Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change.The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalle...Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change.The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalleled reservoir of microbial genetic diversity.Here,by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types,we present a comprehensive Cold Seep Microbiomic Database(CSMD)to archive the genomic and functional diversity of cold seep microbiomes.The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes,which represent 1895 species spanning 105 phyla.In addition,beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition.Heterotrophic and anaerobic metabolisms are prevalent in microbial communities,accompanied by considerable mixotrophs and facultative anaerobes,highlighting the versatile metabolic potential in cold seeps.Furthermore,secondary metabolic gene cluster analysis indicates that at least 98.81%of the sequences potentially encode novel natural products,with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria.Overall,the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.展开更多
Research on CRISPR-Cas（clustered regularly interspaced short palindromic repeats-CRISPR associated protein） systems has led to the revolutionary CRISPR/Cas9 genome editing technique. However, for most archaea and ha...Research on CRISPR-Cas（clustered regularly interspaced short palindromic repeats-CRISPR associated protein） systems has led to the revolutionary CRISPR/Cas9 genome editing technique. However, for most archaea and half of bacteria, exploitation of their native CRISPR-Cas machineries may be more straightforward and convenient. In this study, we harnessed the native type I-B CRISPR-Cas system for precise genome editing in the polyploid haloarchaeon Haloarcula hispanica. After testing different designs, the editing tool was optimized to be a single plasmid that carries both the self-targeting miniCRISPR and a 600-800 bp donor. Significantly, chromosomal modifications, such as gene deletion, gene tagging or single nucleotide substitution, were precisely introduced into the vast majority of the transformants. Moreover, we showed that simultaneous editing of two genomic loci could also be readily achieved by one step. In summary, our data demonstrate that the haloarchaeal CRISPR-Cas system can be harnessed for genome editing in this polyploid archaeon, and highlight the convenience and efficiency of the native CRISPR-based genome editing strategy.展开更多
基金support from the Senior User Project of RV KEXUE(Grant No.KEXUE2019GZ05)the Center for Ocean Mega-Science,Chinese Academy of Sciences+2 种基金funding support from the Second Tibetan Plateau Scientific Expedition and Research Program(Grant No.2021QZKK0100)the National Key R&D Program of China(Grant No.2022YFF1002801)the National Natural Science Foundation of China(Grant No.92251302).
文摘Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change.The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalleled reservoir of microbial genetic diversity.Here,by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types,we present a comprehensive Cold Seep Microbiomic Database(CSMD)to archive the genomic and functional diversity of cold seep microbiomes.The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes,which represent 1895 species spanning 105 phyla.In addition,beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition.Heterotrophic and anaerobic metabolisms are prevalent in microbial communities,accompanied by considerable mixotrophs and facultative anaerobes,highlighting the versatile metabolic potential in cold seeps.Furthermore,secondary metabolic gene cluster analysis indicates that at least 98.81%of the sequences potentially encode novel natural products,with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria.Overall,the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.
基金supported by the grants from the National Natural Science Foundation of China(No.31571283)the CASSAFEA International Partnership Program for Creative Research Teams
文摘Research on CRISPR-Cas（clustered regularly interspaced short palindromic repeats-CRISPR associated protein） systems has led to the revolutionary CRISPR/Cas9 genome editing technique. However, for most archaea and half of bacteria, exploitation of their native CRISPR-Cas machineries may be more straightforward and convenient. In this study, we harnessed the native type I-B CRISPR-Cas system for precise genome editing in the polyploid haloarchaeon Haloarcula hispanica. After testing different designs, the editing tool was optimized to be a single plasmid that carries both the self-targeting miniCRISPR and a 600-800 bp donor. Significantly, chromosomal modifications, such as gene deletion, gene tagging or single nucleotide substitution, were precisely introduced into the vast majority of the transformants. Moreover, we showed that simultaneous editing of two genomic loci could also be readily achieved by one step. In summary, our data demonstrate that the haloarchaeal CRISPR-Cas system can be harnessed for genome editing in this polyploid archaeon, and highlight the convenience and efficiency of the native CRISPR-based genome editing strategy.
