 4245 soil samples. Through our newly established stable isotope probing–metabolic modeling method, uncovered active utilization response changing environments, thus revealing environmental strategy employed at community level. Our study demonstrates widespread their roles setting stage evolutionary subsequent adaptation. These findings provide new insights into evolution growth environments.

Language: Английский

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In vitro and In silico investigation deciphering novel antifungal activity of endophyte Bacillus velezensis CBMB205 against Fusarium oxysporum

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 3, 2025

Endophytes from medicinal plants are potential biocontrol agents against Fusarium oxysporum f. sp. cubense (Foc), which is the causative fungus of banana wilt disease. In present study, endophytic bacterium was isolated Globba racemosa and their antagonistic activities Foc were studied, probable molecular mechanism antagonism predicted by docking studies. The 16SrRNA sequencing confirmed isolate to be Bacillus velezensis CBMB205 (EG2). isolates distortion fungal hyphae illustrated in SEM. metabolites identified FTIR, suggesting presence C-H, CH3 O-H groups. Two major such as β-amyrin dihydroxy octadecenoic acid (DA) LC-MS analysis. Molecular studies suggested that these showed binding with chitin synthase 1 1,3-glucan pathogenic fungi. energy (BE) interaction between synthase-1 (CS-1), (1,3-GS) estimated -10.17 kcal/mol − 9.5 kcal/mol, respectively. BE CS-1 1,3-GS determined -2.43 3.4 current study demonstrated EG2 towards provided a silico also provides insight into developing metabolite-based antifungal for various agricultural applications.

Language: Английский

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Low carbon disposal of urban green waste through biogas slurry recycling for preservation and pretreatment

Chemical Engineering Journal, Journal Year: 2025, Volume and Issue: 505, P. 159204 - 159204

Published: Jan. 5, 2025

Language: Английский

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Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 14, 2025

Language: Английский

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Thermal Enhanced Electrokinetic Bacterial Transport in Porous Media

Environmental Science & Technology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 15, 2025

Soil bacterial communities are crucial to various ecosystem services, with significant implications for environmental processes and human health. Delivering functional strains target locations enhances the preferred ecological features. However, delivery process is often constrained by limited transport through low-permeability soil. Although electrokinetics breaks bottleneck of in thin porous media, its efficiency remains limited. Here, we tested hypothesis that thermal effects enhance electrokinetic shifting net force acting on bacterium. We found heating significantly increased 2.75-fold at 1 V cm–1 media. Thermal enhancement mechanisms were interpreted shift integrating matrix attractive forces verified Quartz Crystal Microbalance Dissipation Monitoring (QCMD) observed adhesion rigidity shift. Thermal-dependent parameters liquid viscosity dielectric constant primary contributors Their variations reduce augment forces, resulting lower enhanced transport. A mechanism-based approach interlinking electric field strength, effect, collision was established facilitate application thermally These findings provide new prospects improving transport, hence optimizing soil functions.

Language: Английский

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Plant-microbiome interactions for enhanced crop production under cadmium stress: A review

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 965, P. 178538 - 178538

Published: Jan. 28, 2025

Language: Английский

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Metagenomic insights into the assembly, function, and key taxa of bacterial community in full-scale pesticide wastewater treatment processes

Environmental Research, Journal Year: 2025, Volume and Issue: unknown, P. 121037 - 121037

Published: Feb. 1, 2025

Language: Английский

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