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Gut microbial interactions based on network construction and bacterial pairwise cultivation

Science China(Life Sciences) 2024年第8期67卷 1751-1762页

作者： Min-Zhi Jiang Chang Liu Chang Xu He Jiang Yulin Wang Shuang-Jiang Liu State Key laboratory of microbial Technology Shandong UniversityQingdao 266000China State Key laboratory of microbial Resources and Environmental Microbiology Research Center(EMRC)Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Association networks are widely applied for the prediction of bacterial interactions in studies of human gut ***,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated *** this study,we addressed this challenge by integrating in vitro time series network(TSN)associations and cocultivation of TSN taxon *** samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 *** cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs)were *** dynamics of bacteria growing on the YCFA agar were used to infer microbial association *** experimentally validate the interactions of taxon pairs in networks,we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank,respectively,for pairwise *** co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism(51.67%),followed by commensalism(21.67%),amensalism(18.33%),competition(5%)and exploitation(3.33%).Genome-centric analysis further revealed that the commensal gut bacteria(helpers and beneficiaries)might interact with each other via the exchanges of amino acids with high biosynthetic costs,short-chain fatty acids,and/or *** also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7%of these strains was significantly *** approach provides new insights into the gut microbiome complexity and microbial interactions in association *** work highlights that the positive relationships in gut microbial communities tend to be overestimated,and that amino acids,short-chain fatty acids,and vitamins are contributed to the positive relationships.

关键词： human gut microbiome gut microbial pairwise interaction co-culture association network microbial community

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Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales

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mLife 2024年第1期3卷 21-41页

作者： Vadakattu V.S.R.Gupta James M.Tiedje CSIRO Agriculture&Food UrrbraeSouth AustraliaAustralia Centre for microbial ecology Michigan State UniversityEast LansingMichiganUSA

The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures *** community structure is mainly a result of the inoculum(dispersal),the selective advantages of those organisms under the habitat-based environmental attributes,and the ability of those colonizers to sustain themselves over *** soil is protective,and its microbial inhabitants have long adapted to varied soil conditions,significant portions of the soil microbial community structure are likely ***,a substantial portion of the community will not correlate to often measured soil *** suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes:(i)those that supply energy,i.e.,organic carbon and electron acceptors;(i)environmental effectors or stressors,i.e.,pH,salt,drought,and toxic chemicals;(ii)macro-organism associations,i.e.,plants and their seasonality,animals and their fecal matter,and soil fauna;and(iv)nutrients,in order,N,P,and probably of lesser importance,other micronutrients,and *** relevance of drivers also varies with spatial and time scales,for example,aggregate to field to regional,and persistent to dynamic populations to transcripts,and with the extent of phylogenetic difference,hence phenotypic differences in organismal *** present a summary matrix to provide guidance on which drivers are important for particular studies,with special emphasis on a wide range of spatial and temporal scales,and illustrate this with genomic and population(rRNA gene)data from selected studies.

关键词： abundance community structure diversity functional microbiome microorganisms

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Recent advances in the culture-independent discovery of natural products using metagenomic approaches

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Chinese Journal of Natural Medicines 2024年第2期22卷 100-111页

作者： SHEN Yiping LIU Nan WANG Zongqiang laboratory of microbial Drug Discovery China Pharmaceutical UniversityNanjing 211198China

Natural products derived from bacterial sources have long been pivotal in the discovery of drug ***,the cultivation of only about 1%of bacteria in laboratory settings has left a significant portion of biosynthetic diversity hidden within the genomes of uncultured *** in sequencing technologies now enable the exploration of genetic material from these metagenomes through culture-independent *** approach involves extracting genetic sequences from environmental DNA and applying a hybrid methodology that combines functional screening,sequence tag-based homology screening,and bioinformatic-assisted chemical *** this process,numerous valuable natural products have been identified and synthesized from previously uncharted metagenomic *** paper provides an overview of the recent advancements in the utilization of culture-independent techniques for the discovery of novel biosynthetic gene clusters and bioactive small molecules within metagenomic libraries.

关键词： Metagenomics Culture-independent approach Natural product Functional screening Sequence tag-based homology screening Syn-BNP

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Mycorrhizal fungi mitigate nitrogen losses of an experimental grassland by facilitating plant uptake and soil microbial immobilization

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Pedosphere 2024年第2期34卷 399-410页

作者： Yangyang JIA Marcel G.A.VAN DER HEIJDEN Alain Y.VALZANO-HELD Markus JOCHER Florian WALDER Postdoctoral Mobile Station of ecology College of Ecology and EnvironmentXinjiang UniversityÜrümqi 830046China Research Group Plant-Soil Interactions AgroscopeZürich 8046Switzerland Research Group Climate and Agriculture AgroscopeZürich 8046Switzerland Department of Plant and microbial Biology University of ZürichZürich 8008Switzerland Research Group Soil Quality and Soil Use AgroscopeZürich 8046Switzerland

Nitrogen(N)is one of the most limited nutrients of terrestrial ecosystems,whose losses are prevented in tightly coupled cycles in finely tuned *** change-induced N enrichment through atmospheric deposition and application of vast amounts of fertilizer are now challenging the terrestrial N *** mycorrhizal fungi(AMF)are known drivers of plant-soil nutrient fluxes,but a comprehensive assessment of AMF involvement in N cycling under global change is still ***,we simulated N enrichment by fertilization(low/high)in experimental grassland microcosms under greenhouse conditions in the presence or absence of AMF and continuously monitored different N pathways over nine *** found that high N enrichment by fertilization decreased the relative abundance of legumes and the plant species dominating the plant community changed from grasses to forbs in the presence of AMF,based on aboveground *** presence of AMF always maintained plant N:phosphorus(P)ratios between 14 and 16,no matter how the soil N availability *** in plant N:P ratios due to the increased plant N and P uptake might thus be a primary pathway of AMF altering plant community ***,we constructed a comprehensive picture of AMF’s role in N cycling,highlighting that AMF reduced N losses primarily by mitigating N leaching,while N_(2)O emissions played a marginal *** mycorrhizal fungi reduced N_(2)O emissions directly through the promotion of N_(2)O-consuming *** underlying mechanism for reducing N leaching is mainly the AMF-mediated improved nutrient uptake and AMF-associated microbial *** results indicate that synergies between AMF and other soil microorganisms cannot be ignored in N cycling and that the integral role of AMF in N cycling terrestrial ecosystems can buffer the upcoming global changes.

关键词： N cycling N enrichment N uptake N:P ratio plant community structure symbiotic soil fungi

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Effect of initial ammonium concentration on a one-stage partial nitrification/anammox biofilm system:Nitrogen removal performance and the microbial community

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Journal of Environmental Sciences 2024年第9期143卷 176-188页

作者： Mengyu Zhou Yun Han Yang Zhuo Fen Yu Gaoyuan Hu Dangcong Peng School of Municipal and Environmental Engineering Xi’an University of Architecture and TechnologyXi’an 710055China Shaanxi Key laboratory of Environmental Engineering Xi’an University of Architecture and TechnologyXi’an 710055China Key laboratory of Northwest Water Resource Environment and EcologyMOEXi’an University of Architecture and TechnologyXi’an 710055China

One-stage partial nitrification coupled with anammox(PN/A)technology effectively reduces the energy consumption of a biological nitrogen removal *** nitrite-oxidizing bacteria(NOB)is essential for this technology to maintain efficient nitrogen removal *** ammonium concentration(IAC)affects the degree of inhibited *** this study,the effect of the IAC on a PN/A biofilm was investigated in a moving bed biofilm *** results showed that nitrogen removal efficiency decreased from 82.49%±1.90%to 64.57%±3.96%after the IAC was reduced from 60 to 20 mg N/L,while the nitrate production ratio increased from 13.87%±0.90%to 26.50%±3.76%.NOB activity increased to1,133.86 mg N/m^(2)/day after the IAC decreased,approximately 4-fold,indicating that the IAC plays an important inhibitory role in *** rate-limiting step in the mature biofilm of the PN/A system is the nitritation process and is not shifted by the *** analysis of the microbial community structure in the biofilm indicates that the IAC was the dominant factor in changes in community *** and *** were the main anammox bacteria,and Nitrosomonas and Nitrospira were the main AOB and NOB,*** did not affect the difference in growth between *** and ***,modulating the IAC promoted the PN/A process with efficient nitrogen removal performance at medium to low ammonium concentrations.

关键词： Biological nitrogen removal Partial nitrification Anammox Ammonium concentration Biofilm

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Variation in Bombyx mori immune response against fungal pathogen Beauveria bassiana with variability in cell wallβ-1,3-glucan

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Insect Science 2024年第1期31卷 211-224页

作者： Yulong Wang Zhen Liu Xuebing Yin Shihong Liu Kai Wang Rongjie Wan Haoran Chen Xinyang Li Bo Huang Anhui Provincial Key laboratory of microbial Pest Control Anhui Agricultural UniversityHefeiChina

Entomopathogenic fungi are protected by a cell wall with dynamic structure for adapting to various environmental conditions.β-1,3-Glucan recognition proteins activate the innate immune system of insects by recognizing surface molecules of ***,the associations between pathogenicity and the different components of entomopathogenic fungal cell walls remain *** Beauveria bassiana strains were selected that have significantly differing virulence against Bombyx *** molecular mechanisms underlying the immune response in *** were investigated using RNA sequencing,which revealed differences in the immune response to different *** strains at 12 h *** assays revealed thatβ-1,3-glucan content had an opposite trend to that of fungal virulence.β-1,3-Glucan injection upregulated BmβGRP4 expression and significantly reduced the virulence of the high-virulence strain but not that of the medium-virulence or low-virulence ***βGRP4 silencing in *** with RNA interference resulted in the opposite virulence pattern,indicating that the virulence of *** was affected by the cell walls’content ofβ-1,3-glucan,which could be recognized by Bmβ***,interference with the gene CnA(calcineurin catalytic A subunit)involved inβ-1,3-glucan synthesis eliminated differences in virulence between *** *** results indicate that strains of a single species of pathogenic fungi that have differing cell wall components are recognized differently by the innate immune system of ***.

关键词： ombyx mori BmβGRP4 innate immunity insect fungal pathogen virulence

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Roles of nanoparticles in arsenic mobility and microbial community composition in arsenic-enriched soils

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Journal of Environmental Sciences 2024年第4期138卷 301-311页

作者： Ting Luo Qining Zheng Jie Yu Weihao Liang Yan Sun Guixiang Quan Feng Zhou School of Environmental Science and Engineering Yancheng Institute of TechnologyYancheng 224051China Jiangsu Provincial Key laboratory of Coastal ecology and Pollution Control Yancheng 224051China School ofEnvironment and Civil Engineering Jiangnan UniversityWuxi 214122China

Environmental effects of nano remediation engineering of arsenic(As)pollution need to be *** this study,the roles of Fe_(2)O_(3)and TiO_(2)nanoparticles(NPs)on the microbial mediated As mobilization from As contaminated soil were *** addition of Fe_(2)O_(3)and TiO_(2)NPs restrained As(V)release,and stimulated As(Ⅲ)***(V)concentration decreased by 94% and 93% after Fe_(2)O_(3)addition,and decreased by 89% and 45% after Ti O_(2)addition compared to the Biotic and Biotic+Acetate(amended with sodium acetate)controls,*** maximum values of As(Ⅲ)were 20.5 and 27.1μg/L at 48 d after Fe_(2)O_(3)and TiO_(2)NPs addition,respectively,and were higher than that in Biotic+Acetate control(12.9μg/L).The released As co-precipitated with Fe in soils in the presence of Fe_(2)O_(3)NPs,but adsorbed on TiO_(2)NPs in the presence of TiO_(2)***,the addition of NPs amended with sodium acetate as the electron donor clearly promoted As(V)reduction induced by *** NPs addition changed the relative abundance of soil bacterial community,while Proteobacteria(42.8%-70.4%),Planctomycetes(2.6%-14.3%),and Firmicutes(3.5%-25.4%)were the dominant microorganisms in *** potential As/Fe reducing bacteria were related to Pseudomonas,Geobacter,Desulfuromonas,and *** addition of Fe_(2)O_(3)and TiO_(2)NPs induced to the decrease of arr A *** results indicated that the addition of NPs had a negative impact on soil microbial population in a long *** findings offer a relatively comprehensive assessment of Fe_(2)O_(3)and TiO_(2)NPs effects on As mobilization and soil bacterial communities.

关键词： Fe_(2)O_(3)and TiO_(2)nanoparticles Arsenic reduction Mobilization Functional gene microbial community

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Rational design of unrestricted pRN1 derivatives and their application in the construction of a dual plasmid vector system for Saccharolobus islandicus

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mLife 2024年第1期3卷 119-128页

作者： Pengpeng Zhao Xiaonan Bi Xiaoning Wang Xu Feng Yulong Shen Guanhua Yuan Qunxin She CRISPR and Archaea Biology Research Center State Key Laboratory of Microbial Technology and Microbial Technology InstituteShandong UniversityQingdaoChina

Saccharolobus islandicus REY15A represents one of the very few archaeal models with versatile genetic tools,which include efficient genome editing,gene silencing,and robust protein expression ***,plasmid vectors constructed for this crenarchaeon thus far are based solely on the pRN2 cryptic *** this plasmid coexists with pRN1 in its original host,early attempts to test pRN1-based vectors consistently failed to yield any stable host-vector system for *** hypothesized that this failure could be due to the occurrence of CRISPR immunity against pRN1 in this *** identified a putative target sequence in orf904 encoding a putative replicase on pRN1(target N1).Mutated targets(N1a,N1b,and N1c)were then designed and tested for their capability to escape the host CRISPR immunity by using a plasmid inter-ference *** results revealed that the original target triggered CRISPR immunity in this archaeon,whereas all three mutated targets did not,indicating that all the designed target mutations evaded host *** mutated targets were then incorporated into orf904 individually,yielding corresponding mutated pRN1 backbones with which shuttle plasmids were constructed(pN1aSD,pN1bSD,and pN1cSD).*** transformation revealed that pN1aSD and pN1bSD were functional shuttle vectors,but pN1cSD lost the capability for *** results indicate that the missense mutations in the conserved helicase domain in pN1c inactivated the *** further showed that pRN1-based and pRN2-based vectors were stably maintained in the archaeal cells either alone or in combination,and this yielded a dual plasmid system for genetic study with this important archaeal model.

关键词： archaeal genetics CRISPR-Cas CRISPR escape mutations dual plasmid vectors Saccharolobus-E.coli shuttle vectors

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Population genomic data reveal low genetic diversity,divergence and local adaptation among threatened Reeves's Pheasant(Syrmaticus reevesii)

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Avian Research 2024年第1期15卷 1-11页

作者： Qi Lu Pengcheng Wang Jiang Chang De Chen Shenghan Gao Jacob Hoglund Zhengwang Zhang Ministry of Education Key laboratory for Biodiversity Science and Ecological Engineering College of Life SciencesBeijing Normal UniversityBeijing100875China Jiangsu Key laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjing210023China State Key laboratory of Environmental Criteria and Risk Assessment Chinese Research Academy of Environmental SciencesBeijing100012China State Key laboratory of microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing100101China Department of ecology and Genetics Animal EcologyUppsala UniversityUppsalaSweden

Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened ***’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat *** is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened ***,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic ***,we identified candidate genes linked with adaptation across the current distribution of Reeves’s *** present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 *** also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those *** comparing with other threatened species,we found that Reeves’s Pheasants have low genetic *** of homozygosity suggest that the Shennongjia population has experienced serious *** demographic history results indicated that three populations experienced several declines during the glacial *** adaptative analysis among the populations identified 241 candidate genes under directional *** are involved in a large variety of processes,including the immune response and *** results suggest that the three populations should be considered as three different conservation *** current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.

关键词： Conservation genetics Local adaptation Pheasant Whole-genome sequencing

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Improved observation of colonized roots reveals the regulation of arbuscule development and senescence by drought stress in the arbuscular mycorrhizae of citrus

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Horticultural Plant Journal 2024年第2期10卷 425-436页

作者： Xilong Yin Wei Zhang Zengwei Feng Guangda Feng Honghui Zhu Qing Yao College of Horticulture South China Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Horticultural Crops(South China)Ministry of Agriculture and Rural AffairsGuangdong Province Key Laboratory of Microbial Signals and Disease ControlGuangzhouGuangdong 510642China Key laboratory of Agricultural Microbiomics and Precision Application Ministry of Agriculture and Rural AffairsGuangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationKey Laboratory of Agricultural MicrobiomicsState Key Laboratory of Applied Microbiology Southern ChinaGuangdong Microbial Culture Collection Center(GDMCC)Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

Citrus is the typical mycorrhizal fruit tree species establishing symbiosis with arbuscular mycorrhizal (AM) fungi. However, arbuscule development and senescence in colonized citrus roots, especially in response to drought stress, remain unclear, which is mainly due to the difficulty in clearing and staining lignified roots with the conventional method. Here, we improved the observation of colonized roots of citrus plants with the sectioning method, which enabled the clear observation of AM fungal structures. Furthermore, we investigated the effects of one week of drought stress on arbuscule development and senescence with the sectioning method. Microscopy observations indicated that drought stress significantly decreased mycorrhizal colonization (F%and M%) although it did not affect plant growth performance. Fluorescence probes (WGA 488 and/or Nile red) revealed that drought stress inhibited arbuscule development by increasing the percentage of arbuscules at the early stage and decreasing the percentages of arbuscules at the midterm and mature stages. Meanwhile, drought stress accelerated arbuscule senescence, which was characterized by the increased accumulation of neutral lipids. Overall, the sectioning method developed in this study enables the in-depth investigation of arbuscule status, and drought stress can inhibit arbuscule development but accelerate arbuscule senescence in the colonized roots of citrus plants. This study paves the way to elaborately dissecting the arbuscule dynamics in the roots of fruit tree species in response to diverse abiotic stresses.

关键词： Arbuscular mycorrhizae Citrus Drought stress Arbuscule development Arbuscule senescence Fruit tree species

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