We report the isolation of a cold-adapted bacterium belonging to the genus Janthinobacterium （named AU 11）, from a water sample collected in Lake Uruguay （King George Island, South Shetlands）. AUI 1 （growth betwe...We report the isolation of a cold-adapted bacterium belonging to the genus Janthinobacterium （named AU 11）, from a water sample collected in Lake Uruguay （King George Island, South Shetlands）. AUI 1 （growth between 4℃ and 30℃） produces a single cold-active extracellular protease （ExPAU11）, differentially expressed at low temperature. ExPAU11 was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MALDI-ToF MS） as an alkaline metallo-protease （70% coverage with an extracellular protease of Janthinobacterium sp. PI12）, and by protease-inhibitor screening identified as a serine-protease. To the best of our knowledge this is the first experimental evidence of a cold-active extracellular protease produced by Janthinobacterium. Furthermore, we identified a serine-protease gene （named JSP8A） showing 60% identity （98% query coverage） to subtilisin peptidases belonging to the $8 family （S8A subfamily） of many cyanobacteria. A phylogenetic analysis of the JSP8A protease, along with related bacterial protein sequences, confirms that JSP8A clusters with S8A subtilisin sequences from different cyanobacteria, and is clearly separated from SSA bacterial sequences of other phyla （including its own）. An analysis of the genomic organization around JSP8A suggests that this protease gene was acquired in an event that duplicated a racemase gene involved in transforming L- to D-amino acids. Our results suggest that AU11 probably acquired this subtilisin-like protease gene by horizontal gene transfer （HGT） from a cyanobacterittrn. We discuss the relevance of a bacterial protease-HGT in the Antarctic environment in light of this hypothesis.展开更多
Mycobacterium is a genus of bacteria with over a hundred non-pathogenic and pathogenic species, best recognized for certain members known to cause diseases such as tuberculosis and leprosy. Two novel protein families ...Mycobacterium is a genus of bacteria with over a hundred non-pathogenic and pathogenic species, best recognized for certain members known to cause diseases such as tuberculosis and leprosy. Two novel protein families important in the pathogenesis of Mycobacterium species are the PE and PPE families. These two protein families affect the antigenic profiles, disturbing host immunity. To better understand the origin and evolution of these gene families and the differences in their composition between pathogenic and non-pathogenic strains, several bioinformatic analyses were conducted both among Mycobacterium and closely related species that contain PE35 and PPE68 gene homologs. The methods included protein homology searches (BLASTP), horizontal gene transfer analysis (IslandViewer), phylogenetic analysis, gene cluster analysis and structural and functional constraints. Results revealed that PE and PPE gene homologs were not only limited to Mycobacterium, but also existed in three other non-mycobacterial genera, Rhodococcus, Tsukamurella and Segniliparus, and were possibly initially acquired from non-mycobacterial microorganisms by multiple horizontal gene transfers. Results also demonstrated that PE and PPE genes were more diverse and more rapidly evolving in pathogenic Mycobacterium as compared with non-pathogenic Mycobacterium and other non-mycobacterial species. These findings possibly shed light on the diverse functions and origins of the PE/PPE proteins among these organisms.展开更多
Horizontal gene transfer(HGT)has been proved a major driving force in prokaryotic evolution.However,the molecular functions of these transferred genes in pathogenic bacteria especially plant pathogenic bacteria are st...Horizontal gene transfer(HGT)has been proved a major driving force in prokaryotic evolution.However,the molecular functions of these transferred genes in pathogenic bacteria especially plant pathogenic bacteria are still not fully investigated.In this study,the whole-genome in silico analysis was performed and found a syringopeptin synthetase(syp)homolog in Burkholderia glumae,which can cause bacterial panicle blight in rice,was predicted to be horizontally transferred from Pseudomonas ancestor with solid confidence by phylogenetic analysis.The comprehensive molecular experiments were performed to study the potential role of this gene in B.glumae.Inoculation of rice panicles with the syp mutant resulted in 60%lower disease index compared with the wild type(WT)parent strain,suggesting the requirement of syp for the full virulence of B.glumae.Chromatography analysis of exudates from B.glumae showed suppression of synthesis of metabolites analogous to syringopeptin in the mutants.All these data raise the possibility of HGT phenomenon in shaping the virulence and adaptation of B.glumae over evolutionary time.展开更多
Leucine rich repeats (LRRs) are present in over 14,000 proteins that have been identified in viruses, bacteria, archaea, and eukaryotes. Two to sixty-two LRRs occur in tandem forming an overall arc shaped domain. Ther...Leucine rich repeats (LRRs) are present in over 14,000 proteins that have been identified in viruses, bacteria, archaea, and eukaryotes. Two to sixty-two LRRs occur in tandem forming an overall arc shaped domain. There are eight classes of LRRs. Plant specific LRRs (class: PS-LRR) had previously been recognized in only plant proteins. However, we find that PS-LRRs are also present in proteins from bacteria. We investigated the origin of bacterial PS-LRR domains. PSLRR proteins are widely distributed in most plants;they are found in only a few bacterial species. There are no PS-LRR proteins from archaea. Bacterial PS-LRRs in twenty proteins from eleven bacterial species (in the three phyla: Proteobacteria, Cyanobacteria, and Bacteroidetes) are significantly more similar to the PS-LRR class than to the other seven classes of LRR proteins. Not only amino acid sequences but also nucleotide sequences of the bacterial PS-LRR domains show highly significant similarity with those of many plant proteins. The program, EGID (Ensemble algorithm for Genomic Island Detection), predicts that Synechococcus sp. CYA_ 1022 came from another organism. Four bacterial PS-LRR proteins contain AhpC-TSA, IgA peptidase M64, the immunoglobulin domain, the Calx-b domain, and the He_PIG domain;these domains show no similarity with any eukaryotic (plant) proteins, in contrast to the similarities of their respective PS-LRRs. The present results indicate that horizontal gene transfer (HGT) of genes/gene fragments encoding PS-LRR domains occurred between bacteria and plants, and HGT among the eleven bacterial species, of the three phyla, as opposed to descent from a common ancestor. There is the possibility of the occurrence of one HGT event from plant to bacteria. A series of HGTs might then have occurred recently and rapidly among these eleven species of bacteria.展开更多
Horizontal gene transfer(HGT) refers to the flow of genetic materials to non-offspring,and occasionally HGT in plants can improve the adaptation of organisms in new niches due to expanded metabolic capability.Anthocya...Horizontal gene transfer(HGT) refers to the flow of genetic materials to non-offspring,and occasionally HGT in plants can improve the adaptation of organisms in new niches due to expanded metabolic capability.Anthocyanins are an important group of water-soluble red,purple,or blue secondary metabolites,whose diversity results from modification after the main skeleton biosynthesis.Cuscuta is a stem holoparasitic genus,whose members form direct connection with hosts to withdraw water,nutrients,and macromolecules.Such intimate association is thought to increase the frequency of HGT.By transcriptome screening for foreign genes in Cuscuta australis,we discovered that one gene encoding a putative anthocyanin acyltransferase gene of the BAHD family,which is likely to be involved in anthocyanin modification,was acquired by C.australis from Fabaceae through HGT.The anthocyanin acyltransferase-like(AT-like) gene was confirmed to be present in the genome assembly of C.australis and the transcriptomes of Cuscuta pentagona.The higher transcriptional level in old stems is consistent with its putative function in secondary metabolism by stabilizing anthocyanin at neutral pH and thus HGT of this AT-like gene may have improved biotic and abiotic resistance of Cuscuta.展开更多
Horizontal gene transfer(HGT)is a common occurrence across all domains of life.However,most HGT events were reported between single-celled organisms or parasites and hosts(Van Etten and Bhattacharya 2020).A type II an...Horizontal gene transfer(HGT)is a common occurrence across all domains of life.However,most HGT events were reported between single-celled organisms or parasites and hosts(Van Etten and Bhattacharya 2020).A type II antifreeze protein(AFP)gene was the first and sole evidence of HGT direct vertebrate-to-vertebrate DNA transmission.AFP is only found in 3 widely separated branches of teleost fishes(herring,sea raven,and smelts),sharing amino acid similarity up to 80%(Graham et al.2008).展开更多
近年来,土壤环境中抗生素抗性基因(ARGs)污染引起广泛关注。以Web of Science核心数据库和万方数据库文献资料为数据源进行文献计量学分析,从年发文量变化、不同国家贡献及研究主题演变(基于关键词)等方面对土壤环境中ARGs污染相关研究...近年来,土壤环境中抗生素抗性基因(ARGs)污染引起广泛关注。以Web of Science核心数据库和万方数据库文献资料为数据源进行文献计量学分析,从年发文量变化、不同国家贡献及研究主题演变(基于关键词)等方面对土壤环境中ARGs污染相关研究进行剖析,以此探讨国内外该领域的研究现状、热点和发展。结果表明,土壤中ARGs污染相关研究的发文数量快速增长。我国文献在发文数量、论文被引频次方面具有重要影响,表明我国在该领域有较强的国际学术影响力。关键词聚类分析表明该领域的研究方向主要集中在以下5个方面:(1)土壤中携带ARGs的微生物及其环境行为;(2)土壤环境中ARGs的来源和持久性;(3)土壤环境中ARGs的传播和消减方法;(4)土壤中共存物质对ARGs丰度和迁移行为的影响;(5)农业生产活动对土壤环境中ARGs污染的影响。同时,在介绍ARGs常用检测方法以及土壤环境中ARGs污染来源和分布的基础上,剖析影响ARGs在土壤中传播的多种因素,探讨土壤环境中ARGs的消减方法,并指出当前研究尚存的不足之处以及今后的研究方向。该文可为未来土壤环境中ARGs污染领域的研究和风险管控提供参考。展开更多
Dimethylsulfoniopropionate(DMSP) is mainly produced by marine phytoplankton as an osmolyte, antioxidant,predator deterrent, or cryoprotectant. DMSP is also an important carbon and sulfur source for marine bacteria.Bac...Dimethylsulfoniopropionate(DMSP) is mainly produced by marine phytoplankton as an osmolyte, antioxidant,predator deterrent, or cryoprotectant. DMSP is also an important carbon and sulfur source for marine bacteria.Bacteria may metabolize DMSP via the demethylation pathway involving the DMSP demethylase gene(dmdA) or the cleavage pathway involving several different DMSP lyase genes. Most DMSP released into seawater is degraded by bacteria via demethylation. To test a hypothesis that the high gene frequency of dmdA among major marine taxa results in part from horizontal gene transfer(HGT) events, a total of thirty-one bacterial strains were isolated from Arctic Kongsfjorden seawater in this study. Analysis of 16S rRNA gene sequences showed that,except for strains BSw22118, BSw22131 and BSw22132 belonging to the genera Colwellia, Pseudomonas and Glaciecola, respectively, all bacteria fell into the genus Pseudoalteromonas. DmdA genes were detected in five distantly related bacterial strains, including four Arctic strains(Pseudoalteromonas sp. BSw22112, Colwellia sp.BSw22118, Pseudomonas sp. BSw22131 and Glaciecola sp. BSw22132) and one Antarctic strain(Roseicitreum antarcticum ZS2–28). Their dmdA genes showed significant similarities(97.7%–98.3%) to that of Ruegeria pomeroyi DSS–3, which was originally isolated from temperate coastal seawater. In addition, the sequence of the gene transfer agent(GTA) capsid protein gene(g5) detected in Antarctic strain ZS2–28 exhibited a genetically closely related to that of Ruegeria pomeroyi DSS–3. Among the five tested strains, only Pseudomonas sp. BSw22131 could grow using DMSP as the sole carbon source. The results of this study support the hypothesis of HGT for dmdA among taxonomically heterogeneous bacterioplankton, and suggest a wide distribution of functional gene(i.e., dmdA) in global marine environments.展开更多
Rapid urbanization has resulted in pervasive occurrence of antibiotic resistance genes(ARGs)in urban aquatic ecosystems.However,limited information is available concerning the ARG profiles and the forces responsible f...Rapid urbanization has resulted in pervasive occurrence of antibiotic resistance genes(ARGs)in urban aquatic ecosystems.However,limited information is available concerning the ARG profiles and the forces responsible for their assembly in urban landscape lagoon systems.Here,we employed high-throughput quantitative PCR(HT-q PCR)to characterize the spatial variations of ARGs in surface and core sediments of Yundang Lagoon,China.The results indicated that the average richness and absolute abundance of ARGs were 11 and 53 times higher in the lagoon sediments as compared to pristine reference Tibetan lake sediments,highlighting the role of anthropogenic activities in ARG pollution.Co-occurrence network analysis indicated that various anaerobic prokaryotic genera belonging to Alpha-,Deltaproteobacteria,Bacteroidetes,Euryarchaeota,Firmicutes and Synergistetes were the potential hosts of ARGs.The partial least squares-path modeling(PLS-PM)analysis revealed positive and negative indirect effects of physicochemical factors and heavy metals on the lagoon ARG profiles,via biotic factors,respectively.The horizontal(mediated by mobile genetic elements)and vertical(mediated by prokaryotic communities)gene transfer may directly contribute the most to drive the abundance and composition of ARGs,respectively.Furthermore,the neutral community model demonstrated that the assembly of sediment ARG communities was jointly governed by deterministic and stochastic processes.Overall,this study provides novel insights into the diversity and distribution of ARGs in the benthic habitat of urban lagoon systems and underlying mechanisms for the spread and proliferation of ARGs.展开更多
The diversity and classification of microbes has been a long-standing issue.Molecular phylogeny of the prokaryotes based on comparison of the 16S rRNA sequences of the small ribosomal subunit has led to a reasonable t...The diversity and classification of microbes has been a long-standing issue.Molecular phylogeny of the prokaryotes based on comparison of the 16S rRNA sequences of the small ribosomal subunit has led to a reasonable tree of life in the late 1970s. How-ever, the availability of more and more complete bacterial genomes has brought about complications instead of refinement of the tree. In particular, it turns out that different choice of genes may tell different history. This might be caused by possible horizontal gene transfer (HGT) among species. There is an urgent need to develop phylogenetic methods that make use of whole genome data. We describe a new approach in molecular phylogeny,namely, tree construction based on K-tuple frequency analysis of the genomic sequences.Putting aside the technicalities, we emphasize the transition from randomness to determin-ism when the string length K increases and try to comment on the challenge mentioned in the title.展开更多
基金supported by PEDECIBA (Programa De Desarrollo de las Ciencias Básicas), Uruguay, and IAU (Instituto Antártico Uruguayo)supported by ANII (Agencia Nacional de Investigación e Innovación)
文摘We report the isolation of a cold-adapted bacterium belonging to the genus Janthinobacterium （named AU 11）, from a water sample collected in Lake Uruguay （King George Island, South Shetlands）. AUI 1 （growth between 4℃ and 30℃） produces a single cold-active extracellular protease （ExPAU11）, differentially expressed at low temperature. ExPAU11 was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MALDI-ToF MS） as an alkaline metallo-protease （70% coverage with an extracellular protease of Janthinobacterium sp. PI12）, and by protease-inhibitor screening identified as a serine-protease. To the best of our knowledge this is the first experimental evidence of a cold-active extracellular protease produced by Janthinobacterium. Furthermore, we identified a serine-protease gene （named JSP8A） showing 60% identity （98% query coverage） to subtilisin peptidases belonging to the $8 family （S8A subfamily） of many cyanobacteria. A phylogenetic analysis of the JSP8A protease, along with related bacterial protein sequences, confirms that JSP8A clusters with S8A subtilisin sequences from different cyanobacteria, and is clearly separated from SSA bacterial sequences of other phyla （including its own）. An analysis of the genomic organization around JSP8A suggests that this protease gene was acquired in an event that duplicated a racemase gene involved in transforming L- to D-amino acids. Our results suggest that AU11 probably acquired this subtilisin-like protease gene by horizontal gene transfer （HGT） from a cyanobacterittrn. We discuss the relevance of a bacterial protease-HGT in the Antarctic environment in light of this hypothesis.
文摘Mycobacterium is a genus of bacteria with over a hundred non-pathogenic and pathogenic species, best recognized for certain members known to cause diseases such as tuberculosis and leprosy. Two novel protein families important in the pathogenesis of Mycobacterium species are the PE and PPE families. These two protein families affect the antigenic profiles, disturbing host immunity. To better understand the origin and evolution of these gene families and the differences in their composition between pathogenic and non-pathogenic strains, several bioinformatic analyses were conducted both among Mycobacterium and closely related species that contain PE35 and PPE68 gene homologs. The methods included protein homology searches (BLASTP), horizontal gene transfer analysis (IslandViewer), phylogenetic analysis, gene cluster analysis and structural and functional constraints. Results revealed that PE and PPE gene homologs were not only limited to Mycobacterium, but also existed in three other non-mycobacterial genera, Rhodococcus, Tsukamurella and Segniliparus, and were possibly initially acquired from non-mycobacterial microorganisms by multiple horizontal gene transfers. Results also demonstrated that PE and PPE genes were more diverse and more rapidly evolving in pathogenic Mycobacterium as compared with non-pathogenic Mycobacterium and other non-mycobacterial species. These findings possibly shed light on the diverse functions and origins of the PE/PPE proteins among these organisms.
基金the National Key R&D Program of China(2018YFD0201202 and 2017YFD0201108)the Agri-X Interdisciplinary Fund of Shanghai Jiao Tong University,China(Agri-X2017010)+3 种基金the State Key Laboratory for Biology of Plant Diseases and Insect Pests of Shanghai Jiao Tong University(SKLOF201802)the Shanghai Committee of Science and Technology(19390743300)the National Natural Science Foundation of China(31200003 and 31770772)Joint Research Funds for Translational Medicine at Shanghai Jiao Tong University(ZH2018ZDA06).
文摘Horizontal gene transfer(HGT)has been proved a major driving force in prokaryotic evolution.However,the molecular functions of these transferred genes in pathogenic bacteria especially plant pathogenic bacteria are still not fully investigated.In this study,the whole-genome in silico analysis was performed and found a syringopeptin synthetase(syp)homolog in Burkholderia glumae,which can cause bacterial panicle blight in rice,was predicted to be horizontally transferred from Pseudomonas ancestor with solid confidence by phylogenetic analysis.The comprehensive molecular experiments were performed to study the potential role of this gene in B.glumae.Inoculation of rice panicles with the syp mutant resulted in 60%lower disease index compared with the wild type(WT)parent strain,suggesting the requirement of syp for the full virulence of B.glumae.Chromatography analysis of exudates from B.glumae showed suppression of synthesis of metabolites analogous to syringopeptin in the mutants.All these data raise the possibility of HGT phenomenon in shaping the virulence and adaptation of B.glumae over evolutionary time.
文摘Leucine rich repeats (LRRs) are present in over 14,000 proteins that have been identified in viruses, bacteria, archaea, and eukaryotes. Two to sixty-two LRRs occur in tandem forming an overall arc shaped domain. There are eight classes of LRRs. Plant specific LRRs (class: PS-LRR) had previously been recognized in only plant proteins. However, we find that PS-LRRs are also present in proteins from bacteria. We investigated the origin of bacterial PS-LRR domains. PSLRR proteins are widely distributed in most plants;they are found in only a few bacterial species. There are no PS-LRR proteins from archaea. Bacterial PS-LRRs in twenty proteins from eleven bacterial species (in the three phyla: Proteobacteria, Cyanobacteria, and Bacteroidetes) are significantly more similar to the PS-LRR class than to the other seven classes of LRR proteins. Not only amino acid sequences but also nucleotide sequences of the bacterial PS-LRR domains show highly significant similarity with those of many plant proteins. The program, EGID (Ensemble algorithm for Genomic Island Detection), predicts that Synechococcus sp. CYA_ 1022 came from another organism. Four bacterial PS-LRR proteins contain AhpC-TSA, IgA peptidase M64, the immunoglobulin domain, the Calx-b domain, and the He_PIG domain;these domains show no similarity with any eukaryotic (plant) proteins, in contrast to the similarities of their respective PS-LRRs. The present results indicate that horizontal gene transfer (HGT) of genes/gene fragments encoding PS-LRR domains occurred between bacteria and plants, and HGT among the eleven bacterial species, of the three phyla, as opposed to descent from a common ancestor. There is the possibility of the occurrence of one HGT event from plant to bacteria. A series of HGTs might then have occurred recently and rapidly among these eleven species of bacteria.
基金Acknowledgments This work was supported by the National Natural Science Foundation of China （No. 31301037 and 31470012 to G.S.）, the Natural Science Foundation of Yunnan Province of China （No. 2013FB068 to G.S.）, the Young Academic and Technical Leader Raising Foundation of Yunnan Province （No. 2014HB046, to G.S.）, the Western Light Talent Culture Project of the Chinese Academy of Sciences （to G.S.）, and the Yunnan Recruitment Program of Experts in Sciences （2012HA016 to J.W.）.
文摘Horizontal gene transfer(HGT) refers to the flow of genetic materials to non-offspring,and occasionally HGT in plants can improve the adaptation of organisms in new niches due to expanded metabolic capability.Anthocyanins are an important group of water-soluble red,purple,or blue secondary metabolites,whose diversity results from modification after the main skeleton biosynthesis.Cuscuta is a stem holoparasitic genus,whose members form direct connection with hosts to withdraw water,nutrients,and macromolecules.Such intimate association is thought to increase the frequency of HGT.By transcriptome screening for foreign genes in Cuscuta australis,we discovered that one gene encoding a putative anthocyanin acyltransferase gene of the BAHD family,which is likely to be involved in anthocyanin modification,was acquired by C.australis from Fabaceae through HGT.The anthocyanin acyltransferase-like(AT-like) gene was confirmed to be present in the genome assembly of C.australis and the transcriptomes of Cuscuta pentagona.The higher transcriptional level in old stems is consistent with its putative function in secondary metabolism by stabilizing anthocyanin at neutral pH and thus HGT of this AT-like gene may have improved biotic and abiotic resistance of Cuscuta.
基金supported by the National Key Research and Development Program of China(2017YFA0604904)the Zhejiang Provincial Natural Science Foundation of China(LR21D060003)to Z.H.
文摘Horizontal gene transfer(HGT)is a common occurrence across all domains of life.However,most HGT events were reported between single-celled organisms or parasites and hosts(Van Etten and Bhattacharya 2020).A type II antifreeze protein(AFP)gene was the first and sole evidence of HGT direct vertebrate-to-vertebrate DNA transmission.AFP is only found in 3 widely separated branches of teleost fishes(herring,sea raven,and smelts),sharing amino acid similarity up to 80%(Graham et al.2008).
文摘近年来,土壤环境中抗生素抗性基因(ARGs)污染引起广泛关注。以Web of Science核心数据库和万方数据库文献资料为数据源进行文献计量学分析,从年发文量变化、不同国家贡献及研究主题演变(基于关键词)等方面对土壤环境中ARGs污染相关研究进行剖析,以此探讨国内外该领域的研究现状、热点和发展。结果表明,土壤中ARGs污染相关研究的发文数量快速增长。我国文献在发文数量、论文被引频次方面具有重要影响,表明我国在该领域有较强的国际学术影响力。关键词聚类分析表明该领域的研究方向主要集中在以下5个方面:(1)土壤中携带ARGs的微生物及其环境行为;(2)土壤环境中ARGs的来源和持久性;(3)土壤环境中ARGs的传播和消减方法;(4)土壤中共存物质对ARGs丰度和迁移行为的影响;(5)农业生产活动对土壤环境中ARGs污染的影响。同时,在介绍ARGs常用检测方法以及土壤环境中ARGs污染来源和分布的基础上,剖析影响ARGs在土壤中传播的多种因素,探讨土壤环境中ARGs的消减方法,并指出当前研究尚存的不足之处以及今后的研究方向。该文可为未来土壤环境中ARGs污染领域的研究和风险管控提供参考。
基金The National Natural Science Foundation of China under contract No.41476171the Chinese Polar Environment Comprehensive Investigation and Assessment Program under contract No.CHINARE04-01
文摘Dimethylsulfoniopropionate(DMSP) is mainly produced by marine phytoplankton as an osmolyte, antioxidant,predator deterrent, or cryoprotectant. DMSP is also an important carbon and sulfur source for marine bacteria.Bacteria may metabolize DMSP via the demethylation pathway involving the DMSP demethylase gene(dmdA) or the cleavage pathway involving several different DMSP lyase genes. Most DMSP released into seawater is degraded by bacteria via demethylation. To test a hypothesis that the high gene frequency of dmdA among major marine taxa results in part from horizontal gene transfer(HGT) events, a total of thirty-one bacterial strains were isolated from Arctic Kongsfjorden seawater in this study. Analysis of 16S rRNA gene sequences showed that,except for strains BSw22118, BSw22131 and BSw22132 belonging to the genera Colwellia, Pseudomonas and Glaciecola, respectively, all bacteria fell into the genus Pseudoalteromonas. DmdA genes were detected in five distantly related bacterial strains, including four Arctic strains(Pseudoalteromonas sp. BSw22112, Colwellia sp.BSw22118, Pseudomonas sp. BSw22131 and Glaciecola sp. BSw22132) and one Antarctic strain(Roseicitreum antarcticum ZS2–28). Their dmdA genes showed significant similarities(97.7%–98.3%) to that of Ruegeria pomeroyi DSS–3, which was originally isolated from temperate coastal seawater. In addition, the sequence of the gene transfer agent(GTA) capsid protein gene(g5) detected in Antarctic strain ZS2–28 exhibited a genetically closely related to that of Ruegeria pomeroyi DSS–3. Among the five tested strains, only Pseudomonas sp. BSw22131 could grow using DMSP as the sole carbon source. The results of this study support the hypothesis of HGT for dmdA among taxonomically heterogeneous bacterioplankton, and suggest a wide distribution of functional gene(i.e., dmdA) in global marine environments.
基金supported by the National Natural Science Foundation of China(Nos.31470539 and U1805244)the Second Tibetan Plateau Scientific Expedition and Research Program(STEP)(No.2019QZKK0503)+1 种基金the 9th China-Croatia Science and Technology cooperation committee program(No.9–21)supported by the China Scholarship Council(No.201804910668)。
文摘Rapid urbanization has resulted in pervasive occurrence of antibiotic resistance genes(ARGs)in urban aquatic ecosystems.However,limited information is available concerning the ARG profiles and the forces responsible for their assembly in urban landscape lagoon systems.Here,we employed high-throughput quantitative PCR(HT-q PCR)to characterize the spatial variations of ARGs in surface and core sediments of Yundang Lagoon,China.The results indicated that the average richness and absolute abundance of ARGs were 11 and 53 times higher in the lagoon sediments as compared to pristine reference Tibetan lake sediments,highlighting the role of anthropogenic activities in ARG pollution.Co-occurrence network analysis indicated that various anaerobic prokaryotic genera belonging to Alpha-,Deltaproteobacteria,Bacteroidetes,Euryarchaeota,Firmicutes and Synergistetes were the potential hosts of ARGs.The partial least squares-path modeling(PLS-PM)analysis revealed positive and negative indirect effects of physicochemical factors and heavy metals on the lagoon ARG profiles,via biotic factors,respectively.The horizontal(mediated by mobile genetic elements)and vertical(mediated by prokaryotic communities)gene transfer may directly contribute the most to drive the abundance and composition of ARGs,respectively.Furthermore,the neutral community model demonstrated that the assembly of sediment ARG communities was jointly governed by deterministic and stochastic processes.Overall,this study provides novel insights into the diversity and distribution of ARGs in the benthic habitat of urban lagoon systems and underlying mechanisms for the spread and proliferation of ARGs.
基金This work was partially supported by the Natural Science Foundation of China,the Special Funds for Major State Basic Research Project,the Innovation Project of the Chinese Academy of Sciences,and the Major Innovation Research Project"248"of Beijing Munic
文摘The diversity and classification of microbes has been a long-standing issue.Molecular phylogeny of the prokaryotes based on comparison of the 16S rRNA sequences of the small ribosomal subunit has led to a reasonable tree of life in the late 1970s. How-ever, the availability of more and more complete bacterial genomes has brought about complications instead of refinement of the tree. In particular, it turns out that different choice of genes may tell different history. This might be caused by possible horizontal gene transfer (HGT) among species. There is an urgent need to develop phylogenetic methods that make use of whole genome data. We describe a new approach in molecular phylogeny,namely, tree construction based on K-tuple frequency analysis of the genomic sequences.Putting aside the technicalities, we emphasize the transition from randomness to determin-ism when the string length K increases and try to comment on the challenge mentioned in the title.
