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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 challenging.microbial 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 time.Since soil is protective,and its microbial inhabitants have long adapted to varied soil conditions,significant portions of the soil microbial community structure are likely stable.Hence,a substantial portion of the community will not correlate to often measured soil attributes.We 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 metals.The 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 groups.We 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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In memoriam:David D.myrold(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 D.myrold,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 15,2021.Dave 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 concern.The 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 development.The 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 probiotics.Strategies 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 resistance.With 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 diseases.This 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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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 Way.It comprises intensity variations vs.time 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 km.These 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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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) transformation in the modern 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：土壤微生物功能多样性水稻种植水稻土新石器时代损失新石器时期遗传多样性

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Acute worsening of microvascular complications of diabetes mellitus during rapid glycemic control:The pathobiology and therapeutic implications

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World Journal of Diabetes 2024年第3期15卷 311-317页

作者： Dania Blaibel Cornelius james Fernandez Joseph m Pappachan Department of Endocrinology and metabolism Lancashire Teaching Hospitals NHS TrustPreston PR29HTUnited Kingdom Department of Endocrinology and metabolism Pilgrim HospitalUnited Lincolnshire Hospitals NHS TrustBoston PE219QSUnited Kingdom Faculty of Science Manchester Metropolitan UniversityManchester M156BHUnited Kingdom Faculty of Biology Medicine and HealthThe University of ManchesterManchester M139PLUnited Kingdom

While chronic hyperglycaemia resulting from poorly controlled diabetes mellitus(Dm)is a well-known precursor to complications such as diabetic retinopathy,neuropathy(including autonomic neuropathy),and nephropathy,a paradoxical intensification of these complications can rarely occur with aggressive glycemic management resulting in a rapid reduction of glycated haemoglobin.Although,acute onset or worsening of retinopathy and treatment induced neuropathy of diabetes are more common among these complications,rarely other problems such as albuminuria,diabetic kidney disease,Charcot’s neuroarthropathy,gastroparesis,and urinary bladder dysfunction are also encountered.The World Journal of Diabetes recently published a rare case of all these complications,occurring in a young type 1 diabetic female intensely managed during pregnancy,as a case report by Huret et al.It is essential to have a comprehensive understanding of the pathobiology,prevalence,predisposing factors,and management strategies for acute onset,or worsening of microvascular complications when rapid glycemic control is achieved,which serves to alleviate patient morbidity,enhance disease management compliance,and possibly to avoid medico-legal issues around this rare clinical problem.This editorial delves into the dynamics surrounding the acute exacerbation of microvascular complications in poorly controlled Dm during rapid glycaemic control.

关键词： Diabetes mellitus microvascular complications Diabetic retinopathy Treatment induced neuropathy of diabetes Diabetic nephropathy Charcot’s neuropathy

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Non-pharmacological interventions for diabetic peripheral neuropathy:Are we winning the battle?

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World Journal of Diabetes 2024年第4期15卷 579-585页

作者： Dania Blaibel Cornelius james Fernandez Joseph m Pappachan Department of Endocrinology and metabolism Lancashire Teaching Hospitals NHS TrustPreston PR29HTUnited Kingdom Department of Endocrinology&metabolism Pilgrim HospitalUnited Lincolnshire Hospitals NHS TrustBoston PE219QSUnited Kingdom Faculty of Science Manchester Metropolitan UniversityManchester M156BHUnited Kingdom Faculty of Biology Medicine&HealthThe University of ManchesterManchester M139PLUnited Kingdom

Despite the advent of relatively reliable modalities of diagnosing diabetic peripheral neuropathy(DPN),such as nerve conduction studies,there is still a knowledge gap about the pathophysiology,and thus limited available in-terventions for symptom control and curtailing disease progression.The pharma-cologic aspect of management is mainly centred on pain control,however,there are several important aspects of DPN such as loss of vibration sense,pressure sense,and proprioception which are associated with risks to lower limb health,which pharmacotherapy does not address.Furthermore,published evidence suggests non-pharmacologic interventions such as glycaemic control through dietary modification and exercise need to be combined with other measures such as psychotherapy,to reach a desired,however modest effect.Acupuncture is emerging as an important treatment modality for several chronic medical conditions including neuropathic and other pain syndromes.In their study published in the World Journal of Diabetes on the potential of acupuncture to reduce DPN symptoms and enhance nerve conduction parameters,Hoerder et al have been able to demonstrate that acupuncture improves sensory function and that this effect is likely sustained two months after treatment cessation.Although previous studies also support these findings,larger multi-center randomized control trials including a sham-controlled arm accounting for a placebo effect are required.Overall,given the satisfactory safety profile and the positive results found in these studies,it is likely that acupuncture may become an important aspect of the repertoire of effective DPN management.

关键词： Diabetic peripheral neuropathy Diabetes mellitus Pharmacotherapy Acupuncture Neuropathic pain Nonpharmacological intervention

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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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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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Rising tide: The global surge of type 2 diabetes in children and adolescents demands action now

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World Journal of Diabetes 2024年第5期15卷 797-809页

作者： Joseph m Pappachan Cornelius james Fernandez Ambika P Ashraf Department of Endocrinology and metabolism Lancashire Teaching Hospitals NHS TrustPreston PR29HTUnited Kingdom Faculty of Science Manchester Metropolitan UniversityManchester M156BHUnited Kingdom Faculty of Biology Medicine&HealthThe University of ManchesterManchester M139PLUnited Kingdom Department of Endocrinology&metabolism Pilgrim HospitalUnited Lincolnshire Hospitals NHS TrustBoston PE219QSUnited Kingdom Division of Pediatric Endocrinology and Diabetes Department of PediatricsUniversity of Alabama at BirminghamBirminghamAL 35233United States

Childhood-onset obesity has emerged as a major public healthcare challenge across the globe,fueled by an obesogenic environment and influenced by both genetic and epigenetic predispositions.This has led to an exponential rise in the incidence of type 2 diabetes mellitus in children and adolescents.The looming wave of diabetes-related complications in early adulthood is anticipated to strain the healthcare budgets in most countries.Unless there is a collective global effort to curb the devastation caused by the situation,the impact is poised to be pro-found.A multifaceted research effort,governmental legislation,and effective social action are crucial in attaining this goal.This article delves into the current epidemiological landscape,explores evidence concerning potential risks and consequences,delves into the pathobiology of childhood obesity,and discusses the latest evidence-based management strategies for diabesity.

关键词： Childhood obesity Diabesity Type 2 diabetes mellitus Adolescence Cardiovascular disease Pharmacotherapy

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