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
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
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
Microplastics(MPs)and antibiotic resistance genes(ARGs)pose significant challenges to the One Health framework due to their intricate and multifaceted ecological and environmental impacts.However,the understanding of ...Microplastics(MPs)and antibiotic resistance genes(ARGs)pose significant challenges to the One Health framework due to their intricate and multifaceted ecological and environmental impacts.However,the understanding of how MP properties influence ARG prevalence in mariculture sediments remains limited.Herein,the polystyrene(PS)and polyvinyl chloride(PVC)MPs with different sizes(20-120μm and 0.5-2.0 mm)were selected to evaluate their impacts and underlying mechanisms driving ARGs dissemination.The results showed that PS and PVC MPs increased the relative abundance of ARGs by 1.41-2.50-fold and 2.01-2.84-fold,respectively,compared with control,particularly high-risk genes.The polymer type effect was identified as more influential than the size effect in driving the sediment resistome evolution.PVC shifted the microbial community assembly from stochastic to deterministic processes,thus enriching ARG host pathogens.Furthermore,the highly hydrophobic PS not only recruited the host bacteria colonization but also facilitated ARG exchange within the plastisphere.The exogenous additives released by PVC(e.g.,heavy metals,bisphenol A,and tridecyl ester)and the particles synergistically promoted ARG conjugative transfer by inducing oxidative stress and enhancing cell membrane permeability.These findings revealed how MPs characteristics facilitated the spread of ARGs in marine benthic ecosystems,underscoring the importance of mitigating MPs pollution to maintain mariculture ecosystem health,prevent zoonotic diseases,and balance global mariculture with ecological health.展开更多
The escalating global dissemination of plasmid-mediated antibiotic resistance poses a formidable threat to global health.Conjugation stands as a pivotal mechanism for horizontal gene transfer among bacterial populatio...The escalating global dissemination of plasmid-mediated antibiotic resistance poses a formidable threat to global health.Conjugation stands as a pivotal mechanism for horizontal gene transfer among bacterial populations,facilitating the spread of antibiotic resistance genes(ARGs).Microelectrolysis has garnered attention as an efficacious strategy for mitigating antibiotic concentrations in wastewater,yet its potential impact on ARG horizontal transfer remain largely unexplored.This comprehensive investigation unveils that microelectrolysis not only influences but significantly accelerates the conjugative transfer of ARG-harboring plasmids.Remarkably,this phenomenon is corroborated at the microbial community scale,underscoring its ecological relevance.Alarmingly,the study highlights the vulnerability of intestinalmicroorganisms to acquire antibiotic resistance under electrolytic stimulation,posing heightened risks to both animal and human health.Delving deeper,the study elucidates the underlyingmechanisms responsible for this enhanced conjugative transfer.It reveals that microelectrolysis augments the abundance of mating-competent cells,triggers the generation of reactive oxygen species,inflicts modest membrane damage,and upregulates the expression of genes critical for conjugation.These findings collectively contribute to a more profound comprehension of the environmental dissemination dynamics and associated public health implications of ARGs in the context of wastewater treatment employing microelectrolytic technologies.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
Horizontal gene transfer(HGT)in the microbiome has profound consequences for human health and disease.The spread of antibiotic resistance genes,virulence,and pathogenicity determinants predominantly occurs by way of H...Horizontal gene transfer(HGT)in the microbiome has profound consequences for human health and disease.The spread of antibiotic resistance genes,virulence,and pathogenicity determinants predominantly occurs by way of HGT.Evidence exists of extensive horizontal transfer in the human gut microbiome.Phage transduction is a type of HGT event in which a bacteriophage transfers non-viral DNA from one bacterial host cell to another.The abundance of tailed bacteriophages in the human gut suggests that transduction could act as a significant mode of HGT in the gut microbiome.Here we review in detail the known mechanisms of phage-mediated HGT,namely specialized and generalized transduction,lateral transduction,gene-transfer agents,and molecular piracy,as well as methods used to detect phage-mediated HGT,and discuss its potential implications for the human gut microbiome.展开更多
Horizontal gene transfer （HGT） has long been considered as a principal force for an organism to gain novel genes in genome evolution. Homology search, phylogenetic analysis and nucleotide composition analysis are th...Horizontal gene transfer （HGT） has long been considered as a principal force for an organism to gain novel genes in genome evolution. Homology search, phylogenetic analysis and nucleotide composition analysis are three major objective approaches to arguably determine the occurrence and directionality of HGT. Here, 21 genes that possess the potential to horizontal transfer were acquired from the whole genome of Magnaporthe grisea according to annotation, among which three candidate genes （corresponding protein accession numbers are EAA55123, EAA47200 and EAA52136） were selected for further analysis. According to BLAST homology results, we subsequently conducted phylogenetic analysis of the three candidate HGT genes. Moreover, nucleotide composition analysis was conducted to further validate these HGTs. In addition, the functions of the three candidate genes were searched in COG database. Consequently, we conclude that the gene encoding protein EAA55123 is transferred from Clostridium perfringens. Another HGT event is between EAA52136 and a certain metazoan＇s corresponding gene, but the direction remains uncertain. Yet, EAA47200 is not a transferred gene.展开更多
Although strand-biased gene distribution （SGD） was described some two decades ago, the underlying molecular mechanisms and their relationship remain elusive. Its facets include, but are not limited to, the degree of...Although strand-biased gene distribution （SGD） was described some two decades ago, the underlying molecular mechanisms and their relationship remain elusive. Its facets include, but are not limited to, the degree of biases, the strand-preference of genes, and the influence of background nucleotide composition variations. Using a dataset composed of 364 non-redundant bacterial genomes, we sought to illus- trate our current understanding of SGD. First, when we divided the collection of bacterial genomes into non-polC and polC groups according to their possession of DnaE isoforms that correlate closely with taxonomy, the SGD of the polC group stood out more sig- nificantly than that of the non-polC group. Second, when examining horizontal gene transfer, coupled with gene functional conservation （essentiality） and expressivity （level of expression）, we realized that they all contributed to SGD. Third, we further demonstrated a weaker G-dominance on the leading strand of the non-polC group but strong purine dominance （both G and A） on the leading strand of the polC group. We propose that strand-biased nucleotide composition plays a decisive role for SGD since the polC-bearing genomes are not only AT-rich but also have pronounced purine-rich leading strands, and we believe that a special mutation spectrum that leads to a strong purine asymmetry and a strong strand-biased nucleotide composition coupled with functional selections for genes and their functions are both at work.展开更多
Alignment-based database search and sequence comparison are commonly used to detect horizontal gene transfer(HGT).However,with the rapid increase of sequencing depth,hundreds of thousands of contigs are routinely asse...Alignment-based database search and sequence comparison are commonly used to detect horizontal gene transfer(HGT).However,with the rapid increase of sequencing depth,hundreds of thousands of contigs are routinely assembled from metagenomics studies,which challenges alignment-based HGT analysis by overwhelming the known reference sequences.Detecting HGT by k-mer statistics thus becomes an attractive alternative.These alignment-free statistics have been demonstrated in high performance and efficiency in wholegenome and transcriptome comparisons.To adapt k-mer statistics for HGT detection,we developed two aggregative statistics T^(S)_(sum ) and T^(*)_(sum),which subsample metagenome contigs by their representative regions,and summarize the regional D^(S) _(2) and D^(*)_(2)metrics by their upper bounds.We systematically studied the aggregative statistics’power at different k-mer size using simulations.Our analysis showed that,in general,the power of T^(S)_(sum) and T^(*)_(sum) increases with sequencing coverage,and reaches a maximum power>80%at k=6,with 5%Type-I error and the coverage ratio>0.2x.The statistical power ofT^(S)_(sum) and T^(*)_(sum) was evaluated with realistic simulations of HGT mechanism,sequencing depth,read length,and base error.We expect these statistics to be useful distance metrics for identifying HGT in metagenomic studies.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
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 global dissemination of antibiotic resistance genes(ARGs),especially via plasmid-mediated horizontal transfer,is becoming a pervasive health threat.While our previous study found that herbicides can accelerate the...The global dissemination of antibiotic resistance genes(ARGs),especially via plasmid-mediated horizontal transfer,is becoming a pervasive health threat.While our previous study found that herbicides can accelerate the horizontal gene transfer(HGT)of ARGs in soil bacteria,the underlying mechanisms by which herbicides promote the HGT of ARGs across and within bacterial genera are still unclear.Here,the underlying mechanism associ-ated with herbicide-promoted HGT was analyzed by detecting intracellular reactive oxygen species(ROS)production,extracellular polymeric substance composition,cell membrane integrity and proton motive force combined with genome-wide RNA sequencing.Exposure to herbicides induced a series of the above bacterial responses to promote HGT except for the ROS response,including compact cell-to-cell contact by enhancing pilus-encoded gene expression and decreasing cell surface charge,increasing cell membrane permeability,and enhancing the proton motive force,providing additional power for DNA uptake.This study provides a mechanistic understanding of the risk of bacterial resistance spread promoted by herbicides,which elucidates a new perspective on nonantibiotic agrochemical acceleration of the HGT of ARGs.展开更多
Microorganisms play a critical role in the biotransformation of arsenic and the form which it exists in the environment. In this study, a methyl parathion-degrading bacterium Caballeronia jiangsuensis, isolated from a...Microorganisms play a critical role in the biotransformation of arsenic and the form which it exists in the environment. In this study, a methyl parathion-degrading bacterium Caballeronia jiangsuensis, isolated from an abandoned pesticide manufacturing plant, was used to analyze arsenic accumulation and transformation. The accumulation of trivalent organoarsenic compounds in C. jiangsuensis occurred to a greater extent than that of their pentavalent counterparts. The chromosome of C. jiangsuensis contains an arsenic gene island whose GC content is significantly lower than that of the genome, suggesting that the island was acquired via horizontal gene transfer. There was approximately 90%-99% similarity between the proteins encoded by the gene island and the corresponding sequence of the plasmid pkk5 from Burkholderia sp. KK1. The biotransformation of different arsenic species by C. jiangsuensis was subsequently analyzed. The results revealed that monomethylarsenic acid(MAs(Ⅴ)) was rapidly demethylated to arsenate with very small amounts of intermediate monomethylarsonous acid(MAs(Ⅲ)), whereas MAs(Ⅲ) was largely oxidized to MAs(Ⅴ) despite the occurrence of the gene arsI probably responsible for aerobic demethylation of MAs(Ⅲ) in C. jiangsuensis. In addition, dimethylarsenic acid was partly demethylated to arsenate. Horizontal gene transfer of ars operon from a plasmid to other bacteria represents an adaptation to a specific environment. This study provides a new perspective for understanding arsenic biogeochemical cycling.展开更多
Strigolactones(SLs)are not only phytohormones that influence multiple aspects of plant growth and development but also signaling molecules for interactions between plants and certain fungi or bacteria.In plants,the SL...Strigolactones(SLs)are not only phytohormones that influence multiple aspects of plant growth and development but also signaling molecules for interactions between plants and certain fungi or bacteria.In plants,the SL receptor is anα/β-hydrolase(ABH)encoded by the DWARF14(D14)/KARRIKIN INSENSITIVE2(KAl2)gene family,which is known to be derived from proteobacterial RsbQthrough horizontal gene transfer(HGT).In the phytopathogenic fungus Cryphonectria parasitica,another ABH named CpD14 was found to possess SL binding and hydrolytic activities and mediate SL responses,exhibiting potential SL perception functions.Here,we demonstrate that CpD14 and its homologs in Leotiomyceta fungi were derived from Actinobacteria through an independent HGT event,forming a distinct CpD14-like(CDL)family across fungi and bacteria.X-ray crystallography and structuralanalyses reveal that actinobacterial and fungal CDL proteins share a conserved core"α/βfold"domain with D14/KAl2/RsbQ but possess a unique lid domain.Biochemical assays show that both actinobacterial CDL and proteobacterial RsbQ can recognize and hydrolyze SLs,suggesting that they are pre-adapted for SL responses and potential perception.Both plant D14/KAl2 and fungal CDL proteins retained these functional activities,whereas they evolved distinct ligand specificities for SL structural variants.Collectively,this work reveals that independent HGT events from two bacterial groups provided plants and their interacting fungi with pre-adapted ABH proteins,which were deployed for SL perception or responses.展开更多
The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health.Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes(AR...The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health.Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes(ARGs)from environments to human beings.Phyllosphere ARGs have been indicated to be changed with plant species,yet the influence of plant cultivar on the phyllospheric resistome is still unclear.Here,we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing,respectively.We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs,mobile genetic elements(MGEs),microbiome and potential bacterial pathogens.The results showed that the cultivars did not affect the ARG abundance and composition,but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere.The relative abundance of potential bacterial pathogenswas significantly higher in the phyllosphere than that in soils.Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens.Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils.These findings extend our knowledge on the vegetable microbiomes,ARGs,and potential pathogens,suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.展开更多
Small non-protein coding micro-RNAs are regularly exported out of cells, both in health and disease. More than ninety percent of extracellular miRNAs are associated with lower-molecular-mass complexes bound to Argonau...Small non-protein coding micro-RNAs are regularly exported out of cells, both in health and disease. More than ninety percent of extracellular miRNAs are associated with lower-molecular-mass complexes bound to Argonaute 2 (Ago2), nucleophosmin-1 (NPM1) and high density lipoproteins (HDL), whereas the rest (~10%) are membrane-vesicle-encapsulated within exosomes, shedding microvesicles and apoptotic bodies. Regardless of the debate of the nature of circulating miRNA as byproducts of routine cell activities or mediators of cell-cell communication, proper understanding of the molecular behaviors of miRNA in health and disease, is expected to open a new gate for the discovery of new diagnostic tools and possibly therapeutic implementation in the near future.展开更多
Horizontal gene transfer （HGT） plays key roles in the evolution of pathogenetic bacteria, especially in pathogenetic associated genes. In this study, the evolutionary dynamics of Xanthomonas at species level were de...Horizontal gene transfer （HGT） plays key roles in the evolution of pathogenetic bacteria, especially in pathogenetic associated genes. In this study, the evolutionary dynamics of Xanthomonas at species level were determined by the comparative analysis of the complete genomes of 15 Xanthomonas strains. A concatenated multiprotein phyletic pattern and a dataset with Xanthomonas clusters of orthologous genes were constructed. Mathematical extrapolation estimates that the core genome will reach a minimum of about 1 547 genes while the pan-genome will increase up to 22 624 genes when sequencing 1 000 genomes. The HGT extent in this genus was assessed by using a Markov-based probabilistic method. The reconstructed gene gain/loss history, which contained several features consistent with biological observations, showed that nearly 60% of the Xanthomonas genes were acquired by HGT. A large fraction of variability was in the clade ancestor nodes and ＂leaves of the tree＂. Coexpression analysis suggested that the pathogenic and metabolic variation between Xanthomonas oryzae pv. oryzicola and Xanthomonas oryzae pv. oryzae might due to recently-transferred genes. Our results strongly supported that the gene gain/loss may play an important role in divergence and pathogenicity variation of Xanthomonas species.展开更多
Soil microbial fuel cells(MFCs),a novel ecosystem technology,have recently been intensively studied for antibiotic-polluted soils.However,actual agricultural soils are always contaminated by mixed pollutants,especiall...Soil microbial fuel cells(MFCs),a novel ecosystem technology,have recently been intensively studied for antibiotic-polluted soils.However,actual agricultural soils are always contaminated by mixed pollutants,especially plasticizers from extensively used agricultural plastic films.The aim of this study was to investigate the effects of di-2-ethylhexyl phthalate(DEHP),a representative plasticizer in soil,on the removal of sulfadiazine(SDZ),a frequently detected antibiotic in natural environments,and antibiotic resistance genes(ARGs)and microbial community in soil MFCs.Soil MFCs maintained a good antibiotic removal ability even under the influence of residual DEHP and achieved a higher removal performance at higher DEHP concentrations due to enhanced power generation.Specifically,a higher DEHP concentration had a favorable effect on antibiotic removal in soil MFCs,with the SDZ concentration decreased in both the upper and lower layers(from 4.867±0.221 to 0.268±0.021 and 0.293±0.047 mg kg^(-1),respectively)of polluted soils.Moreover,a high DEHP concentration significantly promoted the abundance of bacteria associated with electricity generation compared with a lower DEHP concentration,resulting in the promotion of extracellular electron transfer and enhancing SDZ degradation.The increased ARG abundance may be caused by the enrichment of ARG potential hosts brought about by high DEHP concentration,likely due to the increased conjugative transfer frequencies of plasmid RP4 by decreasing cell membrane permeability and increasing reactive oxygen species content.The results revealed the ecological risk of residual DEHP in soil that promotes ARG transmission in soil MFCs,although it has the potential to reduce SDZ toxicity through horizontal gene transfer.We also highlight concerns regarding the management of antibiotics and plasticizers in soil.The negative effects of plasticizers on antibiotic removal should be carefully evaluated when using soil MFCs for the in-situ remediation of antibiotic-contaminated soil.展开更多
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.
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.
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).
基金was supported by the National Natural Science Foundation of China(42077115,42377238,42307515)the National Science Fund for Distinguished Young Scholars of Shandong Province(ZR2021JQ13)+1 种基金the Hainan Provincial Key Research and Development Projects(ZDYF2022SHFZ018)the Postdoctoral Fellowship Program of CPSF(GZC20232496).
文摘Microplastics(MPs)and antibiotic resistance genes(ARGs)pose significant challenges to the One Health framework due to their intricate and multifaceted ecological and environmental impacts.However,the understanding of how MP properties influence ARG prevalence in mariculture sediments remains limited.Herein,the polystyrene(PS)and polyvinyl chloride(PVC)MPs with different sizes(20-120μm and 0.5-2.0 mm)were selected to evaluate their impacts and underlying mechanisms driving ARGs dissemination.The results showed that PS and PVC MPs increased the relative abundance of ARGs by 1.41-2.50-fold and 2.01-2.84-fold,respectively,compared with control,particularly high-risk genes.The polymer type effect was identified as more influential than the size effect in driving the sediment resistome evolution.PVC shifted the microbial community assembly from stochastic to deterministic processes,thus enriching ARG host pathogens.Furthermore,the highly hydrophobic PS not only recruited the host bacteria colonization but also facilitated ARG exchange within the plastisphere.The exogenous additives released by PVC(e.g.,heavy metals,bisphenol A,and tridecyl ester)and the particles synergistically promoted ARG conjugative transfer by inducing oxidative stress and enhancing cell membrane permeability.These findings revealed how MPs characteristics facilitated the spread of ARGs in marine benthic ecosystems,underscoring the importance of mitigating MPs pollution to maintain mariculture ecosystem health,prevent zoonotic diseases,and balance global mariculture with ecological health.
基金supported by Jiangsu Agriculture Science and Technology Innovation Fund(No.CX(22)3001)。
文摘The escalating global dissemination of plasmid-mediated antibiotic resistance poses a formidable threat to global health.Conjugation stands as a pivotal mechanism for horizontal gene transfer among bacterial populations,facilitating the spread of antibiotic resistance genes(ARGs).Microelectrolysis has garnered attention as an efficacious strategy for mitigating antibiotic concentrations in wastewater,yet its potential impact on ARG horizontal transfer remain largely unexplored.This comprehensive investigation unveils that microelectrolysis not only influences but significantly accelerates the conjugative transfer of ARG-harboring plasmids.Remarkably,this phenomenon is corroborated at the microbial community scale,underscoring its ecological relevance.Alarmingly,the study highlights the vulnerability of intestinalmicroorganisms to acquire antibiotic resistance under electrolytic stimulation,posing heightened risks to both animal and human health.Delving deeper,the study elucidates the underlyingmechanisms responsible for this enhanced conjugative transfer.It reveals that microelectrolysis augments the abundance of mating-competent cells,triggers the generation of reactive oxygen species,inflicts modest membrane damage,and upregulates the expression of genes critical for conjugation.These findings collectively contribute to a more profound comprehension of the environmental dissemination dynamics and associated public health implications of ARGs in the context of wastewater treatment employing microelectrolytic technologies.
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.
基金financial support from Science Foundation Ireland[grant number SFI/12/RC/2273_P2]and Wellcome Trust under a Wellcome Trust Research Career Development Fellowship[220646/Z/20/Z](A.N.S.)whole,or in part,by the Wellcome Trust[220646/Z/20/Z].
文摘Horizontal gene transfer(HGT)in the microbiome has profound consequences for human health and disease.The spread of antibiotic resistance genes,virulence,and pathogenicity determinants predominantly occurs by way of HGT.Evidence exists of extensive horizontal transfer in the human gut microbiome.Phage transduction is a type of HGT event in which a bacteriophage transfers non-viral DNA from one bacterial host cell to another.The abundance of tailed bacteriophages in the human gut suggests that transduction could act as a significant mode of HGT in the gut microbiome.Here we review in detail the known mechanisms of phage-mediated HGT,namely specialized and generalized transduction,lateral transduction,gene-transfer agents,and molecular piracy,as well as methods used to detect phage-mediated HGT,and discuss its potential implications for the human gut microbiome.
基金supported in part by grants from the National Natural Science Foundation of China (General Programs No. 30270331 and No. 30670469)Director Fund of the State Key Laboratory of Oral Diseases (Sichuan University)+1 种基金the Science and Technology Fund for Distinguished Young Scholars of Sichuan Province (No.06ZQ026-035)the Key Technologies R&D Program of Sichuan Province (2006Z08-010)
文摘Horizontal gene transfer （HGT） has long been considered as a principal force for an organism to gain novel genes in genome evolution. Homology search, phylogenetic analysis and nucleotide composition analysis are three major objective approaches to arguably determine the occurrence and directionality of HGT. Here, 21 genes that possess the potential to horizontal transfer were acquired from the whole genome of Magnaporthe grisea according to annotation, among which three candidate genes （corresponding protein accession numbers are EAA55123, EAA47200 and EAA52136） were selected for further analysis. According to BLAST homology results, we subsequently conducted phylogenetic analysis of the three candidate HGT genes. Moreover, nucleotide composition analysis was conducted to further validate these HGTs. In addition, the functions of the three candidate genes were searched in COG database. Consequently, we conclude that the gene encoding protein EAA55123 is transferred from Clostridium perfringens. Another HGT event is between EAA52136 and a certain metazoan＇s corresponding gene, but the direction remains uncertain. Yet, EAA47200 is not a transferred gene.
基金supported by grants from Knowledge Innovation Program of the Chinese Academy of Sciences(Grant No.KSCX2-EW-R-01-04)Natural Science Foundation of China(Grant No.90919024 and 30900831)+2 种基金the Ministry of Science and Technology of China as the National Science and Technology Key Project (Grant No.2008ZX10004-013)the Special Foundation Work Program(Grant No.2009FY120100)the National Basic Research Program(Grant No. 2011CB944100)
文摘Although strand-biased gene distribution （SGD） was described some two decades ago, the underlying molecular mechanisms and their relationship remain elusive. Its facets include, but are not limited to, the degree of biases, the strand-preference of genes, and the influence of background nucleotide composition variations. Using a dataset composed of 364 non-redundant bacterial genomes, we sought to illus- trate our current understanding of SGD. First, when we divided the collection of bacterial genomes into non-polC and polC groups according to their possession of DnaE isoforms that correlate closely with taxonomy, the SGD of the polC group stood out more sig- nificantly than that of the non-polC group. Second, when examining horizontal gene transfer, coupled with gene functional conservation （essentiality） and expressivity （level of expression）, we realized that they all contributed to SGD. Third, we further demonstrated a weaker G-dominance on the leading strand of the non-polC group but strong purine dominance （both G and A） on the leading strand of the polC group. We propose that strand-biased nucleotide composition plays a decisive role for SGD since the polC-bearing genomes are not only AT-rich but also have pronounced purine-rich leading strands, and we believe that a special mutation spectrum that leads to a strong purine asymmetry and a strong strand-biased nucleotide composition coupled with functional selections for genes and their functions are both at work.
基金L.C.X.was supported by the Innovation in Cancer Informatics Fund.
文摘Alignment-based database search and sequence comparison are commonly used to detect horizontal gene transfer(HGT).However,with the rapid increase of sequencing depth,hundreds of thousands of contigs are routinely assembled from metagenomics studies,which challenges alignment-based HGT analysis by overwhelming the known reference sequences.Detecting HGT by k-mer statistics thus becomes an attractive alternative.These alignment-free statistics have been demonstrated in high performance and efficiency in wholegenome and transcriptome comparisons.To adapt k-mer statistics for HGT detection,we developed two aggregative statistics T^(S)_(sum ) and T^(*)_(sum),which subsample metagenome contigs by their representative regions,and summarize the regional D^(S) _(2) and D^(*)_(2)metrics by their upper bounds.We systematically studied the aggregative statistics’power at different k-mer size using simulations.Our analysis showed that,in general,the power of T^(S)_(sum) and T^(*)_(sum) increases with sequencing coverage,and reaches a maximum power>80%at k=6,with 5%Type-I error and the coverage ratio>0.2x.The statistical power ofT^(S)_(sum) and T^(*)_(sum) was evaluated with realistic simulations of HGT mechanism,sequencing depth,read length,and base error.We expect these statistics to be useful distance metrics for identifying HGT in metagenomic studies.
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 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 supported by the National Natural Science Foundation of China(31972521)the Fujian Agriculture and Forest University Program for Distinguished Young Scholar(No.XJQ2017001).
文摘The global dissemination of antibiotic resistance genes(ARGs),especially via plasmid-mediated horizontal transfer,is becoming a pervasive health threat.While our previous study found that herbicides can accelerate the horizontal gene transfer(HGT)of ARGs in soil bacteria,the underlying mechanisms by which herbicides promote the HGT of ARGs across and within bacterial genera are still unclear.Here,the underlying mechanism associ-ated with herbicide-promoted HGT was analyzed by detecting intracellular reactive oxygen species(ROS)production,extracellular polymeric substance composition,cell membrane integrity and proton motive force combined with genome-wide RNA sequencing.Exposure to herbicides induced a series of the above bacterial responses to promote HGT except for the ROS response,including compact cell-to-cell contact by enhancing pilus-encoded gene expression and decreasing cell surface charge,increasing cell membrane permeability,and enhancing the proton motive force,providing additional power for DNA uptake.This study provides a mechanistic understanding of the risk of bacterial resistance spread promoted by herbicides,which elucidates a new perspective on nonantibiotic agrochemical acceleration of the HGT of ARGs.
基金supported by the National Natural Science Foundation of China(Nos.42077289,42277197,and 41877422).
文摘Microorganisms play a critical role in the biotransformation of arsenic and the form which it exists in the environment. In this study, a methyl parathion-degrading bacterium Caballeronia jiangsuensis, isolated from an abandoned pesticide manufacturing plant, was used to analyze arsenic accumulation and transformation. The accumulation of trivalent organoarsenic compounds in C. jiangsuensis occurred to a greater extent than that of their pentavalent counterparts. The chromosome of C. jiangsuensis contains an arsenic gene island whose GC content is significantly lower than that of the genome, suggesting that the island was acquired via horizontal gene transfer. There was approximately 90%-99% similarity between the proteins encoded by the gene island and the corresponding sequence of the plasmid pkk5 from Burkholderia sp. KK1. The biotransformation of different arsenic species by C. jiangsuensis was subsequently analyzed. The results revealed that monomethylarsenic acid(MAs(Ⅴ)) was rapidly demethylated to arsenate with very small amounts of intermediate monomethylarsonous acid(MAs(Ⅲ)), whereas MAs(Ⅲ) was largely oxidized to MAs(Ⅴ) despite the occurrence of the gene arsI probably responsible for aerobic demethylation of MAs(Ⅲ) in C. jiangsuensis. In addition, dimethylarsenic acid was partly demethylated to arsenate. Horizontal gene transfer of ars operon from a plasmid to other bacteria represents an adaptation to a specific environment. This study provides a new perspective for understanding arsenic biogeochemical cycling.
基金supported in part by grants from the National Natural Science Foundation of China(NSFC)(32170242 and 32470244)the Youth Innovation Promotion Association CAS(2022398)+4 种基金the Yunnan Revitalization Talent Support Program"Young Talent"Project(XDYCQNRC-2022-0046)the Yunnan Fundamental Research Projects(202201AT070163)the Second Tibetan Plateau Scientific Expedition and Research(STEP)Program(2019QZKK0502)the National Key R&D Program of China(2024YFF1306700)the Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture(CE200100015).
文摘Strigolactones(SLs)are not only phytohormones that influence multiple aspects of plant growth and development but also signaling molecules for interactions between plants and certain fungi or bacteria.In plants,the SL receptor is anα/β-hydrolase(ABH)encoded by the DWARF14(D14)/KARRIKIN INSENSITIVE2(KAl2)gene family,which is known to be derived from proteobacterial RsbQthrough horizontal gene transfer(HGT).In the phytopathogenic fungus Cryphonectria parasitica,another ABH named CpD14 was found to possess SL binding and hydrolytic activities and mediate SL responses,exhibiting potential SL perception functions.Here,we demonstrate that CpD14 and its homologs in Leotiomyceta fungi were derived from Actinobacteria through an independent HGT event,forming a distinct CpD14-like(CDL)family across fungi and bacteria.X-ray crystallography and structuralanalyses reveal that actinobacterial and fungal CDL proteins share a conserved core"α/βfold"domain with D14/KAl2/RsbQ but possess a unique lid domain.Biochemical assays show that both actinobacterial CDL and proteobacterial RsbQ can recognize and hydrolyze SLs,suggesting that they are pre-adapted for SL responses and potential perception.Both plant D14/KAl2 and fungal CDL proteins retained these functional activities,whereas they evolved distinct ligand specificities for SL structural variants.Collectively,this work reveals that independent HGT events from two bacterial groups provided plants and their interacting fungi with pre-adapted ABH proteins,which were deployed for SL perception or responses.
基金supported by the National Key Research and Development Plan from Ministry of Science and Technology of the People’s Republic of China(No.2020YFC1806902)the Alliance of International Science Organizations(No.ANSO-PA-2020-18).
文摘The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health.Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes(ARGs)from environments to human beings.Phyllosphere ARGs have been indicated to be changed with plant species,yet the influence of plant cultivar on the phyllospheric resistome is still unclear.Here,we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing,respectively.We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs,mobile genetic elements(MGEs),microbiome and potential bacterial pathogens.The results showed that the cultivars did not affect the ARG abundance and composition,but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere.The relative abundance of potential bacterial pathogenswas significantly higher in the phyllosphere than that in soils.Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens.Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils.These findings extend our knowledge on the vegetable microbiomes,ARGs,and potential pathogens,suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.
文摘Small non-protein coding micro-RNAs are regularly exported out of cells, both in health and disease. More than ninety percent of extracellular miRNAs are associated with lower-molecular-mass complexes bound to Argonaute 2 (Ago2), nucleophosmin-1 (NPM1) and high density lipoproteins (HDL), whereas the rest (~10%) are membrane-vesicle-encapsulated within exosomes, shedding microvesicles and apoptotic bodies. Regardless of the debate of the nature of circulating miRNA as byproducts of routine cell activities or mediators of cell-cell communication, proper understanding of the molecular behaviors of miRNA in health and disease, is expected to open a new gate for the discovery of new diagnostic tools and possibly therapeutic implementation in the near future.
基金supported by the Natural Science Foundation of Zhejiang Province of China (Y3090150)the Fundamental Research Funds for the Central Universities,China+4 种基金the Zhejiang Provincial Project, China (2010R10091)the Research Project for Commonweal Industry of Agricultural Ministry, China (nyhyzx 201003029 201003066)the Specialized Research Fund for the Doctoral Program of Higher Education, China (20090101120083)the Key Subject Construction Program for Modern Agricultural Biotechnology and Crop Disease Control of Zhejiang, China
文摘Horizontal gene transfer （HGT） plays key roles in the evolution of pathogenetic bacteria, especially in pathogenetic associated genes. In this study, the evolutionary dynamics of Xanthomonas at species level were determined by the comparative analysis of the complete genomes of 15 Xanthomonas strains. A concatenated multiprotein phyletic pattern and a dataset with Xanthomonas clusters of orthologous genes were constructed. Mathematical extrapolation estimates that the core genome will reach a minimum of about 1 547 genes while the pan-genome will increase up to 22 624 genes when sequencing 1 000 genomes. The HGT extent in this genus was assessed by using a Markov-based probabilistic method. The reconstructed gene gain/loss history, which contained several features consistent with biological observations, showed that nearly 60% of the Xanthomonas genes were acquired by HGT. A large fraction of variability was in the clade ancestor nodes and ＂leaves of the tree＂. Coexpression analysis suggested that the pathogenic and metabolic variation between Xanthomonas oryzae pv. oryzicola and Xanthomonas oryzae pv. oryzae might due to recently-transferred genes. Our results strongly supported that the gene gain/loss may play an important role in divergence and pathogenicity variation of Xanthomonas species.
基金supported by the National Natural Science Foundation of China(Nos.42477014 and 52070101)Huixiang Wang would like to acknowledge the Postgraduate Research Practice Innovation Program of Jiangsu Province,China(No.181200003023218)。
文摘Soil microbial fuel cells(MFCs),a novel ecosystem technology,have recently been intensively studied for antibiotic-polluted soils.However,actual agricultural soils are always contaminated by mixed pollutants,especially plasticizers from extensively used agricultural plastic films.The aim of this study was to investigate the effects of di-2-ethylhexyl phthalate(DEHP),a representative plasticizer in soil,on the removal of sulfadiazine(SDZ),a frequently detected antibiotic in natural environments,and antibiotic resistance genes(ARGs)and microbial community in soil MFCs.Soil MFCs maintained a good antibiotic removal ability even under the influence of residual DEHP and achieved a higher removal performance at higher DEHP concentrations due to enhanced power generation.Specifically,a higher DEHP concentration had a favorable effect on antibiotic removal in soil MFCs,with the SDZ concentration decreased in both the upper and lower layers(from 4.867±0.221 to 0.268±0.021 and 0.293±0.047 mg kg^(-1),respectively)of polluted soils.Moreover,a high DEHP concentration significantly promoted the abundance of bacteria associated with electricity generation compared with a lower DEHP concentration,resulting in the promotion of extracellular electron transfer and enhancing SDZ degradation.The increased ARG abundance may be caused by the enrichment of ARG potential hosts brought about by high DEHP concentration,likely due to the increased conjugative transfer frequencies of plasmid RP4 by decreasing cell membrane permeability and increasing reactive oxygen species content.The results revealed the ecological risk of residual DEHP in soil that promotes ARG transmission in soil MFCs,although it has the potential to reduce SDZ toxicity through horizontal gene transfer.We also highlight concerns regarding the management of antibiotics and plasticizers in soil.The negative effects of plasticizers on antibiotic removal should be carefully evaluated when using soil MFCs for the in-situ remediation of antibiotic-contaminated soil.
