Genome‐Wide Analysis Reveals Genetic Potential for Aromatic Compounds Biodegradation of <i>Sphingopyxis</i>

Yang, Fei; Feng, Hai; Massey, Isaac Yaw; Huang, Feiyu; Guo, Jian; Zhang, Xian

doi:10.1155/2020/5849123

Cited by 15 publications

(10 citation statements)

References 57 publications

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“…Specifically, Sphingopyxis was found to be one of the genera with a greater number of genes encoding aromatic-degrading enzymes identified in the metagenome (Figure 8). The genetic potential for the degradation of aromatic compounds of Sphingopyxis has been previously analyzed (Yang et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Soil Microbiome Structure and Function in Ecopiles Used to Remediate Petroleum-Contaminated Soil

Wang

Garrido‐Sanz

Sansegundo‐Lobato

et al. 2021

Front. Environ. Sci.

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The soil microbiome consists of a vast variety of microorganisms which contribute to essential ecosystem services including nutrient recycling, protecting soil structure, and pathogen suppression. Recalcitrant organic compounds present in soils contaminated with fuel oil can lead to a decrease in functional redundancy within soil microbiomes. Ecopiling is a passive bioremediation technique involving biostimulation of indigenous hydrocarbon degraders, bioaugmentation through inoculation with known petroleum-degrading consortia, and phytoremediation. The current study investigates the assemblage of soil microbial communities and pollutant-degrading potential in soil undergoing the Ecopiling process, through the amplicon marker gene and metagenomics analysis of the contaminated soil. The analysis of key community members including bacteria, fungi, and nematodes revealed a surprisingly diverse microbial community composition within the contaminated soil. The soil bacterial community was found to be dominated by Alphaproteobacteria (60–70%) with the most abundant genera such as Lysobacter, Dietzia, Pseudomonas, and Extensimonas. The fungal community consisted mainly of Ascomycota (50–70% relative abundance). Soil sequencing data allowed the identification of key enzymes involved in the biodegradation of hydrocarbons, providing a novel window into the function of individual bacterial groups in the Ecopile. Although the genus Lysobacter was identified as the most abundant bacterial genus (11–46%) in all of the contaminated soil samples, the metagenomic data were unable to confirm a role for this group in petrochemical degradation. Conversely, genera with relatively low abundance such as Dietzia (0.4–9.0%), Pusillimonas (0.7–2.3%), and Bradyrhizobium (0.8–1.8%) did possess genes involved in aliphatic or aromatic compound degradation.

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Section: Discussionmentioning

confidence: 99%

Soil Microbiome Structure and Function in Ecopiles Used to Remediate Petroleum-Contaminated Soil

Wang

Garrido‐Sanz

Sansegundo‐Lobato

et al. 2021

Front. Environ. Sci.

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“…The genus Sphingopyxis dominated in both drawings. Sphingopyxis isolates have been reported to degrade aromatic compounds in various habitats (Yang F. et al, 2020). In addition, the genus Paracoccus was only relevant in drawing L7 with the dominance of P. yeei, which has been isolated from diverse natural environments, including human skin (Lim et al, 2018).…”

Section: Bacteriamentioning

confidence: 99%

The Microbiome of Leonardo da Vinci’s Drawings: A Bio-Archive of Their History

Piñar

Sclocchi²,

Pinzari³

et al. 2020

Front. Microbiol.

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Seven emblematic Leonardo da Vinci’s drawings were investigated through third generation sequencing technology (Nanopore). In addition, SEM analyses were carried out to acquire photographic documentation and to infer the nature of the micro-objects removed from the surface of the drawings. The Nanopore generated microbiomes can be used as a “bio-archive” of the drawings, offering a kind of fingerprint for current and future biological comparisons. This information might help to create a biological catalog of the drawings (cataloging), a microbiome-fingerprint for each single analyzed drawing, as a reference dataset for future studies (monitoring) and last but not least a bio-archive of the history of each single object (added value). Results showed a relatively high contamination with human DNA and a surprising dominance of bacteria over fungi. However, it was possible to identify typical bacteria of the human microbiome, which are mere contaminants introduced by handling of the drawings as well as other microorganisms that seem to have been introduced through vectors, such as insects and their droppings, visible through the SEM analyses. All drawings showed very specific bio-archives, but a core microbiome of bacteria and fungi that are repeatedly found in this type of material as true degraders were identified, such as members of the phyla Proteobacteria, Actinobacteria, and Firmicutes among bacteria, and fungi belonging to the classes Sordariomycetes and Eurotiomycetes. In addition, some similarities were observed that could be influenced by their geographical location (Rome or Turin), indicating the influence of this factor and denoting the importance of environmental and storage conditions on the specific microbiomes.

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“…In contrast, Rubellimicrobium are mainly isolated from soil and are also found in the air ( 36 ); Marinococcus usually lives in high-salinity environments like the sea, salt lakes, and salt mines ( 37 ); its accumulation in cancer tissue might be due to salt body fluid effusion. Intriguingly, Sphingomonas and Sphingopyxis are soil microbes; both are famous for their degradation of PAHs, pesticide, and organometallic compounds ( 38 – 41 ). Therefore, enrichment of these microbes in subjects exposed to IAP indicated: PAHs and other pollutants accumulated in patients’ lungs provided a substrate for the microbes, and possibly support their growth.…”

Section: Resultsmentioning

confidence: 99%

A Multi-Omics Study of Familial Lung Cancer: Microbiome and Host Gene Expression Patterns

et al. 2022

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BackgroundInherited susceptibility and environmental carcinogens are crucial players in lung cancer etiology. The lung microbiome is getting rising attention in carcinogenesis. The present work sought to investigate the microbiome in lung cancer patients affected by familial lung cancer (FLC) and indoor air pollution (IAP); and further, to compare host gene expression patterns with their microbiome for potential links.MethodsTissue sample pairs (cancer and adjacent nonmalignant tissue) were used for 16S rRNA (microbiome) and RNA-seq (host gene expression). Subgroup microbiome diversities and their matched gene expression patterns were analyzed. Significantly enriched taxa were screened out, based on different clinicopathologic characteristics.ResultsOur FLC microbiome seemed to be smaller, low-diversity, and inactive to change; we noted microbiome differences in gender, age, blood type, anatomy site, histology type, TNM stage as well as IAP and smoking conditions. We also found smoking and IAP dramatically decreased specific-OTU biodiversity, especially in normal lung tissue. Intriguingly, enriched microbes were in three categories: opportunistic pathogens, probiotics, and pollutant-detoxication microbes; this third category involved Sphingomonas, Sphingopyxis, etc. which help degrade pollutants, but may also cause epithelial damage and chronic inflammation. RNA-seq highlighted IL17, Ras, MAPK, and Notch pathways, which are associated with carcinogenesis and compromised immune system.ConclusionsThe lung microbiome can play vital roles in carcinogenesis. FLC and IAP subjects were affected by fragile lung epithelium, vulnerable host-microbes equilibrium, and dysregulated immune surveillance and response. Our findings provided useful information to study the triple interplay among environmental carcinogens, population genetic background, and diversified lung microbiome.

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Genome‐Wide Analysis Reveals Genetic Potential for Aromatic Compounds Biodegradation of Sphingopyxis

Cited by 15 publications

References 57 publications

Soil Microbiome Structure and Function in Ecopiles Used to Remediate Petroleum-Contaminated Soil

Soil Microbiome Structure and Function in Ecopiles Used to Remediate Petroleum-Contaminated Soil

The Microbiome of Leonardo da Vinci’s Drawings: A Bio-Archive of Their History

A Multi-Omics Study of Familial Lung Cancer: Microbiome and Host Gene Expression Patterns

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