Novel tetrahydrofuran (THF) degradation-associated genes and cooperation patterns of a THF-degrading microbial community as revealed by metagenomic

Qi, Minbo; Huang, Hui; Zhang, Ying; Wang, Haixia; Li, Hanbo; Lü, Zhenmei

doi:10.1016/j.chemosphere.2019.05.137

Cited by 12 publications

(3 citation statements)

References 63 publications

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“…These considered through bioinformatics tools such as MG-RAST, MetaVelvet, Genovo, etc., most of which borrowed from the areas of data mining, manufactured insights and measurements, have incredibly enhanced our information on microbial compositions and network-based relationship examinations [88]. Qi et al [89] have utilized the metagenomics by utilizing the Illumina MiSeq highthroughput sequencing of the 16S rRNA quality to uncover the composition of the microbial community. Advance investigation of the shotgun metagenomic sequencing comes about uncovered a Scedosporium beginning CYP450 encoding quality, assigned cyp450q1 (GenBank no.…”

Section: Metagenome Analysis and Interpretationmentioning

confidence: 99%

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

et al. 2020

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The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.

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Section: Metagenome Analysis and Interpretationmentioning

confidence: 99%

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

et al. 2020

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“…With recent rapid developments in genome sequencing, more and more Pseudonocardia genomic data have been accumulated in the database. Many Pseudonocardia -specific gene clusters are now available, and their functions, concerning, for example, synthesis of many natural bioactive products ( Miyamoto et al, 2014 ; Caffrey et al, 2016 ; Won et al, 2017 ; Geddis et al, 2018 ; Fang et al, 2019 ; Strecker et al, 2019 ; Subramani and Sipkema, 2019 ), biodegradation of large amounts of industrially discharged environmental pollutants ( Grostern et al, 2012 ; Sales et al, 2013 ; Inoue et al, 2016 ; Yamamoto et al, 2018 ; Qi et al, 2019 ), defense against invading genetic elements ( Doron et al, 2018 ), have been and will continue to be deduced or demonstrated, showing great application potentials in human medicine, animal health, and crop protection, etc. Indeed, current applications of Pseudonocardia have been summarized very recently ( Riahi et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Enabling Efficient Genetic Manipulations in a Rare Actinomycete Pseudonocardia alni Shahu

Wang

Yang

et al. 2022

Front. Microbiol.

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Pseudonocardia species are emerging as important microorganisms of global concern with unique and increasingly significant ecological roles and represent a prominent source of bioactive natural products, but genetic engineering of these organisms for biotechnological applications is greatly hindered due to the limitation of efficient genetic manipulation tools. In this regard, we report here the establishment of an efficient genetic manipulation system for a newly isolated strain, Pseudonocardia alni Shahu, based on plasmid conjugal transfer from Escherichia coli to Pseudonocardia. Conjugants were yielded upon determining the optimal ratio between the donor and recipient cells, and designed genome modifications were efficiently accomplished, including exogenous gene integration based on an integrative plasmid and chromosomal stretch removal by homologous recombination using a suicidal non-replicating vector. Collectively, this work has made the P. alni Shahu accessible for genetic engineering, and provided an important reference for developing genetic manipulation methods in other rare actinomycetes.

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“…Yet, a thiamine-mediated cooperation for the degradation of tetrahydrofuran (a structural analog and co-metabolic substrate of 1,4-dioxane) has been veri ed [21]. The potential degraders and main cooperators in the degradation of tetrahydrofuran were also identi ed by metagenomic analysis [22]. A recent study discovered potential novel pathways and enzymes for 1,4-dioxane degradation using the integration of metagenomics and metabolomics [23].…”

Section: Introductionmentioning

confidence: 99%

Network And Meta-Omics Reveal The Key Degrader And Cooperation Patterns In An Efficient 1,4-Dioxane-Degrading Microbial Community

Dai

Wang

et al. 2021

Preprint

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Background: 1,4-dioxane is an emerging wastewater contaminant with probable human carcinogenicity. Our current understanding of microbial interactions during 1,4-dioxane biodegradation process in mix cultures is limited. Here, we applied metagenomic, metatranscriptomic and co-occurrence network analyses to unraveling the microbial cooperation between degrader and non-degraders in an efficient 1,4-dioxane-degrading microbial community CH1.Results: The 1,4-dioxane degrading bacterium, Ancylobacter polymorphus ZM13, was isolated from CH1 and proved to be the key degrader because of the high relative abundance, highly expressed toluene monooxygenase genes tmoABCDEF and high betweenness centrality of networks. The strain ZM13 cooperated obviously with 6 bacterial genera in the network, among which Xanthobacter and Mesorhizobium were proved to be involved in the intermediate metabolism with responsible genes encoding alcohol dehydrogenase (adh), aldehyde dehydrogenase (aldh), glycolate oxidase (glcDEF), glyoxylate carboligase (gcl), malate synthase (glcB) and 2-isopropylmalate synthase (leuA) upregulated. Also, 1,4-dioxane facilitated the shift of biodiversity and function of CH1, and those cooperators of CH1 cooperated with ZM13 in the way of providing amino acids or fatty acids and relieving environmental stresses to promote biodegradation.Conclusions: This study revealed the biodiversity, community structure, microbial functions and interactions in a microbial community CH1 during the efficient 1,4-dioxane degradation and proved the degrader Ancylobacter polymorphus ZM13 that isolated from CH1 was the key degrading bacterium. These results provide new insights into our understanding of how the key degrading bacterium interacted with cooperators in a 1,4-dioxane-degrading community, and has important implications for predicting microbial cooperation and constructing highly efficient synthetic 1,4-dioxane-degrading communities.

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Novel tetrahydrofuran (THF) degradation-associated genes and cooperation patterns of a THF-degrading microbial community as revealed by metagenomic

Cited by 12 publications

References 63 publications

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

Enabling Efficient Genetic Manipulations in a Rare Actinomycete Pseudonocardia alni Shahu

Network And Meta-Omics Reveal The Key Degrader And Cooperation Patterns In An Efficient 1,4-Dioxane-Degrading Microbial Community

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