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soil microbial ecology through the lens of metatranscriptomics

soil ecology Letters 2024年第3期6卷 1-15页

作者： Jingjing Peng Xi Zhou Christopher Rensing Werner Liesack Yong-Guan Zhu State Key Laboratory of Nutrient Use and Management College of Resources and Environmental SciencesNational Academy of Agriculture Green DevelopmentKey Laboratory of Plant-Soil InteractionsMinistry of EducationChina Agricultural UniversityBeijing 100193China Institute of Environmental Microbiology College of Resource and EnvironmentFujian Agriculture and Forestry UniversityFuzhou 350002China Max Planck Institute for Terrestrial Microbiology Marburg 35043Germany State Key Laboratory of Urban and Regional ecology Research Centre for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China Key Laboratory of Urban Environment and Health Institute of Urban EnvironmentChinese Academy of SciencesXiamen 361021China

Metatranscriptomics is a cutting-edge technology for exploring the gene expression by,and functional activities of,the microbial community across diverse ecosystems at a given time,thereby shedding light on their metabolic responses to the prevailing environmental *** double-RNA approach involves the simultaneous analysis of rRNA and mRNA,also termed structural and functional *** contrast,mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles,but requires either deep sequencing or effective rRNA *** this review,we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional *** particular,we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields,such as rhizobiomes,antibiotic resistomes,methanomes,and *** review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.

关键词： metatranscriptomics mRNA MAGs rhizobiont resistome virome

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Special Issue on soil microbial ecology

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soil ecology Letters 2021年第4期3卷 289-289页

作者： Haiyan Chu Yunfeng Yang State Key Laboratory of soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China University of Chinese Academy of Sciences Beijing 100049China State Key Joint Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijing 100084China

soils would not exist without the activity and diversity of residential *** microbes are fundamental to maintaining key soil processes associated with organic matter decomposition,nutrient cycling,and plant productivity and are thus integral to human well*** technological advances have exponentially increased our knowledge concerning soil microbial composition,diversity,distribution,and ecological func*** special issue on soil microbial ecology focuses on various aspects of soil microbiology,including soil microbial spatial distribution,microbial succession,community assembly processes,microbial biogeochemical cycles,the associations between microbial communities and plant health,and the identification and isolation of benefiting microbes for crop *** call for papers was widely recognized within the community,reflected by 12 research papers now published in the issue.

关键词： soil cycling ecology

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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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Mycorrhizal fungi mitigate nitrogen losses of an experimental grassland by facilitating plant uptake and soil microbial immobilization

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Pedosphere 2024年第2期34卷 399-410页

作者： Yangyang JIA Marcel G.A.VAN DER HEIJDEN Alain Y.VALZANO-HELD Markus JOCHER Florian WALDER Postdoctoral Mobile Station of ecology College of Ecology and EnvironmentXinjiang UniversityÜrümqi 830046China Research Group Plant-soil Interactions AgroscopeZürich 8046Switzerland Research Group Climate and Agriculture AgroscopeZürich 8046Switzerland Department of Plant and microbial Biology University of ZürichZürich 8008Switzerland Research Group soil Quality and soil Use AgroscopeZürich 8046Switzerland

Nitrogen(N)is one of the most limited nutrients of terrestrial ecosystems,whose losses are prevented in tightly coupled cycles in finely tuned *** change-induced N enrichment through atmospheric deposition and application of vast amounts of fertilizer are now challenging the terrestrial N *** mycorrhizal fungi(AMF)are known drivers of plant-soil nutrient fluxes,but a comprehensive assessment of AMF involvement in N cycling under global change is still ***,we simulated N enrichment by fertilization(low/high)in experimental grassland microcosms under greenhouse conditions in the presence or absence of AMF and continuously monitored different N pathways over nine *** found that high N enrichment by fertilization decreased the relative abundance of legumes and the plant species dominating the plant community changed from grasses to forbs in the presence of AMF,based on aboveground *** presence of AMF always maintained plant N:phosphorus(P)ratios between 14 and 16,no matter how the soil N availability *** in plant N:P ratios due to the increased plant N and P uptake might thus be a primary pathway of AMF altering plant community ***,we constructed a comprehensive picture of AMF’s role in N cycling,highlighting that AMF reduced N losses primarily by mitigating N leaching,while N_(2)O emissions played a marginal *** mycorrhizal fungi reduced N_(2)O emissions directly through the promotion of N_(2)O-consuming *** underlying mechanism for reducing N leaching is mainly the AMF-mediated improved nutrient uptake and AMF-associated microbial *** results indicate that synergies between AMF and other soil microorganisms cannot be ignored in N cycling and that the integral role of AMF in N cycling terrestrial ecosystems can buffer the upcoming global changes.

关键词： N cycling N enrichment N uptake N:P ratio plant community structure symbiotic soil fungi

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Adsorption and Desorption of Cry1Ab Proteins on Differently Textured Paddy soils

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Pedosphere 2018年第1期28卷 94-102页

作者： Ling LIU Stefan KNAUTH Thilo EICKHORST soil microbial ecology University of Bremen

In recent years, selected cry genes from Bacillus thuringiensis（Bt） encoding the production of Cry proteins（Bt toxins） have been engineered into crop plants（Bt-crops）. Through the cultivation of Bt crops and the application of Bt pesticides, Cry proteins could be introduced into arable soils. The interaction between the proteins and soils was analyzed in this study to investigate the affinity of Cry proteins in paddy soil ecosystems. Four Paddy soils were selected to represent different soil textures. Cry proteins were spiked in soils, and the amount of protein adsorbed was measured over 24 h. Desorption of Cry1Ab proteins from paddy soils was performed by washing with sterile Milli-Q water（H_2O_（MQ））, and subsequently extracted with an extraction buffer. The paddy soils had a strong affinity for Cry1Ab proteins. Most of the Cry1Ab proteins added（＆gt; 98%） were rapidly adsorbed on the paddy soils tested. More Cry1Ab proteins were adsorbed on non-sterile soils than on sterile soils. Less than 2% of the adsorbed Cry1Ab proteins were desorbed using H2 OMQ, while a considerable proportion of the adsorbed proteins could be desorbed with the buffer, ranging from 20% to 40%.The amount of proteins desorbed increased with the increases in the initial amount of Cry1Ab proteins added to the paddy soils. The concentration of Cry1Ab proteins desorbed from the paddy soils was higher for sterile soils than non-sterile ones. Our results indicate that Bt toxins released via the cultivation of Bt crops, the application of Bt pesticides can be adsorbed on paddy soils, and soil texture could impose an impact on the adsorption capability.

关键词： affinity Bt toxin extraction protein solution soil texture sterile soil

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Land Use Effects on soil Organic Carbon, microbial Biomass and microbial Activity in Changbai Mountains of Northeast China

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Chinese Geographical Science 2014年第3期24卷 297-306页

作者： FANG Xiangmin WANG Qingli ZHOU Wangming ZHAO Wei WEI Yawei NIU Lijun DAI Limin State Key Laboratory of Forest and soil ecology Institute of Applied EcologyChinese Academy of Sciences University of Chinese Academy of Sciences Changbai Mountains Academy of Sciences

Land use changes are known to alter soil organic carbon （SOC） and microbial properties, however, information about how conversion of natural forest to agricultural land use as well as plantations affects SOC and microbial properties in the Changbai Moun- tains of Northeast China is meager. soil carbon content, microbial biomass carbon （MBC）, basal respiration and soil carbon mineraliza- tion were studied in five selected types of land use： natural old-growth broad-leaved Korean pine mixed forest （NF）; spruce plantation （SP） established following clear-cutting of NF; cropland （CL）; ginseng farmland （GF） previously under NF; and a five-year Mongolian oak young forest （YF） reforested on an abandoned GF, in the Changbai Mountains of Northeast China in 2011. Results showed that SOC content was significantly lower in SP, CL, GF, and YF than in NF. MBC ranged from 304.4 mg/kg in CL to 1350.3 mg/kg in NF, which was significantly higher in the soil of NF than any soil of the other four land use types. The SOC and MBC contents were higher in SP soil than in CL, GF, and YF soils, yielding a significant difference between SP and CL. The value of basal respiration was also higher in NF than in SP, CL, GF, and YF. Simultaneously, higher values of the metabolic quotient were detected in CL, GF, and YF soils, indicat- ing low substrate utilization of the soil microbial community compared with that in NF and SP soil. The values of cumulative mineral- ized carbon and potentially mineralized carbon （Co） in NF were significantly higher than those in CL and GF, while no significant dif- ference was observed between NF and SP. In addition, YF had higher values of Co and C mineralization rate compared with GF. The results indicate that conversion from NF into agricultural land （CL and GF） uses and plantation may lead to a reduction in soil nutrients （SOC and MBC） and substrate utilization efficiency of the microbial community. By contrast, soils below SP were more conducive to the preserv

关键词： land use soil organic carbon (SOC) microbial biomass carbon (MBC) carbon mineralization basal respiration ChangbaiMountains

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soil microbial activity and nutrients of evergreen broad-leaf forests in mid-subtropical region of China

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Journal of Forestry Research 2015年第3期26卷 673-678页

作者： Zhangquan Zeng Silong Wang Canming Zhang Hong Tang Xiquan Li Zijian Wu Jia Luo Hunan Academy of Forestry Hengshan Station of Forest Ecology Huitong Experimental Station of Forest ecology State Key Laboratory of Forest and Soil Ecology Institute of Applied Ecology Chinese Academy of Sciences Huitong National Research Station of Forest Ecosystem College of Environment and Life Science Kaili University

To better understand the effects of forest suc- cession on soil microbial activity, a comparison of soil microbial properties and nutrients was conducted between three forest types representing a natural forest succession chronosequence. The study compared a pine （Pinus mas- soniana） forest （PF）, a pine and broadleaf mixed forest （MF） and an evergreen broadleaf forest （BF）, in the Yingzuijie Biosphere Reserve, Hunan Province, China. Results showed that soil nutrients in the MF and BF plots were higher than in the PF plots. The range in microbial biomass carbon followed a similar pattem with Be havingthe greatest values, 522-1022 mg kg-1, followed by Mr 368-569 mg kg-1, and finally, PF 193--449 mg kg-1. soil nutrients were more strongly correlated with microbial biomass carbon than basal respiration or metabolic quo- tient. Overall, forest succession in the study site improved soil microbial properties and soil fertility, which in turn can increase primary productivity and carbon sequestration.

关键词： Keywords qCO2 soil microbial biomass C soil nutrient

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Effect of Groundwater Irrigation on soil PAHs Pollution Abatement and soil microbial Characteristics:A Case Study in Northeast China

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Pedosphere 2010年第5期20卷 557-567页

作者： ZHANG Jing ZHANG Hui-Wen ZHANG Cheng-Gang Institute of Applied ecology Chinese Academy of Sciences Shenyang 110016 (China) State Key Laboratory of soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing 210008 (China)

To evaluate the effect of groundwater irrigation on the polycyclic aromatic hydrocarbons(PAHs) pollution abatement and soil microbial characteristics,a case study was performed in the Shenfu irrigation area of Shenyang,Northeast China,where the irrigation with petroleum wastewater had lasted for more than fifty years,and then groundwater irrigation instead of wastewater irrigation was applied due to the gradually serious PAHs pollution in *** chemical properties,including PAHs and nutrients contents,and soil microbial characteristics,including microbial biomass carbon,substrateinduced respiration,microbial quotient(qM),metabolic quotient(qCO2),dehydrogenase(DH),polyphenol oxidase(PO),urease(UR) and cellulase(CE) in surface and subsurface were *** organic C,total N,total P,and available K were significantly different between the sites *** PAHs concentrations ranged from 610.9 to 6362.8 μg kg-1 in the surface layers(0-20 cm) and from 404.6 to 4318.5 μg kg-1 in the subsurface layers(20-40 cm).From the principal component analysis,the first principal component was primarily weighed by total PAHs,total organic C,total N,total P and available K,and it was the main factor that influencing the soil microbial *** the tested microbial characteristics,DH,PO,UR,CE,qM and qCO2 were more sensitive to the PAHs stress than the others,thus they could serve as useful ecological assessment indicators for soil PAHs pollution.

关键词： microbial biomass paddy soil polycyclic aromatic hydrocarbons soil enzyme activities

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Nitrogen addition promotes soil carbon accumulation globally

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Science China Life Sciences 2025年第1期68卷 284-293页

作者： Xuemei Yang Suhui Ma Erhan Huang Danhua Zhang Guoping Chen Jiangling Zhu Chengjun Ji Biao Zhu Lingli Liu Jingyun Fang Institute of ecology College of Urban and Environmental Sciencesand Key Laboratory for Earth Surface Processes of the Ministry of EducationPeking University Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China School of Ecology and Environmental ScienceYunnan University State Key Laboratory of Vegetation and Environmental Change Institute of BotanyChinese Academy of Sciences

soil is the largest carbon(C) reservoir in terrestrial ecosystems and plays a crucial role in regulating the global C cycle and climate *** nitrogen(N) deposition has been widely considered as a critical factor affecting soil organic carbon(SOC) storage, but its effect on SOC components with different stability remains unclear. Here, we analyzed extensive empirical data from 304 sites worldwide to investigate how SOC and its components respond to N addition. Our analysis showed that N addition led to a significant increase in bulk SOC(6.7%), with greater increases in croplands(10.6%) and forests(6.0%) compared to grasslands(2.1%). Regarding SOC components, N addition promoted the accumulation of plant-derived C(9.7%–28.5%) over microbial-derived C(0.2%), as well as labile(5.7%) over recalcitrant components(–1.2%), resulting in a shift towards increased accumulation of plant-derived labile C. Consistently, N addition led to a greater increase in particulate organic C(11.9%) than mineral-associated organic C(3.6%), suggesting that N addition promotes C accumulation across all pools, with more increase in unstable than stable pools. The responses of SOC and its components were best predicted by the N addition rate and net primary productivity. Overall, our findings suggest that N enrichment could promote the accumulation of plant-derived and non-mineral associated C and a subsequent decrease in the overall stability of soil C pool, which underscores the importance of considering the effects of N enrichment on SOC components for a better understanding of C dynamics in soils.

关键词： meta-analysis nitrogen enrichment soil organic carbon carbon accumulation carbon stability

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Effect of Rhizobacterium Rhodopseudomonas palustris Inoculation on Stevia rebaudiana Plant Growth and soil microbial Community

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Pedosphere 2018年第5期28卷 793-803页

作者： XU Jiangbing FENG Youzhi WANG Yanling LIN Xiangui International Center for ecology Meteorologyand Environment (IceMe)School of Applied MeteorologyNanjing University of Information Science and Technology State Key Laboratory of soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of Sciences

There is an increasing concern that the continuous use of chemical fertilizers might lead to harmful effects on soil ***, a biocompatible approach involving inoculation of beneficial microorganisms is presented to promote plant growth and simultaneously minimize the negative effect of chemical fertilizers. In this study, Rhodopseudomonas palustris, a plant growth-promoting rhizobacterium(PGPR), was inoculated into both fertilized and unfertilized soils to assess its influence on Stevia rebaudiana plant growth and microbial community in rhizosphere soils in a 122-d field experiment. soil enzyme assays(dehydrogenase, urease, invertase, and phosphomonoesterase), real-time quantitative polymerase chain reaction(RT-_qPCR), and a high-throughput sequencing technique were employed to determine the microbial activity and characterize the bacterial community. Results showed that the *** inoculation did not significantly influence Stevia yields and root biomass in either the fertilized or unfertilized soil. Chemical fertilization had strong negative effects on soil bacterial community properties, especially on dehydrogenase and urease ***, R. palustris inoculation counteracted the effect of chemical fertilizer on dehydrogenase and urease activities, and increased the abundances of some bacterial lineages(including Bacteroidia, Nitrospirae, Planctomycetacia, Myxococcales, and Legionellales). In contrast, inoculation into the unfertilized soil did not significantly change the soil enzyme activities or the soil bacterial community structure. For both the fertilized and unfertilized soils, R. palustris inoculation decreased the relative abundances of some bacterial lineages possessing photosynthetic ability, such as Cyanobacteria, Rhodobacter, Sphingomonadales, and Burkholderiales. Taken together, our observations stress the potential utilization of R. palustris as PGPR in agriculture, which might further ameliorate the soil microbial prop

关键词： bacterial community structure beneficial microorganism chemical fertilization plant growth-promoting rhizobacterium,soil enzyme activity

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