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Functional profiles of soil microbial communities in the alpine and temperate grasslands of China

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Grassland Research 2022年第1期1卷 3-13页

作者： Yunfeng Yang jizhong zhou Xue Guo 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 School of Civil Engineering and Environmental Sciences University of OklahomaNormanOklahomaUSA Earth and Environmental Sciences Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA

Grassland ecosystems in cold regions are typical of short growing seasons and limited primary productivity,rendering soil microorganisms as major ecosystem engineers in governing biogeochemical cycling.Climate warming and extensive livestock grazing have dramatically influenced soil microbial diversity and function in grassland worldwide,but it remains elusive how functional microbial communities exist and respond to global changes.Here,we present a review to highlight similarities and differences in soil functional microbial communities between alpine grasslands in the Qinghai-Tibet Plateau and temperate grasslands in the Inner Mongolian Plateau,both of which are major plateaus in China,but differ substantially in geography.We show that many specialized functional groups thrive under harsh conditions,exhibiting a high functional diversity.Their community compositions mirror the heterogeneity and complexity of grassland soils.Moreover,functional microbial responses to environmental changes have been extremely variable,with few consistent patterns across both plateaus.Because we identify a lack of technical standardization that prevents in-depth comparative studies for functional microbial communities,we conclude the review by outlining several research gaps that need to be filled in future studies.

关键词： climate changes functional microbial communities grassland soils grazing Inner Mongolian Plateau Qinghai-Tibet Plateau

The diversity and ecological significance of microbial traits potentially involved in B_(12) biosynthesis in the global ocean

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mLife 2023年第4期2卷 416-427页

作者： Jiayin zhou Wei Qin Xinda Lu Yunfeng Yang David Stahl Nianzhi Jiao jizhong zhou Jihua Liu Qichao Tu Institute of Marine Science and Technology Shandong UniversityQingdaoChina Joint Lab for Ocean Research and Education at Dalhousie University Shandong University and Xiamen UniversityQingdaoChina School of Biological Sciences University of OklahomaNormanOklahomaUSA Department of Civil and Environmental Engineering Massachusetts Institute of TechnologyCambridgeMassachusettsUSA State Key Joint Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijingChina Department of Civil and Environmental Engineering University of WashingtonSeattleWashingtonUSA Institute of Marine Microbes and Ecospheres Xiamen UniversityXiamenChina Earth and Environmental Sciences Lawrence Berkeley NationalLaboratoryBerkeley CaliforniaUSA Institutefr Environmental Genomics University of OklahomaNormanOklahomaUSA School of Civil Engineering and Environmental Sciences University of OklahomaNormanOklahomaUSA School of Computer Sciences University of OklahomaNormanOklahomaUSA DermBiont Inc. BostonMassachusettsUSA

Cobalamin(B_(12)),an essential nutrient and growth cofactor for many living organisms on Earth,can be fully synthesized only by selected prokaryotes in nature.Therefore,microbial communities related to B_(12) biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomic make-up of complex functional assemblages.By anchoring microbial traits potentially involved in B_(12) biosynthesis,we depict the biogeographic patterns of B_(12) biosynthesis genes and the taxa harboring them in the global ocean,despite the limitations of detecting de novo B_(12) synthesizers via metagenomes alone.Both the taxonomic and functional composition of B_(12) biosynthesis genes were strongly shaped by depth,differentiating the epipelagic zones from the mesopelagic layers.Functional genes related to B_(12) biosynthesis were relatively stably distributed across different oceans,but the taxa harboring them varied considerably,showing clear functional redundancy among microbial systems.Microbial taxa carrying B_(12) biosynthesis genes in the surface water were influenced by environmental factors such as temperature,oxygen,and nitrate.However,the composition of functional genes was only weakly associated with these environmental factors.Null model analyses demonstrated that determinism governed the variations in B_(12) biosynthesis genes,whereas a higher degree of stochasticity was associated with taxonomic variations.Significant associations were observed between the chlorophyll a concentration and B_(12) biosynthesis,confirming its importance in primary production in the global ocean.The results of this study reveal an essential ecological mechanism governing the assembly of microbes in nature:the environment selects for function rather than taxonomy;functional redundancy underlies stochastic community assembly.

关键词： B_(12)biosynthesis community assembly functional genes functional redundancy ocean primary production

Assessing mechanisms for microbial taxa and community dynamics using process models

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mLife 2023年第3期2卷 239-252页

作者： Linwei Wu Yunfeng Yang Daliang Ning Qun Gao Huaqun Yin Naija Xiao Benjamin Yzhou Si Chen Qiang He jizhong zhou Institute of Ecology Key Laboratory for Earth Surface Processes of the Ministry of EducationCollege of Urban and Environmental SciencesPeking UniversityBeijingChina Institute for Environmental Genomics University of OklahomaNormanOKUSA Department of Microbiology and Plant Biology University of OklahomaNormanOKUSA State Key Joint Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijingChina School of Minerals Processing and Bioengineering Central South UniversityChangshaChina Department of Mathematics Lunt HallNorthwestern UniversityEvanstonIllinoisUSA Department of Civil and Environmental Engineering The University of TennesseeKnoxvilleTennesseeUSA Institute for a Secure and Sustainable Environment The University of TennesseeKnoxvilleTennesseeUSA School of Civil Engineering and Environmental Sciences University of OklahomaNormanOklahomaUSA Earth and Environmental Sciences Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA School of Computer Science University of OklahomaNormanOKUSA

Disentangling the assembly mechanisms controlling community composition,structure,distribution,functions,and dynamics is a central issue in ecology.Although various approaches have been proposed to examine community assembly mechanisms,quanti-tative characterization is challenging,particularly in microbial ecology.Here,we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer–resource model with a neutral model in stochastic differential equations.Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes,we tested the applicability of three ecological models:the consumer–resource model,the neutral model,and the combined model.Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions.The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated.In contrast,the neutral model showed the best performance for rare taxa.Our analysis further indicated that immigration rates decreased with taxa abundance and com-petitions between taxa were strongly correlated with phylogeny,but within a certain phylogenetic distance only.The determinism underlying taxa and community dynamics were quantitatively assessed,showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning.Given its mechanistic basis,the framework developed here is expected to be potentially applicable beyond microbial ecology.

关键词： community assembly mechanisms consumer-resource model neutral model species dynamics

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 cycle.In temperate ecosystems,soil microbial communities function along seasonal cycles.However,little is known about how the responses of soil microbial communities to warming vary when the season changes.In this study,we investigated the seasonal dynamics of soil bacterial community under experimental warming in a temperate tall‐grass prairie ecosystem.Our 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 winter.Also,warming significantly(p<0.050)increased microbial network complexity and robustness,especially during the colder seasons,despite large variations in network size and complexity in different seasons.In addition,the relative importance of stochastic processes in shaping the microbial community decreased by warming in fall and winter but not in spring and summer.Our study indicates that climate warming restructures the seasonal dynamics of soil microbial community in a temperate ecosystem.Such 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

mLife:Your journal for cutting-edge research in all microbiological disciplines

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mLife 2022年第1期1卷 1-2页

作者： Li Huang jizhong zhou State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijingChina College of Life Science University of Chinese Academy of SciencesBeijingChina Institute for Environmental Genomics University of OklahomaNormanOKUSA Department of Microbiology and Plant Biology University of OklahomaNormanOKUSA School of Civil Engineering and Environmental Sciences University of OklahomaNormanOKUSA Earth and Environmental Sciences Lawrence Berkeley National LaboratoryBerkeleyCAUSA

After years of deliberations,the Institute of Microbiology of the Chinese Academy of Sciences(IMCAS;http://***)and the Chinese Society for Microbiology(CSM;http://***/)decided early in 2021 to jointly launch mLife,a new high-profile open-access microbiology journal with a scope spanning the entire spectrum of microbiological sciences.An editorial board consisting of over 70 internationally well-established scientists with expertise in various areas of microbiology has been established.It is a great honor for both of us to work with our outstanding board members in getting this new journal off the ground.

关键词： journal jointly http

Resistance potential of soil bacterial communities along a biodiversity gradient in forest ecosystems

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mLife 2022年第4期1卷 399-411页

作者： Jialiang Kuang Dongmei Deng Shun Han Colin T.Bates Daliang Ning Wensheng Shu jizhong zhou The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters Ministry of EducationSchool of Environment and EnergySouth China University of TechnologyGuangzhouChina Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA State Key Laboratory of Biocontrol Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education InstitutesCollege of Ecology and EvolutionSun Yat-sen UniversityGuangzhouChina Guangxi Key Laboratory of Green Processing of Sugar Resources College of Biological and Chemical EngineeringGuangxi University of Science and TechnologyLiuzhouChina School of Life Sciences South China Normal UniversityGuangzhouChina School of Civil Engineering and Environmental Sciences University of OklahomaNormanOklahomaUSA School of Computer Sciences University of OklahomaNormanOklahomaUSA.8Earth and Environmental SciencesLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA.

Higher biodiversity is often assumed to be a more desirable scenario for maintaining the functioning of ecosystems,but whether species-richer communities are also more disturbance-tolerant remains controversial.In this study,we investigated the bacterial communities based on 472 soil samples from 28 forests across China with associated edaphic and climatic properties.We developed two indexes(i.e.,community mean tolerance breadth[CMTB]and community mean response asynchrony[CMRA])to explore the relationship between diversity and community resistance potential.Moreover,we examined this resistance potential along the climatic and latitudinal gradients.We revealed that CMTB was significantly and negatively related to species richness,resulting from the changes in balance between relative abundances of putative specialists and generalists.In comparison,we found a unimodal relationship between CMRA and richness,suggesting that higher biodiversity might not always lead to higher community resistance.Moreover,our results showed differential local patterns along latitude.In particular,local patterns in the northern region mainly followed general relationships rather than those for the southern forests,which may be attributed to the differences in annual means and annual variations of climate conditions.Our findings highlight that the community resistance potential depends on the composition of diverse species with differential environmental tolerance and responses.This study provides a new,testable evaluation by considering tolerance breadth and response asynchrony at the community level,which will be helpful in assessing the influence of disturbance under rapid shifts in biodiversity and species composition as a result of global environmental change.

关键词： ecological resistance forest soil bacterial community latitudinal gradient specialist–generalist balance species richness

Antibiotic resistome mostly relates to bacterial taxonomy along a suburban transmission chain

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Frontiers of Environmental Science & Engineering 2022年第3期16卷 63-72页

作者： Ziyan Qin Qun Gao Qiang Dong Joy D.Van Nostrand Qi Qi Yifan Su Suo Liu Tianjiao Dai Jingmin Cheng jizhong zhou Yunfeng Yang State Key Joint Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijing 100084China Institute of Chemical Defense Beijing 102205China Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOK 73019USA School of Civil Engineering and Environmental Sciences University of OklahomaNormanOK 73019USA Earth and Environmental Sciences Lawrence Berkeley National LaboratoryBerkeleyCA 94720USA

Antibiotic resistance genes comprising antibiotic resistome are of great concern due to their increase in the environment.Recent evidence of shared resistomes between soils and animal husbandry has imposed potential risks to human health.However,the correlation between a given community’s resistome and bacterial taxonomic composition is controversial.Here,a transmission chain of resistomes from swine manure to compost and compost-amended soil were analyzed in five suburban areas of Beijing,China,with unamended agricultural soils as control soils.Antibiotic resistomes and bacterial taxonomic compositions were distinct between(I)manure and compost;and(II)compost-amended and control soils.In manure,compost,and compost-amended soils,theβ-diversity of the resistome and bacterial taxonomic composition was significantly correlated,while no correlation was detected in control soils.Bacterial taxonomic composition explained 36.0%of total variations of the resistome composition,much higher than environmental factors.Together,those results demonstrated that antibiotic resistome was closely related to bacterial taxonomic composition along the suburban transmission chain.

关键词： Antibiotic resistance genes Resistome Bacterial taxonomy Transmission chain

A successful start for mLife

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mLife 2023年第1期2卷 1-1页

作者： Li Huang jizhong zhou State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijingChina College of Life Sciences University of Chinese Academy of SciencesBeijingChina Institute for Environmental Genomics University of OklahomaNormanOKUSA Department of Microbiology and Plant Biology University of OklahomaNormanOKUSA School of Civil Engineering and Environmental Sciences University of OklahomaNormanOKUSA School of Computer Science University of OklahomaNormanOKUSA Earth and Environmental Sciences Lawrence Berkeley National LaboratoryBerkeleyCAUSA

mLife made its debut with the publication of the inaugurating issue on March 30,2022.We are pleased to have published 42 high-quality articles,including reviews,research articles,and application notes,which cover microbial genetics,biochemistry and physiology,ecology and evolution,pathogenic and public health microbiology,and so forth.Nine of the articles concern technical innovations and applications in areas including genome editing,single-cell analysis,and database.

关键词： editing notes ecology

Effects of Fe(II) on anammox community activity and physiologic response

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Frontiers of Environmental Science & Engineering 2021年第1期15卷 113-123页

作者： Jing Ding Wanyi Seow jizhong zhou Raymond Jianxiong Zeng Jun Gu Yan zhou Advanced Environmental Biotechnology Centre Nanyang Environment and Water Research InstituteNanyang Technological UniversitySingapore 637141Singapore School of Civil and Environmental Engineering Nanyang Technological UniversitySingapore 639798Singapore Centre of Wastewater Resource Recovery College of Resources and EnvironmentFujian Agriculture and Forestry UniversityFuzhou 350002China Institute for Environmental Genomics and Department of Microbiology and Plant University of OklahomaNormanOK 73019USA Earth and Environmental Sciences Lawrence Berkeley National LaboratoryBerkeleyCA 94720USA School of Environment Tsinghua UniversityBeijing 100084China

Though there are many literatures studying the effects of iron on anammox process,these studies only focus on the reactor performance and/or the microbial community changes,the detailed effects and mechanisms of Fe(II)on anammox bacterial activity and physiology have not been explored.In this study,four Fe(II)concentrations(0.03,0.09,0.12 and 0.75 mmol/L)were employed into the enriched anammox culture.The enhancement and inhibition effects of Fe(II)on anammox process and bacterial physiology were investigated.It was discovered that the anammox process and bacterial growth were enhanced by 0.09 and 0.12 mmol/L Fe(II),in which the 0.12 mmol/L Fe(II)had advantage in stimulating the total anammox activity and bacterial abundance,while 0.09 mmol/L Fe(II)enhanced the relative anammox activity better.The anammox activity could be inhibited by 0.75 mmol/L Fe(II)immediately,while the inhibition was recoverable.Both 0.09 and 0.12 mmol/L Fe(II)induced more genes being expressed,while didn’t show a stimulation on the relative expression level of functional genes.And anammox bacteria showed a stress response to detoxify the Fe inhibition once inhibited by 0.75 mmol/L Fe(II).This study provides more information about physiologic response of anammox bacteria to external influence(enhancement and inhibition),and may also instruct the future application of anammox process in treating various sources of wastewater(containing external disturbances such as heavy metals)and/or different treatment strategies(e.***.from side-stream to main-stream).

关键词： Anaerobic ammonium oxidation(Anammox) Candidatus Kuenenia stuttgartiensis Ferrous iron GeoChip