古菌作为海洋微生物的重要组分广泛分布于各种海洋环境,在碳、氮、硫等元素的生物地球化学循环和地球生命演化过程中扮演着极为重要的角色。目前古菌主要分为4个超级门(广古菌、TACK古菌、阿斯加德古菌和DPANN古菌),近30个门类。本文综...古菌作为海洋微生物的重要组分广泛分布于各种海洋环境,在碳、氮、硫等元素的生物地球化学循环和地球生命演化过程中扮演着极为重要的角色。目前古菌主要分为4个超级门(广古菌、TACK古菌、阿斯加德古菌和DPANN古菌),近30个门类。本文综述了广泛分布于近岸或深渊等海洋沉积环境中的四类常见的古菌类群[深古菌门(Bathyarchaeota)、乌斯古菌门(Woesearchaeota)、阿斯加德(Asgard)古菌超门和底栖古菌目(Thermoprofundales,Marine Benthic Group D)]的分布与代谢特征的研究进展,以期为进一步开展这几类古菌方面的研究提供线索和启示。展开更多
Theionarchaea is a recently described archaeal class within the Euryarchaeota.While it is widely distributed in sediment ecosystems,little is known about its metabolic potential and ecological features.Here,we used me...Theionarchaea is a recently described archaeal class within the Euryarchaeota.While it is widely distributed in sediment ecosystems,little is known about its metabolic potential and ecological features.Here,we used metagenomics and metatranscriptomics to characterize 12 theionarchaeal metagenome-assembled genomes,which were further divided into two subgroups,from coastal mangrove sediments of China and seawater columns of the Yap Trench.Genomic analysis revealed that apart from the canonical sulfhydrogenase,Theionarchaea harbor genes encoding heliorhodopsin,group 4[NiFe]-hydrogenase,and flagellin,in which genes for heliorhodopsin and group 4[NiFe]-hydrogenase were transcribed in mangrove sediment.Further,the theionarchaeal substrate spectrum may be broader than previously reported as revealed by metagenomics and metatranscriptomics,and the potential carbon substrates include detrital proteins,hemicellulose,ethanol,and CO_(2).The genes for organic substrate metabolism(mainly detrital protein and amino acid metabolism genes)have relatively higher transcripts in the top sediment layers in mangrove wetlands.In addition,co-occurrence analysis suggested that the degradation of these organic compounds by Theionarchaea might be processed in syntrophy with fermenters(e.g.,Chloroflexi)and methanogens.Collectively,these observations expand the current knowledge of the metabolic potential of Theionarchaea,and shed light on the metabolic strategies and roles of these archaea in the marine ecosystems.展开更多
After explorations in a diversity of single-atom nanozymes(SAzymes),developing dual-centered SAzymes becomes a promising approach for superior catalytic performance.But confusing mechanisms including atomic coordinati...After explorations in a diversity of single-atom nanozymes(SAzymes),developing dual-centered SAzymes becomes a promising approach for superior catalytic performance.But confusing mechanisms including atomic coordination,spatial configuration,and metal–metal atom interaction hinder the development and design of SAzymes.Herein,a dual-centered Fe-Cu-N_(x)SAzyme exhibits excellent peroxidase(POD)-and catalase(CAT)-like activities with d-band center(ε_(d))coordination of Fe and Cu in multiple reaction stages,which plays a critical role in the adsorption of H_(2)O_(2)molecule and H_(2)O and O_(2)release.Therefore,the dband center coordination,which can be represented byε_(d)(Fe)–ε_(d)(Cu)shifts,leads to the competition between one-side and bilateral adsorption,which determines the favorable reaction path with lower energy barriers.Based on experimental statistics,simulated formation energies,and reaction barriers,3 configurations,Fe-Cu-N6-I,Fe-Cu-N_(8)-II,and Fe-Cu-N_(8)-III,are modeled and validated.Impressively,configuration-dependent catalytic selectivity and the competition between one-side and bilateral adsorption can be unveiled by d-band center coordination paradigm analysis.Theoretical simulations suggest that the unsymmetrical charge distribution over the three Fe-Cu configurations could tune the adsorption strength compared with the counterparts FeN_(4)and CuN_(4).The present work provides a potential route for optimizing enzyme-like catalysis by designing the dual-or even triple-metal SAzymes,which demonstrates the large space to modulate the metal atomic configuration and interaction.展开更多
Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance.Here,we retrieved 11 metagenomic-assembled genomes(MAGs)a...Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance.Here,we retrieved 11 metagenomic-assembled genomes(MAGs)affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench.Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum,subsequently named Candidatus Qinglongiota,Candidatus Heilongiota,and Candidatus Canglongiota.Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle,with the potential to utilize various types of sugars,proteins,and/or short-chain fatty acids through anaerobic pathways.This was further confirmed by a global distribution map of the three phyla,indicating a preference for oxygen-limited or particle-attached niches,such as anoxic sedimentary environments.Of note,Candidatus Canglongiota genomes harbor genes for the complete WoodLjungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria.Evolutionary analysis indicated that gene gain and loss events,and horizontal gene transfer(HGT)play important roles in shaping the genomic and metabolic features of the three new phyla.This study presents the genomic insight into the ecology,metabolism,and evolution of three new phyla,which broadens the phylum-level diversity within the domain Bacteria.展开更多
文摘古菌作为海洋微生物的重要组分广泛分布于各种海洋环境,在碳、氮、硫等元素的生物地球化学循环和地球生命演化过程中扮演着极为重要的角色。目前古菌主要分为4个超级门(广古菌、TACK古菌、阿斯加德古菌和DPANN古菌),近30个门类。本文综述了广泛分布于近岸或深渊等海洋沉积环境中的四类常见的古菌类群[深古菌门(Bathyarchaeota)、乌斯古菌门(Woesearchaeota)、阿斯加德(Asgard)古菌超门和底栖古菌目(Thermoprofundales,Marine Benthic Group D)]的分布与代谢特征的研究进展,以期为进一步开展这几类古菌方面的研究提供线索和启示。
基金supported by the National Natural Science Foundation of China(91851105,31970105,31600093,3170043091951102)+1 种基金the Innovation Team Project of Universities in Guangdong Province(2020KCXTD023)the Shenzhen Science and Technology Program(JCYJ20200109105010363,JCYJ20180305163524811 and JCYJ20190808152403587)。
文摘Theionarchaea is a recently described archaeal class within the Euryarchaeota.While it is widely distributed in sediment ecosystems,little is known about its metabolic potential and ecological features.Here,we used metagenomics and metatranscriptomics to characterize 12 theionarchaeal metagenome-assembled genomes,which were further divided into two subgroups,from coastal mangrove sediments of China and seawater columns of the Yap Trench.Genomic analysis revealed that apart from the canonical sulfhydrogenase,Theionarchaea harbor genes encoding heliorhodopsin,group 4[NiFe]-hydrogenase,and flagellin,in which genes for heliorhodopsin and group 4[NiFe]-hydrogenase were transcribed in mangrove sediment.Further,the theionarchaeal substrate spectrum may be broader than previously reported as revealed by metagenomics and metatranscriptomics,and the potential carbon substrates include detrital proteins,hemicellulose,ethanol,and CO_(2).The genes for organic substrate metabolism(mainly detrital protein and amino acid metabolism genes)have relatively higher transcripts in the top sediment layers in mangrove wetlands.In addition,co-occurrence analysis suggested that the degradation of these organic compounds by Theionarchaea might be processed in syntrophy with fermenters(e.g.,Chloroflexi)and methanogens.Collectively,these observations expand the current knowledge of the metabolic potential of Theionarchaea,and shed light on the metabolic strategies and roles of these archaea in the marine ecosystems.
基金supported by the National Key Research and Development Program of China(Nos.2021YFF1200700 and 2021YFF1200701)the National Natural Science Foundation of China(Nos.91859101,81971744,U1932107,82001952,11804248,82302361,and 82302381)+5 种基金Outstanding Youth Funds of Tianjin(No.2021FJ-0009)STI 2030-Major Projects(No.2022ZD0210200)National Natural Science Foundation of Tianjin(Nos.19JCZDJC34000,20JCYBJC00940,21JCYBJC00550,21JCZDJC00620,and 21JCYBJC00490)the Key Projects of Tianjin Natural Fund(No.21JCZDJC00490)the Innovation Foundation of Tianjin University,China Postdoctoral Science Foundation(No.2023M732601)CAS Interdisciplinary Innovation Team(No.JCTD-2020-08).
文摘After explorations in a diversity of single-atom nanozymes(SAzymes),developing dual-centered SAzymes becomes a promising approach for superior catalytic performance.But confusing mechanisms including atomic coordination,spatial configuration,and metal–metal atom interaction hinder the development and design of SAzymes.Herein,a dual-centered Fe-Cu-N_(x)SAzyme exhibits excellent peroxidase(POD)-and catalase(CAT)-like activities with d-band center(ε_(d))coordination of Fe and Cu in multiple reaction stages,which plays a critical role in the adsorption of H_(2)O_(2)molecule and H_(2)O and O_(2)release.Therefore,the dband center coordination,which can be represented byε_(d)(Fe)–ε_(d)(Cu)shifts,leads to the competition between one-side and bilateral adsorption,which determines the favorable reaction path with lower energy barriers.Based on experimental statistics,simulated formation energies,and reaction barriers,3 configurations,Fe-Cu-N6-I,Fe-Cu-N_(8)-II,and Fe-Cu-N_(8)-III,are modeled and validated.Impressively,configuration-dependent catalytic selectivity and the competition between one-side and bilateral adsorption can be unveiled by d-band center coordination paradigm analysis.Theoretical simulations suggest that the unsymmetrical charge distribution over the three Fe-Cu configurations could tune the adsorption strength compared with the counterparts FeN_(4)and CuN_(4).The present work provides a potential route for optimizing enzyme-like catalysis by designing the dual-or even triple-metal SAzymes,which demonstrates the large space to modulate the metal atomic configuration and interaction.
基金supported by the National Natural Science Foundation of China(91951102,31800105,31970105,32061133009)the Innovation Team Project of Universities in Guangdong Province(2020KCXTD023)+1 种基金the Scientific Research Foundation of Third Institute of Oceanography,MNR(2019022)the Science and Technology Innovation Committee of Shenzhen(JCYJ20190808152403587,JCYJ20180305163524811,JCYJ20200109105010363)。
文摘Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance.Here,we retrieved 11 metagenomic-assembled genomes(MAGs)affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench.Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum,subsequently named Candidatus Qinglongiota,Candidatus Heilongiota,and Candidatus Canglongiota.Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle,with the potential to utilize various types of sugars,proteins,and/or short-chain fatty acids through anaerobic pathways.This was further confirmed by a global distribution map of the three phyla,indicating a preference for oxygen-limited or particle-attached niches,such as anoxic sedimentary environments.Of note,Candidatus Canglongiota genomes harbor genes for the complete WoodLjungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria.Evolutionary analysis indicated that gene gain and loss events,and horizontal gene transfer(HGT)play important roles in shaping the genomic and metabolic features of the three new phyla.This study presents the genomic insight into the ecology,metabolism,and evolution of three new phyla,which broadens the phylum-level diversity within the domain Bacteria.
