Metatranscriptomics is a cutting-edge technology for exploring the gene expression by,and functional activities of,the microbial community across diverse ecosystems at a given time,thereby shedding light on their meta...Metatranscriptomics is a cutting-edge technology for exploring the gene expression by,and functional activities of,the microbial community across diverse ecosystems at a given time,thereby shedding light on their metabolic responses to the prevailing environmental conditions.The double-RNA approach involves the simultaneous analysis of rRNA and mRNA,also termed structural and functional metatranscriptomics.By contrast,mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles,but requires either deep sequencing or effective rRNA depletion.In this review,we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional metatranscriptomics.In particular,we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields,such as rhizobiomes,antibiotic resistomes,methanomes,and viromes.Our review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.展开更多
In real environment, it is unlikely that contaminants exist singly; environmental contamination with chemical mixtures is a norm. However, the impacts of chemical mixtures on environmental quality and ecosystem health...In real environment, it is unlikely that contaminants exist singly; environmental contamination with chemical mixtures is a norm. However, the impacts of chemical mixtures on environmental quality and ecosystem health have been overlooked in the past.Among the complex interactions between different contaminants, their relationship with the rise of antibiotic resistance（AR） is an emerging environmental concern. In this paper,we review recent progresses on how chemicals or chemical mixtures promote AR. We propose that, through co-selection, agents causing stress to bacteria may induce AR. The mechanisms for chemical mixtures to promote AR are also discussed. We also propose that,mechanistic understanding of co-selection of chemical mixtures for AR should be a future research priority in environmental health research.展开更多
文摘Metatranscriptomics is a cutting-edge technology for exploring the gene expression by,and functional activities of,the microbial community across diverse ecosystems at a given time,thereby shedding light on their metabolic responses to the prevailing environmental conditions.The double-RNA approach involves the simultaneous analysis of rRNA and mRNA,also termed structural and functional metatranscriptomics.By contrast,mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles,but requires either deep sequencing or effective rRNA depletion.In this review,we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional metatranscriptomics.In particular,we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields,such as rhizobiomes,antibiotic resistomes,methanomes,and viromes.Our review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.
基金supported by the National Key Research and Development Plan(No.2016YFD0800205)the National Natural Science Foundation of China(Nos.41571130063 and31770127)the Strategic Priority Research Program of Chinese Academy of Sciences(No.XDB15020402)
文摘In real environment, it is unlikely that contaminants exist singly; environmental contamination with chemical mixtures is a norm. However, the impacts of chemical mixtures on environmental quality and ecosystem health have been overlooked in the past.Among the complex interactions between different contaminants, their relationship with the rise of antibiotic resistance（AR） is an emerging environmental concern. In this paper,we review recent progresses on how chemicals or chemical mixtures promote AR. We propose that, through co-selection, agents causing stress to bacteria may induce AR. The mechanisms for chemical mixtures to promote AR are also discussed. We also propose that,mechanistic understanding of co-selection of chemical mixtures for AR should be a future research priority in environmental health research.
