Shigella species and Escherichia coli are closely related organisms. Early phenotyping experiments and several recent molecular studies put Shigella within the species E. coli. However, the whole-genome-based, alignme...Shigella species and Escherichia coli are closely related organisms. Early phenotyping experiments and several recent molecular studies put Shigella within the species E. coli. However, the whole-genome-based, alignment-free and parameter-free CVTree approach shows convincingly that four established Shigella species, Shigella boydii, Shigella sonnei, Shigella felxneri and Shigella dysenteriae, are distinct from E. coli strains, and form sister species to E. coli within the genus Esch- erichia. In view of the overall success and high resolution power of the CVTree approach, this result should be taken seriously. We hope that the present report may promote further in-depth study of the Shigella-E. coli relationship.展开更多
The full length cDNA sequence of CBF3 （CRT/DRE-binding factor） was cloned from Vitis amurensis by reverse transcription polymerase chain reaction （RT-PCR） using the primers designed based on CBF genes available in...The full length cDNA sequence of CBF3 （CRT/DRE-binding factor） was cloned from Vitis amurensis by reverse transcription polymerase chain reaction （RT-PCR） using the primers designed based on CBF genes available in GenBank. Sequence analysis showed that the gene had 854 bp long and its coding sequence contained 720 bp, encoding a protein with 239 amino acids and an AP2 structural domain. The molecular mass of CBF3 was predicted to be 25.9 kDa and its theoretical isoelectric point was 7.02 and aliphatic index was 59.29. The average hydropathicity of the protein was -0.551. The tertiary structures of CBF3 were also analyzed. The prokaryotic expression vector pGEX-4T-CBF3 containing CBF3 gene was constructed and CBF3 fusion protein （52 kDa） was produced in Escherichia coli after induction with 1 mmol L-1 IPTG. Further studies are needed to evaluate its potential application for improving plant resistance to cold and other stress condition such as drought and salinity.展开更多
We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacte-riologists' taxo...We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacte-riologists' taxonomy-primarily the latest online Outline of the Bergey's Manual of Systematic Bacteri-ology. The CVTree phylogeny agrees very well with the Bergey's taxonomy in majority of fine branchings and overall structures. At the same time most of the differences between the trees and the Manual have been known to biologists to some extent and may hint at taxonomic revisions. Instead of demonstrating the overwhelming agreement this paper puts emphasis on the biological implications of the differences.展开更多
热带—亚热带潮间带沉积物中丰富的菌—藻类微生物及其复杂的生命活动对颗粒的早期胶结过程起重要作用。本文通过16S r RNA高通量基因测序方法分析西沙群岛石屿、全富岛及海南龙湾珊瑚礁滨岸带海滩岩表生微生物群落结构,确定主导海滩岩...热带—亚热带潮间带沉积物中丰富的菌—藻类微生物及其复杂的生命活动对颗粒的早期胶结过程起重要作用。本文通过16S r RNA高通量基因测序方法分析西沙群岛石屿、全富岛及海南龙湾珊瑚礁滨岸带海滩岩表生微生物群落结构,确定主导海滩岩快速胶结的共性菌株/微生物功能群。表层生长草皮海藻的全富岛海滩岩原核生物多样性最高。龙湾潮间带上部暴露时间较长的海滩岩比潮间带下部海滩岩原核生物多样性高。相对固结的石屿海滩岩原核生物多样性最低。4个取样点具有较为相似的细菌门类组成,物种丰度由大到小依次为变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、放线菌门(Actinobacteriota)、蓝细菌门(Cyanobacteria)、绿弯菌门(Chloroflexi)、芽单胞菌门(Gemmatimonadota)和脱硫杆菌门(Desulfobacterota)。不同点位的海滩岩形成环境中蓝细菌主要种类大体相同,其中眉藻(Calothrixsp.)是主导海滩岩早期胶结的共性钙化菌株,通过分泌胞外聚合物成为碳酸盐矿物沉淀的“热点”。群落中检出的反硝化细菌和硫酸盐还原菌表明海滩岩内部氧化还原梯度较大,表面下极浅处即存在缺氧微环境。微生物群落内强烈的光合作用、硫酸盐还原作用和反硝化作用不断提高微环境pH值,有利碳酸盐矿物在粒间孔内的成核和生长并加速颗粒胶结。展开更多
Prokaryotes play a fundamental role in global ocean biogeochemical cycles.However,how the abundance and metabolic activity of ecologically distinct subgroups(i.e.,high nucleic acid(HNA)and low nucleic acid(LNA)cells),...Prokaryotes play a fundamental role in global ocean biogeochemical cycles.However,how the abundance and metabolic activity of ecologically distinct subgroups(i.e.,high nucleic acid(HNA)and low nucleic acid(LNA)cells),and their regulating factors,change in response to changing marine environmental conditions remains poorly understood.Here,we delved into the time-evolving dynamic responses of the HNA and LNA prokaryotic subgroups to declining resource availability and selective grazing by protozoa by conducting a 73-day incubation experiment in a large-volume(117,000 L)macrocosm that facilitates community-level exploration.We found that the metabolic activity of the HNA subgroup was higher than that of the LNA subgroup when the macrocosm was resource replete but that the HNA subgroup declined more rapidly than the LNA subgroup as the resources became increasingly scarce,leading to a steadily increasing contribution of LNA cells to prokaryotic activity.Meanwhile,as resources in the macrocosm became limited,protozoan grazing preference shifted from the HNA to the LNA subgroup and the contributions of the LNA subgroup to the carbon flow within the macrocosm increased.The findings highlight the resilience of LNA cells in resource-limited environments,illuminate the critical role of selective grazing by protozoa in balancing distinct prokaryotic subgroups under changing resource conditions,and demonstrate the complex and adaptive interactions between protozoa and prokaryotes across diverse environmental contexts.展开更多
Many investigations suggest that dissimilatory arsenate-respiring prokaryotes (DARPs) play a key role in stimulating reductive mobilization of As from solid phase into groundwater,but it is not clear how environmental...Many investigations suggest that dissimilatory arsenate-respiring prokaryotes (DARPs) play a key role in stimulating reductive mobilization of As from solid phase into groundwater,but it is not clear how environmental Mn(Ⅱ) affects the DARPs-mediated reductive mobilization of arsenic.To resolve this issue,we collected soil samples from a realgar tailingsaffected area.We found that there were diverse arsenate-respiratory reductase (arr) genes in the soils.The microbial communities had high arsenate-respiring activity,and were able to efficiently stimulate the reductive mobilization of As.Compared to the microcosms without Mn(Ⅱ),addition of 10 mmol/L Mn(Ⅱ) to the microcosms led to 23.99%-251.79% increases in the microbial mobilization of As,and led to 133.3%-239.2% increases in the abundances of arr genes.We further isolated a new cultivable DARP,Bacillus sp.F11,from the arseniccontaminated soils.It completely reduced 1 mmol/L As(V) in 5 days under the optimal reaction conditions.We further found that it was able to efficiently catalyze the reductive mobilization and release of As from the solid phase;the addition of 2 mmol/L Mn(Ⅱ) led to 98.49%-248.78% increases in the F11 cells-mediated reductive mobilization of As,and70.6%-104.4% increases in the arr gene abundances.These data suggest that environmental Mn(Ⅱ) markedly increased the DARPs-mediated reductive mobilization of As in arseniccontaminated soils.This work provided a new insight into the close association between the biogeochemical cycles of arsenic and manganese.展开更多
基金supported by the National Basic Research Program of China (973 Project, Grant No. 2007CB814800 and2013CB834100)the Shanghai Leading Academic Discipline Project (Grant No. B111)the National Key Laboratory of Applied Surface Physics and the Department of Physics, Fu-dan University
文摘Shigella species and Escherichia coli are closely related organisms. Early phenotyping experiments and several recent molecular studies put Shigella within the species E. coli. However, the whole-genome-based, alignment-free and parameter-free CVTree approach shows convincingly that four established Shigella species, Shigella boydii, Shigella sonnei, Shigella felxneri and Shigella dysenteriae, are distinct from E. coli strains, and form sister species to E. coli within the genus Esch- erichia. In view of the overall success and high resolution power of the CVTree approach, this result should be taken seriously. We hope that the present report may promote further in-depth study of the Shigella-E. coli relationship.
基金supported by the Fundamental Research Funds for the Central Universities,China(DL09EAQ02)the Natural Science Foundation of Heilongjiang Province and Harbin City,China(C200606nd and 2006RFQN005)
文摘The full length cDNA sequence of CBF3 （CRT/DRE-binding factor） was cloned from Vitis amurensis by reverse transcription polymerase chain reaction （RT-PCR） using the primers designed based on CBF genes available in GenBank. Sequence analysis showed that the gene had 854 bp long and its coding sequence contained 720 bp, encoding a protein with 239 amino acids and an AP2 structural domain. The molecular mass of CBF3 was predicted to be 25.9 kDa and its theoretical isoelectric point was 7.02 and aliphatic index was 59.29. The average hydropathicity of the protein was -0.551. The tertiary structures of CBF3 were also analyzed. The prokaryotic expression vector pGEX-4T-CBF3 containing CBF3 gene was constructed and CBF3 fusion protein （52 kDa） was produced in Escherichia coli after induction with 1 mmol L-1 IPTG. Further studies are needed to evaluate its potential application for improving plant resistance to cold and other stress condition such as drought and salinity.
文摘We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacte-riologists' taxonomy-primarily the latest online Outline of the Bergey's Manual of Systematic Bacteri-ology. The CVTree phylogeny agrees very well with the Bergey's taxonomy in majority of fine branchings and overall structures. At the same time most of the differences between the trees and the Manual have been known to biologists to some extent and may hint at taxonomic revisions. Instead of demonstrating the overwhelming agreement this paper puts emphasis on the biological implications of the differences.
文摘热带—亚热带潮间带沉积物中丰富的菌—藻类微生物及其复杂的生命活动对颗粒的早期胶结过程起重要作用。本文通过16S r RNA高通量基因测序方法分析西沙群岛石屿、全富岛及海南龙湾珊瑚礁滨岸带海滩岩表生微生物群落结构,确定主导海滩岩快速胶结的共性菌株/微生物功能群。表层生长草皮海藻的全富岛海滩岩原核生物多样性最高。龙湾潮间带上部暴露时间较长的海滩岩比潮间带下部海滩岩原核生物多样性高。相对固结的石屿海滩岩原核生物多样性最低。4个取样点具有较为相似的细菌门类组成,物种丰度由大到小依次为变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、放线菌门(Actinobacteriota)、蓝细菌门(Cyanobacteria)、绿弯菌门(Chloroflexi)、芽单胞菌门(Gemmatimonadota)和脱硫杆菌门(Desulfobacterota)。不同点位的海滩岩形成环境中蓝细菌主要种类大体相同,其中眉藻(Calothrixsp.)是主导海滩岩早期胶结的共性钙化菌株,通过分泌胞外聚合物成为碳酸盐矿物沉淀的“热点”。群落中检出的反硝化细菌和硫酸盐还原菌表明海滩岩内部氧化还原梯度较大,表面下极浅处即存在缺氧微环境。微生物群落内强烈的光合作用、硫酸盐还原作用和反硝化作用不断提高微环境pH值,有利碳酸盐矿物在粒间孔内的成核和生长并加速颗粒胶结。
基金supported by the National Natural Science Foundation of China(Grant Nos.42188102,41861144018)the Natural Science Foundation of Fujian Province of China(Grant No.2023J05017)+3 种基金the Marine Economic Development Special Fund Project of Fujian Province of China(Grant No.FJHJF-L-2022-11)supported by the China Postdoctoral Science Foundation(Grant No.2021M691863)supported by the Innovation Team Project of Universities in Guangdong Province(Grant No.2023KCXTD028)supported by the Ph.D.Fellowship of the State Key Laboratory of Marine Environmental Science at Xiamen University。
文摘Prokaryotes play a fundamental role in global ocean biogeochemical cycles.However,how the abundance and metabolic activity of ecologically distinct subgroups(i.e.,high nucleic acid(HNA)and low nucleic acid(LNA)cells),and their regulating factors,change in response to changing marine environmental conditions remains poorly understood.Here,we delved into the time-evolving dynamic responses of the HNA and LNA prokaryotic subgroups to declining resource availability and selective grazing by protozoa by conducting a 73-day incubation experiment in a large-volume(117,000 L)macrocosm that facilitates community-level exploration.We found that the metabolic activity of the HNA subgroup was higher than that of the LNA subgroup when the macrocosm was resource replete but that the HNA subgroup declined more rapidly than the LNA subgroup as the resources became increasingly scarce,leading to a steadily increasing contribution of LNA cells to prokaryotic activity.Meanwhile,as resources in the macrocosm became limited,protozoan grazing preference shifted from the HNA to the LNA subgroup and the contributions of the LNA subgroup to the carbon flow within the macrocosm increased.The findings highlight the resilience of LNA cells in resource-limited environments,illuminate the critical role of selective grazing by protozoa in balancing distinct prokaryotic subgroups under changing resource conditions,and demonstrate the complex and adaptive interactions between protozoa and prokaryotes across diverse environmental contexts.
基金supported by the General Programs (No. 41472219)the Foundations for Innovative Research Groups (No. 41521001) from the National Natural Science Foundation of China。
文摘Many investigations suggest that dissimilatory arsenate-respiring prokaryotes (DARPs) play a key role in stimulating reductive mobilization of As from solid phase into groundwater,but it is not clear how environmental Mn(Ⅱ) affects the DARPs-mediated reductive mobilization of arsenic.To resolve this issue,we collected soil samples from a realgar tailingsaffected area.We found that there were diverse arsenate-respiratory reductase (arr) genes in the soils.The microbial communities had high arsenate-respiring activity,and were able to efficiently stimulate the reductive mobilization of As.Compared to the microcosms without Mn(Ⅱ),addition of 10 mmol/L Mn(Ⅱ) to the microcosms led to 23.99%-251.79% increases in the microbial mobilization of As,and led to 133.3%-239.2% increases in the abundances of arr genes.We further isolated a new cultivable DARP,Bacillus sp.F11,from the arseniccontaminated soils.It completely reduced 1 mmol/L As(V) in 5 days under the optimal reaction conditions.We further found that it was able to efficiently catalyze the reductive mobilization and release of As from the solid phase;the addition of 2 mmol/L Mn(Ⅱ) led to 98.49%-248.78% increases in the F11 cells-mediated reductive mobilization of As,and70.6%-104.4% increases in the arr gene abundances.These data suggest that environmental Mn(Ⅱ) markedly increased the DARPs-mediated reductive mobilization of As in arseniccontaminated soils.This work provided a new insight into the close association between the biogeochemical cycles of arsenic and manganese.
