Dear Editor ：The sustainable cultivation of rice, which serves as staple food crop for more than half of the world＇s population, is under serious threat due to the huge yield losses inflicted by rice blast disease c...Dear Editor ：The sustainable cultivation of rice, which serves as staple food crop for more than half of the world＇s population, is under serious threat due to the huge yield losses inflicted by rice blast disease caused by the globally destructive fungus Magnaporthe oryzae （Pyricularia oryzae） （Dean et al., 2012; Nalley et al., 2016; Deng et al., 2017）. This filamentous ascomycete fungus is also capable of causing blast infection on other economically important cereal crops, including wheat, millet, and barley, making it the world＇s most important plant pathogenic fungus （Zhong et al., 2016）.展开更多
Cylasformicarius is one of the most important pests of sweet potato worldwide, causing considerable ecological and economic damage.This study improved the effect of comprehensive management and understanding of geneti...Cylasformicarius is one of the most important pests of sweet potato worldwide, causing considerable ecological and economic damage.This study improved the effect of comprehensive management and understanding of genetic mechanisms by examining the functional genomics of C. formicarius.Using Illumina and PacBio sequencing, this study obtained a chromosome-level genome assembly of adult weevils from lines inbred for 15 generations.The high-quality assembly obtained was 338.84 Mb, with contig and scaffold N50 values of 14.97 and 34.23 Mb, respectively.In total, 157.51 Mb of repeat sequences and 11 907 protein-coding genes were predicted.A total of 337.06 Mb of genomic sequences was located on the 11 chromosomes, accounting for 99.03%of the total length of the associated chromosome.Comparative genomic analysis showed that C. formicarius was sister to Dendroctonus ponderosae, and C. formicarius diverged from D. ponderosae approximately 138.89 million years ago (Mya).Many important gene families expanded in the C. formicarius genome were involved in the detoxification of pesticides, tolerance to cold stress and chemosensory system.To further study the role of odorant-binding proteins (OBPs) in olfactory recognition of C. formicarius, the binding assay results indicated that Cfor OBP4–6 had strong binding affinities for sex pheromones and other ligands.The high-quality C. formicarius genome provides a valuable resource to reveal the molecular ecological basis, genetic mechanism, and evolutionary process of major agricultural pests;it also offers new ideas and new technologies for ecologically sustainable pest control.展开更多
The analysis of bacterial diversity in aquatic systems particularly in rivers, lakes, and streams can provide useful data on the effect of anthropogenic activities on such water bodies to humans and fishes. Idah River...The analysis of bacterial diversity in aquatic systems particularly in rivers, lakes, and streams can provide useful data on the effect of anthropogenic activities on such water bodies to humans and fishes. Idah River, the focal point of this study, is an offshoot of the two major Nigerian rivers characterized by observed human activities and pollution sources. Water samples were collected from four designated sites and assessed for their bacterial assemblages and structure, using PacBio Single-Molecule Real-Time (SMRT) sequencing technology. The full length of the 16S rRNA gene was sequenced, and Amplicon Sequence Variants were generated using the DADA2 workflow optimised for PacBio long-read amplicons in Rstudio. A total of 8751 high-quality reads obtained were taxonomically classified as 24 phyla, 42 classes, 84 orders, 125 families, 156 genera, and 106 species. Taxonomical composition revealed Proteobacteria as the most abundant phyla across all sample sites. At the genera level, Azospira (57.03%) was the most dominant ASV in Docking Point A, while Acinetobacter (66.67%) was the most abundant ASV in Docking Point B. In Idah Axis Confluence, hgcl clade (65.66%) was the most prevalent ASV, whereas Holophaga (42.86%) was the most common ASV in Idah Axis Midstream. Genera analysis also revealed that 12.9% of the total ASVs were discovered across all sample sites. Among these were pathogenic bacteria, reducers, and degraders of domestic and animal wastes. Observed results provide evidence that sampled sites of Idah River are contaminated, most likely through constant human activities and thus, could have an impact on resident fishes as well. This study, therefore, agrees with a previous report from the river, which used standard microbial procedures. However, next-generation sequencing techniques employed revealed more bacterial community than the former, including unresolved taxonomic sequences that may be novel.展开更多
Sulfate-reducing bacteria(SRB)are ubiquitous anaerobic microorganisms that play signifi cant roles in the global biogeochemical cycle.Coastal wetlands,one of the major habitats of SRB,exhibit high sulfate-reducing act...Sulfate-reducing bacteria(SRB)are ubiquitous anaerobic microorganisms that play signifi cant roles in the global biogeochemical cycle.Coastal wetlands,one of the major habitats of SRB,exhibit high sulfate-reducing activity and thus play signifi cant roles in organic carbon remineralization,benthic geochemical action,and plant-microbe interactions.Recent studies have provided credible evidence that the functional rather than the taxonomic composition of microbes responds more closely to environmental factors.Therefore,in this study,functional gene prediction based on PacBio single molecular real-time sequencing of 16S rDNA was applied to determine the sulfate-reducing and organic substrate-decomposing activities of SRB in the rhizospheres of two typical coastal wetland plants in North and South China:Zostera japonica and Scirpus mariqueter.To this end,some physicochemical characteristics of the sediments as well as the phylogenetic structure,community composition,diversity,and proportions of several functional genes of the SRB in the two plant rhizospheres were analyzed.The Z.japonic a meadow had a higher dissimilatory sulfate reduction capability than the S.mariqueter-comprising saltmarsh,owing to its larger proportion of SRB in the microbial community,larger proportions of functional genes involved in dissimilatory sulfate reduction,and the stronger ability of the SRB to degrade organic substrates completely.This study confi rmed the feasibility of applying microbial community function prediction in research on the metabolic features of SRB,which will be helpful for gaining new knowledge of the biogeochemical and ecological roles of these bacteria in coastal wetlands.展开更多
Molecular identification methods,in particular high-throughput sequencing tools,have greatly improved our knowledge about fungal diversity and biogeography,but many of the recovered taxa from natural environments cann...Molecular identification methods,in particular high-throughput sequencing tools,have greatly improved our knowledge about fungal diversity and biogeography,but many of the recovered taxa from natural environments cannot be identified to species or even higher taxonomic levels.This study addresses the phylogenetic placement of previously unrecognized fungal groups by using two complementary approaches:(i)third-generation amplicon sequencing analysis of DNA from global soil samples,screening out ITS reads of<90%similarity to other available Sanger sequences,and(ii)analysis of common fungal taxa that were previously indicated to be enigmatic in terms of taxonomic placement based on the ITS sequences alone(so-called top50 sequences).For the global soil samples,we chose to amplify the full rRNA gene operon using four partly overlapping amplicons and multiple newly developed primers or primer combinations that cover nearly all fungi and a vast majority of non-fungal eukaryotes.We extracted the rRNA 18S(SSU)and 28S(LSU)genes and performed phylogenetic analyses against carefully selected reference material.Both SSU and LSU analyses placed most soil sequences and top50 sequences to known orders and classes,but tens of monophyletic groups and single sequences remained outside described taxa.Furthermore,the LSU analyses recovered a few small groups of sequences that may potentially represent novel phyla.We conclude that rRNA genes-based phylogenetic analyses are efficient tools for determining phylogenetic relationships of fungal taxa that cannot be placed to any order or class using ITS sequences alone.However,in many instances,longer rRNA gene sequences and availability of both SSU and LSU reads are needed to improve taxonomic resolution.By leveraging third-generation sequencing from global soil samples,we successfully provided phylogenetic placement for many previously unidentified sequences and broadened our view on the fungal tree of life,with 10-20%new order-level taxa.In addition,the PacBio sequence data greatly extends fungal class-level information in reference databases.展开更多
Fungi are highly important biotic components of terrestrial ecosystems,but we still have a very limited understanding about their diversity and distribution.This data article releases a global soil fungal dataset of t...Fungi are highly important biotic components of terrestrial ecosystems,but we still have a very limited understanding about their diversity and distribution.This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium(GSMc)to boost further research in fungal diversity,biogeography and macroecology.The dataset comprises 722,682 fungal operational taxonomic units(OTUs)derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all continents.The plots are supplied with geographical and edaphic metadata.The OTUs are taxonomically and functionally assigned to guilds and other functional groups.The entire dataset has been corrected by excluding chimeras,index-switch artefacts and potential contamination.The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data.The GSMc dataset is available over the PlutoF repository.展开更多
Sepsis-induced liver injury(SILI)is an important cause of septicemia deaths.BaWeiBaiDuSan(BWBDS)was extracted from a formula of Panax ginseng C.A.Meyer,Lilium brownie F.E.Brown ex Miellez var.viridulum Baker,Polygonat...Sepsis-induced liver injury(SILI)is an important cause of septicemia deaths.BaWeiBaiDuSan(BWBDS)was extracted from a formula of Panax ginseng C.A.Meyer,Lilium brownie F.E.Brown ex Miellez var.viridulum Baker,Polygonatum sibiricum Delar.ex Redoute,Lonicera japonica Thunb.,Hippophae rhamnoides Linn.,Amygdalus Communis Vas,Platycodon grandiflorus(Jacq.)A.DC.,and Cortex Phelloderdri.Herein,we investigated whether the BWBDS treatment could reverse SILI by the mechanism of modulating gut microbiota.BWBDS protected mice against SILI,which was associated with promoting macrophage anti-inflammatory activity and enhancing intestinal integrity.BWBDS selectively promoted the growth of Lactobacillus johnsonii(L.johnsonii)in cecal ligation and puncture treated mice.Fecal microbiota transplantation treatment indicated that gut bacteria correlated with sepsis and was required for BWBDS anti-sepsis effects.Notably,L.johnsonii significantly reduced SILI by promoting macrophage anti-inflammatory activity,increasing interleukin-10+M2 macrophage production and enhancing intestinal integrity.Furthermore,heat inactivation L.johnsonii(HI-L.johnsonii)treatment promoted macrophage anti-inflammatory activity and alleviated SILI.Our findings revealed BWBDS and gut microbiota L.johnsonii as novel prebiotic and probiotic that may be used to treat SILI.The potential underlying mechanism was at least in part,via L.johnsonii-dependent immune regulation and interleukin-10+M2 macrophage production.展开更多
文摘Dear Editor ：The sustainable cultivation of rice, which serves as staple food crop for more than half of the world＇s population, is under serious threat due to the huge yield losses inflicted by rice blast disease caused by the globally destructive fungus Magnaporthe oryzae （Pyricularia oryzae） （Dean et al., 2012; Nalley et al., 2016; Deng et al., 2017）. This filamentous ascomycete fungus is also capable of causing blast infection on other economically important cereal crops, including wheat, millet, and barley, making it the world＇s most important plant pathogenic fungus （Zhong et al., 2016）.
基金supported by the Natural Science Foundation of Guangxi Autonomous Region,China(2022GXNSFAA035558)the Technology Development Foundation of Guangxi Academy of Agricultural Sciences(2021ZX09)+2 种基金the China Agriculture Research System of MOF and MARA(CARS-10-B3 and CARS-10-C19)the Guangxi Innovation Team Construction Project(nycytxgxcxtd-11-03)the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD),China。
文摘Cylasformicarius is one of the most important pests of sweet potato worldwide, causing considerable ecological and economic damage.This study improved the effect of comprehensive management and understanding of genetic mechanisms by examining the functional genomics of C. formicarius.Using Illumina and PacBio sequencing, this study obtained a chromosome-level genome assembly of adult weevils from lines inbred for 15 generations.The high-quality assembly obtained was 338.84 Mb, with contig and scaffold N50 values of 14.97 and 34.23 Mb, respectively.In total, 157.51 Mb of repeat sequences and 11 907 protein-coding genes were predicted.A total of 337.06 Mb of genomic sequences was located on the 11 chromosomes, accounting for 99.03%of the total length of the associated chromosome.Comparative genomic analysis showed that C. formicarius was sister to Dendroctonus ponderosae, and C. formicarius diverged from D. ponderosae approximately 138.89 million years ago (Mya).Many important gene families expanded in the C. formicarius genome were involved in the detoxification of pesticides, tolerance to cold stress and chemosensory system.To further study the role of odorant-binding proteins (OBPs) in olfactory recognition of C. formicarius, the binding assay results indicated that Cfor OBP4–6 had strong binding affinities for sex pheromones and other ligands.The high-quality C. formicarius genome provides a valuable resource to reveal the molecular ecological basis, genetic mechanism, and evolutionary process of major agricultural pests;it also offers new ideas and new technologies for ecologically sustainable pest control.
文摘The analysis of bacterial diversity in aquatic systems particularly in rivers, lakes, and streams can provide useful data on the effect of anthropogenic activities on such water bodies to humans and fishes. Idah River, the focal point of this study, is an offshoot of the two major Nigerian rivers characterized by observed human activities and pollution sources. Water samples were collected from four designated sites and assessed for their bacterial assemblages and structure, using PacBio Single-Molecule Real-Time (SMRT) sequencing technology. The full length of the 16S rRNA gene was sequenced, and Amplicon Sequence Variants were generated using the DADA2 workflow optimised for PacBio long-read amplicons in Rstudio. A total of 8751 high-quality reads obtained were taxonomically classified as 24 phyla, 42 classes, 84 orders, 125 families, 156 genera, and 106 species. Taxonomical composition revealed Proteobacteria as the most abundant phyla across all sample sites. At the genera level, Azospira (57.03%) was the most dominant ASV in Docking Point A, while Acinetobacter (66.67%) was the most abundant ASV in Docking Point B. In Idah Axis Confluence, hgcl clade (65.66%) was the most prevalent ASV, whereas Holophaga (42.86%) was the most common ASV in Idah Axis Midstream. Genera analysis also revealed that 12.9% of the total ASVs were discovered across all sample sites. Among these were pathogenic bacteria, reducers, and degraders of domestic and animal wastes. Observed results provide evidence that sampled sites of Idah River are contaminated, most likely through constant human activities and thus, could have an impact on resident fishes as well. This study, therefore, agrees with a previous report from the river, which used standard microbial procedures. However, next-generation sequencing techniques employed revealed more bacterial community than the former, including unresolved taxonomic sequences that may be novel.
基金Supported by the Scientifi c Research Fund of the Second Institute of Oceanography,Ministry of Natural Resources(MNR)(Nos.JB1906,JG1616,JG1910)the Zhejiang Qingshan Lake Innovation Platform for Marine Science and Technology(No.2017E80001)+4 种基金the Key Projects of Philosophy and Social Sciences Research,Ministry of Education(No.18JZD059)the National Key Technology Research and Development Program of the Ministry of Science and Technology of the China(No.2015BAD08B01)the State Key Laboratory of Satellite Ocean Environment Dynamics(No.SOEDZZ1902)the National Natural Science Foundation of China(No.41806136)the Project of Long Term Observation and Research Plan in the Changjiang Estuary and the Adjacent East China Sea(LORCE,14282)。
文摘Sulfate-reducing bacteria(SRB)are ubiquitous anaerobic microorganisms that play signifi cant roles in the global biogeochemical cycle.Coastal wetlands,one of the major habitats of SRB,exhibit high sulfate-reducing activity and thus play signifi cant roles in organic carbon remineralization,benthic geochemical action,and plant-microbe interactions.Recent studies have provided credible evidence that the functional rather than the taxonomic composition of microbes responds more closely to environmental factors.Therefore,in this study,functional gene prediction based on PacBio single molecular real-time sequencing of 16S rDNA was applied to determine the sulfate-reducing and organic substrate-decomposing activities of SRB in the rhizospheres of two typical coastal wetland plants in North and South China:Zostera japonica and Scirpus mariqueter.To this end,some physicochemical characteristics of the sediments as well as the phylogenetic structure,community composition,diversity,and proportions of several functional genes of the SRB in the two plant rhizospheres were analyzed.The Z.japonic a meadow had a higher dissimilatory sulfate reduction capability than the S.mariqueter-comprising saltmarsh,owing to its larger proportion of SRB in the microbial community,larger proportions of functional genes involved in dissimilatory sulfate reduction,and the stronger ability of the SRB to degrade organic substrates completely.This study confi rmed the feasibility of applying microbial community function prediction in research on the metabolic features of SRB,which will be helpful for gaining new knowledge of the biogeochemical and ecological roles of these bacteria in coastal wetlands.
基金funded by the Estonian Science Foundation(Grants PUT1399,PRG632,MOBERC21)。
文摘Molecular identification methods,in particular high-throughput sequencing tools,have greatly improved our knowledge about fungal diversity and biogeography,but many of the recovered taxa from natural environments cannot be identified to species or even higher taxonomic levels.This study addresses the phylogenetic placement of previously unrecognized fungal groups by using two complementary approaches:(i)third-generation amplicon sequencing analysis of DNA from global soil samples,screening out ITS reads of<90%similarity to other available Sanger sequences,and(ii)analysis of common fungal taxa that were previously indicated to be enigmatic in terms of taxonomic placement based on the ITS sequences alone(so-called top50 sequences).For the global soil samples,we chose to amplify the full rRNA gene operon using four partly overlapping amplicons and multiple newly developed primers or primer combinations that cover nearly all fungi and a vast majority of non-fungal eukaryotes.We extracted the rRNA 18S(SSU)and 28S(LSU)genes and performed phylogenetic analyses against carefully selected reference material.Both SSU and LSU analyses placed most soil sequences and top50 sequences to known orders and classes,but tens of monophyletic groups and single sequences remained outside described taxa.Furthermore,the LSU analyses recovered a few small groups of sequences that may potentially represent novel phyla.We conclude that rRNA genes-based phylogenetic analyses are efficient tools for determining phylogenetic relationships of fungal taxa that cannot be placed to any order or class using ITS sequences alone.However,in many instances,longer rRNA gene sequences and availability of both SSU and LSU reads are needed to improve taxonomic resolution.By leveraging third-generation sequencing from global soil samples,we successfully provided phylogenetic placement for many previously unidentified sequences and broadened our view on the fungal tree of life,with 10-20%new order-level taxa.In addition,the PacBio sequence data greatly extends fungal class-level information in reference databases.
基金the Estonian Science Foundation(Grant Nos.PRG632,PSG136,MOBTP198,PUT1170)Norway-Baltic EEA financial mechanism(Grant No.EMP442)RSF19-14-00038,DSFP-2021 and Novo Nordisk Fonden(Silva Nova).
文摘Fungi are highly important biotic components of terrestrial ecosystems,but we still have a very limited understanding about their diversity and distribution.This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium(GSMc)to boost further research in fungal diversity,biogeography and macroecology.The dataset comprises 722,682 fungal operational taxonomic units(OTUs)derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all continents.The plots are supplied with geographical and edaphic metadata.The OTUs are taxonomically and functionally assigned to guilds and other functional groups.The entire dataset has been corrected by excluding chimeras,index-switch artefacts and potential contamination.The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data.The GSMc dataset is available over the PlutoF repository.
基金funded by regular grants and joint grant(File No.0096/2018/A3,0111/2020/A3 and 0056/2020/AMJ)Dr.Neher’s Biophysics Laboratory for Innovative Drug Discovery(File No.001/2020/ALC)+4 种基金supported by the Macao Science and Technology Development Fundsupported by 2020 Young Qihuang Scholar funded by the National Administration of Traditional Chinese Medicinesupported by National Natural Science Foundation of China(82025036)supported by the Start-up Research Grant of University of Macao(SRG2022-00020-FHS,China)the Faculty of Health Science,University of Macao(Macao,China).
文摘Sepsis-induced liver injury(SILI)is an important cause of septicemia deaths.BaWeiBaiDuSan(BWBDS)was extracted from a formula of Panax ginseng C.A.Meyer,Lilium brownie F.E.Brown ex Miellez var.viridulum Baker,Polygonatum sibiricum Delar.ex Redoute,Lonicera japonica Thunb.,Hippophae rhamnoides Linn.,Amygdalus Communis Vas,Platycodon grandiflorus(Jacq.)A.DC.,and Cortex Phelloderdri.Herein,we investigated whether the BWBDS treatment could reverse SILI by the mechanism of modulating gut microbiota.BWBDS protected mice against SILI,which was associated with promoting macrophage anti-inflammatory activity and enhancing intestinal integrity.BWBDS selectively promoted the growth of Lactobacillus johnsonii(L.johnsonii)in cecal ligation and puncture treated mice.Fecal microbiota transplantation treatment indicated that gut bacteria correlated with sepsis and was required for BWBDS anti-sepsis effects.Notably,L.johnsonii significantly reduced SILI by promoting macrophage anti-inflammatory activity,increasing interleukin-10+M2 macrophage production and enhancing intestinal integrity.Furthermore,heat inactivation L.johnsonii(HI-L.johnsonii)treatment promoted macrophage anti-inflammatory activity and alleviated SILI.Our findings revealed BWBDS and gut microbiota L.johnsonii as novel prebiotic and probiotic that may be used to treat SILI.The potential underlying mechanism was at least in part,via L.johnsonii-dependent immune regulation and interleukin-10+M2 macrophage production.
