Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2024.05.31.596902

Biodegradation Potential of Neptunomonas naphthovoran - NAG-2N-126 for Crude Oil Pollution Mitigation: Experimental and Modelling Insights

Mutallimov, T.·Wu, K.·Deng, H.·Ibrahimov, Y.
View original source ↗Export metadata ↓

Abstract

Crude oil contamination poses a significant threat to the environment, demanding effective bioremediation strategies. While microbial biodegradation holds promise, there is a notable absence of exploration, particularly regarding the biodegradation potential of Neptunomonas naphthovoran strain NAG-2N-126. This study addresses this gap by investigating the bioremediation potential of NAG-2N-126 through experimental analyses and mathematical modelling. Our findings reveal the strains rapid growth on crude oil, with the microbial biomass predicted to undergo a 3.5-fold increase over the experimental period. Additionally, the strain exhibited high efficiency in degrading aromatic compounds, achieving an impressive 41% degradation rate within the initial 20-day period. Oxygen availability emerged as a critical factor influencing microbial growth and biodegradation processes, with simulations indicating a 20% decrease in degradation rates under oxygen-deprived conditions. Mathematical modelling provided insights into the complex dynamics involved, contributing to the understanding of microbial hydrocarbon degradation. However, further research is warranted to optimize growth conditions and scale up findings for practical applications in environmental cleanup efforts. By delving into this underexplored area, this study highlights the importance of NAG-2N-126 in crude oil bioremediation and underscores the need for further research to optimize its application in environmental cleanup efforts. IMPORTANCEThis study presents novel insights into microbial biodegradation of crude oil, addressing a critical environmental challenge. With an estimated 24 billion BOE potentially remaining in the North Sea reservoir and over 2,000 oil spills reported since 2011, including 215 in marine protection areas, the urgency of developing effective bioremediation strategies is paramount. By investigating the growth kinetics and biodegradation efficiency of the bacterial strain N. naphthovoran NAG-2N-126 under controlled laboratory conditions, we elucidate its potential for crude oil remediation. Our findings highlight the strains remarkable ability to degrade aromatic hydrocarbons, offering promise for sustainable bioremediation strategies. Furthermore, through the development of mathematical models, we provide valuable insights into microbial population dynamics and substrate utilization rates during crude oil degradation. This research contributes to advancing our understanding of bioremediation processes and offers practical implications for mitigating environmental pollution and promoting ecosystem health.

Explore related subjects

microbiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Mutallimov, T., Wu, K., Deng, H., Ibrahimov, Y.. 2024-06-01. Biodegradation Potential of Neptunomonas naphthovoran - NAG-2N-126 for Crude Oil Pollution Mitigation: Experimental and Modelling Insights. https://doi.org/10.1101/2024.05.31.596902

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

Periodontitis is an archetypical mucosal inflammatory disease in which microbiome dysbiosis at the tooth-epithelial interface interacts with host genetic and behavioral risk factors to drive immune-mediated tissue destruction. Although subgingival microbiome compositional shifts are thought to parallel disease severity, microbiome variation at the population-level and its relationship to periodontal clinical phenotypes and disease-modifying factors remain poorly defined. Here, we use unsupervised manifold learning to map the compositional landscape of the subgingival microbiome in 1,355 adults spanning periodontal health to severe periodontitis. We identified eight latent microbiome states organized along a branching continuum from eubiosis to dysbiosis. An intermediate microbial configuration marked ecological destabilization and bifurcation into two distinct periodontitis-associated dysbiotic trajectories, distinguished by links to gingival inflammation and smoking. Although the microbiome trajectories broadly tracked periodontal destruction, a minority of individuals showed discordant microbiome-clinical phenotypes, with some individuals with periodontitis retaining otherwise eubiotic microbiomes enriched for low-abundance pathobionts, while some cases of health or mild disease had highly dysbiotic communities, suggesting distinct host susceptibility. Together, these findings define a population-scale ecological landscape of the subgingival microbiome, reveal divergent trajectories to periodontal dysbiosis, and highlight heterogeneity in the relationship between microbial community structure and clinical disease expression.

microbiology↗
bioRxiv2026

The iron-binding siderophore enterobactin is required for the response of multi-drug resistant Klebsiella pneumoniae to zinc limitation

To persist during infection Klebsiella pneumoniae must overcome nutrient iron and zinc limitation imposed by the host immune system through a process called nutritional immunity. Secreted small molecule siderophores are a major virulence determinant of Klebsiella pneumoniae pathogenesis and are presumed to overcome nutritional immunity by binding iron for bacterial acquisition. In this work, we set out to identify how a multi-drug resistant K. pneumoniae grows in zinc limited environments. Using unbiased transcriptomics, proteomics, and an arrayed transposon screen, we identified that synthesis and uptake of the siderophore enterobactin is required to allow for growth in low zinc conditions. Iron-specific chelators did not replicate this phenotype and addition of supplemental iron through heme in growth media could not complement severe growth defects of enterobactin mutant K. pneumoniae experiencing zinc limitation. Finally, zinc starvation induced enterobactin production independent of the canonical zinc uptake regulator (Zur) transcription factor suggesting an unidentified regulatory mechanism by which Gram-negative pathogens may respond to zinc stress. Together, these studies expand the role of enterobactin beyond iron regulation and highlight a previously unreported link between iron and zinc homeostasis in Klebsiella pneumoniae.

microbiology↗
bioRxiv2026

A microbiota-derived protease links phage susceptibility to host epithelial responses

Bacteriophages are major ecological drivers of gut microbial ecology, yet whether bacterial mechanisms that determine phage susceptibility have consequences for the mammalian host remains poorly understood. Here, we identify dipeptidyl peptidase 11 (Dpp11a), the predominant active serine protease of the prevalent gut commensal Phocaeicola vulgatus, as an unexpected bacterial defence factor. Dpp11a protects against environmental proteases and confers resistance to bacteriophage infection. Metatranscriptomic analyses further reveal increased expression of both dpp11a and P. vulgatus-associated phage transcripts in ulcerative colitis stool samples, indicating that both components of this interaction are transcriptionally active in disease-associated human microbiomes. Using the microfluidic gut-on-a-chip co-culture model HuMiX, we show that the absence of Dpp11 is accompanied by altered epithelial tight-junction remodelling during phage-bacterial infection. Together, our findings reveal that the consequences of bacterial phage defence can extend beyond phage-bacterium interactions to the mammalian epithelium.

microbiology↗