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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

Antibiotic Resistance Genes in the Human-Impacted Environment:A One Health Perspective

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Pedosphere 2019年第3期29卷 273-282页

作者： james M. tiedje WANG Fang Celia M. MANAIA Marko VIRTA SHENG Hongjie MA Liping ZHANG Tong Edward TOPP Key Laboratory of Soil Environment and Pollution Remediation Institute of Soil Science Chinese Academy of Sciences Nanjing 210008 (China) Center for Microbial Ecology Department of Plant Soil and Microbial Sciences Michigan State University East Lansing MI 48824 (USA) University of Chinese Academy of Sciences Beijing 100049 (China) Universidade Catolica Portuguesa CBQF-Centro de Biotecnologia e Quimica Fina一Laboratorio Associado Escola Superior de Biotecnologia Porto 4200-374 (Portugal) Department of Microbiology University of Helsinki Helsinki 00014 (Finland) Environmental Biotechnology Lab The University of Hong Kong Hong Kong (China) London Research and Development Centre Agriculture and Agri-Food Canada and University of Western Ontario London ON N6G 0J3 (Canada)

Antibiotic resistance and its environmental component are gaining more attention as part of combating the growing healthcare crisis. The One Health framework, promulgated by many global health agencies, recognizes that antimicrobial resistance is a truly inter-domain problem in which human health, animal agriculture, and the environment are the core and interrelated *** prospectus presents the status and issues relevant to the environmental component of antibiotic resistance, namely, the needs for advancing surveillance methodology: the environmental reservoirs and sources of resistance, namely, urban wastewater treatment plants, aquaculture production systems, soil receiving manure and biosolid, and the atmosphere which includes longer range ***, much work has been done describing antibiotic resistance genes in various environments;now quantitative, mechanistic,and hypothesis-driven studies are needed to identify practices that reduce real risks and maintain the effectiveness of our current antibiotics as long as possible. Advanced deployable detection methods for antibiotic resistance in diverse environmental samples are needed in order to provide the surveillance information to identify risks and define barriers that can reduce risks. Also needed are practices that reduce antibiotic use and thereby reduce selection for resistance, as well as practices that limit the dispersal of or destroy antibiotic-resistant bacteria or their resistance genes that are feasible for these varied environmental domains.

关键词： animal agriculture antibiotic-resistant bacteria antimicrobial resistance aquaculture human health One Health framework soil contamination wastewater and sludge

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

From Waste to H2:GeoChip-based Analysis of Microbial Community Structure and Functions in Bio-electrochemically Assisted Microbial Reactor (BEAMR)

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From Waste to H2:GeoChip-based Analysis of Microbial Communi...

Exploring the Biofrontier:the Microbial World

第十次全国环境微生物学术研讨会

作者： Bruce Logan james tiedje Department of Environmental Science and Engineering Pennsylvanian State UniversityUSA Center for Microbial Ecology Michigan State UniversityUSA

Hydrogen is one of the most promising alternative clean energy and has been received great attention in research and *** hydrogen can be produced via a variety of biology-based processes such as photosynthesis,fermentation and gasification of plant biomass, the fermentation-based hydrogen production appears to be a more efficient approach than others.

关键词： bio-hydrogen BEAMR Geochip community structure and functions

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Exploring the Biofrontier:the Microbial World

两个分离菌株对2,4-D降解效率的微生态系统模拟

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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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

Microbial communities biostimulated by ethanol during uranium （VI） bioremediation in contaminated sediment as shown by stable isotope probing

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Frontiers of Environmental Science & Engineering 2015年第3期9卷 453-464页

作者： Mary Beth LEIGH Wei-Min WU Erick CARDENAS Ondrej UHLIK Sue CARROLL Terry GENTRY Terence L. MARSH Jizhong ZHOU Philip JARDINE Craig S. CRIDDLE james M. tiedje Center for Microbial Ecology Michigan State University East Lansing MI 48824 USA Institute of Arctic Biology University of Alaska Fairbanks Fairbanks AK 99775 USA Department of Civil and Environmental Engineering Center for Sustainable Development & Global Competitiveness Codiga Resource Recovery Center Stanford University Stanford CA 94305-4020 USA Department of Biochemistry and Microbiology Institute of Chemical Technology Prague Technicka 3 166 28 Prague Czech Republic Environmental Sciences Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA Department of Botany and Microbiology University of Oklahoma Norman OK 73019 USA Department of Crop and Soil Sciences Texas A&M University College Station TX 77843 USA

Stable isotope probing （SIP） was used to identify microbes stimulated by ethanol addition in microcosms containing two sediments collected from the bioremediation test zone at the US Department of Energy Oak Ridge site, TN, USA. One sample was highly bioreduced with ethanol while another was less reduced. Microcosms with the respective sediments were amended with ^13C labeled ethanol and incubated for 7 days for SIP. Ethanol was rapidly converted to acetate within 24h accompanied with the reduction of nitrate and sulfate. The accumulation of acetate persisted beyond the 7 d period. Aqueous U did not decline in the microcosm with the reduced sediment due to desorption of U but continuously declined in the less reduced sample. Microbial growth and concomitant 13C-DNA production was detected when ethanol was exhausted and abundant acetate had accumulated in both microcosms. This coincided with U（VI） reduction in the less reduced sample. I3C originating from ethanol was ultimately utilized for growth, either directly or indirectly, by the dominant microbial community members within 7 days of incubation. The microbial community was comprised predominantly of known denitrifiers, sulfate-reducing bacteria and iron （Ⅲ） reducing bacteria including Desulfovibrio, Sphingomonas, Ferribacterium, Rhodanobacter, Geothrix, Thiobacillus and others, including the known U（VI）-redueing bacteria Acidovorax, Anaeromyxobacter, Desulfovibrio, Geobac- ter and Desulfosporosinus. The findings suggest that ethanol biostimulates the U（VI）-reducing microbial com- munity by first serving as an electron donor for nitrate, sulfate, iron （IH） and U（VI） reduction, and acetate which then functions as electron donor for U（VI） reduction and carbon source for microbial growth.

关键词： Stable isotope probing (S/P) ethanol acetate uranium reduction sediment bioremediation

不同土地利用方式下典型黑土区土壤微生物群落演替规律

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土壤学报 2022年第5期59卷 1238-1247页

作者：胡芳王芳韩晓增许敏付玉豪严君贾仲君 tiedje james M. 蒋新中国科学院土壤环境与污染修复重点实验室(南京土壤研究所) 南京210008 中国科学院东北地理与农业生态研究所黑土区农业生态重点实验室哈尔滨150081 中国科学院大学北京100049 密歇根州立大学植物、土壤和微生物科学系微生物生态中心美国密歇根州48824

利用先进的分子生态学技术,针对中国科学院海伦农业生态试验站长期定位实验,研究了典型黑土区经过长期(32年)裸地、农田和草地三种土地利用后,土壤微生物区系的演替规律及其环境驱动机制。结果表明:与裸地相比,32年玉米-大豆-小麦轮作... 详细信息

利用先进的分子生态学技术,针对中国科学院海伦农业生态试验站长期定位实验,研究了典型黑土区经过长期(32年)裸地、农田和草地三种土地利用后,土壤微生物区系的演替规律及其环境驱动机制。结果表明:与裸地相比,32年玉米-大豆-小麦轮作种植或自然草地恢复后,土壤有机质含量从52.07 g·kg^(–1)显著增加至54.83 g·kg^(–1)和61.54 g·kg^(–1),增幅分别为8.0%和27.5%,土壤氮磷钾养分有效性也显著增加。同时,每克干燥土壤中微生物丰度从2.25×10^(7)拷贝数增加至8.08×10^(7)拷贝数和1.69×10^(8)拷贝数,分别增加了2.58倍和6.51倍。裸地、农田和草地土壤的优势微生物菌门均为变形菌、酸杆菌和放线菌,其相对丰度均高于19%,且三者无显著差异(P>0.05)。然而,所有检测到的228个微生物属中,高达54个微生物属有显著差异(P<0.05),但绝大多数为相对丰度较低的微生物。分析表明土壤养分含量是微生物群落分异的主要环境驱动力,Granulicella微生物属可作为指示类群评估黑土环境的变化。上述研究结果表明,植被覆盖是土壤微生物群落演替的重要影响因素,未来应深入研究原位条件下黑土微生物的功能及其农业环境意义,为维系土壤养分元素循环和发展可持续农业生态管理模式提供理论参考。

关键词：长期试验黑土土壤微生物高通量测序农田草地

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