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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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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

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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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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

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Toward the Fourth Industrial Revolution on Real-Time Customization

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Journal of Systems Science and Systems Engineering 2020年第2期29卷 127-142页

作者： james.m.Tien College of Engineering University of MiamiCoral GablesFlorida 33146USA

The outputs of a national economy can be partitioned into three sets of products:tangible goods(due to manufacturing,construction,extraction and agriculture),intangible services(due to an act of useful effort),and an integration of services and goods or,as initially defined by Tien(2012),***,these products can also be considered in terms of their relation to the first three Industrial Revolutions:the First Industrial Revolution(circa 1800)was primarily focused on the production of goods;the Second Industrial Revolution(circa 1900)was primarily focused on the mass production of goods;and the Third Industrial Revolution(circa 2000)has been primarily focused on the mass customization of goods,services or *** this follow-up paper,the Third Industrial Revolution of mass customization continues to accelerate in its evolution and,in many respects,is subsuming the earlier Industrial Revolutions of production and mass *** importantly,with the advent of real-time decision making,artificial intelligence,Internet of Things,mobile networks,and other advanced digital technologies,customization has been extensively enabled,thereby advancing mass customization into a Fourth Industrial Revolution of real-time ***,the moral,ethical,security and employment problems associated with both mass and real-time customization must be carefully assessed and mitigated,especially in regard to unintended *** ahead and with the advance of artificial general intelligence,this Fourth Industrial Revolution could be forthcoming in about the middle of the 21st Century;it would allow for multiple activities to be simultaneously tackled in real-time and in a customized manner.

关键词： Industrial revolutions big data goods services servgoods connected production mass customization real-time decision making Internet of Things artificial intelligence general

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THE NEXT INDUSTRIAL REVOLUTION:INTEGRATED SERVICES AND GOODS

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Journal of Systems Science and Systems Engineering 2012年第3期21卷 257-296页

作者： james.m.TIEN College of Engineering University of MiamiCoral GablesFlorida 33146USA

The outputs or products of an economy can be divided into services products ana gooas products （due to manufacturing, construction, agriculture and mining）. To date, the services and goods products have, for the most part, been separately mass produced. However, in contrast to the first and second industrial revolutions which respectively focused on the development and the mass production of goods, the next - or third - industrial revolution is focused on the integration of services and/or goods; it is beginning in this second decade of the 21st Century. The Third Industrial Revolution （TIR） is based on the confluence of three major technological enablers （i.e., big data analytics, adaptive services and digital manufacturing）; they underpin the integration or mass customization of services and/or goods. As detailed in an earlier paper, we regard mass customization as the simultaneous and real-time management of supply and demand chains, based on a taxonomy that can be defined in terms of its underpinning component and management foci. The benefits of real-time mass customization cannot be over-stated as goods and services become indistinguishable and are co-produced - as ＂servgoods＂ - in real-time, resulting in an overwhelming economic advantage to the industrialized countries where the consuming customers are at the same time the co-producing producers.

关键词： Big data decision analytics goods adaptive services digital manufacturing value chain supply chain demand chain mass production mass customization industrial revolution

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ON INTEGRATION AND ADAPTATION IN COmPLEX SERVICE SYSTEmS

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Journal of Systems Science and Systems Engineering 2008年第4期17卷 385-415页

作者： james.m.TIEN College of Engineering University of miami Coral GablesFloridaUSA

The services sector employs a large and growing proportion of workers in the industrialized nations, and it is increasingly dependent on information and communication technologies. While the interdependences, similarities and complementarities of manufacturing and services are significant, there are considerable differences between goods and services, including the shift in focus from mass production to mass customization （whereby a service is produced and delivered in response to a customer＇s stated or imputed needs）. In general, services can be considered to be knowledge-intensive agents or components which work together as providers and consumers to create or co-produce value. Like manufacturing systems, an efficient service system must be an integrated system of systems, leading to greater connectivity and interdependence. Integration must occur over the physical, temporal, organizational and functional dimensions, and must include methods concerned with the component, the management, and the system. moreover, an effective service system must also be an adaptable system, leading to greater value and responsiveness. Adaptation must occur over the dimensions of monitoring, feedback, cybernetics and learning, and must include methods concerned with space, time, and system. In sum, service systems are indeed complex, especially due to the uncertainties associated with the human-centered aspects of such systems. moreover, the system complexities can only be dealt with methods that enhance system integration and adaptation. The paper concludes with several insights, including a plea to shift the current misplaced focus on developing a science or discipline for services to further developing a systems engineering approach to services, an approach based on the integration and adaptation of a host of sciences or disciplines （e.g., physics, mathematics, statistics, psychology, sociology, etc.）. In fact, what is required is a services-related transdisciplinary - beyond a s

关键词： Services service system system components system integration system adaptation system of systems decision informatics real-time decision making

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BIG DATA:UNLEASHING INFORmATION

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Journal of Systems Science and Systems Engineering 2013年第2期22卷 127-151页

作者： james.m.TIEN College of Engineering University of Miami

At present, it is projected that about 4 zettabytes （or 10^＊＊21 bytes） of digital data are being generated per year by everything from underground physics experiments to retail transactions to security cameras to global positioning systems. In the U. S., major research programs are being funded to deal with big data in all five sectors （i.e., services, manufacturing, construction, agriculture and mining） of the economy. Big Data is a term applied to data sets whose size is beyond the ability of available tools to undertake their acquisition, access, analytics and/or application in a reasonable amount of time. Whereas Tien （2003） forewarned about the data rich, information poor （DRIP） problems that have been pervasive since the advent of large-scale data collections or warehouses, the DRIP conundrum has been somewhat mitigated by the Big Data approach which has unleashed information in a manner that can support informed - yet, not necessarily defensible or valid - decisions or choices. Thus, by somewhat overcoming data quality issues with data quantity, data access restrictions with on-demand cloud computing, causative analysis with correlative data analytics, and model-driven with evidence-driven applications, appropriate actions can be undertaken with the obtained information. New acquisition, access, analytics and application technologies are being developed to further Big Data as it is being employed to help resolve the 14 grand challenges （identified by the National Academy of Engineering in 2008）, underpin the 10 breakthrough technologies （compiled by the massachusetts Institute of Technology in 2013） and support the Third Industrial Revolution of mass customization.

关键词： Big data data acquisition data access data analytics data application decision informatics products processes adaptive services digital manufacturing mass customization third industrial revolution

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