Metagenomic insights into bacterial communities’ structures in polycyclic aromatic hydrocarbons degrading consortia

Patel, A. B.; Manvar, Toral; Jain, Kunal; Desai, Chirayu; Madamwar, Datta

doi:10.1016/j.jece.2021.106578

Cited by 23 publications

(6 citation statements)

References 39 publications

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“…A network analysis of polycyclic aromatic hydrocarbon-degrading microbial communities showed that a Chelatococcus sp. was one of the most abundant organisms and had many positive interactions with other organisms (Patel et al, 2021 ). A few organisms from the genera Hyphomonas and Luteimonas also degrade polycyclic aromatic hydrocarbons (Dong et al, 2015 ; Singleton et al, 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Versatile microbial communities rapidly assimilate ammonium hydroxide-treated plastic waste

Schaerer

Wood

Aloba

et al. 2023

Journal of Industrial Microbiology and Biotechnology

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Most plastic waste accumulates in landfills or the environment. Natural microbial metabolisms can degrade plastic polymers. Unfortunately, biodegradation of plastics is slow even under ideal conditions; depolymerization of plastic is the rate limiting step. Rapid chemical depolymerization yields biodegradable plastic monomers, improving biodegradation rates. Here we demonstrate that ammonium hydroxide depolymerizes PET into terephthalic acid and terephthalic acid monoamide which are rapidly metabolized by diverse consortia obtained from compost and sediment. By neutralizing the product with phosphoric acid prior to bioprocessing, the final product contains plastic-derived carbon and biologically accessible nitrogen and phosphorus from the process reactants, removing the need for culture medium. Three microbial consortia were able to degrade chemically deconstructed PET in ultrapure water and scavenged river water without the addition of nutrients, with no statistically significant difference in growth rate compared to communities grown on deconstructed PET in Bushnell Haas minimal culture medium. The consortia were dominated by Rhodococcus spp., Hydrogenophaga spp., and many lower abundance genera. All taxa were related to species known to degrade aromatic compounds. Microbial consortia are known to confer flexibility in processing diverse substrates. To highlight the versatility of these consortia, we also demonstrate that two microbial consortia can grow on similarly deconstructed polyesters, polyamides, and polyurethanes in water instead of medium. Our findings suggest that using microbial communities enable flexible bioprocessing of mixed plastic wastes. We also demonstrate the flexibility of this approach for coupled chemical deconstruction and bioprocessing.

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Section: Discussionmentioning

confidence: 99%

Versatile microbial communities rapidly assimilate ammonium hydroxide-treated plastic waste

Schaerer

Wood

Aloba

et al. 2023

Journal of Industrial Microbiology and Biotechnology

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“…Our RDA analyses revealed a positive correlation between both environmental factors and the abundance of Firmicutes and Chloroflexi, two taxa that play a crucial role in the symbiotic network. The functional enrichment of the bacterial community is predominantly focused on the carbon and energy cycles ( Patel et al, 2021 ). Upon introducing fresh tobacco into the curing room, the temperature increase led to a notable rise in the respiration rate of the tobacco.…”

Section: Discussionmentioning

confidence: 99%

Bacterial dynamic of flue-cured tobacco leaf surface caused by change of environmental conditions

Ding,

Wei,

Shang

et al. 2023

Front. Microbiol.

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Microorganisms present on the surface of tobacco leaves play a significant role in shaping the composition of the tobacco microbial ecosystem, which undergoes continuous changes throughout the curing process. In the present study, a total of four distinct tobacco curing periods were selected for sampling, namely the fresh, yellowing, leaf-drying, and stem-drying stages. The bacterial 16S rRNA gene sequences of the collected samples were subsequently analyzed to identify operational taxonomic units (OTUs). The findings indicated that the complete dataset of leaf microbial samples was clustered, resulting in the identification of 1,783 operational taxonomic units (OTUs). Furthermore, the analysis of diversity revealed a pattern of initially increasing and subsequently decreasing community diversity. Redundancy Analysis (RDA) and weighted gene correlation networks for analysis (WGCNA) were employed in conjunction with environmental factors to assign OTUs to 22 modules for functional analysis. Additionally, a classification model utilizing the random forest algorithm was utilized to identify seven marker microorganisms (Escherichia coli, Faecalibacterium prausnitzii, Faecalibacterium, Escherichia-Shigella, Peptostreptococcaceae, Peptostreptococcales-Tissierellales, and Proteobacteria) that exhibited discriminative characteristics across different time periods. This study aimed to investigate the dynamic changes in the bacterial community throughout the curing process and their impact on the community’s function. Additionally, certain bacteria were identified as potential markers for detecting changes in the curing stage. These findings offer a novel opportunity to accurately regulate the curing environment, thereby enhancing the overall quality of tobacco leaf curing.

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“…Network analysis has been employed to large sequencing data sets of environmental samples to reveal microbial co-occurrence patterns in different ecosystems, including marine water and soil, even at the global scale . Network analysis has also been used in numerous studies investigating microbial community structure at contaminated sites to provide guidance for environmental management and bioremediation of pollutants, including rare earth elements and polycyclic aromatic hydrocarbons (PAHs). , However, very few studies have applied network analysis to investigating microbial communities related to PFAS biotransformations. , …”

Section: Introductionmentioning

confidence: 99%

“…32 Network analysis has also been used in numerous studies investigating microbial community structure at contaminated sites to provide guidance for environmental management and bioremediation of pollutants, including rare earth elements and polycyclic aromatic hydrocarbons (PAHs). 33,34 However, very few studies have applied network analysis to investigating microbial communities related to PFAS biotransformations. 35,36 PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a powerful computational tool that uses marker gene information and a reference genome database to predict the functional composition of a metagenome.…”

Section: Introductionmentioning

confidence: 99%

Using Network Analysis and Predictive Functional Analysis to Explore the Fluorotelomer Biotransformation Potential of Soil Microbial Communities

Dong,

Yan,

Mezzari

et al. 2024

Environ. Sci. Technol.

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Microbial transformation of per-and polyfluoroalkyl substances (PFAS), including fluorotelomer-derived PFAS, by native microbial communities in the environment has been widely documented. However, few studies have identified the key microorganisms and their roles during the PFAS biotransformation processes. This study was undertaken to gain more insight into the structure and function of soil microbial communities that are relevant to PFAS biotransformation. We collected 16S rRNA gene sequencing data from 8:2 fluorotelomer alcohol and 6:2 fluorotelomer sulfonate biotransformation studies conducted in soil microcosms under various redox conditions. Through co-occurrence network analysis, several genera, including Variovorax, Rhodococcus, and Cupriavidus, were found to likely play important roles in the biotransformation of fluorotelomers. Additionally, a metagenomic prediction approach (PICRUSt2) identified functional genes, including 6-oxocyclohex-1-ene-carbonyl-CoA hydrolase, cyclohexa-1,5-dienecarbonyl-CoA hydratase, and a fluoride-proton antiporter gene, that may be involved in defluorination. This study pioneers the application of these bioinformatics tools in the analysis of PFAS biotransformation-related sequencing data. Our findings serve as a foundational reference for investigating enzymatic mechanisms of microbial defluorination that may facilitate the development of efficient microbial consortia and/or pure microbial strains for PFAS biotransformation.

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Metagenomic insights into bacterial communities’ structures in polycyclic aromatic hydrocarbons degrading consortia

Cited by 23 publications

References 39 publications

Versatile microbial communities rapidly assimilate ammonium hydroxide-treated plastic waste

Versatile microbial communities rapidly assimilate ammonium hydroxide-treated plastic waste

Bacterial dynamic of flue-cured tobacco leaf surface caused by change of environmental conditions

Using Network Analysis and Predictive Functional Analysis to Explore the Fluorotelomer Biotransformation Potential of Soil Microbial Communities

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