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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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A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation

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Science Bulletin 2016年第13期61卷 1052-1060页

作者： Yong-Guan Zhu Jian-Qiang Su Zhihong Cao Kai Xue John Quensen Guang-Xia Guo Yun-Feng Yang Jizhong Zhou Hai-Yan Chu james m.tiedje Key Laboratory of Urban Environment and Health Institute of Urban Environment Chinese Academy of Sciences State Key Laboratory of Urban and Regional Ecology Research Center for Eco-environmental Sciences Chinese Academy of Sciences Institute of Soil Science Chinese Academy of Sciences Institute for Environmental Genomics University of Oklahoma Center for microbial Ecology Department of Plant Soil and Microbial Sciences Michigan State University State Key Joint Laboratory of Environment Simulation and Pollution Control School of Environment Tsinghua University

It has been documented that human activities are causing the rapid loss of taxonomic, phylogenetic, genetic and functional diversity in soils. However, it remains unclear how modern intensive rice cultivation impacts the soil microbiome and its functionality. Here we examined the microbial composition and function differences between a buried Neolithic paddy soil and an adjacent, currently-cultivated paddy soil using high throughput metagenomics technologies. Our results showed that the currently cultivated soil contained about 10-fold more microbial biomass than the buried one. Analyses based on both 16S rRNA genes and functional gene array showed that the currently cultivated soil had significantly higher phylogenetic diversity, but less functional diversity than the buried Neolithic one. The community structures were significantly different between modern and ancient soils, with functional structure shifting towards accelerated organic carbon （C） degradation and nitrogen （N） transfor- mation in the modem soils. This study implies that, modern intensive rice cultivation has substantially altered soil microbial functional structure, leading to functional homogenization and the promotion of soil ecological functions related to the acceleration of nutrient cycling which is necessary for high crop yields.

关键词： Neolithic paddy soil Long-term ricecultivation 16S rRNA gene pyrosequencing -Bacterial community - Functional gene diversityGeoChip

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Exploring the Biofrontier:the microbial World

Exploring the Biofrontier:the Microbial World

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2008年中国微生物学会学术年会

作者： james m.tiedje Center for microbial Ecology Plant and Soil Sciences Building Michigan State University

The microbial world is arguably the greatest under-explored resource for biological discovery, both for basic contributions to knowledge about the diversity and strategies for Ufe,and for harvesting that novelty for apphcations from medicines to *** from 16S rRNA gene sequences,metagenomic studies,descriptions of new isolates,and from habitat,spatial and organism studies all suggest that the diversity of the microbial world is *** is not

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两个分离菌株对2,4-D降解效率的微生态系统模拟

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中山大学学报（自然科学版） 2000年第3期39卷 111-115页

作者：夏北成李婉华 David S.Treves james m.tiedje 中山大学环境科学研究所广东广州5102752 广州污水处理总厂 Center for microbial Ecology Michigan State University

在微生态系统模拟条件下 ,2个分离菌株Sphingomonaspaucimobilis 92 56 ,Ralstoniaeu trophusJmP表现出对除草剂 2 ,4 D的高效降解性能 .但R eutrophusJmP能在更多的模拟条件下成为优势种群 .对 2个菌株的种群消长影响最大的生态因子... 详细信息

在微生态系统模拟条件下 ,2个分离菌株Sphingomonaspaucimobilis 92 56 ,Ralstoniaeu trophusJmP表现出对除草剂 2 ,4 D的高效降解性能 .但R eutrophusJmP能在更多的模拟条件下成为优势种群 .对 2个菌株的种群消长影响最大的生态因子是湿度和 2 ,4 D的浓度 .种群增长与 2 ,4 D降解有约 2 4h的时滞 ;种群的增长量不完全受底物 2 ,4 D消耗的多少制约 .多个生态因子的综合作用说明模拟的微生态系统离自然系统还有较大的差别 .

关键词：生物降解二氯苯氧基乙酸微生态系统模拟菌株

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In memoriam:David ***(1955–2021)

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Pedosphere 2022年第1期32卷 222-222页

作者： Zhongjun JIA Jeanette m.NORTON Joshua P.SCHImEL james m.tiedje State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNo.71 East Beijing RoadNanjing 210008China Department of Plants Soils and ClimateUtah State UniversityLogan UT 84322-4820USA Department of Ecology Evolutionand Marine BiologyUniversity of CaliforniaSanta Barbara CA 93106USA Center for microbial Ecology Michigan State UniversityEast Lansing MI 48824-1325USA

David ***,65,Professor of Soil microbiology in the Department of Crop and Soil Science at Oregon State University,passed away in Corvallis,Oregon,USA on July 15,*** was well known to many soil scientists for his work on soil nitrogen cycling,a career of research work that was summarized in his latest 2021 publication—Transformation of Nitrogen.

关键词： soil cycling Crop

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Gut microbiota research nexus:One Health relationshipbetween human,animal,and environmental resistomes

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mLife 2023年第4期2卷 350-364页

作者： Yuhao Fu Qingyuan Dou Kornelia Smalla Yu Wang Timothy A.Johnson Kristian K.Brandt Zhi mei maoyuan Liao Syed A.Hashsham Andreas Schäffer Hauke Smidt Tong Zhang Hui Li Robert Stedtfeld Hongjie Sheng Benli Chai marko Virta Xin Jiang Fang Wang Yong-Guan Zhu james m.tiedje State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjingChina University of Chinese Academy of Sciences BeijingChina Julius Kühn Institute(JKI)Federal Research Centre for Cultivated Plants BraunschweigGermany Department of Animal Sciences Purdue UniversityWestLafayetteIndianaUSA Section for microbial Ecology and Biotechnology Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark Sino-Danish Center(SDC) BeijingChina Department of microbiology University of HelsinkiHelsinkiFinland Department of Plant Soil and MicrobialSciencesCenter for Microbial EcologyMichigan State UniversityMichiganUSA Department of Civil and Environmental Engineering Michigan State UniversityMichiganUSA Institute for Environmental Research RWTH Aachen UniversityAachenGermany Laboratory of microbiology Wageningen University&ResearchWageningenThe Netherlands Environmental microbiome Engineering and Biotechnology Laboratory Center for Environmental Engineering ResearchDepartment of Civil EngineeringTheUniversity of Hong KongPokfulamHong KongChina Institute of Agricultural Resources and Environment Jiangsu Academy of Agricultural SciencesNanjingChina KeyLaboratory of Urban Environment and Health Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina State Key Laboratory of Urban and Regional Ecology Chinese Academy of SciencesBeijingChina

The emergence and rapid spread of antimicrobial resistance is of global public health *** gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and vertical gene transfers is considered an important reservoir and sink of antibiotic resistance genes(ARGs).In this review,we describe the reservoirs of gut ARGs and their dynamics in both animals and humans,use the One Health perspective to track the transmission of ARG-containing bacteria between humans,animals,and the environment,and assess the impact of antimicrobial resistance on human health and socioeconomic *** gut resistome can evolve in an environment subject to various selective pressures,including antibiotic administration and environmental and lifestyle factors(e.g.,diet,age,gender,and living conditions),and interventions through *** to reduce the abundance of clinically relevant antibiotic-resistant bacteria and their resistance determinants in various environmental niches are needed to ensure the mitigation of acquired antibiotic *** the help of effective measures taken at the national,local,personal,and intestinal management,it will also result in preventing or minimizing the spread of infectious *** review aims to improve our understanding of the correlations between intestinal microbiota and antimicrobial resistance and provide a basis for the development of management strategies to mitigate the antimicrobial resistance crisis.

关键词： antibiotic antimicrobial resistance gut microbiota modulatory strategies One Health

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土壤中抗生素抗性基因的环境行为与阻控研究进展

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土壤学报 2023年第1期60卷 39-49页

作者：生弘杰王芳相雷雷付玉豪王紫泉许敏梅芝刘雨豆庆圆蒋新 james m.tiedje 中国科学院土壤环境与污染修复重点实验室中国科学院南京土壤研究所南京210008 农业农村部长江下游平原农业环境重点实验室江苏省农业科学院农业资源与环境研究所南京210014 中国科学院大学北京100049 Department of Plant Soil and Microbial SciencesMichigan State UniversityMI 48824USA

抗生素抗性基因(Antibiotic resistance genes,ARGs)的传播威胁着生态环境安全和人体健康,已成为一个全球性的问题。土壤中抗生素抗性基因的分布、来源、扩散传播以及消减技术已成为一个研究热点。本文在简要介绍自然环境和受人类活动... 详细信息

抗生素抗性基因(Antibiotic resistance genes,ARGs)的传播威胁着生态环境安全和人体健康,已成为一个全球性的问题。土壤中抗生素抗性基因的分布、来源、扩散传播以及消减技术已成为一个研究热点。本文在简要介绍自然环境和受人类活动干扰土壤中抗生素抗性基因分布水平的基础上,分析了土壤中抗生素抗性基因的主要来源,剖析了抗生素抗性基因由土壤向其他环境介质(水、植物)传播的规律及其影响因素,如土壤理化性质、农艺调控和环境中污染物等。进而探讨了环境中各种生物和非生物因素对土壤中抗生素抗性基因持久性的影响和环境中抗生素抗性基因的消减技术,包括好氧堆肥、厌氧发酵、水处理工艺等。最后,提出遵循“大健康(One Health)”准则,以跨学科的方法控制抗生素抗性基因在环境中的传播,以更全面地将抗生素抗性基因对人类的健康风险降低至最低水平。

关键词：抗生素抗性基因抗生素抗性细菌土壤水平基因转移大健康

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Climate warming restructures seasonal dynamics of grassland soil microbial communities

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mLife 2022年第3期1卷 245-256页

作者： Xue Guo mengting Yuan Jiesi Lei Zhou Shi Xishu Zhou Jiabao Li Ye Deng Yunfeng Yang Liyou Wu Yiqi Luo james mtiedje Jizhong Zhou State Key Joint Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijingChina Institute for Environmental Genomics and Department of microbiology and Plant Biology University of OklahomaNormanOklahomaUSA Department of Environmental Science Policyand ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA Gladstone Institutes and Chan‐Zuckerberg Biohub San FranciscoCaliforniaUSA School of minerals Processing and Bioengineering Central South UniversityChangshaChina Key Laboratory of Environmental and Applied microbiology Chinese Academy of Sciences and Environmental Microbiology&Key Laboratory of Sichuan ProvinceChengdu Institute of BiologyChinese Academy of SciencesChengduChina Key Laboratory of Environmental Biotechnology Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina Department of Biological Sciences Center for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA Center for microbial Ecology Michigan State UniversityEast LansingMichiganUSA School of Civil Engineering and Environmental Sciences University of OklahomaNormanOklahomaUSA Earth and Environmental Sciences Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA School of Computer Sciences University of OklahomaNormanOklahomaUSA.

Soil microbial community's responses to climate warming alter the global carbon *** temperate ecosystems,soil microbial communities function along seasonal ***,little is known about how the responses of soil microbial communities to warming vary when the season *** this study,we investigated the seasonal dynamics of soil bacterial community under experimental warming in a temperate tall‐grass prairie *** results showed that warming significantly(p=0.001)shifted community structure,such that the differences of microbial communities between warming and control plots increased nonlinearly(R^(2)=0.578,p=0.021)from spring to ***,warming significantly(pmicrobial network complexity and robustness,especially during the colder seasons,despite large variations in network size and complexity in different *** addition,the relative importance of stochastic processes in shaping the microbial community decreased by warming in fall and winter but not in spring and *** study indicates that climate warming restructures the seasonal dynamics of soil microbial community in a temperate *** seasonality of microbial responses to warming may enlarge over time and could have significant impacts on the terrestrial carbon cycle.

关键词： climate warming microbial community microbial network seasonal dynamics

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地下水铀污染的原位微生物还原与固定：在美国能源部田纳西橡树岭放射物污染现场的试验

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环境科学学报 2011年第3期31卷 449-459页

作者：吴唯民 Jack Carley David Watson 顾宝华 Scott Brooks Shelly D.Kelly Kenneth Kemner Joy D.van Nostrand 吴力游许玫英周集中罗剑 Erick Cardenas 黄家琪 matthew W.Fields Terence L.marsh james m.tiedje Stefan J.Green Joel E.Kostka Peter K.Kitanidis Philip m.Jardme CraigS.Criddle 美国斯坦福大学土木与环境工程系 StanfordCA94305USA 美国橡树岭国家实验室环境科学部 OakRidgeTN37831USA 美国阿岗国家实验室生物科学部 ArgonneIL60439USA 美国俄克拉荷马大学植物-与微生物学系 NormanOK73019USA 广东省微生物研究所广州510070 美国乔冶亚理工学院土木与环境工程系 AtlantaGA30332USA 美国密歇根州立大学微生物生态中心 EastLansingMI48823USA 美国蒙大拿州立大学生物膜工程中心 BozemanMT59717USA 美国佛罗里达州立大学地球海洋大气科学系 TallahasseeFL32306USA 美国田纳西大学生物系统工程与土壤科学系 KnoxvilleTN37996USA

总结了美国斯坦福大学和橡树岭国家实验室等在美国能源部田纳西州橡树岭综合试验基地进行的铀污染原位微生物修复阶段性试验结果.本试验利用微生物以乙醇为电子供体还原地下水和沉积物中的六价铀为不溶解的四价铀,使之原位固定化.随后... 详细信息

总结了美国斯坦福大学和橡树岭国家实验室等在美国能源部田纳西州橡树岭综合试验基地进行的铀污染原位微生物修复阶段性试验结果.本试验利用微生物以乙醇为电子供体还原地下水和沉积物中的六价铀为不溶解的四价铀,使之原位固定化.随后通过加入溶解氧和硝酸盐来试验微生物还原后的地下水层中还原固定态铀的稳定性.通过预处理和长期间隔注入乙醇溶液,地下水中铀浓度从40～60mg·L-1降至0.03mg·L-1以下,达到了美国环保署饮用水的标准.还原的四价铀主要以U(Ⅳ)-Fe复合物的形态存在.结果表明,固定化后的四价铀只有在厌氧条件下才是稳定的,溶解氧和硝酸盐侵入地下水层后会使固定化的四价铀重新氧化为溶解态的六价铀.在试验过程中,采用多种分子生物学方法检测了微生物种群的变化和与铀氧化还原反应有关的功能微生物.本研究表明,在维持试验系统无氧和无硝酸盐的条件下,通过添加乙醇为电子供体可有效地促进地下水中土著功能微生物的活性,从而实现铀的原位还原固定与稳定.

关键词：铀污染微生物还原原位生物修复地下水沉积物

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Probing turbulence in galaxies with fast radio burst scintillation

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Science China(Physics,mechanics & Astronomy) 2024年第1期67卷 177-178页

作者： james m.Cordes Department of Astronomy the Cornell Center for Astrophysics and Planetary ScienceCornell UniversityIthaca NY 14853USA

Interstellar scintillation(ISS)is a well-known phenomenon observed from pulsars in the milky *** comprises intensity variations *** and frequency caused by constructive and destructive interference from multipath propagation,which is due to diffraction from fluctuations in electron density in the interstellar medium(ISm)on scales as small as~100 *** density fluctuations appear to be part of a turbulence process combined with discrete structures in electron density from other astrophysical processes;together these fluctuations extend to scales of pc or larger.

关键词： scales galaxies turbulence

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