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Beyond microbial carbon use efficiency

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National Science Review 2024年第4期11卷 33-35页

作者： Ke-Qing Xiao Chao Liang Zimeng Wang Jingjing Peng Yao Zhao Ming Zhang Mingyu Zhao Shuiqing Chen Yong-Guan Zhu Caroline L.Peacock State Key Lab of Urban and Regional Ecology Research Center for Eco-Environmental SciencesChinese Academy of Sciences University of Chinese Academy of Sciences Institute of Applied Ecology Chinese Academy of Sciences Department of environmental Science and Engineering Fudan University College of Resources and environmental Sciences China Agricultural University State Key laboratory of environmental Criteria and Risk Assessment Chinese Research Academy of Environmental Sciences State Key laboratory of Agricultural microbiology College of Resources and Environment Huazhong Agricultural University Key laboratory of Cenozoic Geology and Environment Institute of Geology and Geophysics Chinese Academy of Sciences School of Earth and Environment University of Leeds

Microbial carbon use efficiency (CUE)is defined as the proportion of microbial biomass growth C versus substrate C uptake, and thus provides a useful measure of microbially driven accumulation and loss of soil organic carbon (SOC)[1]. In a recent study published in Nature [2],the authors used a data-driven machinelearning approach to conclude that CUE promotes global SOC storage based on a positive correlation between CUE and SOC content and that, based on sensitivity analysis, CUE is at least four times as important as six other evaluated factors,namely plant C inputs, C input allocation, non-microbial C transfer, substrate decomposability, environmental modifications and vertical transport.

关键词： SOIL-CARBON ORGANIC-MATTER

Selenium-oxidizing Agrobacterium sp.T3F4 decreases arsenic uptake by Brassica rapa L.under a native polluted soil

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Journal of environmental Sciences 2024年第4期138卷 506-515页

作者： Lijin An Chunzhi Zhou Lipeng Zhao Ao Wei Yiting Wang Huimin Cui Shixue Zheng State Key laboratory of Agricultural microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China

Toxic arsenic(As)and trace element selenium(Se)are transformed by microorganisms but their complex interactions in soil-plant systems have not been fully understood.An Asand Se-oxidizing bacterium,Agrobacterium sp.T3F4,was applied to a native seleniferous As-polluted soil to investigate As/Se uptake by the vegetable Brassica rapa L.and As-Se interaction as mediated by strain T3F4.The Se content in the aboveground plants was significantly enhanced by 34.1%,but the As content was significantly decreased by 20.5% in the T3F4-inoculated pot culture compared to the control(P<0.05).Similar result was shown in treatment with additional 5 mg/kg of Se(IV)in soil.In addition,the As contents in roots were significantly decreased by more than 35% under T3F4 or Se(IV)treatments(P<0.05).Analysis of As-Se-bacterium interaction in a soil simulation experiment showed that the bioavailability of Se significantly increased and As was immobilized with the addition of the T3F4strain(P<0.05).Furthermore,an As/Se co-exposure hydroponic experiment demonstrated that As uptake and accumulation in plants was reduced by increasing Se(IV)concentrations.The 50% growth inhibition concentration(IC50)values for As in plants were increased about one-fold and two-fold under co-exposure with 5 and 10μmol/L Se(IV),respectively.In conclusion,strain T3F4 improves Se uptake but decreases As uptake by plants via oxidation of As and Se,resulting in decrease of soil As bioavailability and As/Se competitive absorption by plants.This provides a potential bioremediation strategy for Se biofortification and As immobilization in As-polluted soil.

关键词： Selenium oxidation Selenium biofortification Arsenite-oxidizing bacteria Arsenic immobilization Brassica rapa L

Alcohol solvent effect on the self-assembly behaviors of lignin oligomers

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Green Energy & Environment 2024年第4期9卷 597-603页

作者： Ya Ma Zhicheng Jiang Yafei Luo Xingjie Guo Xudong Liu Yiping Luo Bi Shi College of Biomass Science and Engineering Sichuan UniversityChengdu610065China National Engineering Research Center of Clean Technology in Leather Industry Sichuan UniversityChengdu610065China College of Pharmacy(International Academy of Targeted Therapeutics and Innovation) Chongqing University of Arts and SciencesChongqing402160China State Key laboratory of Utilization of Woody Oil Resource Hunan Academy of ForestryChangsha410004China CAS Key laboratory of environmental and Applied microbiology Environmental Microbiology Key Laboratory of Sichuan ProvinceChengdu Institute of BiologyChinese Academy of SciencesChengdu610041China

The interactions between lignin oligomers and solvents determine the behaviors of lignin oligomers self-assembling into uniform lignin nanoparticles(LNPs).Herein,several alcohol solvents,which readily interact with the lignin oligomers,were adopted to study their effects during solvent shifting process for LNPs’production.The lignin oligomers with widely distributed molecular weight and abundant guaiacyl units were extracted from wood waste(mainly consists of pine wood),exerting outstanding self-assembly capability.Uniform and spherical LNPs were generated in H_(2)O-n-propanol cosolvent,whereas irregular LNPs were obtained in H_(2)O-methanol cosolvent.The unsatisfactory self-assembly performance of the lignin oligomers in H_(2)O-methanol cosolvent could be attributed to two aspects.On one hand,for the initial dissolution state,the distinguishing Hansen solubility parameter and polarity between methanol solvent and lignin oligomers resulted in the poor dispersion of the lignin oligomers.On the other hand,strong hydrogen bonds between methanol solvent and lignin oligomers during solvent shifting process,hindered the interactions among the lignin oligomers for self-assembly.

关键词： Lignin oligomers Alcohol solvent Self-assembly LNPs Solvent effects

Staying hungry:a roadmap to harnessing central regulators of symbiotic nitrogen fixation under fluctuating nitrogen availability

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aBIOTECH 2024年第1期5卷 107-113页

作者： Lijin Qiao Jieshun Lin Takuya Suzaki Pengbo Liang State Key laboratory of Plant environmental Resilience College of Biological SciencesChina Agricultural UniversityBeijingChina MOA Key laboratory of Soil microbiology Rhizobium Research CenterChina Agricultural UniversityBeijingChina Department of Molecular Biology and Genetics Aarhus UniversityAarhusDenmark Faculty of Life and environmental Sciences University of TsukubaTsukubaIbarakiJapan Tsukuba Plant-Innovation Research Center University of TsukubaTsukubaIbarakiJapan

Legumes have evolved specific inventions to enhance nitrogen(N)acquisition by establishing symbiotic interactions with N-fixing rhizobial bacteria.Because symbiotic N fixation is energetically costly,legumes have developed sophisticated mechanisms to ensure carbon-nitrogen balance,in a variable environment,both locally and at the whole plant level,by monitoring nodule number,nodule development,and nodular nitrogenase activity,as well as controlling nodule senescence.Studies of the autoregulation of nodulation and regulation of nodulation by nodule inception(NIN)and NIN-LIKE PROTEINs(NLPs)have provided great insights into the genetic mechanisms underlying the nitrateinduced regulation of root nodulation for adapting to N availability in the rhizosphere.However,many aspects of N-induced pleiotropic regulation remain to be fully explained,such as N-triggered senescence in mature nodules.Wang et al.determined that this process is governed by a transcriptional network regulated by NAC-type transcription factors.Characterization and dissection of these soybean nitrogenassociated NAPs(SNAPs)transcription factor-mastered networks have yielded a roadmap for exploring how legumes rewire nodule functions across a range of N levels,laying the foundation for enhancing the growth of N-deprived crops in agricultural settings.

关键词： Symbiotic nitrogen fixation N-adapted nodulation Nodule senescence NIN NLPs SNAPs

Gut microbial interactions based on network construction and bacterial pairwise cultivation

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Science China Life Sciences 2024年第8期 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 University State Key laboratory of Microbial Resources and Environmental Microbiology Research Center (EMRC)Institute of MicrobiologyChinese Academy of Sciences University of Chinese Academy of Sciences

Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes.However,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria.In this study,we addressed this challenge by integrating in vitro time series network(TSN) associations and cocultivation of TSN taxon pairs.Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days.Enriched cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs) were recovered.Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks.To 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-cultures.The 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 vitamins.We 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 promoted.This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks.Our 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.

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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 pheasants.Reeves’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat loss.There is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened bird.Here,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic divergence.Furthermore,we identified candidate genes linked with adaptation across the current distribution of Reeves’s Pheasant.The present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 genes.We also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those populations.By comparing with other threatened species,we found that Reeves’s Pheasants have low genetic diversity.Runs of homozygosity suggest that the Shennongjia population has experienced serious inbreeding.The demographic history results indicated that three populations experienced several declines during the glacial period.Local adaptative analysis among the populations identified 241 candidate genes under directional selection.They are involved in a large variety of processes,including the immune response and pigmentation.Our results suggest that the three populations should be considered as three different conservation units.The 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

Multi-omics analysis of attenuated variant reveals potential evaluation marker of host damaging for SARS-CoV-2 variants

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Science China(Life Sciences) 2024年第1期67卷 83-95页

作者： Guangshan Xie Lin Zhu Siwen Liu Cun Li Xin Diao Yanhao Zhang Xiuli Su Yuanyuan Song Guodong Cao Li Zhong Pui Wang Xiaojuan Liu Bobo Wing-Yee Mok Shusheng Zhang Dong-Yan Jin Jie Zhou Honglin Chen Zongwei Cai State Key laboratory of environmental and Biological Analysis Hong Kong Baptist UniversityHong Kong SARChina State Key laboratory for Emerging Infectious Diseases and Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina College of Chemistry Zhengzhou UniversityZhengzhou 450001China School of Biomedical Sciences The University of Hong KongHong Kong SARChina HKBU Shenzhen Institute of Research and Continuing Education Shenzhen 518000China

SARS-CoV-2 continues to threaten human society by generating novel variants via mutation and recombination.The high number of mutations that appeared in emerging variants not only enhanced their immune-escaping ability but also made it difficult to predict the pathogenicity and virulence based on viral nucleotide sequences.Molecular markers for evaluating the pathogenicity of new variants are therefore needed.By comparing host responses to wild-type and variants with attenuated pathogenicity at proteome and metabolome levels,six key molecules on the polyamine biosynthesis pathway including putrescine,SAM,dc-SAM,ODC1,SAMS,and SAMDC were found to be differentially upregulated and associated with pathogenicity of variants.To validate our discovery,human airway organoids were subsequently used which recapitulates SARS-CoV-2 replication in the airway epithelial cells of COVID-19 patients.Using ODC1 as a proof-ofconcept,differential activation of polyamine biosynthesis was found to be modulated by the renin-angiotensin system(RAS)and positively associated with ACE2 activity.Further experiments demonstrated that ODC1 expression could be differentially activated upon a panel of SARS-CoV-2 variants of concern(VOCs)and was found to be correlated with each VOCs’pathogenic properties.Particularly,the presented study revealed the discriminative ability of key molecules on polyamine biosynthesis as a predictive marker for virulence evaluation and assessment of SARS-CoV-2 variants in cell or organoid models.Our work,therefore,presented a practical strategy that could be potentially applied as an evaluation tool for the pathogenicity of current and emerging SARS-CoV-2 variants.

关键词： SARS-CoV-2 multi-omics attenuated variant predictive pathogenic marker polyamine biosynthesis

Plant virology in the 21st century in China:Recent advances and future directions

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Journal of Integrative Plant Biology 2024年第3期66卷 579-622页

作者： Jianguo Wu Yongliang Zhang Fangfang Li Xiaoming Zhang Jian Ye Taiyun Wei Zhenghe Li Xiaorong Tao Feng Cui Xianbing Wang Lili Zhang Fei Yan Shifang Li Yule Liu Dawei Li Xueping Zhou Yi Li State Key laboratory for Ecological Pest Control of Fujian and Taiwan Crops Vector-borne Virus Research CenterCollege of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhou 350002China State Key laboratory of Plant environmental Resilience and Ministry of Agriculture Key laboratory of Soil microbiology College of Biological SciencesChina Agricultural UniversityBeijing 100193China State Key laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China State Key laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China State Key laboratory of Plant Genomics Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China State Key laboratory of Rice Biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China Department of Plant Pathology The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjing 210095China State Key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products Institute of Plant VirologyNingbo UniversityNingbo 315211China MOE Key laboratory of Bioinformatics Center for Plant BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China State Key laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China

Plant viruses are a group of intracellular pathogens that persistently threaten global food security.Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years,including basic research and technologies for preventing and controlling plant viral diseases.Here,we review these milestones and advances,including the identification of new crop-infecting viruses,dissection of pathogenic mechanisms of multiple viruses,examination of multilayered interactions among viruses,their host plants,and virus-transmitting arthropod vectors,and in-depth interrogation of plantencoded resistance and susceptibility determinants.Notably,various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants.We also recommend future plant virology studies in China.

关键词： China emerging plant viruses plant virology plant resistance/susceptibility to viral infection plant-virus transmission vector interactions plant virus-based vectors viral pathogenesis

Different mechanisms underlie similar species-area relationships in two tropical archipelagoes

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Plant Diversity 2024年第2期46卷 238-246页

作者： Shengchun Li Tieyao Tu Shaopeng Li Xian Yang Yong Zheng Liang-Dong Guo Dianxiang Zhang Lin Jiang Key laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China ECNU-Alberta Joint Lab for Biodiversity Study Tiantong Forest Ecosystem National Observation and Research StationSchool of Ecological and Environmental SciencesEast China Normal UniversityShanghai 200241China School of Biological Sciences Georgia Institute of TechnologyAtlantaGA 30332USA Jiangxi Academy of Forestry Nanchang 330032China Institute of Eco-Chongming(IEC) Shanghai 202162China State Key laboratory of Biocontrol School of EcologySun Yat-sen UniversityGuangzhou 510275China School of Geographical Sciences Fujian Normal UniversityFuzhou 350007China State Key laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Despite much research in the field of island biogeography,mechanisms regulating insular diversity remain elusive.Here,we aim to explore mechanisms underlying plant species-area relationships in two tropical archipelagoes in the South China Sea.We found positive plant species-area relationships for both coral and continental archipelagoes.However,our results showed that different mechanisms contributed to similar plant species-area relationships between the two archipelagoes.For coral islands,soil nutrients and spatial distance among communities played major roles in shaping plant community structure and species diversity.By contrast,the direct effect of island area,and to a lesser extent,soil nutrients determined plant species richness on continental islands.Intriguingly,increasing soil nutrients availability(N,P,K)had opposite effects on plant diversity between the two archipelagoes.In summary,the habitat quality effect and dispersal limitation are important for regulating plant diversity on coral islands,whereas the passive sampling effect,and to a lesser extent,the habitat quality effect are important for regulating plant diversity on continental islands.More generally,our findings indicate that island plant species-area relationships are outcomes of the interplay of both niche and neutral processes,but the driving mechanisms behind these relationships depends on the type of islands.

关键词： Coral and continental islands Plant diversity Soil nutrients Species-area relationships The sampling effect